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Conserved domains on  [gi|150865289|ref|XP_001384440|]
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Part of small ribosomal subunit (SSU) processosome (contains U3 snoRNA) [Scheffersomyces stipitis CBS 6054]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1246-1322 2.39e-28

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member cd05708:

Pssm-ID: 471952 [Multi-domain]  Cd Length: 77  Bit Score: 109.34  E-value: 2.39e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 150865289 1246 VGEIFEGSVKRATDFGVFIKLDGTlNITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLGMKASYF 1322
Cdd:cd05708     2 VGQKIDGTVRRVEDYGVFIDIDGT-NVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKASYF 77
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 881-950 4.62e-28

S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 108.45  E-value: 4.62e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  881 TKAVIKSVKGTQLNVQLADNLQGRIAATECFNSWneiKDKKQPLSQFHKGQVIDVKIIGFHDAKNHKFLP 950
Cdd:cd05702     4 VKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEW---PDGKNPLSKFKIGQKIKARVIGGHDAKTHRFLP 70
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 988-1060 5.36e-28

S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 108.43  E-value: 5.36e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 150865289  988 GSQHIVFVNNIAKGYVWASLSPNIRGRISFMELTDNVSVFDDLENNLPIGSAISATVKEVDNEHHSVVLTARK 1060
Cdd:cd05703     1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 96-223 1.78e-27

S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 107.69  E-value: 1.78e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   96 LIPGTLVLGQITAVGKLDITLALGDNLVGYIPITSISEELTIQIEQYEKAEDsdeesedeedeqesedgkirtatlKSKS 175
Cdd:cd05693     1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESE------------------------EEDD 56

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 150865289  176 RPEFPELKTLFSIGQWLRAKVVQPSSSqnqnQKQKKRIQLTIEPETVN 223
Cdd:cd05693    57 EEELPDLEDLFSVGQLVRCKVVSLDKS----KSGKKRIELSLEPELVN 100
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1159-1225 5.41e-26

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 102.37  E-value: 5.41e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 150865289 1159 GDVVKGFVKNVANNGVYVSLGRSVHALVRVADLSDAYLKDWKKYFKPHQPILGKISACKEE-GRVLMT 1225
Cdd:cd05707     1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDnGRIEMT 68
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 594-663 8.29e-26

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member cd05698:

Pssm-ID: 471952 [Multi-domain]  Cd Length: 70  Bit Score: 101.92  E-value: 8.29e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  594 GFKTPAIVEKFVHNGAIVSFFGNLRAFLPKNEISETFVSNASDYLRLGQTVNVRVLDVKQEEKRMLVTLR 663
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1069-1141 9.99e-25

S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240211 [Multi-domain]  Cd Length: 73  Bit Score: 98.86  E-value: 9.99e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 150865289 1069 VKVGQKYPARILKVRDTYVLVELGEKVVASAFITDALDNYSDKLESVFTTNEFATATVLDIDTDSEKIAVSLR 1141
Cdd:cd05706     1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 764-847 1.10e-21

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member cd04461:

Pssm-ID: 471952 [Multi-domain]  Cd Length: 83  Bit Score: 90.72  E-value: 1.10e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  764 KQDAIPAYFKDIKVdNKMLRGFVKSVTNKGLFVSFAGKLTGLVLAKYATSNENEDLLKKFYKYQSIACRVINIDEENKRF 843
Cdd:cd04461     1 KEGTLPTNFSDLKP-GMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRF 79


                  ....
gi 150865289  844 LLTL 847
Cdd:cd04461    80 LLSL 83
rpsA super family cl36730
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 511-848 3.35e-21

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


The actual alignment was detected with superfamily member TIGR00717:

Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 99.42  E-value: 3.35e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   511 IIKVLPEAGGIVIkvLDEFEGFVPGSHMSDIKLVYPERKFKVGSKVRGRVLSKQGNKLVVTFkkSLVNIEDDEVLARFED 590
Cdd:TIGR00717  194 VVKNITDFGAFVD--LGGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISL--SLKQLGEDPWEAIEKK 269

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   591 AKIGFKTPAIVEKFVHNGAIVSFFGNLRAFLPKNEIS-ETFVSNASDYLRLGQTVNVRVLDVKQEEKRMLVTLRhssELT 669
Cdd:TIGR00717  270 FPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK---QCK 346

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   670 NTQKSSIDDLQPGKSIVTVSVVEKTKDSVIVELEGNsLRGVIytgHLTDGNYEQNRAYAKKLSIGEK-LEVLVLEKDLKA 748
Cdd:TIGR00717  347 ANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGG-IDGLI---HLSDISWDKDGREADHLYKKGDeIEAVVLAVDKEK 422

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   749 RTVIVSAKKsLIDAAKQDAIPAYFKDIKVdnkmlRGFVKSVTNKGLFVSFAGKLTGLVLAKYATSNENEDLLKKFYKYQS 828
Cdd:TIGR00717  423 KRISLGVKQ-LTENPWEKFAAKYKVGSVV-----KGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDE 496

                          330       340
                   ....*....|....*....|
gi 150865289   829 IACRVINIDEENKRFLLTLK 848
Cdd:TIGR00717  497 VEAKVVDIDKKNRKVSLSVK 516
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1430-1688 8.33e-12

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 67.83  E-value: 8.33e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1430 LNTRAPQSVADFERLLVGNPNSSILWMNYMSFQLQLSEADKAREIGERALKtinyRDEQEKLniwiALLNLENTF---GT 1506
Cdd:COG2956    20 LNGQPDKAIDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYlkaGL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1507 DESLEEIFKRSTQ-YMDSLTMHQKLVSIYSMSEKYYQAEELYKVMTKKFGKSISVWVQYGSFLLDRKLQEETHEVLAKAL 1585
Cdd:COG2956    92 LDRAEELLEKLLElDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKAL 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1586 QTLPkrDHIEVVRKFAQLEFSKGDAEQGRSLFEGLVADAPKRIDLWNVYVDQEIKQDNKSKVEDIFERALAKKlsrKQAK 1665
Cdd:COG2956   172 KLDP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKALELD---PSDD 246

                         250       260
                  ....*....|....*....|...
gi 150865289 1666 FFFTKWLAFEEEKGDEQMAARIK 1688
Cdd:COG2956   247 LLLALADLLERKEGLEAALALLE 269
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 230-312 7.04e-11

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member cd05694:

Pssm-ID: 471952 [Multi-domain]  Cd Length: 74  Bit Score: 59.57  E-value: 7.04e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  230 DLIPGNALQCSVKSVEDHGIIMNTGRDGLSGFISNKEIKNtpdldVEILKPGKVLLTSIVSKSASRTVnlrpIHSTSVSK 309
Cdd:cd05694     1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGN-----FSKLKVGQLLLCVVEKVKDDGRV----VSLSADPS 71


                  ...
gi 150865289  310 KSA 312
Cdd:cd05694    72 KVS 74
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 418-485 3.28e-07

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member cd05696:

Pssm-ID: 471952 [Multi-domain]  Cd Length: 71  Bit Score: 49.18  E-value: 3.28e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 150865289  418 GHVLEDAEVVGSDPNY-VFLKFGGSILGQVHNSKIDKDK--TLEHDFNLGSKHSARVIGFNSIDNLLVLTM 485
Cdd:cd05696     1 GAVVDSVKVTKVEPDLgAVFELKDGLLGFVHISHLSDDKvpSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 325-395 5.56e-03

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member cd05697:

Pssm-ID: 471952 [Multi-domain]  Cd Length: 69  Bit Score: 37.22  E-value: 5.56e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 150865289  325 GILVDALVADVTKNGLIVKVFGLVDATINLAQLQEFdfnALKH---KYAIGNNIKARVMAVltRAGSKKLILSH 395
Cdd:cd05697     1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADV---RLKHpekKFKPGLKVKCRVLSV--EPERKRLVLTL 69
 
Name Accession Description Interval E-value
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1246-1322 2.39e-28

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 109.34  E-value: 2.39e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 150865289 1246 VGEIFEGSVKRATDFGVFIKLDGTlNITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLGMKASYF 1322
Cdd:cd05708     2 VGQKIDGTVRRVEDYGVFIDIDGT-NVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKASYF 77
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 881-950 4.62e-28

S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 108.45  E-value: 4.62e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  881 TKAVIKSVKGTQLNVQLADNLQGRIAATECFNSWneiKDKKQPLSQFHKGQVIDVKIIGFHDAKNHKFLP 950
Cdd:cd05702     4 VKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEW---PDGKNPLSKFKIGQKIKARVIGGHDAKTHRFLP 70
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 988-1060 5.36e-28

S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 108.43  E-value: 5.36e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 150865289  988 GSQHIVFVNNIAKGYVWASLSPNIRGRISFMELTDNVSVFDDLENNLPIGSAISATVKEVDNEHHSVVLTARK 1060
Cdd:cd05703     1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 96-223 1.78e-27

S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 107.69  E-value: 1.78e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   96 LIPGTLVLGQITAVGKLDITLALGDNLVGYIPITSISEELTIQIEQYEKAEDsdeesedeedeqesedgkirtatlKSKS 175
Cdd:cd05693     1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESE------------------------EEDD 56

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 150865289  176 RPEFPELKTLFSIGQWLRAKVVQPSSSqnqnQKQKKRIQLTIEPETVN 223
Cdd:cd05693    57 EEELPDLEDLFSVGQLVRCKVVSLDKS----KSGKKRIELSLEPELVN 100
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1159-1225 5.41e-26

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 102.37  E-value: 5.41e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 150865289 1159 GDVVKGFVKNVANNGVYVSLGRSVHALVRVADLSDAYLKDWKKYFKPHQPILGKISACKEE-GRVLMT 1225
Cdd:cd05707     1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDnGRIEMT 68
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 594-663 8.29e-26

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 101.92  E-value: 8.29e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  594 GFKTPAIVEKFVHNGAIVSFFGNLRAFLPKNEISETFVSNASDYLRLGQTVNVRVLDVKQEEKRMLVTLR 663
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1069-1141 9.99e-25

S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240211 [Multi-domain]  Cd Length: 73  Bit Score: 98.86  E-value: 9.99e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 150865289 1069 VKVGQKYPARILKVRDTYVLVELGEKVVASAFITDALDNYSDKLESVFTTNEFATATVLDIDTDSEKIAVSLR 1141
Cdd:cd05706     1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 764-847 1.10e-21

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 90.72  E-value: 1.10e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  764 KQDAIPAYFKDIKVdNKMLRGFVKSVTNKGLFVSFAGKLTGLVLAKYATSNENEDLLKKFYKYQSIACRVINIDEENKRF 843
Cdd:cd04461     1 KEGTLPTNFSDLKP-GMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRF 79


                  ....
gi 150865289  844 LLTL 847
Cdd:cd04461    80 LLSL 83
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 511-848 3.35e-21

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 99.42  E-value: 3.35e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   511 IIKVLPEAGGIVIkvLDEFEGFVPGSHMSDIKLVYPERKFKVGSKVRGRVLSKQGNKLVVTFkkSLVNIEDDEVLARFED 590
Cdd:TIGR00717  194 VVKNITDFGAFVD--LGGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISL--SLKQLGEDPWEAIEKK 269

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   591 AKIGFKTPAIVEKFVHNGAIVSFFGNLRAFLPKNEIS-ETFVSNASDYLRLGQTVNVRVLDVKQEEKRMLVTLRhssELT 669
Cdd:TIGR00717  270 FPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK---QCK 346

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   670 NTQKSSIDDLQPGKSIVTVSVVEKTKDSVIVELEGNsLRGVIytgHLTDGNYEQNRAYAKKLSIGEK-LEVLVLEKDLKA 748
Cdd:TIGR00717  347 ANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGG-IDGLI---HLSDISWDKDGREADHLYKKGDeIEAVVLAVDKEK 422

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   749 RTVIVSAKKsLIDAAKQDAIPAYFKDIKVdnkmlRGFVKSVTNKGLFVSFAGKLTGLVLAKYATSNENEDLLKKFYKYQS 828
Cdd:TIGR00717  423 KRISLGVKQ-LTENPWEKFAAKYKVGSVV-----KGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDE 496

                          330       340
                   ....*....|....*....|
gi 150865289   829 IACRVINIDEENKRFLLTLK 848
Cdd:TIGR00717  497 VEAKVVDIDKKNRKVSLSVK 516
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 1064-1319 5.60e-19

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 90.49  E-value: 5.60e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1064 ASIKDVKVGQKYPARILKVRDTYVLVELGEK---VVASAFITDALDNYS----DKLEsvfttnefatATVLDIDTDSEKI 1136
Cdd:COG0539    11 ESLKELKEGDIVKGTVVSIDDDEVLVDIGYKsegIIPLSEFSDEPGELEvkvgDEVE----------VYVEKVEDGEGEI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1137 AVSL-RTDspTDKVINSIAD-LNRGDVVKGFVKNVANNGVYVSLGrSVHALVRVADLSDAYLKDWKKYFKphQPILGKIS 1214
Cdd:COG0539    81 VLSKkKAD--REKAWEELEEaFENGEPVEGKVKGVVKGGLIVDIG-GVRAFLPASQVDVRPVRDLDEYVG--KTLEFKII 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1215 ACKEEG-------RVLMTLKESEVSGELnvlkrFDDLVVGEIFEGSVKRATDFGVFIKLDGtlnITGLCHHSQIADKDVD 1287
Cdd:COG0539   156 KLDRKRnnvvvsrRAVLEEEREEKREEL-----LEKLEEGDVVEGTVKNITDFGAFVDLGG---VDGLLHISEISWGRVK 227

                         250       260       270
                  ....*....|....*....|....*....|..
gi 150865289 1288 NVTSLFGEGDRVKVKLLAIDSDKKQLSLGMKA 1319
Cdd:COG0539   228 HPSEVLKVGDEVEVKVLKIDREKERISLSLKQ 259
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 1156-1319 1.40e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 89.93  E-value: 1.40e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1156 LNRGDVVKGFVKNVANNGVYVSLGrSVHALVRVADLSDAYLKDWKKYFKPHQPILGKI-SACKEEGRVLMTLKESEVSGE 1234
Cdd:PRK06676  190 LKEGDVVEGTVARLTDFGAFVDIG-GVDGLVHISELSHERVEKPSEVVSVGQEVEVKVlSIDWETERISLSLKDTLPGPW 268

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1235 LNVLKRFddlVVGEIFEGSVKRATDFGVFIKL-DGtlnITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQL 1313
Cdd:PRK06676  269 EGVEEKL---PEGDVIEGTVKRLTDFGAFVEVlPG---VEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRI 342


                  ....*.
gi 150865289 1314 SLGMKA 1319
Cdd:PRK06676  343 SLSIKA 348
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1067-1318 1.02e-16

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 85.56  E-value: 1.02e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  1067 KDVKVGQKYPARILKVRDTYVLVELGEKVVASAFITD-ALDNYSDKLESVFTTNEFATATVLDIDTDSEKIAVSLR--TD 1143
Cdd:TIGR00717  268 KKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEmSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKqcKA 347

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  1144 SPTDKVInsiADLNRGDVVKGFVKNVANNGVYVSLGRSVHALVRVADLS-DAYLKDWKKYFKPHQPILGKISAC-KEEGR 1221
Cdd:TIGR00717  348 NPWEQFE---EKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVdKEKKR 424

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  1222 VLMTLKESEVSGELNVLKRFDdlvVGEIFEGSVKRATDFGVFIKLDGtlNITGLCHHSQIADKDVDNVTSLFGEGDRVKV 1301
Cdd:TIGR00717  425 ISLGVKQLTENPWEKFAAKYK---VGSVVKGKVTEIKDFGAFVELPG--GVEGLIRNSELSENRDEDKTDEIKVGDEVEA 499

                          250
                   ....*....|....*..
gi 150865289  1302 KLLAIDSDKKQLSLGMK 1318
Cdd:TIGR00717  500 KVVDIDKKNRKVSLSVK 516
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 547-874 3.14e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 80.98  E-value: 3.14e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  547 ERKFKVGSKVRGRVlskqgnklvvtfkkslVNIEDDEVLARFEDAkigfktpaiVEKFVHngaiVSffgnlraflpknEI 626
Cdd:PRK06299  281 EKKYPVGSKVKGKV----------------TNITDYGAFVELEEG---------IEGLVH----VS------------EM 319

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  627 SET-FVSNASDYLRLGQTVNVRVLDVKQEEKRMLVTLRhsseltNTQKSSIDDL----QPGkSIVTVSVVEKTKDSVIVE 701
Cdd:PRK06299  320 SWTkKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLK------QCKENPWEEFaekyPVG-DVVEGKVKNITDFGAFVG 392

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  702 LEGNsLRGVIytgHLTDGNYEQNRAYAKKL-SIGEKLEVLVLEKDLKARtvivsaKKSL-IDAAKQDAIPAYFKDIKVDN 779
Cdd:PRK06299  393 LEGG-IDGLV---HLSDISWDKKGEEAVELyKKGDEVEAVVLKVDVEKE------RISLgIKQLEEDPFEEFAKKHKKGS 462

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  780 KmLRGFVKSVTNKGLFVSFAGKLTGLVLAKYATSNENEDLLKKFYKYQSIACRVINIDEENKRFLLTLKDVNGSKNIDSE 859
Cdd:PRK06299  463 I-VTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEAEEKEAI 541

                         330
                  ....*....|....*
gi 150865289  860 AVVNPVDTSKKLIGD 874
Cdd:PRK06299  542 AEYNSASDSKTTLGD 556
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 503-571 1.08e-13

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 67.26  E-value: 1.08e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 150865289  503 GTAVKSCeIIKVLPEagGIVIKVLDEFEGFVPGSHMSDIKLVYPERKFKVGSKVRGRVLS--KQGNKLVVT 571
Cdd:cd05697     1 GQVVKGT-IRKLRPS--GIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSvePERKRLVLT 68
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1246-1318 2.53e-13

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 66.47  E-value: 2.53e-13
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 150865289   1246 VGEIFEGSVKRATDFGVFIKLDGtlNITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLGMK 1318
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGN--GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1430-1688 8.33e-12

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 67.83  E-value: 8.33e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1430 LNTRAPQSVADFERLLVGNPNSSILWMNYMSFQLQLSEADKAREIGERALKtinyRDEQEKLniwiALLNLENTF---GT 1506
Cdd:COG2956    20 LNGQPDKAIDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYlkaGL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1507 DESLEEIFKRSTQ-YMDSLTMHQKLVSIYSMSEKYYQAEELYKVMTKKFGKSISVWVQYGSFLLDRKLQEETHEVLAKAL 1585
Cdd:COG2956    92 LDRAEELLEKLLElDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKAL 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1586 QTLPkrDHIEVVRKFAQLEFSKGDAEQGRSLFEGLVADAPKRIDLWNVYVDQEIKQDNKSKVEDIFERALAKKlsrKQAK 1665
Cdd:COG2956   172 KLDP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKALELD---PSDD 246

                         250       260
                  ....*....|....*....|...
gi 150865289 1666 FFFTKWLAFEEEKGDEQMAARIK 1688
Cdd:COG2956   247 LLLALADLLERKEGLEAALALLE 269
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1159-1227 2.88e-11

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 60.70  E-value: 2.88e-11
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   1159 GDVVKGFVKNVANNGVYVSLGRSVHALVRVADLSDAYLKDWKKYFKPHQPILGKISAC-KEEGRVLMTLK 1227
Cdd:smart00316    3 GDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVdEEKGRIILSLK 72
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 230-312 7.04e-11

S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240199 [Multi-domain]  Cd Length: 74  Bit Score: 59.57  E-value: 7.04e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  230 DLIPGNALQCSVKSVEDHGIIMNTGRDGLSGFISNKEIKNtpdldVEILKPGKVLLTSIVSKSASRTVnlrpIHSTSVSK 309
Cdd:cd05694     1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGN-----FSKLKVGQLLLCVVEKVKDDGRV----VSLSADPS 71


                  ...
gi 150865289  310 KSA 312
Cdd:cd05694    72 KVS 74
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1246-1317 3.10e-10

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 57.68  E-value: 3.10e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 150865289  1246 VGEIFEGSVKRATDFGVFIKLDGtlNITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLGM 1317
Cdd:pfam00575    3 KGDVVEGEVTRVTKGGAFVDLGN--GVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 548-947 3.82e-10

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 63.52  E-value: 3.82e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  548 RKFKVGSKVRGRVlskqgnklvvtfkkslVNIEDDEVLArfeDakIGFKTPAIVekfvhngaivsffgnlraflPKNEIS 627
Cdd:COG0539    14 KELKEGDIVKGTV----------------VSIDDDEVLV---D--IGYKSEGII--------------------PLSEFS 52

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  628 EtfvSNASDYLRLGQTVNVRVLDVKQEEKRMLVTLRHSSELTNTQKssIDDLQPGKSIVTVSVVEKTKDSVIVELEGnsL 707
Cdd:COG0539    53 D---EPGELEVKVGDEVEVYVEKVEDGEGEIVLSKKKADREKAWEE--LEEAFENGEPVEGKVKGVVKGGLIVDIGG--V 125

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  708 RGVIYTGHLTDGnyeqnraYAKKLS--IGEKLEVLVLEKDLKARTVIVSAKKsLIDAAKQDAIPAYFKDIKVdNKMLRGF 785
Cdd:COG0539   126 RAFLPASQVDVR-------PVRDLDeyVGKTLEFKIIKLDRKRNNVVVSRRA-VLEEEREEKREELLEKLEE-GDVVEGT 196

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  786 VKSVTNKGLFVSFAGkLTGLV----LAkYATSNENEDLLKkfyKYQSIACRVINIDEENKRFLLTLKDVNGsknidseav 861
Cdd:COG0539   197 VKNITDFGAFVDLGG-VDGLLhiseIS-WGRVKHPSEVLK---VGDEVEVKVLKIDREKERISLSLKQLQP--------- 262

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  862 vNPVDT-SKKL-IGDFVPGIATK-----AViksvkgtqlnVQLADNLQGRIAATECfnSWNeiKDKKQPLSQFHKGQVID 934
Cdd:COG0539   263 -DPWENiAEKYpVGDVVKGKVTRltdfgAF----------VELEPGVEGLVHISEM--SWT--KRVAHPSDVVKVGDEVE 327

                         410
                  ....*....|...
gi 150865289  935 VKIIGFhDAKNHK 947
Cdd:COG0539   328 VKVLDI-DPEERR 339
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
592-663 4.40e-10

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 57.23  E-value: 4.40e-10
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 150865289    592 KIGFKTPAIVEKFVHNGAIVSFFGNLRAFLPKNEISETFVSNASDYLRLGQTVNVRVLDVKQEEKRMLVTLR 663
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
782-848 5.52e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 51.45  E-value: 5.52e-08
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 150865289    782 LRGFVKSVTNKGLFVSFAGKLTGLVLAKYATSNENEDLLKKFYKYQSIACRVINIDEENKRFLLTLK 848
Cdd:smart00316    6 VEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_Rrp5_repeat_hs4 cd05696
S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 418-485 3.28e-07

S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240201 [Multi-domain]  Cd Length: 71  Bit Score: 49.18  E-value: 3.28e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 150865289  418 GHVLEDAEVVGSDPNY-VFLKFGGSILGQVHNSKIDKDK--TLEHDFNLGSKHSARVIGFNSIDNLLVLTM 485
Cdd:cd05696     1 GAVVDSVKVTKVEPDLgAVFELKDGLLGFVHISHLSDDKvpSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
509-573 2.07e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 46.83  E-value: 2.07e-06
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 150865289    509 CEIIKVLPeaGGIVIKVLDEFEGFVPGSHMSDIKLVYPERKFKVGSKVRGRVLS--KQGNKLVVTFK 573
Cdd:smart00316    8 GTVTEITP--GGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSvdEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1070-1141 2.49e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.75  E-value: 2.49e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 150865289   1070 KVGQKYPARILKVRDTYVLVELGEKVVASAFITDALDNYSDKLESVFTTNEFATATVLDIDTDSEKIAVSLR 1141
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 599-658 2.76e-04

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 40.73  E-value: 2.76e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   599 AIVEKFVHNGAIVSFFGNLRAFLPKNEISETFVSNASDYLRLGQTVNVRVLDVKQEEKRM 658
Cdd:pfam00575    9 GEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRI 68
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1159-1221 5.54e-04

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 39.96  E-value: 5.54e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 150865289  1159 GDVVKGFVKNVANNGVYVSLGRSVHALVRVADLSDAYLKDWKKYFKPHQPILGKISACKEEGR 1221
Cdd:pfam00575    4 GDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRR 66
PRK05807 PRK05807
RNA-binding protein S1;
1156-1230 7.78e-04

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 41.27  E-value: 7.78e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 150865289 1156 LNRGDVVKGFVKNVANNGVYVSL-GRSvhALVRVADLSDAYLKDWKKYFKPHQPILGKISACKEEGRVLMTLKESE 1230
Cdd:PRK05807    3 LKAGSILEGTVVNITNFGAFVEVeGKT--GLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQAM 76
PRK08059 PRK08059
general stress protein 13; Validated
 595-663 1.30e-03

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 40.42  E-value: 1.30e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 150865289  595 FKTPAIVEKFVHN----GAIVSFFGNLRAFLPKNEISETFVSNASDYLRLGQTVNVRVLDVKQEEKRMLVTLR 663
Cdd:PRK08059    5 YEVGSVVTGKVTGiqpyGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR 77
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 325-395 5.56e-03

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 37.22  E-value: 5.56e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 150865289  325 GILVDALVADVTKNGLIVKVFGLVDATINLAQLQEFdfnALKH---KYAIGNNIKARVMAVltRAGSKKLILSH 395
Cdd:cd05697     1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADV---RLKHpekKFKPGLKVKCRVLSV--EPERKRLVLTL 69
 
Name Accession Description Interval E-value
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1246-1322 2.39e-28

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 109.34  E-value: 2.39e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 150865289 1246 VGEIFEGSVKRATDFGVFIKLDGTlNITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLGMKASYF 1322
Cdd:cd05708     2 VGQKIDGTVRRVEDYGVFIDIDGT-NVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKASYF 77
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 881-950 4.62e-28

S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 108.45  E-value: 4.62e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  881 TKAVIKSVKGTQLNVQLADNLQGRIAATECFNSWneiKDKKQPLSQFHKGQVIDVKIIGFHDAKNHKFLP 950
Cdd:cd05702     4 VKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEW---PDGKNPLSKFKIGQKIKARVIGGHDAKTHRFLP 70
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 988-1060 5.36e-28

S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 108.43  E-value: 5.36e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 150865289  988 GSQHIVFVNNIAKGYVWASLSPNIRGRISFMELTDNVSVFDDLENNLPIGSAISATVKEVDNEHHSVVLTARK 1060
Cdd:cd05703     1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 96-223 1.78e-27

S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 107.69  E-value: 1.78e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   96 LIPGTLVLGQITAVGKLDITLALGDNLVGYIPITSISEELTIQIEQYEKAEDsdeesedeedeqesedgkirtatlKSKS 175
Cdd:cd05693     1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESE------------------------EEDD 56

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 150865289  176 RPEFPELKTLFSIGQWLRAKVVQPSSSqnqnQKQKKRIQLTIEPETVN 223
Cdd:cd05693    57 EEELPDLEDLFSVGQLVRCKVVSLDKS----KSGKKRIELSLEPELVN 100
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1159-1225 5.41e-26

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 102.37  E-value: 5.41e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 150865289 1159 GDVVKGFVKNVANNGVYVSLGRSVHALVRVADLSDAYLKDWKKYFKPHQPILGKISACKEE-GRVLMT 1225
Cdd:cd05707     1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDnGRIEMT 68
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 594-663 8.29e-26

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 101.92  E-value: 8.29e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  594 GFKTPAIVEKFVHNGAIVSFFGNLRAFLPKNEISETFVSNASDYLRLGQTVNVRVLDVKQEEKRMLVTLR 663
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1069-1141 9.99e-25

S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240211 [Multi-domain]  Cd Length: 73  Bit Score: 98.86  E-value: 9.99e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 150865289 1069 VKVGQKYPARILKVRDTYVLVELGEKVVASAFITDALDNYSDKLESVFTTNEFATATVLDIDTDSEKIAVSLR 1141
Cdd:cd05706     1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 764-847 1.10e-21

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 90.72  E-value: 1.10e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  764 KQDAIPAYFKDIKVdNKMLRGFVKSVTNKGLFVSFAGKLTGLVLAKYATSNENEDLLKKFYKYQSIACRVINIDEENKRF 843
Cdd:cd04461     1 KEGTLPTNFSDLKP-GMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRF 79


                  ....
gi 150865289  844 LLTL 847
Cdd:cd04461    80 LLSL 83
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 511-848 3.35e-21

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 99.42  E-value: 3.35e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   511 IIKVLPEAGGIVIkvLDEFEGFVPGSHMSDIKLVYPERKFKVGSKVRGRVLSKQGNKLVVTFkkSLVNIEDDEVLARFED 590
Cdd:TIGR00717  194 VVKNITDFGAFVD--LGGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISL--SLKQLGEDPWEAIEKK 269

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   591 AKIGFKTPAIVEKFVHNGAIVSFFGNLRAFLPKNEIS-ETFVSNASDYLRLGQTVNVRVLDVKQEEKRMLVTLRhssELT 669
Cdd:TIGR00717  270 FPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK---QCK 346

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   670 NTQKSSIDDLQPGKSIVTVSVVEKTKDSVIVELEGNsLRGVIytgHLTDGNYEQNRAYAKKLSIGEK-LEVLVLEKDLKA 748
Cdd:TIGR00717  347 ANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGG-IDGLI---HLSDISWDKDGREADHLYKKGDeIEAVVLAVDKEK 422

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   749 RTVIVSAKKsLIDAAKQDAIPAYFKDIKVdnkmlRGFVKSVTNKGLFVSFAGKLTGLVLAKYATSNENEDLLKKFYKYQS 828
Cdd:TIGR00717  423 KRISLGVKQ-LTENPWEKFAAKYKVGSVV-----KGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDE 496

                          330       340
                   ....*....|....*....|
gi 150865289   829 IACRVINIDEENKRFLLTLK 848
Cdd:TIGR00717  497 VEAKVVDIDKKNRKVSLSVK 516
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 1064-1319 5.60e-19

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 90.49  E-value: 5.60e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1064 ASIKDVKVGQKYPARILKVRDTYVLVELGEK---VVASAFITDALDNYS----DKLEsvfttnefatATVLDIDTDSEKI 1136
Cdd:COG0539    11 ESLKELKEGDIVKGTVVSIDDDEVLVDIGYKsegIIPLSEFSDEPGELEvkvgDEVE----------VYVEKVEDGEGEI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1137 AVSL-RTDspTDKVINSIAD-LNRGDVVKGFVKNVANNGVYVSLGrSVHALVRVADLSDAYLKDWKKYFKphQPILGKIS 1214
Cdd:COG0539    81 VLSKkKAD--REKAWEELEEaFENGEPVEGKVKGVVKGGLIVDIG-GVRAFLPASQVDVRPVRDLDEYVG--KTLEFKII 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1215 ACKEEG-------RVLMTLKESEVSGELnvlkrFDDLVVGEIFEGSVKRATDFGVFIKLDGtlnITGLCHHSQIADKDVD 1287
Cdd:COG0539   156 KLDRKRnnvvvsrRAVLEEEREEKREEL-----LEKLEEGDVVEGTVKNITDFGAFVDLGG---VDGLLHISEISWGRVK 227

                         250       260       270
                  ....*....|....*....|....*....|..
gi 150865289 1288 NVTSLFGEGDRVKVKLLAIDSDKKQLSLGMKA 1319
Cdd:COG0539   228 HPSEVLKVGDEVEVKVLKIDREKERISLSLKQ 259
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 1153-1319 7.12e-19

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 90.10  E-value: 7.12e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1153 IADLNRGDVVKGFVKNVANNGVYVSLGrSVHALVRVADLSdaylkdWKK------YFKPHQPILGKI-SACKEEGRVLMT 1225
Cdd:COG0539   184 LEKLEEGDVVEGTVKNITDFGAFVDLG-GVDGLLHISEIS------WGRvkhpseVLKVGDEVEVKVlKIDREKERISLS 256

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1226 LKESEVSGELNVLKRFddlVVGEIFEGSVKRATDFGVFIKL-DGtlnITGLCHHSQIA-DKDVDNVTSLFGEGDRVKVKL 1303
Cdd:COG0539   257 LKQLQPDPWENIAEKY---PVGDVVKGKVTRLTDFGAFVELePG---VEGLVHISEMSwTKRVAHPSDVVKVGDEVEVKV 330

                         170
                  ....*....|....*.
gi 150865289 1304 LAIDSDKKQLSLGMKA 1319
Cdd:COG0539   331 LDIDPEERRISLSIKQ 346
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 1156-1319 1.40e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 89.93  E-value: 1.40e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1156 LNRGDVVKGFVKNVANNGVYVSLGrSVHALVRVADLSDAYLKDWKKYFKPHQPILGKI-SACKEEGRVLMTLKESEVSGE 1234
Cdd:PRK06676  190 LKEGDVVEGTVARLTDFGAFVDIG-GVDGLVHISELSHERVEKPSEVVSVGQEVEVKVlSIDWETERISLSLKDTLPGPW 268

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1235 LNVLKRFddlVVGEIFEGSVKRATDFGVFIKL-DGtlnITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQL 1313
Cdd:PRK06676  269 EGVEEKL---PEGDVIEGTVKRLTDFGAFVEVlPG---VEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRI 342


                  ....*.
gi 150865289 1314 SLGMKA 1319
Cdd:PRK06676  343 SLSIKA 348
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 1126-1319 1.43e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 91.76  E-value: 1.43e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1126 VLDIDTDSEKIAVSLR--TDSPTDKVINSIadlNRGDVVKGFVKNVANNGVYVSLGRSVHALVRVADLS-DAYLKDWKKY 1202
Cdd:PRK06299  342 VLEIDEEKRRISLGLKqcKENPWEEFAEKY---PVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVEL 418

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1203 FKPHQPILGKI-SACKEEGRVLMTLKESEVSGELNVLKRFDdlvVGEIFEGSVKRATDFGVFIKLDGtlNITGLCHHSQI 1281
Cdd:PRK06299  419 YKKGDEVEAVVlKVDVEKERISLGIKQLEEDPFEEFAKKHK---KGSIVTGTVTEVKDKGAFVELED--GVEGLIRASEL 493

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 150865289 1282 ADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLGMKA 1319
Cdd:PRK06299  494 SRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKA 531
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 1064-1319 5.00e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 88.39  E-value: 5.00e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1064 ASIKDVKVGQKYPARILKVRDTYVLVEL----GEKVVAsafITDALDNYSDKLESVFTTNEFATATVLDIDTDSEKIAVS 1139
Cdd:PRK06676   10 NSVKEVEVGDVVTGEVLKVEDKQVFVNIegykVEGVIP---ISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLS 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1140 LRTDSpTDKVINSI-ADLNRGDVVKGFVKNVANNGVYVSLGrSVHALVRVADLSDAYLKDWKKYFKphQPILGKISACKE 1218
Cdd:PRK06676   87 KRRLE-AEKAWDKLeEKFEEGEVVEVKVTEVVKGGLVVDVE-GVRGFIPASLISTRFVEDFSDFKG--KTLEVKIIELDP 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1219 EGRVLMtLKESEVSGELNVLKR---FDDLVVGEIFEGSVKRATDFGVFIKLDGtlnITGLCHHSQIADKDVDNVTSLFGE 1295
Cdd:PRK06676  163 EKNRVI-LSRRAVVEEERAAKKeelLSSLKEGDVVEGTVARLTDFGAFVDIGG---VDGLVHISELSHERVEKPSEVVSV 238

                         250       260
                  ....*....|....*....|....
gi 150865289 1296 GDRVKVKLLAIDSDKKQLSLGMKA 1319
Cdd:PRK06676  239 GQEVEVKVLSIDWETERISLSLKD 262
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1013-1318 9.25e-18

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 89.24  E-value: 9.25e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1013 GRISFMELTDNVSvfDDLENNLPIGSAISATVKEVDNEHHSVVLTARKNMVASIKDV-----KVGQKYPARILKVRDTYV 1087
Cdd:PRK00087  328 GVIPLRELTLDEI--SSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKEleeafENGEPVKGKVKEVVKGGL 405

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1088 LVELGEkvvASAFITDAL--DNYSDKLeSVFTTNEFaTATVLDIDTDSEKIAVSLRTD-------SPTDKVINSiadLNR 1158
Cdd:PRK00087  406 LVDYGG---VRAFLPASHveLGYVEDL-SEYKGQEL-EVKIIEFNRKRRKKVVLSRKAileeekeKKKEETWNS---LEE 477

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1159 GDVVKGFVKNVANNGVYVSLGrSVHALVRVADLSdaylkdWKKYFKPHQpILG---KISAC-----KEEGRVLMTLKESE 1230
Cdd:PRK00087  478 GDVVEGEVKRLTDFGAFVDIG-GVDGLLHVSEIS------WGRVEKPSD-VLKvgdEIKVYildidKENKKLSLSLKKLL 549

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1231 VSGELNVLKRFDdlvVGEIFEGSVKRATDFGVFIKL-DGtlnITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSD 1309
Cdd:PRK00087  550 PDPWENVEEKYP---VGSIVLGKVVRIAPFGAFVELePG---VDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPE 623


                  ....*....
gi 150865289 1310 KKQLSLGMK 1318
Cdd:PRK00087  624 EKRIRLSIK 632
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1062-1319 9.95e-17

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 86.15  E-value: 9.95e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1062 MVASIKDVKVGQKYPARILKVRDTYVLVELGEK---VVASAFITDALDNysdKLESVFTTNEFATATVLDIDTDSEKIAV 1138
Cdd:PRK00087  293 MNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKsegVIPLRELTLDEIS---SLKESVKVGDEIEVKVLKLEDEDGYVVL 369

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1139 S-LRTDSptDKVINSIADLNR-GDVVKGFVKNVANNGVYVSLGrSVHALVRVADLSDAYLKDWKKYFKphQPILGKISAC 1216
Cdd:PRK00087  370 SkKEADR--EKAWKELEEAFEnGEPVKGKVKEVVKGGLLVDYG-GVRAFLPASHVELGYVEDLSEYKG--QELEVKIIEF 444

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1217 KEEGRVLMTLKESEVSGELNVLKR---FDDLVVGEIFEGSVKRATDFGVFIKLDGtlnITGLCHHSQIADKDVDNVTSLF 1293
Cdd:PRK00087  445 NRKRRKKVVLSRKAILEEEKEKKKeetWNSLEEGDVVEGEVKRLTDFGAFVDIGG---VDGLLHVSEISWGRVEKPSDVL 521

                         250       260
                  ....*....|....*....|....*.
gi 150865289 1294 GEGDRVKVKLLAIDSDKKQLSLGMKA 1319
Cdd:PRK00087  522 KVGDEIKVYILDIDKENKKLSLSLKK 547
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1067-1318 1.02e-16

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 85.56  E-value: 1.02e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  1067 KDVKVGQKYPARILKVRDTYVLVELGEKVVASAFITD-ALDNYSDKLESVFTTNEFATATVLDIDTDSEKIAVSLR--TD 1143
Cdd:TIGR00717  268 KKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEmSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKqcKA 347

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  1144 SPTDKVInsiADLNRGDVVKGFVKNVANNGVYVSLGRSVHALVRVADLS-DAYLKDWKKYFKPHQPILGKISAC-KEEGR 1221
Cdd:TIGR00717  348 NPWEQFE---EKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVdKEKKR 424

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  1222 VLMTLKESEVSGELNVLKRFDdlvVGEIFEGSVKRATDFGVFIKLDGtlNITGLCHHSQIADKDVDNVTSLFGEGDRVKV 1301
Cdd:TIGR00717  425 ISLGVKQLTENPWEKFAAKYK---VGSVVKGKVTEIKDFGAFVELPG--GVEGLIRNSELSENRDEDKTDEIKVGDEVEA 499

                          250
                   ....*....|....*..
gi 150865289  1302 KLLAIDSDKKQLSLGMK 1318
Cdd:TIGR00717  500 KVVDIDKKNRKVSLSVK 516
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 601-1059 1.69e-16

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 84.79  E-value: 1.69e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   601 VEKFVHNGAIVSFFGnLRAFLPKNEISETFVSNASDYlrLGQTVNVRVLDVKQEEKRMLVTLRHSSELTNTQK--SSIDD 678
Cdd:TIGR00717  108 IVGKVKGGFIVDLNG-VEAFLPGSQVDVKPIKDLDSL--IGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAreELLEN 184

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   679 LQPGKSIVTVsVVEKTKDSVIVELEGnsLRGVIytgHLTDGNYEQNRAYAKKLSIGEKLEVLVLEKDLKARTVIVSAKks 758
Cdd:TIGR00717  185 LKEGDVVKGV-VKNITDFGAFVDLGG--VDGLL---HITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLK-- 256

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   759 lidAAKQDAIPAYFKDIKVdNKMLRGFVKSVTNKGLFVSFAGKLTGLV-LAKYATSNENEDLLKKFYKYQSIACRVINID 837
Cdd:TIGR00717  257 ---QLGEDPWEAIEKKFPV-GDKITGRVTNLTDYGVFVEIEEGIEGLVhVSEMSWVKKNSHPSKVVKKGDEVEVMILDID 332

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   838 EENKRFLLTLKdvngsknidsEAVVNPVDT--SKKLIGDFVpgiatKAVIKSVKGTQLNVQLADNLQGRIAATECfnSWN 915
Cdd:TIGR00717  333 PERRRLSLGLK----------QCKANPWEQfeEKHPVGDRV-----TGKIKKITDFGAFVELEGGIDGLIHLSDI--SWD 395

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   916 eiKDKKQPLSQFHKGQVIDVKIIGFhDAKNHKflpithtrsnkniileLSLIKKDLESStPYQELT----FSSIVPGSqh 991
Cdd:TIGR00717  396 --KDGREADHLYKKGDEIEAVVLAV-DKEKKR----------------ISLGVKQLTEN-PWEKFAakykVGSVVKGK-- 453

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 150865289   992 ivfVNNIAKGYVWASLSPNIRGRISFMELTDNvsVFDDLENNLPIGSAISATVKEVDNEHHSVVLTAR 1059
Cdd:TIGR00717  454 ---VTEIKDFGAFVELPGGVEGLIRNSELSEN--RDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 978-1318 8.23e-16

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 82.47  E-value: 8.23e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   978 QELTFSSIVPGSQHIVFVNNIAKGYVWASLSPNIRGRISfmeltdnVSVFDDLENNLPIGSAISATVKEVDNEHHSVVLT 1057
Cdd:TIGR00717    9 ESLKTEETRPGSIVKGTVVAINKDTVFVDVGLKSEGRIP-------KEEFLDAPLEIQVGDEVEVYLDRVEDRFGETVLS 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  1058 ArknmvasIKDVKVGQKYPARILKVRDTYVlVELGEKVVASAFITD-------------ALDNYSDKLESVFTTNEFAta 1124
Cdd:TIGR00717   82 R-------EKAQRHELWIKLEKAYEEGSIV-EGKIVGKVKGGFIVDlngveaflpgsqvDVKPIKDLDSLIGKTLKFK-- 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  1125 tVLDIDTDSEKIAVSLRT------DSPTDKVINSIADlnrGDVVKGFVKNVANNGVYVSLGrSVHALVRVADLSDAYLKD 1198
Cdd:TIGR00717  152 -IIKLDQKRNNIVVSRRAyleeerSQAREELLENLKE---GDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKH 226

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  1199 WKKYFKPHQPILGK-ISACKEEGRVLMTLKESEVSGELNVLKRFDdlvVGEIFEGSVKRATDFGVFIKL-DGtlnITGLC 1276
Cdd:TIGR00717  227 PSEYVKVGQEVKVKvIKFDKEKGRISLSLKQLGEDPWEAIEKKFP---VGDKITGRVTNLTDYGVFVEIeEG---IEGLV 300

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|...
gi 150865289  1277 HHSQIA-DKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLGMK 1318
Cdd:TIGR00717  301 HVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK 343
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 1246-1319 2.06e-15

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 82.02  E-value: 2.06e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 150865289 1246 VGEIFEGSVKRATDFGVFIK-LDGTlniTGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDsDKKQLSLGMKA 1319
Cdd:PRK11824  621 VGEIYEGKVVRIVDFGAFVEiLPGK---DGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID-KRGRIRLSRKA 691
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 547-874 3.14e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 80.98  E-value: 3.14e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  547 ERKFKVGSKVRGRVlskqgnklvvtfkkslVNIEDDEVLARFEDAkigfktpaiVEKFVHngaiVSffgnlraflpknEI 626
Cdd:PRK06299  281 EKKYPVGSKVKGKV----------------TNITDYGAFVELEEG---------IEGLVH----VS------------EM 319

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  627 SET-FVSNASDYLRLGQTVNVRVLDVKQEEKRMLVTLRhsseltNTQKSSIDDL----QPGkSIVTVSVVEKTKDSVIVE 701
Cdd:PRK06299  320 SWTkKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLK------QCKENPWEEFaekyPVG-DVVEGKVKNITDFGAFVG 392

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  702 LEGNsLRGVIytgHLTDGNYEQNRAYAKKL-SIGEKLEVLVLEKDLKARtvivsaKKSL-IDAAKQDAIPAYFKDIKVDN 779
Cdd:PRK06299  393 LEGG-IDGLV---HLSDISWDKKGEEAVELyKKGDEVEAVVLKVDVEKE------RISLgIKQLEEDPFEEFAKKHKKGS 462

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  780 KmLRGFVKSVTNKGLFVSFAGKLTGLVLAKYATSNENEDLLKKFYKYQSIACRVINIDEENKRFLLTLKDVNGSKNIDSE 859
Cdd:PRK06299  463 I-VTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEAEEKEAI 541

                         330
                  ....*....|....*
gi 150865289  860 AVVNPVDTSKKLIGD 874
Cdd:PRK06299  542 AEYNSASDSKTTLGD 556
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 530-947 1.23e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 79.05  E-value: 1.23e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  530 EGFVPGSHmSDIKLVyPERKFKVGSKVRGRVLS---KQGNkLVVTFKKSL--VNIEDDEVLArfEDAKIGFKTPAIVEKF 604
Cdd:PRK06299  138 EAFLPGSQ-VDVRPV-RDTDPLEGKELEFKVIKldkKRNN-IVVSRRAVLeeERAEEREELL--ENLEEGQVVEGVVKNI 212

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  605 VHNGAIVSFfGNLRAFLPKNEISETFVSNASDYLRLGQTVNVRVLDVKQEEKRMLVTLRhssELTNTQKSSIDDLQPGKS 684
Cdd:PRK06299  213 TDYGAFVDL-GGVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLK---QLGEDPWEAIEKKYPVGS 288

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  685 IVTVSVVEKTKDSVIVELEgNSLRGVIytgHLTDGNYEQNRAYAKK-LSIGEKLEVLVLEKDLKARTVIVSAKKSLID-- 761
Cdd:PRK06299  289 KVKGKVTNITDYGAFVELE-EGIEGLV---HVSEMSWTKKNKHPSKvVSVGQEVEVMVLEIDEEKRRISLGLKQCKENpw 364

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  762 ---AAKQdaipayfkdiKVDNKmLRGFVKSVTNKGLFVSFAGKLTGLV-LAKYATSNENEDLLKKFYKYQSIACRVINID 837
Cdd:PRK06299  365 eefAEKY----------PVGDV-VEGKVKNITDFGAFVGLEGGIDGLVhLSDISWDKKGEEAVELYKKGDEVEAVVLKVD 433

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  838 EENKRFLLTLKDVNGsknidseavvNPVDtskKLIGDFVPGIATKAVIKSVKGTQLNVQLADNLQGRIAATEcfNSWNEI 917
Cdd:PRK06299  434 VEKERISLGIKQLEE----------DPFE---EFAKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASE--LSRDRV 498

                         410       420       430
                  ....*....|....*....|....*....|
gi 150865289  918 KDKKqplSQFHKGQVIDVKIIGFhDAKNHK 947
Cdd:PRK06299  499 EDAT---EVLKVGDEVEAKVINI-DRKNRR 524
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1119-1318 1.57e-14

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 78.62  E-value: 1.57e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  1119 NEFATATVLDIDTDSEKIAVSLRT--DSPTDKVINsiaDLNRGDVVKGFVKNVANNGVYVSLGRSVHALVRVADLS-DAY 1195
Cdd:TIGR00717  234 GQEVKVKVIKFDKEKGRISLSLKQlgEDPWEAIEK---KFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKK 310

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  1196 LKDWKKYFKPHQPILGKI-SACKEEGRVLMTLKESEVSGELNVLKRFDdlvVGEIFEGSVKRATDFGVFIKLDGtlNITG 1274
Cdd:TIGR00717  311 NSHPSKVVKKGDEVEVMIlDIDPERRRLSLGLKQCKANPWEQFEEKHP---VGDRVTGKIKKITDFGAFVELEG--GIDG 385

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 150865289  1275 LCHHSQIA-DKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLGMK 1318
Cdd:TIGR00717  386 LIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVK 430
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 1246-1319 2.97e-14

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 70.98  E-value: 2.97e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 150865289 1246 VGEIFEGSVKRATDFGVFIKLDGtlNITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKqLSLGMKA 1319
Cdd:COG1098     5 VGDIVEGKVTGITPFGAFVELPE--GTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDGK-ISLSIKQ 75
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
520-851 8.69e-14

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 76.52  E-value: 8.69e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  520 GIVIKVLDEF---------EGFVPGSHMSDIKLVYPERKFKVGSKVRGRVLSKQGN--KLVVTFKKSLVNIEDDEVLARF 588
Cdd:PRK00087  308 GTVVSVNENEvfvdvgyksEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEdgYVVLSKKEADREKAWKELEEAF 387

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  589 EDakigfKTP--AIVEKFVHNGAIVSFfGNLRAFLPKNEISETFVSNASDYlrLGQTVNVRVLDVKQEEKRMLVTLRHS- 665
Cdd:PRK00087  388 EN-----GEPvkGKVKEVVKGGLLVDY-GGVRAFLPASHVELGYVEDLSEY--KGQELEVKIIEFNRKRRKKVVLSRKAi 459

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  666 --SELTNTQKSSIDDLQPGKsIVTVSVVEKTKDSVIVELEGnsLRGVIytgHLTDGNYEQNRAYAKKLSIGEKLEVLVLE 743
Cdd:PRK00087  460 leEEKEKKKEETWNSLEEGD-VVEGEVKRLTDFGAFVDIGG--VDGLL---HVSEISWGRVEKPSDVLKVGDEIKVYILD 533

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  744 KDLKARTVIVSAKKSLIDAAKQDAipayfKDIKVDNKMLrGFVKSVTNKGLFVSFAGKLTGLVLAKYATSNENEDLLKKF 823
Cdd:PRK00087  534 IDKENKKLSLSLKKLLPDPWENVE-----EKYPVGSIVL-GKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVL 607

                         330       340
                  ....*....|....*....|....*...
gi 150865289  824 YKYQSIACRVINIDEENKRFLLTLKDVN 851
Cdd:PRK00087  608 SEGEEVKAKILEVDPEEKRIRLSIKEVE 635
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 1244-1319 9.63e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 76.36  E-value: 9.63e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 150865289 1244 LVVGEIFEGSVKRATDFGVFIKLDGtlnITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLGMKA 1319
Cdd:PRK06299  199 LEEGQVVEGVVKNITDYGAFVDLGG---VDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQ 271
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 503-571 1.08e-13

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 67.26  E-value: 1.08e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 150865289  503 GTAVKSCeIIKVLPEagGIVIKVLDEFEGFVPGSHMSDIKLVYPERKFKVGSKVRGRVLS--KQGNKLVVT 571
Cdd:cd05697     1 GQVVKGT-IRKLRPS--GIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSvePERKRLVLT 68
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 520-850 1.43e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 74.53  E-value: 1.43e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  520 GIVIKVLDE----------FEGFVPGSHMSDIKLVYPERKFKVGSKVRGRVLSKQGNKLVVTFKKSLVNIED--DEVLAR 587
Cdd:PRK06676   23 GEVLKVEDKqvfvniegykVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEKawDKLEEK 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  588 FEDAKIgFKtpAIVEKFVHNGAIVSFFGnLRAFLPKNEISETFVSNASDYlrLGQTVNVRVLDVKQEEKRMLVTLRH--S 665
Cdd:PRK06676  103 FEEGEV-VE--VKVTEVVKGGLVVDVEG-VRGFIPASLISTRFVEDFSDF--KGKTLEVKIIELDPEKNRVILSRRAvvE 176

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  666 SELTNTQKSSIDDLQPGkSIVTVSVVEKTKDSVIVELEGnsLRGVIytgHLTDGNYEQNRAYAKKLSIGEKLEVLVLEKD 745
Cdd:PRK06676  177 EERAAKKEELLSSLKEG-DVVEGTVARLTDFGAFVDIGG--VDGLV---HISELSHERVEKPSEVVSVGQEVEVKVLSID 250

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  746 LKARTVIVSAKkslidaakqDAIPAYFKDIK---VDNKMLRGFVKSVTNKGLFVSFAGKLTGLV-LAKYATSNEN--EDL 819
Cdd:PRK06676  251 WETERISLSLK---------DTLPGPWEGVEeklPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVhISQISHKHIAtpSEV 321

                         330       340       350
                  ....*....|....*....|....*....|.
gi 150865289  820 LKkfyKYQSIACRVINIDEENKRFLLTLKDV 850
Cdd:PRK06676  322 LE---EGQEVKVKVLEVNEEEKRISLSIKAL 349
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1246-1318 2.53e-13

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 66.47  E-value: 2.53e-13
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 150865289   1246 VGEIFEGSVKRATDFGVFIKLDGtlNITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLGMK 1318
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGN--GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1246-1316 5.68e-13

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 65.34  E-value: 5.68e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 150865289 1246 VGEIFEGSVKRATDFGVFIKLDGtlnITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLG 1316
Cdd:cd05688     1 EGDVVEGTVKSITDFGAFVDLGG---VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1247-1318 6.83e-13

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 65.00  E-value: 6.83e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 150865289 1247 GEIFEGSVKRATDFGVFIKLDGtlNITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKqLSLGMK 1318
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGG--GISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGR-ISLSIK 69
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 580-662 1.03e-12

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 65.30  E-value: 1.03e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  580 EDDEVLARFEDAKIGFKTPAIVEKFVHNGAIVSFFGNLRAFLPKNEISETFVSNASDYLRLGQTVNVRVLDVKQEEKRML 659
Cdd:cd04461     1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80


                  ...
gi 150865289  660 VTL 662
Cdd:cd04461    81 LSL 83
PRK05807 PRK05807
RNA-binding protein S1;
1244-1318 2.06e-12

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 65.92  E-value: 2.06e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 150865289 1244 LVVGEIFEGSVKRATDFGVFIKLDGTlniTGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDsDKKQLSLGMK 1318
Cdd:PRK05807    3 LKAGSILEGTVVNITNFGAFVEVEGK---TGLVHISEVADTYVKDIREHLKEQDKVKVKVISID-DNGKISLSIK 73
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 1247-1315 2.39e-12

S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 63.72  E-value: 2.39e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1247 GEIFEGSVKRATDFGVFIK-LDGTlniTGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDsDKKQLSL 1315
Cdd:cd04472     1 GKIYEGKVVKIKDFGAFVEiLPGK---DGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD-DRGRISL 66
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1430-1688 8.33e-12

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 67.83  E-value: 8.33e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1430 LNTRAPQSVADFERLLVGNPNSSILWMNYMSFQLQLSEADKAREIGERALKtinyRDEQEKLniwiALLNLENTF---GT 1506
Cdd:COG2956    20 LNGQPDKAIDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYlkaGL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1507 DESLEEIFKRSTQ-YMDSLTMHQKLVSIYSMSEKYYQAEELYKVMTKKFGKSISVWVQYGSFLLDRKLQEETHEVLAKAL 1585
Cdd:COG2956    92 LDRAEELLEKLLElDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKAL 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1586 QTLPkrDHIEVVRKFAQLEFSKGDAEQGRSLFEGLVADAPKRIDLWNVYVDQEIKQDNKSKVEDIFERALAKKlsrKQAK 1665
Cdd:COG2956   172 KLDP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKALELD---PSDD 246

                         250       260
                  ....*....|....*....|...
gi 150865289 1666 FFFTKWLAFEEEKGDEQMAARIK 1688
Cdd:COG2956   247 LLLALADLLERKEGLEAALALLE 269
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 1247-1318 1.63e-11

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.


Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 61.49  E-value: 1.63e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 150865289 1247 GEIFEGSVKRATDFGVFIKLDGTLNIT-GLCHHSQI-ADKDVDNVTSLFGEGDRVKVKLLAIDSDKkqLSLGMK 1318
Cdd:cd05684     1 GKIYKGKVTSIMDFGCFVQLEGLKGRKeGLVHISQLsFEGRVANPSDVVKRGQKVKVKVISIQNGK--ISLSMK 72
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 1153-1318 2.01e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 68.65  E-value: 2.01e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1153 IADLNRGDVVKGFVKNVANNGVYVSLGrSVHALVRVADLSdaylkdWK------KYFKPHQPILGK-ISACKEEGRVLMT 1225
Cdd:PRK06299  196 LENLEEGQVVEGVVKNITDYGAFVDLG-GVDGLLHITDIS------WKrvnhpsEVVNVGDEVKVKvLKFDKEKKRVSLG 268

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1226 LKESEVSGELNVLKRFDdlvVGEIFEGSVKRATDFGVFIKL-DGtlnITGLCHHSQIA-DKDVDNVTSLFGEGDRVKVKL 1303
Cdd:PRK06299  269 LKQLGEDPWEAIEKKYP---VGSKVKGKVTNITDYGAFVELeEG---IEGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMV 342

                         170
                  ....*....|....*
gi 150865289 1304 LAIDSDKKQLSLGMK 1318
Cdd:PRK06299  343 LEIDEEKRRISLGLK 357
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1159-1227 2.88e-11

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 60.70  E-value: 2.88e-11
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   1159 GDVVKGFVKNVANNGVYVSLGRSVHALVRVADLSDAYLKDWKKYFKPHQPILGKISAC-KEEGRVLMTLK 1227
Cdd:smart00316    3 GDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVdEEKGRIILSLK 72
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 1247-1315 4.55e-11

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 59.94  E-value: 4.55e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 150865289 1247 GEIFEGSVKRATDFGVFIklDGTLNITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSL 1315
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFV--DIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISL 67
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 549-879 4.93e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 66.82  E-value: 4.93e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  549 KFKVGSKVRGRVLSkqgnklvvtfkkslvnIEDDEVLARFEDAKIgfktpaivekfvhNGAIvsffgnlraflPKNEISE 628
Cdd:PRK06676   14 EVEVGDVVTGEVLK----------------VEDKQVFVNIEGYKV-------------EGVI-----------PISELSN 53

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  629 TFVSNASDYLRLGQTVNVRVLDVKQEEKRMLVTLRHSSEltntqKSSIDDLQ---PGKSIVTVSVVEKTKDSVIVELEGn 705
Cdd:PRK06676   54 DHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEA-----EKAWDKLEekfEEGEVVEVKVTEVVKGGLVVDVEG- 127

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  706 sLRGVIYTGHLTDGNYEQNRAYakklsIGEKLEVLVLEKDLKARTVIVSAkKSLIDAAKQDAIPAYFKDIKVDNKmLRGF 785
Cdd:PRK06676  128 -VRGFIPASLISTRFVEDFSDF-----KGKTLEVKIIELDPEKNRVILSR-RAVVEEERAAKKEELLSSLKEGDV-VEGT 199

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  786 VKSVTNKGLFVSFAGkLTGLV----LAkYATSNENEDLLKkfyKYQSIACRVINIDEENKRFLLTLKDVNGS--KNIDSE 859
Cdd:PRK06676  200 VARLTDFGAFVDIGG-VDGLVhiseLS-HERVEKPSEVVS---VGQEVEVKVLSIDWETERISLSLKDTLPGpwEGVEEK 274

                         330       340
                  ....*....|....*....|....*..
gi 150865289  860 AVVNPV--DTSKKLI--GDFV---PGI 879
Cdd:PRK06676  275 LPEGDVieGTVKRLTdfGAFVevlPGV 301
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 230-312 7.04e-11

S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240199 [Multi-domain]  Cd Length: 74  Bit Score: 59.57  E-value: 7.04e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  230 DLIPGNALQCSVKSVEDHGIIMNTGRDGLSGFISNKEIKNtpdldVEILKPGKVLLTSIVSKSASRTVnlrpIHSTSVSK 309
Cdd:cd05694     1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGN-----FSKLKVGQLLLCVVEKVKDDGRV----VSLSADPS 71


                  ...
gi 150865289  310 KSA 312
Cdd:cd05694    72 KVS 74
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1246-1317 3.10e-10

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 57.68  E-value: 3.10e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 150865289  1246 VGEIFEGSVKRATDFGVFIKLDGtlNITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLGM 1317
Cdd:pfam00575    3 KGDVVEGEVTRVTKGGAFVDLGN--GVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 548-947 3.82e-10

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 63.52  E-value: 3.82e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  548 RKFKVGSKVRGRVlskqgnklvvtfkkslVNIEDDEVLArfeDakIGFKTPAIVekfvhngaivsffgnlraflPKNEIS 627
Cdd:COG0539    14 KELKEGDIVKGTV----------------VSIDDDEVLV---D--IGYKSEGII--------------------PLSEFS 52

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  628 EtfvSNASDYLRLGQTVNVRVLDVKQEEKRMLVTLRHSSELTNTQKssIDDLQPGKSIVTVSVVEKTKDSVIVELEGnsL 707
Cdd:COG0539    53 D---EPGELEVKVGDEVEVYVEKVEDGEGEIVLSKKKADREKAWEE--LEEAFENGEPVEGKVKGVVKGGLIVDIGG--V 125

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  708 RGVIYTGHLTDGnyeqnraYAKKLS--IGEKLEVLVLEKDLKARTVIVSAKKsLIDAAKQDAIPAYFKDIKVdNKMLRGF 785
Cdd:COG0539   126 RAFLPASQVDVR-------PVRDLDeyVGKTLEFKIIKLDRKRNNVVVSRRA-VLEEEREEKREELLEKLEE-GDVVEGT 196

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  786 VKSVTNKGLFVSFAGkLTGLV----LAkYATSNENEDLLKkfyKYQSIACRVINIDEENKRFLLTLKDVNGsknidseav 861
Cdd:COG0539   197 VKNITDFGAFVDLGG-VDGLLhiseIS-WGRVKHPSEVLK---VGDEVEVKVLKIDREKERISLSLKQLQP--------- 262

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  862 vNPVDT-SKKL-IGDFVPGIATK-----AViksvkgtqlnVQLADNLQGRIAATECfnSWNeiKDKKQPLSQFHKGQVID 934
Cdd:COG0539   263 -DPWENiAEKYpVGDVVKGKVTRltdfgAF----------VELEPGVEGLVHISEM--SWT--KRVAHPSDVVKVGDEVE 327

                         410
                  ....*....|...
gi 150865289  935 VKIIGFhDAKNHK 947
Cdd:COG0539   328 VKVLDI-DPEERR 339
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
592-663 4.40e-10

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 57.23  E-value: 4.40e-10
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 150865289    592 KIGFKTPAIVEKFVHNGAIVSFFGNLRAFLPKNEISETFVSNASDYLRLGQTVNVRVLDVKQEEKRMLVTLR 663
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 510-851 7.47e-10

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 62.75  E-value: 7.47e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  510 EIIKvlpeagGIVIKVLDEF---------EGFVPGSHMSDIKlvyPERKFKVGSKVRGRVLSKQGNK--LVVTFKKSLVN 578
Cdd:COG0539    20 DIVK------GTVVSIDDDEvlvdigyksEGIIPLSEFSDEP---GELEVKVGDEVEVYVEKVEDGEgeIVLSKKKADRE 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  579 IEDDEVLARFEDAKIgFKtpAIVEKFVHNGAIVSFFGnLRAFLPKNEISETFVSNASDYLrlGQTVNVRVLDVKQEEKRM 658
Cdd:COG0539    91 KAWEELEEAFENGEP-VE--GKVKGVVKGGLIVDIGG-VRAFLPASQVDVRPVRDLDEYV--GKTLEFKIIKLDRKRNNV 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  659 LVTLRHSSELTNTQKSS--IDDLQPGKsIVTVSVVEKTKDSVIVELEGnsLRGVIytgHLTDGNYEQNRAYAKKLSIGEK 736
Cdd:COG0539   165 VVSRRAVLEEEREEKREelLEKLEEGD-VVEGTVKNITDFGAFVDLGG--VDGLL---HISEISWGRVKHPSEVLKVGDE 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  737 LEVLVLEKDLKARTVIVSAKKSLID-----AAKqdaipayfkdIKVDNKmLRGFVKSVTNKGLFVSFAGKLTGLV-LAKY 810
Cdd:COG0539   239 VEVKVLKIDREKERISLSLKQLQPDpweniAEK----------YPVGDV-VKGKVTRLTDFGAFVELEPGVEGLVhISEM 307

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|.
gi 150865289  811 ATSNENEDLLKKFYKYQSIACRVINIDEENKRFLLTLKDVN 851
Cdd:COG0539   308 SWTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIKQLA 348
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 683-1227 7.82e-10

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 63.60  E-value: 7.82e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   683 KSIVTVSVVEKTKDSVIVELEGNSlRGVIYTGHLTDGNYEqnrayakkLSIGEKLEVLVLEKDLKARTVIVSAKKSLIDA 762
Cdd:TIGR00717   19 GSIVKGTVVAINKDTVFVDVGLKS-EGRIPKEEFLDAPLE--------IQVGDEVEVYLDRVEDRFGETVLSREKAQRHE 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   763 AKQDAIPAYFKDIKVDNKMLrGFVKSvtnkGLFVSFAGkltglvlakyatsnenedlLKKFYKYQSIACRVINIDEE--N 840
Cdd:TIGR00717   90 LWIKLEKAYEEGSIVEGKIV-GKVKG----GFIVDLNG-------------------VEAFLPGSQVDVKPIKDLDSliG 145

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   841 KRF---LLTLKDVNGSKNIDSEAVVNPVDTSKK--LIGDFVPGIATKAVIKSVKGTQLNVQLaDNLQGRIAATECfnSWN 915
Cdd:TIGR00717  146 KTLkfkIIKLDQKRNNIVVSRRAYLEEERSQAReeLLENLKEGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDM--SWK 222

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   916 EIKdkkQPLSQFHKGQVIDVKIIGFHDAKNHKFLPITHTRSNkniilelslikkdlesstPYQELTfSSIVPGSQHIVFV 995
Cdd:TIGR00717  223 RVK---HPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGED------------------PWEAIE-KKFPVGDKITGRV 280

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   996 NNIAKGYVWASLSPNIRG--RISFMELTDNVSvfdDLENNLPIGSAISATVKEVDNEHHSVVLtarknmvaSIKDVK--- 1070
Cdd:TIGR00717  281 TNLTDYGVFVEIEEGIEGlvHVSEMSWVKKNS---HPSKVVKKGDEVEVMILDIDPERRRLSL--------GLKQCKanp 349

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  1071 ---------VGQKYPARILKVRDTYVLVELGEKVVASAFITDA--LDNYSDKLESVFTTNEFAtATVLDIDTDSEKIAVS 1139
Cdd:TIGR00717  350 weqfeekhpVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDIswDKDGREADHLYKKGDEIE-AVVLAVDKEKKRISLG 428

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  1140 LR--TDSPTDKvinsIADLNR-GDVVKGFVKNVANNGVYVSLGRSVHALVRVADLSDAYLKDWKKYFKPHQPILGKISAC 1216
Cdd:TIGR00717  429 VKqlTENPWEK----FAAKYKvGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDI 504

                          570
                   ....*....|..
gi 150865289  1217 -KEEGRVLMTLK 1227
Cdd:TIGR00717  505 dKKNRKVSLSVK 516
rpsA PRK13806
30S ribosomal protein S1; Provisional
 1064-1316 1.14e-09

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 62.82  E-value: 1.14e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1064 ASIKDVKVGQKYPARILKVRDTYVLVELGEKVVASAFITDALDNYSDKLESVFTTNEFATATVLDIDTDSE----KIAVS 1139
Cdd:PRK13806  195 AFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLS 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1140 LR--TDSPTDkvinSIAD-LNRGDVVKGFVKNVANNGVYVSLGRSVHALVRVADLSDAylkdwKKYFKPHQPI-LGKISA 1215
Cdd:PRK13806  275 IKqaGGDPWD----TVGDrLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWT-----RRVNKPEDVVaPGDAVA 345

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1216 CK------EEGRVLMTLKESEVSGELNVLKRFddlVVGEIFEGSVKRATDFGVFIKLDGtlNITGLCHHSQIADKDVDNV 1289
Cdd:PRK13806  346 VKikdidpAKRRISLSLRDAEGDPWADVAERF---APGTTVTGTVEKRAQFGLFVNLAP--GVTGLLPASVISRAGKPAT 420

                         250       260
                  ....*....|....*....|....*..
gi 150865289 1290 TSLFGEGDRVKVKLLAIDSDKKQLSLG 1316
Cdd:PRK13806  421 YEKLKPGDSVTLVVEEIDTAKRKISLA 447
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1228-1319 1.93e-09

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 62.06  E-value: 1.93e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  1228 ESEVSGELNVLkrFDDLVVGEIFEGSVKRATDFGVFIKLDGtlnITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAID 1307
Cdd:TIGR00717  171 EEERSQAREEL--LENLKEGDVVKGVVKNITDFGAFVDLGG---VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFD 245

                           90
                   ....*....|..
gi 150865289  1308 SDKKQLSLGMKA 1319
Cdd:TIGR00717  246 KEKGRISLSLKQ 257
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 1237-1317 2.25e-09

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 55.67  E-value: 2.25e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1237 VLKRFDDLVVGEIFEGSVKRATDFGVFIKLDGtlNITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLG 1316
Cdd:cd04461     5 LPTNFSDLKPGMVVHGYVRNITPYGVFVEFLG--GLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLS 82


                  .
gi 150865289 1317 M 1317
Cdd:cd04461    83 L 83
rpsA PRK13806
30S ribosomal protein S1; Provisional
 1153-1320 4.23e-09

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 60.89  E-value: 4.23e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1153 IADLNRGDVVKGFVKNVANNGVYVSLGRSVHALVRVADLSdaylkdWKKYFKPHQPI-LG--------KISACKEEGRVL 1223
Cdd:PRK13806  197 METVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELS------WSRVQKADEAVsVGdtvrvkvlGIERAKKGKGLR 270

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1224 MTLKESEVSGE--LNVLKRFDDlvvGEIFEGSVKRATDFGVFIK-LDGtlnITGLCHHSQIA-----DKDVDNVTSlfge 1295
Cdd:PRK13806  271 ISLSIKQAGGDpwDTVGDRLKA---GDKVTGKVVRLAPFGAFVEiLPG---IEGLVHVSEMSwtrrvNKPEDVVAP---- 340

                         170       180
                  ....*....|....*....|....*
gi 150865289 1296 GDRVKVKLLAIDSDKKQLSLGMKAS 1320
Cdd:PRK13806  341 GDAVAVKIKDIDPAKRRISLSLRDA 365
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1247-1316 5.23e-09

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 54.04  E-value: 5.23e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 150865289 1247 GEIFEGSVKRATDFGVFIKLDGtlNITGLCHHSQIA-DKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLG 1316
Cdd:cd05690     1 GTVVSGKIKSITDFGIFVGLDG--GIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG 69
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 502-851 8.66e-09

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 60.50  E-value: 8.66e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  502 NGTAVKScEIIKVLPEAGGIVIKVLDEFEGFVPGSHMSDIKLVYPERKFKVGSKVRGRVLSK----QGNKLVVTFKKSLv 577
Cdd:PRK12269  398 DGTPVEG-RIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPESLIGLTSKFYIERISQskqhRGNDNIVINRRRY- 475

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  578 nIEDDEVLAR---FEDAKIGFKTPAIVEKFVHNGAIVSFfGNLRAFLPKNEISETFVSNASDYLRLGQTVNVRVLDVKQE 654
Cdd:PRK12269  476 -LEERARQAReefFNSVHIEDSVSGVVKSFTSFGAFIDL-GGFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQA 553

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  655 EKRMLVTLRHSSE---LTNTQKSSIDDLQPGKsivtvsvVEKTKD-SVIVELEgnslRGVIYTGHLTDGNY-EQNRAYAK 729
Cdd:PRK12269  554 EKRINLSLKHFQPdpwLEFENKFGVNDVVKGR-------VTKIADfGAFIELA----EGIEGLAHISEFSWvKKTSKPSD 622

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  730 KLSIGEKLEVLVLEKDLKARTVIVSAKKslIDAAKQDAIPAYFkdiKVDNKMLRGFVKsVTNKGLFVSFAGKLTG----- 804
Cdd:PRK12269  623 MVKIGDEVECMILGYDIQAGRVSLGLKQ--VTANPWEEIEARY---PVGARFTRRIVK-VTNAGAFIEMEEGIDGflhvd 696

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*...
gi 150865289  805 -LVLAKYATSNENEDLLKKfykyqSIACRVINIDEENKRFLLTLKDVN 851
Cdd:PRK12269  697 dLSWVKRTRPADHELEVGK-----EIECMVIECDPQARRIRLGVKQLS 739
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 171-663 1.09e-08

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 59.75  E-value: 1.09e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   171 LKSKSR---PEFPELKTLFSIGQWLRAKVVQ-------PSSSQNQNQKQKKRIQLTI---EPETVnqpledEDLIPGNal 237
Cdd:TIGR00717   40 LKSEGRipkEEFLDAPLEIQVGDEVEVYLDRvedrfgeTVLSREKAQRHELWIKLEKayeEGSIV------EGKIVGK-- 111

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   238 qcsVKSvedhGIIMNTGrdGLSGF--ISNKEIKNTPDLDVEILKPGKVLLTSIVSKSASRTVNLRPIHSTSVSKKSAVts 315
Cdd:TIGR00717  112 ---VKG----GFIVDLN--GVEAFlpGSQVDVKPIKDLDSLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREE-- 180

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   316 isSVDAVLPGILVDALVADVTKNGLIVKVfGLVDAtinLAQLQEFDFNALKHKYAI---GNNIKARVMAVLTRAGSKKLI 392
Cdd:TIGR00717  181 --LLENLKEGDVVKGVVKNITDFGAFVDL-GGVDG---LLHITDMSWKRVKHPSEYvkvGQEVKVKVIKFDKEKGRISLS 254

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   393 LSHLPHaisytstasNP--DALEAFPIGHVLEdAEVVGSDPNYVFLKFGGSILGQVHNSKIDKDKTLEHD---FNLGSKH 467
Cdd:TIGR00717  255 LKQLGE---------DPweAIEKKFPVGDKIT-GRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPskvVKKGDEV 324

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   468 SARVIGFNSIDNLLVLTMESHVINSQYLHASDVPNGTAVKScEIIKVlpEAGGIVIKVLDEFEGFVpgsHMSDIKLV--- 544
Cdd:TIGR00717  325 EVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTG-KIKKI--TDFGAFVELEGGIDGLI---HLSDISWDkdg 398

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   545 -YPERKFKVGSKVRGRVLS--KQGNKLVVTFKKSLVNieddevlaRFEDAKIGFKTPAIVEKFVHN----GAIVSFFGNL 617
Cdd:TIGR00717  399 rEADHLYKKGDEIEAVVLAvdKEKKRISLGVKQLTEN--------PWEKFAAKYKVGSVVKGKVTEikdfGAFVELPGGV 470

                          490       500       510       520
                   ....*....|....*....|....*....|....*....|....*.
gi 150865289   618 RAFLPKNEISETFVSNASDYLRLGQTVNVRVLDVKQEEKRMLVTLR 663
Cdd:TIGR00717  471 EGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 1248-1315 2.27e-08

S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.


Pssm-ID: 240191 [Multi-domain]  Cd Length: 73  Bit Score: 52.48  E-value: 2.27e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 150865289 1248 EIFEGSVKRATDFGVFIKLDGTLNiTGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKK-QLSL 1315
Cdd:cd05686     5 QIFKGEVASVTEYGAFVKIPGCRK-QGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKmKLSL 72
PRK08059 PRK08059
general stress protein 13; Validated
 1246-1319 2.36e-08

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 53.90  E-value: 2.36e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 150865289 1246 VGEIFEGSVKRATDFGVFIKLDGTLNitGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLGMKA 1319
Cdd:PRK08059    7 VGSVVTGKVTGIQPYGAFVALDEETQ--GLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRA 78
rpsA PRK13806
30S ribosomal protein S1; Provisional
 423-859 2.41e-08

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 58.58  E-value: 2.41e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  423 DAEVVGSDPNYVFLKFGGSILGQVhnskiDKDKTLEHDFNL----GSKHSARVIGFNSIDNLLVLTMESHVINSQYLHAS 498
Cdd:PRK13806   39 TGTVIAITEDSVFVDTGSKVDGVV-----DRAELLDADGELtvavGDEVELYVVSVNGQEIRLSKALSGQGGAAMLEEAY 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  499 DvpNGTAV--KSCEIIKvlpeaGGIVIKVLDEfEGFVPGSHMsDIKLVYPERKFkVGSKVRGRV--LSKQGNKLVVTfKK 574
Cdd:PRK13806  114 E--NGVPVegKVTGTCK-----GGFNVEVLGR-RAFCPVSQI-DLRYVEDPESY-VGQTFQFLItrVEENGRNIVVS-RR 182

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  575 SLVNIEDDEVLARF-EDAKIGFKTPAIVEKFVHNGAIVSFFGNLRAFLPKNEISETFVSNASDYLRLGQTVNVRVLDVKQ 653
Cdd:PRK13806  183 ALLEREQKEALEAFmETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIER 262

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  654 EEK----RMLVTLRHSSEltNTQKSSIDDLQPGkSIVTVSVVEKTKDSVIVELegnsLRGVIYTGHLTDGNYEQNRAYAK 729
Cdd:PRK13806  263 AKKgkglRISLSIKQAGG--DPWDTVGDRLKAG-DKVTGKVVRLAPFGAFVEI----LPGIEGLVHVSEMSWTRRVNKPE 335

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  730 K-LSIGEKLEVLVLEKDLKARTVIVSAKKSL----IDAAKQDAIPAyfkdikvdnkMLRGFVKSVTNKGLFVSFAGKLTG 804
Cdd:PRK13806  336 DvVAPGDAVAVKIKDIDPAKRRISLSLRDAEgdpwADVAERFAPGT----------TVTGTVEKRAQFGLFVNLAPGVTG 405

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 150865289  805 LVLAKYATSNENEDLLKKFYKYQSIACRVINIDEENKRFLLTLKDVNGSKNIDSE 859
Cdd:PRK13806  406 LLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLAPAGAAGSGADDDD 460
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1250-1316 3.89e-08

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 51.61  E-value: 3.89e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 150865289 1250 FEGSVKRATDFGVFIKLDGtlNITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLG 1316
Cdd:cd00164     1 VTGKVVSITKFGVFVELED--GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
782-848 5.52e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 51.45  E-value: 5.52e-08
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 150865289    782 LRGFVKSVTNKGLFVSFAGKLTGLVLAKYATSNENEDLLKKFYKYQSIACRVINIDEENKRFLLTLK 848
Cdd:smart00316    6 VEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 978-1318 1.28e-07

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 56.64  E-value: 1.28e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  978 QELTFSSIVPGSQHIVFVNNIAKGYVWASLSPNIRGRISFMELT------DNVSVFddLENNLPIGSAISATVKEvdneh 1051
Cdd:PRK12269  312 ERYSFEAPEPGSVRMGTVVQVNAGTVFVDIGGKSEGRVPVEEFEappkagDGVRVY--VERVTPYGPELSKTKAD----- 384

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1052 hsvvltaRKNMVASIKDV-KVGQKYPARILKV--RDTYVLVELGEKVVASAFITDALDNYSDKLESVF-TTNEFATATVL 1127
Cdd:PRK12269  385 -------RLGLKVKLRDAeRDGTPVEGRIVRLteKKSGFEVDLGAGMMAFLPISQSDCQKVDAPESLIgLTSKFYIERIS 457

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1128 --------DIDTDSEKIAVSLRTDSPTDKVINSIadlNRGDVVKGFVKNVANNGVYVSLGrSVHALVRVADLSDAYLKDW 1199
Cdd:PRK12269  458 qskqhrgnDNIVINRRRYLEERARQAREEFFNSV---HIEDSVSGVVKSFTSFGAFIDLG-GFDGLLHVNDMSWGHVARP 533

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1200 KKYFKPHQPI-LGKISACKEEGRVLMTLKESEVSGELNVLKRFDdlvVGEIFEGSVKRATDFGVFIKLdgTLNITGLCHH 1278
Cdd:PRK12269  534 REFVKKGQTIeLKVIRLDQAEKRINLSLKHFQPDPWLEFENKFG---VNDVVKGRVTKIADFGAFIEL--AEGIEGLAHI 608

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|.
gi 150865289 1279 SQIA-DKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLGMK 1318
Cdd:PRK12269  609 SEFSwVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLK 649
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 1246-1318 2.78e-07

S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein.


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 49.50  E-value: 2.78e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 150865289 1246 VGEIFEGSVKRATDFGVFIKLDGTLNITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLGMK 1318
Cdd:cd04452     3 EGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK 75
S1_Rrp5_repeat_hs4 cd05696
S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 418-485 3.28e-07

S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240201 [Multi-domain]  Cd Length: 71  Bit Score: 49.18  E-value: 3.28e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 150865289  418 GHVLEDAEVVGSDPNY-VFLKFGGSILGQVHNSKIDKDK--TLEHDFNLGSKHSARVIGFNSIDNLLVLTM 485
Cdd:cd05696     1 GAVVDSVKVTKVEPDLgAVFELKDGLLGFVHISHLSDDKvpSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1162-1223 5.93e-07

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 48.15  E-value: 5.93e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 150865289 1162 VKGFVKNVANNGVYVSLGRSVHALVRVADLSDAYLKDWKKYFKPHQPILGKISACKEEGRVL 1223
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRI 62
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 1226-1319 7.71e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 52.88  E-value: 7.71e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1226 LKESEVSGELN----------VLKRFDDLVVGEIFEGSVKRATDFGVFIKLDGtlnITGLCHHSQIADKDVDNVTSLFGE 1295
Cdd:PRK07400  166 LKFLEVDEERNrlvlshrralVERKMNRLEVGEVVVGTVRGIKPYGAFIDIGG---VSGLLHISEISHEHIETPHSVFNV 242

                          90       100
                  ....*....|....*....|....
gi 150865289 1296 GDRVKVKLLAIDSDKKQLSLGMKA 1319
Cdd:PRK07400  243 NDEMKVMIIDLDAERGRISLSTKQ 266
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1533-1658 1.30e-06

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 49.42  E-value: 1.30e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1533 IYSMSEKYYQAEELYKVMTKKFGKSISVWVQYGSFLLDRKLQEETHEVLAKALQTLPkrDHIEVVRKFAQLEFSKGDAEQ 1612
Cdd:COG4783    13 ALLLAGDYDEAEALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLHEALELDP--DEPEARLNLGLALLKAGDYDE 90

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 150865289 1613 GRSLFEGLVADAPKRIDLWNVYVDQEIKQDNKSKVEDIFERALAKK 1658
Cdd:COG4783    91 ALALLEKALKLDPEHPEAYLRLARAYRALGRPDEAIAALEKALELD 136
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
509-573 2.07e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 46.83  E-value: 2.07e-06
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 150865289    509 CEIIKVLPeaGGIVIKVLDEFEGFVPGSHMSDIKLVYPERKFKVGSKVRGRVLS--KQGNKLVVTFK 573
Cdd:smart00316    8 GTVTEITP--GGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSvdEEKGRIILSLK 72
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 1246-1315 2.15e-06

S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.


Pssm-ID: 239917 [Multi-domain]  Cd Length: 83  Bit Score: 47.01  E-value: 2.15e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1246 VGEIFEGSVKRATDFGVFIKLDGTLnITGLCHHSQIAD---KDVDNVTSLFGE--------GDRVKVKLLAIDSDKKQLS 1314
Cdd:cd04471     1 VGEEFDGVISGVTSFGLFVELDNLT-VEGLVHVSTLGDdyyEFDEENHALVGErtgkvfrlGDKVKVRVVRVDLDRRKID 79


                  .
gi 150865289 1315 L 1315
Cdd:cd04471    80 F 80
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 674-842 2.16e-06

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 51.97  E-value: 2.16e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  674 SSIDDLQPGkSIVTVSVVEKTKDSVIVELEGNSlRGVIYTGHLTDGNYEqnrayaKKLSIGEKLEVLVLEKDLKARTVIV 753
Cdd:COG0539    11 ESLKELKEG-DIVKGTVVSIDDDEVLVDIGYKS-EGIIPLSEFSDEPGE------LEVKVGDEVEVYVEKVEDGEGEIVL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  754 SAKKSLIDAAKQDAIPAYFKDIKVDnkmlrGFVKSVTNKGLFVSFAGkLTG-----LVLAKYAtsnenEDLLKkfYKYQS 828
Cdd:COG0539    83 SKKKADREKAWEELEEAFENGEPVE-----GKVKGVVKGGLIVDIGG-VRAflpasQVDVRPV-----RDLDE--YVGKT 149

                         170
                  ....*....|....
gi 150865289  829 IACRVINIDEENKR 842
Cdd:COG0539   150 LEFKIIKLDRKRNN 163
PRK08582 PRK08582
RNA-binding protein S1;
1246-1318 2.26e-06

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 48.88  E-value: 2.26e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 150865289 1246 VGEIFEGSVKRATDFGVFIKLDGtlNITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKqLSLGMK 1318
Cdd:PRK08582    5 VGSKLQGKVTGITNFGAFVELPE--GKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGK-IGLSIK 74
S1_Rrp5_repeat_hs4 cd05696
S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 503-561 2.70e-06

S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240201 [Multi-domain]  Cd Length: 71  Bit Score: 46.49  E-value: 2.70e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 150865289  503 GTAVKSCEIIKVLPEAGgIVIKVLDEFEGFVPGSHMSDIKLVYPERKFKVGSKVRGRVL 561
Cdd:cd05696     1 GAVVDSVKVTKVEPDLG-AVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARII 58
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 1247-1315 2.78e-06

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 46.46  E-value: 2.78e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 150865289 1247 GEIFEGSVKRATDFGVFIKLDGtlNITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSL 1315
Cdd:cd05697     1 GQVVKGTIRKLRPSGIFVKLSD--HIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVL 67
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 784-848 3.37e-06

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 46.06  E-value: 3.37e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 150865289  784 GFVKSVTNKGLFVSFAGKLTGLVLAKYATSNENEDLLKKFYKYQSIACRVINIDEENKRFLLTLK 848
Cdd:cd05698     6 GTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 1241-1306 6.45e-06

S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.


Pssm-ID: 239919 [Multi-domain]  Cd Length: 77  Bit Score: 45.68  E-value: 6.45e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 150865289 1241 FDDLVVGEIFEGSVKRATDFGVFIKLDGtlNITGLCHHSqiadkdvdNVTSLFGEGDRVKVKLLAI 1306
Cdd:cd04473    11 MEDLEVGKLYKGKVNGVAKYGVFVDLND--HVRGLIHRS--------NLLRDYEVGDEVIVQVTDI 66
VacB COG0557
Exoribonuclease R [Transcription];
1246-1313 8.32e-06

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 50.88  E-value: 8.32e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 150865289 1246 VGEIFEGSVKRATDFGVFIKLDGTLnITGLCHHSQIADK--DVDNVT-SLFGE--------GDRVKVKLLAIDSDKKQL 1313
Cdd:COG0557   622 VGEEFEGVISGVTSFGLFVELDELG-VEGLVHVSSLGDDyyEYDERRqALVGErtgkryrlGDRVEVRVVRVDLDRRQI 699
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 1148-1226 1.40e-05

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 44.89  E-value: 1.40e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1148 KVINSIADLNRGDVVKGFVKNVANNGVYVSLGRSVHALVRVADLSDAYLKDWKKYFKPHQPILGKISACKEE-GRVLMTL 1226
Cdd:cd04461     4 TLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEkQRFLLSL 83
rpsA PRK13806
30S ribosomal protein S1; Provisional
 1221-1318 1.75e-05

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 49.34  E-value: 1.75e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1221 RVLMTLKESEVSGELnvlkrFDDLVVGEIFEGSVKRATDFGVFIKLDGTLNitGLCHHSQIADKDVDNVTSLFGEGDRVK 1300
Cdd:PRK13806  182 RALLEREQKEALEAF-----METVKEGDVVEGTVTRLAPFGAFVELAPGVE--GMVHISELSWSRVQKADEAVSVGDTVR 254

                          90       100
                  ....*....|....*....|..
gi 150865289 1301 VKLLAIDSDKK----QLSLGMK 1318
Cdd:PRK13806  255 VKVLGIERAKKgkglRISLSIK 276
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 520-1141 2.37e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 49.01  E-value: 2.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  520 GIVIKVLDEF---------EGFVPgshMSDIKLVYPERKFKVGSKVRgRVLSKQGNK---LVVTFKKSLVniedDEVLAR 587
Cdd:PRK06299   36 GTVVAIDKDYvlvdvglksEGRIP---LEEFKNEQGELEVKVGDEVE-VYVERIEDGfgeTVLSREKAKR----LEAWDK 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  588 FEDAkigFKTPAIVEKFVHN----GAIVSFFGnLRAFLPKNEISETFVSNASDYLrlGQTVNVRVLDVKQEEKRMLVTLR 663
Cdd:PRK06299  108 LEKA---FENGEIVEGVINGkvkgGFTVDLNG-VEAFLPGSQVDVRPVRDTDPLE--GKELEFKVIKLDKKRNNIVVSRR 181

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  664 HSSELTNTQKSS--IDDLQPGkSIVTVSVVEKTKDSVIVELEGnsLRGVIytgHLTDGNYEQNRAYAKKLSIGEKLEVLV 741
Cdd:PRK06299  182 AVLEEERAEEREelLENLEEG-QVVEGVVKNITDYGAFVDLGG--VDGLL---HITDISWKRVNHPSEVVNVGDEVKVKV 255

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  742 LEKDLKARTVivsakkSL-IDAAKQD---AIPAyfkDIKVDNKmLRGFVKSVTNKGLFVSFAGKLTGLV-LAKYATSNEN 816
Cdd:PRK06299  256 LKFDKEKKRV------SLgLKQLGEDpweAIEK---KYPVGSK-VKGKVTNITDYGAFVELEEGIEGLVhVSEMSWTKKN 325

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  817 ---EDLLKKfykYQSIACRVINIDEENKRFLLTLKDVNgsknidseavVNPVD--TSKKLIGDFVpgiatKAVIKSVKGT 891
Cdd:PRK06299  326 khpSKVVSV---GQEVEVMVLEIDEEKRRISLGLKQCK----------ENPWEefAEKYPVGDVV-----EGKVKNITDF 387

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  892 QLNVQLADNLQGRIAATECfnSWNeiKDKKQPLSQFHKGQVIDVKIIGFhDAKNHKflpithtrsnkniileLSLIKKDL 971
Cdd:PRK06299  388 GAFVGLEGGIDGLVHLSDI--SWD--KKGEEAVELYKKGDEVEAVVLKV-DVEKER----------------ISLGIKQL 446

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  972 ESStpyqeltfssivpgsqhivfvnniakgyvwaslsPnirgrisfmeltdnvsvFDDLENNLPIGSAISATVKEVDneh 1051
Cdd:PRK06299  447 EED----------------------------------P-----------------FEEFAKKHKKGSIVTGTVTEVK--- 472

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1052 hsvvltarknmvasikdvkvgqkyparilkvrDTYVLVELGEKVVASAFITDALDNYSDKLESVFTTNEFATATVLDIDT 1131
Cdd:PRK06299  473 --------------------------------DKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDR 520

                         650
                  ....*....|
gi 150865289 1132 DSEKIAVSLR 1141
Cdd:PRK06299  521 KNRRISLSIK 530
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 434-573 2.47e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 49.01  E-value: 2.47e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289  434 VFLKFGGSILGQVHNSKIDKDKTLEH---DFNLGSKHSARVIGFNSIDNLLVLTM---ESHVINSqylHASDVPNGTAVK 507
Cdd:PRK06299  389 AFVGLEGGIDGLVHLSDISWDKKGEEaveLYKKGDEVEAVVLKVDVEKERISLGIkqlEEDPFEE---FAKKHKKGSIVT 465

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 150865289  508 sCEIIKVlpEAGGIVIKVLDEFEGFVPGSHMSDIKLVYPERKFKVGSKVRGRVLS--KQGNKLVVTFK 573
Cdd:PRK06299  466 -GTVTEV--KDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINidRKNRRISLSIK 530
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1070-1141 2.49e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.75  E-value: 2.49e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 150865289   1070 KVGQKYPARILKVRDTYVLVELGEKVVASAFITDALDNYSDKLESVFTTNEFATATVLDIDTDSEKIAVSLR 1141
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 599-661 2.88e-05

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 43.52  E-value: 2.88e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 150865289  599 AIVEKFVHNGAIVSFFGNLRAFLPKNEISETFVSNASDYLRLGQTVNVRVLDVKQEEKRMLVT 661
Cdd:cd00164     3 GKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 1246-1318 3.90e-05

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 47.13  E-value: 3.90e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 150865289 1246 VGEIFEGSVKRATDFGVFIKLDGTLNITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLGMK 1318
Cdd:PRK03987    8 EGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 1159-1226 5.18e-05

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 43.00  E-value: 5.18e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 150865289 1159 GDVVKGFVKNVANNGVYVSLGRSVHALVRVADLSDAYLKDWKKYFKPHQPILGKISACK-EEGRVLMTL 1226
Cdd:cd05697     1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEpERKRLVLTL 69
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 594-656 5.21e-05

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 42.66  E-value: 5.21e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 150865289  594 GFKTPAIVEKFVHNGAIVSFFGNLRAFLPKNEISETFVSNASDYLRLGQTVNVRVLDVKQEEK 656
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGR 63
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
684-756 5.57e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.98  E-value: 5.57e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 150865289    684 SIVTVSVVEKTKDSVIVELEGNsLRGVIYTGHLTDGNYEQNRayaKKLSIGEKLEVLVLEKDLKARTVIVSAK 756
Cdd:smart00316    4 DVVEGTVTEITPGGAFVDLGNG-VEGLIPISELSDKRVKDPE---EVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 782-847 6.30e-05

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 42.61  E-value: 6.30e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 150865289  782 LRGFVKSVTNKGLFVSFAGKLTGLVlakyaTSNENEDLL-----KKFYKYQSIACRVINIDEENKRFLLTL 847
Cdd:cd05697     4 VKGTIRKLRPSGIFVKLSDHIKGLV-----PPMHLADVRlkhpeKKFKPGLKVKCRVLSVEPERKRLVLTL 69
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 599-663 6.51e-05

S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 239911 [Multi-domain]  Cd Length: 67  Bit Score: 42.45  E-value: 6.51e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 150865289  599 AIVEKFVHNGAIVSFFGnLRAFLPKNEISETFVSNASDYlrLGQTVNVRVLDVKQEEKRMLVTLR 663
Cdd:cd04465     6 GKVTEKVKGGLIVDIEG-VRAFLPASQVDLRPVEDLDEY--VGKELKFKIIEIDRERNNIVLSRR 67
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 1077-1318 1.08e-04

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 47.01  E-value: 1.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1077 ARILKVRDTYVLVELGEKVVASAFITD-ALDNYSDKLESVFTTNEFATATVLDIDTDSEKIAVSLR--TDSPTDKVInsi 1153
Cdd:PRK12269  584 GRVTKIADFGAFIELAEGIEGLAHISEfSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKqvTANPWEEIE--- 660

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1154 ADLNRGDVVKGFVKNVANNGVYVSLGRSVHALVRVADLSdaylkdWKKYFKP--HQPILGK-----ISACKEEGRVLmTL 1226
Cdd:PRK12269  661 ARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLS------WVKRTRPadHELEVGKeiecmVIECDPQARRI-RL 733

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1227 KESEVSGelNVLKRFDDLV-VGEIFEGSVKRATDFGVFIKLDGtlNITGLCHHSQIA---DKDVDNVTSLFGEGDRVKVK 1302
Cdd:PRK12269  734 GVKQLSD--NPWQVFANAYgVGSTVEGEVSSVTDFGIFVRVPG--GVEGLVRKQHLVenrDGDPGEALRKYAVGDRVKAV 809

                         250
                  ....*....|....*.
gi 150865289 1303 LLAIDSDKKQLSLGMK 1318
Cdd:PRK12269  810 IVDMNVKDRKVAFSVR 825
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 783-846 1.20e-04

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 41.90  E-value: 1.20e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 150865289  783 RGFVKSVTNKGLFVSFAGKLTGLVLAKYATSNENEDLLKKFYKYQSIACRVINIDEENKRFLLT 846
Cdd:cd05707     5 RGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1533-1641 1.57e-04

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 43.46  E-value: 1.57e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1533 IYSMSEKYYQAEELYKVMTKKFGKSISVWVQYGSFLLDRKLQEETHEVLAKALQTLPkrDHIEVVRKFAQLEFSKGDAEQ 1612
Cdd:COG4235    26 AYLRLGRYDEALAAYEKALRLDPDNADALLDLAEALLAAGDTEEAEELLERALALDP--DNPEALYLLGLAAFQQGDYAE 103

                          90       100
                  ....*....|....*....|....*....
gi 150865289 1613 GRSLFEGLVADAPKriDLWNVYVDQEIKQ 1641
Cdd:COG4235   104 AIAAWQKLLALLPA--DAPARLLEASIAE 130
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 782-846 1.81e-04

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 41.21  E-value: 1.81e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 150865289  782 LRGFVKSVTNKGLFVSFAGKLTGLVLAKYATSNENEDLLKKFYKYQSIACRVINIDEENKRFLLT 846
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1247-1319 2.05e-04

S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 41.10  E-value: 2.05e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 150865289 1247 GEIFEGSVKRATDFGVFIKLDGtlNITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDSDKKQLSLGMKA 1319
Cdd:cd05691     1 GSIVTGKVTEVDAKGATVKLGD--GVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKA 71
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 599-658 2.76e-04

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 40.73  E-value: 2.76e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289   599 AIVEKFVHNGAIVSFFGNLRAFLPKNEISETFVSNASDYLRLGQTVNVRVLDVKQEEKRM 658
Cdd:pfam00575    9 GEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRI 68
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1448-1696 4.47e-04

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 43.84  E-value: 4.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1448 NPNSSILWMNYMSFQLQLSEADKAREIGERALKtINYRDEQEKLNIWIALLNLENtfgTDESLEEiFKRSTQYM-DSLTM 1526
Cdd:COG0457     4 DPDDAEAYNNLGLAYRRLGRYEEAIEDYEKALE-LDPDDAEALYNLGLAYLRLGR---YEEALAD-YEQALELDpDDAEA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1527 HQKLVSIYSMSEKYYQAEELYKVMTKKFGKSISVWVQYGSFLLDRKLQEETHEVLAKALQTLPkrDHIEVVRKFAQLEFS 1606
Cdd:COG0457    79 LNNLGLALQALGRYEEALEDYDKALELDPDDAEALYNLGLALLELGRYDEAIEAYERALELDP--DDADALYNLGIALEK 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1607 KGDAEQGRSLFEglvaDAPKRIDLWNVYVDQEIKQDNKSKVEDIFERALAKKLSRKQAKFFFTKWLAFEEEKGDEQMAAR 1686
Cdd:COG0457   157 LGRYEEALELLE----KLEAAALAALLAAALGEAALALAAAEVLLALLLALEQALRKKLAILTLAALAELLLLALALLLA 232

                         250
                  ....*....|
gi 150865289 1687 IKARAVEYAQ 1696
Cdd:COG0457   233 LRLAALALYQ 242
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 517-562 5.49e-04

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 39.67  E-value: 5.49e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 150865289  517 EAGGIVIKVLDEFEGFVPGSHMSDIKLVYPERKFKVGSKVRGRVLS 562
Cdd:cd00164     9 TKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLE 54
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1159-1221 5.54e-04

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 39.96  E-value: 5.54e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 150865289  1159 GDVVKGFVKNVANNGVYVSLGRSVHALVRVADLSDAYLKDWKKYFKPHQPILGKISACKEEGR 1221
Cdd:pfam00575    4 GDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRR 66
PRK05807 PRK05807
RNA-binding protein S1;
1156-1230 7.78e-04

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 41.27  E-value: 7.78e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 150865289 1156 LNRGDVVKGFVKNVANNGVYVSL-GRSvhALVRVADLSDAYLKDWKKYFKPHQPILGKISACKEEGRVLMTLKESE 1230
Cdd:PRK05807    3 LKAGSILEGTVVNITNFGAFVEVeGKT--GLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQAM 76
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 601-663 1.00e-03

S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein.


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 39.49  E-value: 1.00e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 150865289  601 VEKFVHNGAIVSF--FGNLRAFLPKNEISETFVSNASDYLRLGQTVNVRVLDVKQEEKRMLVTLR 663
Cdd:cd04452    11 VKSIADMGAYVSLleYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK 75
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 1520-1625 1.03e-03

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 41.48  E-value: 1.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1520 YMDSLTMHQKLVSIYSMSEKYYQAEELYKVMTKKFGKSISVWVQYGSFLLDRKLQEETHEVLAKALQTLPkrDHIEVVRK 1599
Cdd:COG5010    50 LAKAFAIESPSDNLYNKLGDFEESLALLEQALQLDPNNPELYYNLALLYSRSGDKDEAKEYYEKALALSP--DNPNAYSN 127

                          90       100
                  ....*....|....*....|....*.
gi 150865289 1600 FAQLEFSKGDAEQGRSLFEGLVADAP 1625
Cdd:COG5010   128 LAALLLSLGQDDEAKAALQRALGTSP 153
PRK11642 PRK11642
ribonuclease R;
1246-1320 1.12e-03

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 43.96  E-value: 1.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1246 VGEIFEGSVKRATDFGVFIKLDgTLNITGLCHHSQIaDKD---VDNV-TSLFGE--------GDRVKVKLLAIDSDKKQL 1313
Cdd:PRK11642  643 VGNVFKGVISSVTGFGFFVRLD-DLFIDGLVHVSSL-DNDyyrFDQVgQRLIGEssgqtyrlGDRVEVRVEAVNMDERKI 720


                  ....*..
gi 150865289 1314 SLGMKAS 1320
Cdd:PRK11642  721 DFSLISS 727
PRK08059 PRK08059
general stress protein 13; Validated
 595-663 1.30e-03

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 40.42  E-value: 1.30e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 150865289  595 FKTPAIVEKFVHN----GAIVSFFGNLRAFLPKNEISETFVSNASDYLRLGQTVNVRVLDVKQEEKRMLVTLR 663
Cdd:PRK08059    5 YEVGSVVTGKVTGiqpyGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR 77
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 608-651 1.31e-03

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 42.50  E-value: 1.31e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 150865289  608 GAIVSF--FGNLRAFLPKNEISETFVSNASDYLRLGQTVNVRVLDV 651
Cdd:PRK03987   23 GAFVTLdeYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRV 68
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1159-1222 1.45e-03

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 38.76  E-value: 1.45e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 150865289 1159 GDVVKGFVKNVANNGVYVSLGrSVHALVRVADLSDAYLKDWKKYFKPHQPILGKI-SACKEEGRV 1222
Cdd:cd05688     2 GDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVlKIDKERKRI 65
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1527-1626 1.45e-03

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 40.56  E-value: 1.45e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1527 HQKLVSIYSMSEKYYQAEELYKVMTKKFGKSISVWVQYGSFLLDRKLQEETHEVLAKALQTLPkrDHIEVVRKFAQLEFS 1606
Cdd:COG4783    41 FALLGEILLQLGDLDEAIVLLHEALELDPDEPEARLNLGLALLKAGDYDEALALLEKALKLDP--EHPEAYLRLARAYRA 118

                          90       100
                  ....*....|....*....|
gi 150865289 1607 KGDAEQGRSLFEGLVADAPK 1626
Cdd:COG4783   119 LGRPDEAIAALEKALELDPD 138
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 1246-1319 1.50e-03

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 43.34  E-value: 1.50e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 150865289 1246 VGEIFEG-SVKRATDFGVFIKLdgTLNITGLCHHSQIADKDVDNVTSLFGEGDRVKVKLLAIDsDKKQLSLGMKA 1319
Cdd:PLN00207  753 VGDIYRNcEIKSIAPYGAFVEI--APGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVN-DKGQLRLSRRA 824
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
1533-1626 1.66e-03

Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 39.38  E-value: 1.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1533 IYSMSEKYYQAEELYKVMTKKFGKSISVWVQYGSFLLDRKLQEETHEvLAKALQTLPkrDHIEVVRKFAQLEFSKGDAEQ 1612
Cdd:COG3063     1 LYLKLGDLEEAEEYYEKALELDPDNADALNNLGLLLLEQGRYDEAIA-LEKALKLDP--NNAEALLNLAELLLELGDYDE 77

                          90
                  ....*....|....
gi 150865289 1613 GRSLFEGLVADAPK 1626
Cdd:COG3063    78 ALAYLERALELDPS 91
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 683-756 1.89e-03

S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 239911 [Multi-domain]  Cd Length: 67  Bit Score: 38.21  E-value: 1.89e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 150865289  683 KSIVTVSVVEKTKDSVIVELEGnsLRGVIYTGHLTDGNYEQNRAYakklsIGEKLEVLVLEKDLKARTVIVSAK 756
Cdd:cd04465     1 GEIVEGKVTEKVKGGLIVDIEG--VRAFLPASQVDLRPVEDLDEY-----VGKELKFKIIEIDRERNNIVLSRR 67
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 601-651 2.02e-03

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 42.73  E-value: 2.02e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 150865289  601 VEKFVHNGAIVSFFGNLRAFLPKNEISETFVSNASDYLRLGQTVNVRVLDV 651
Cdd:PRK11824  629 VVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEI 679
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 780-841 2.38e-03

S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240210 [Multi-domain]  Cd Length: 74  Bit Score: 38.15  E-value: 2.38e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 150865289  780 KMLRGFVKSVTNKGLFVSFAGKLTGLVLAKYATS---NENEDLLKKFYKYQSIACRVINIDEENK 841
Cdd:cd05705     5 QLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKyfvSDPSLYNKYLPEGKLLTAKVLSVNSEKN 69
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 600-657 2.53e-03

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 37.99  E-value: 2.53e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 150865289  600 IVEKFVHNGAIVSFfGNLRAFLPKNEISETFVSNASDYLRLGQTVNVRVLDVKQEEKR 657
Cdd:cd05688     8 TVKSITDFGAFVDL-GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKR 64
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1159-1226 2.93e-03

S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 37.94  E-value: 2.93e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 150865289 1159 GDVVKGFVKNVANNGVYVSLGRSVHALVRVADLSDAY--LKDWKKYFKPHQPILGKI-SACKEEGRVLMTL 1226
Cdd:cd05703     1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVsvLEHPEKKFPIGQALKAKVvGVDKEHKLLRLSA 71
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1533-1698 3.16e-03

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 41.25  E-value: 3.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1533 IYSMSEKYYQAEELYKVMTKKFGKSISVWVQYGSFLLDRKLQEETHEVLAKALQTLPkrDHIEVVRKFAQLEFSKGDAEQ 1612
Cdd:COG2956    17 NYLLNGQPDKAIDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLERDP--DRAEALLELAQDYLKAGLLDR 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 150865289 1613 GRSLFEGLVADAPKRIDLWNVYVDQEIKQDNKSKVEDIFERALakKLSRKQAKFFFTKWLAFeEEKGDEQMAARIKARAV 1692
Cdd:COG2956    95 AEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLL--KLGPENAHAYCELAELY-LEQGDYDEAIEALEKAL 171


                  ....*.
gi 150865289 1693 EYAQSH 1698
Cdd:COG2956   172 KLDPDC 177
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 782-845 4.43e-03

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 37.47  E-value: 4.43e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 150865289  782 LRGFVKSVTNKGLFVSFAGKLTGLV-LAKYATSNENEDLLKKFYKYQSIACRVINIDEENKRFLL 845
Cdd:cd05690     4 VSGKIKSITDFGIFVGLDGGIDGLVhISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 511-573 4.59e-03

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 37.21  E-value: 4.59e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 150865289  511 IIKVLPeaGGIVIKVLDEFEGFVPGSHMSDIKLVYPERKFKVGSKVRGRVLS--KQGNKLVVTFK 573
Cdd:cd05698     8 IVKVKP--NGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLScdPEQQRLLLSCK 70
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 325-395 5.56e-03

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 37.22  E-value: 5.56e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 150865289  325 GILVDALVADVTKNGLIVKVFGLVDATINLAQLQEFdfnALKH---KYAIGNNIKARVMAVltRAGSKKLILSH 395
Cdd:cd05697     1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADV---RLKHpekKFKPGLKVKCRVLSV--EPERKRLVLTL 69
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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