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Conserved domains on  [gi|1832390731|emb|CAB3402481|]
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unnamed protein product [Caenorhabditis bovis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Astacin pfam01400
Astacin (Peptidase family M12A); The members of this family are enzymes that cleave peptides. ...
 103-290 1.86e-100

Astacin (Peptidase family M12A); The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family contain two conserved disulphide bridges, these are joined 1-4 and 2-3. Members of this family have an amino terminal propeptide which is cleaved to give the active protease domain. All other linked domains are found to the carboxyl terminus of this domain. This family includes: Astacin, a digestive enzyme from Crayfish. Meprin, a multiple domain membrane component that is constructed from a homologous alpha and beta chain. Proteins involved in morphogenesis such as Swiss:P13497, and Tolloid from drosophila.


:

Pssm-ID: 426242 [Multi-domain]  Cd Length: 192  Bit Score: 320.77  E-value: 1.86e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  103 RRWPNGEIPYTLSSQYGAYARSVIANAMNEYHKKTCVRFVARDPARHHDYLWIHPDEGCYSLVGKTGGKQPVSLDSGCIQ 182
Cdd:pfam01400    1 KKWPNGPIPYVIDGSLTGLARALIRQAMRHWENKTCIRFVERTPAPDNNYLFFFKGDGCYSYVGRVGGRQPVSIGDGCDK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  183 VGTIVHELMHAVGFFHEQSRQDRDNYIDVVWQNVMNGADDQFEKYNLNVISHLDEPYDYSSIMHYGPYAFS-GSGKKTLI 261
Cdd:pfam01400   81 FGIIVHELGHALGFFHEQSRPDRDDYVSINWDNIDPGQEGNFDKYDPSEVDSYGVPYDYGSIMHYGPNAFSkNGSLPTIV 160

                          170       180       190
                   ....*....|....*....|....*....|
gi 1832390731  262 PKKSGAE-RMGQRVKFSDIDVRKINKLYNC 290
Cdd:pfam01400  161 PKDNDYQaTIGQRVKLSFYDIKKINKLYKC 190
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1774-2033 5.93e-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: 68.22  E-value: 5.93e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1774 ESEEDLSKQLRGDPNSAILWIKYMSLFLQKADLAaarataeralESINYRETAELRNVWTAYLNMEVAF-----GDASTV 1848
Cdd:COG2956     26 KAIDLLEEALELDPETVEAHLALGNLYRRRGEYD----------RAIRIHQKLLERDPDRAEALLELAQdylkaGLLDRA 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1849 QKVFERACN-NVDSYTMHLQLAQIYQNSKKNQEAKQILETMVKKfRAQHIEVWVLLAEHLMKQKEHKAARDLLTRALSSV 1927
Cdd:COG2956     96 EELLEKLLElDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKL-GPENAHAYCELAELYLEQGDYDEAIEALEKALKLD 174

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1928 PKQQ--HTMLiskfAQLEFKYGDSERGTTLFEGLLTAHPKKTDLWLVYADAAVKHMGIEQARKIMDRACNSNNSLHKMRP 2005
Cdd:COG2956    175 PDCAraLLLL----AELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKALELDPSDDLLLA 250

                          250       260
                   ....*....|....*....|....*...
gi 1832390731 2006 LYKKwleIENRHGDSVSVELVRAKAEKY 2033
Cdd:COG2956    251 LADL---LERKEGLEAALALLERQLRRH 275
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
750-820 1.28e-10

Ribosomal protein S1-like RNA-binding domain;


:

Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 59.15  E-value: 1.28e-10
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1832390731   750 GDIVEGKVVHVSPQGIHLNVCNFVRAFAPASMLSDKPIIgKLKSKFPLGSTVKCRIWQICKDRKKLIVSCK 820
Cdd:smart00316    3 GDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVK-DPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 483-546 4.50e-06

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: 46.09  E-value: 4.50e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1832390731  483 LVAGLVIHTCVTSLEEKGAVLDIGLDQMTGFLEKAQFP-PSGVFEGQPL--IVRVLSTTSRVVKVSA 546
Cdd:cd05694      2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGnFSKLKVGQLLlcVVEKVKDDGRVVSLSA 68
rpsA super family cl36730
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 486-850 5.01e-06

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: 51.66  E-value: 5.01e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  486 GLVIHTCVTSLEEKGAVLDIGLdQMTGFLEKAQFP--PSGVFEGQPLIVRVLSTTSR----VVKVSALVEQDNLnmtscE 559
Cdd:TIGR00717   19 GSIVKGTVVAINKDTVFVDVGL-KSEGRIPKEEFLdaPLEIQVGDEVEVYLDRVEDRfgetVLSREKAQRHELW-----I 92

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  560 KLqLNHLMPGTILECEPTGDepVSNGVFVSIgNGLKGILPRRNLPPRLRENPEKL-GKAIRAVVM-FCQQNSKVLVlhAH 637
Cdd:TIGR00717   93 KL-EKAYEEGSIVEGKIVGK--VKGGFIVDL-NGVEAFLPGSQVDVKPIKDLDSLiGKTLKFKIIkLDQKRNNIVV--SR 166

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  638 PDIVAISKIEKR-TSFEGISIGDTVKCTVLDVIPSKctVFFSLPPTDGkkSLVTGLCSRGFLDNPDNIaenYNIGAEKLC 716
Cdd:TIGR00717  167 RAYLEEERSQAReELLENLKEGDVVKGVVKNITDFG--AFVDLGGVDG--LLHITDMSWKRVKHPSEY---VKVGQEVKV 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  717 RVIAYRYVERSIVVStrkdiLKQKITSYMDAV-----CGDIVEGKVVHVSPQGIHLNVCNFVRAFAPASMLSDKPIIGKL 791
Cdd:TIGR00717  240 KVIKFDKEKGRISLS-----LKQLGEDPWEAIekkfpVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHP 314

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1832390731  792 KSKFPLGSTVKCRIWQICKDRKKLIVS---CKERmlelktPLANTKEKLSVGDLLPCTVRKI 850
Cdd:TIGR00717  315 SKVVKKGDEVEVMILDIDPERRRLSLGlkqCKAN------PWEQFEEKHPVGDRVTGKIKKI 370
PRK00087 super family cl35061
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1416-1675 5.07e-04

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


The actual alignment was detected with superfamily member PRK00087:

Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 44.94  E-value: 5.07e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1416 NNFNVGDVVRcfgsaGTVES--DSEIRVEINGIWTGHIARENISDD----LKVETGIGGIIDVKLAPGQLREARVVAVDK 1489
Cdd:PRK00087   298 KQIRRGDIVK-----GTVVSvnENEVFVDVGYKSEGVIPLRELTLDeissLKESVKVGDEIEVKVLKLEDEDGYVVLSKK 372

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1490 KSNTLELSLNVEKnpKFEIGEKLTGRVFSepqKDNSVMLKLASGDQAILTATGITSIYesvDKKISEnfGKGEILDVica 1569
Cdd:PRK00087   373 EADREKAWKELEE--AFENGEPVKGKVKE---VVKGGLLVDYGGVRAFLPASHVELGY---VEDLSE--YKGQELEV--- 439

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1570 KVTQSKPRRYYVVTPSRYHDLKSCKNEKRKLILdpNNVTIGQNYDGIVVQASPSGVIVEIGpGIVGKIPVNE-------E 1642
Cdd:PRK00087   440 KIIEFNRKRRKKVVLSRKAILEEEKEKKKEETW--NSLEEGDVVEGEVKRLTDFGAFVDIG-GVDGLLHVSEiswgrveK 516

                          250       260       270
                   ....*....|....*....|....*....|....
gi 1832390731 1643 NSDIIDIGVK-SVVTVEIEKSTPKgFLLKLKEII 1675
Cdd:PRK00087   517 PSDVLKVGDEiKVYILDIDKENKK-LSLSLKKLL 549
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 391-475 1.58e-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 cd05693:

Pssm-ID: 471952 [Multi-domain]  Cd Length: 100  Bit Score: 39.89  E-value: 1.58e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  391 EGLLGLGVVSDVFDDGIILHTAGNQNVRINVSEVANKFSQLINA------------EKIEMSDAFKIGQMVPFRVISK-K 457
Cdd:cd05693      3 EGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEEldeeseeeddeeELPDLEDLFSVGQLVRCKVVSLdK 82

                           90
                   ....*....|....*...
gi 1832390731  458 SKQDKGSVKGTCNPAKLN 475
Cdd:cd05693     83 SKSGKKRIELSLEPELVN 100
 
Name Accession Description Interval E-value
Astacin pfam01400
Astacin (Peptidase family M12A); The members of this family are enzymes that cleave peptides. ...
 103-290 1.86e-100

Astacin (Peptidase family M12A); The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family contain two conserved disulphide bridges, these are joined 1-4 and 2-3. Members of this family have an amino terminal propeptide which is cleaved to give the active protease domain. All other linked domains are found to the carboxyl terminus of this domain. This family includes: Astacin, a digestive enzyme from Crayfish. Meprin, a multiple domain membrane component that is constructed from a homologous alpha and beta chain. Proteins involved in morphogenesis such as Swiss:P13497, and Tolloid from drosophila.


Pssm-ID: 426242 [Multi-domain]  Cd Length: 192  Bit Score: 320.77  E-value: 1.86e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  103 RRWPNGEIPYTLSSQYGAYARSVIANAMNEYHKKTCVRFVARDPARHHDYLWIHPDEGCYSLVGKTGGKQPVSLDSGCIQ 182
Cdd:pfam01400    1 KKWPNGPIPYVIDGSLTGLARALIRQAMRHWENKTCIRFVERTPAPDNNYLFFFKGDGCYSYVGRVGGRQPVSIGDGCDK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  183 VGTIVHELMHAVGFFHEQSRQDRDNYIDVVWQNVMNGADDQFEKYNLNVISHLDEPYDYSSIMHYGPYAFS-GSGKKTLI 261
Cdd:pfam01400   81 FGIIVHELGHALGFFHEQSRPDRDDYVSINWDNIDPGQEGNFDKYDPSEVDSYGVPYDYGSIMHYGPNAFSkNGSLPTIV 160

                          170       180       190
                   ....*....|....*....|....*....|
gi 1832390731  262 PKKSGAE-RMGQRVKFSDIDVRKINKLYNC 290
Cdd:pfam01400  161 PKDNDYQaTIGQRVKLSFYDIKKINKLYKC 190
ZnMc_astacin_like cd04280
Zinc-dependent metalloprotease, astacin_like subfamily or peptidase family M12A, a group of ...
 107-288 1.42e-93

Zinc-dependent metalloprotease, astacin_like subfamily or peptidase family M12A, a group of zinc-dependent proteolytic enzymes with a HExxH zinc-binding site/active site. Members of this family may have an amino terminal propeptide, which is cleaved to yield the active protease domain, which is consequently always found at the N-terminus in multi-domain architectures. This family includes: astacin, a digestive enzyme from Crayfish; meprin, a multiple domain membrane component that is constructed from a homologous alpha and beta chain, proteins involved in (bone) morphogenesis, tolloid from drosophila, and the sea urchin SPAN protein, which may also play a role in development.


Pssm-ID: 239807 [Multi-domain]  Cd Length: 180  Bit Score: 300.26  E-value: 1.42e-93
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  107 NGEIPYTLSSQYGAYARSVIANAMNEYHKKTCVRFVARDParHHDYLWIHPDEGCYSLVGKTGGKQPVSLDSGCIQVGTI 186
Cdd:cd04280      1 NGTVPYVIDGSFDESDRSLILRAMREIESNTCIRFVPRTT--EKDYIRIVKGSGCWSYVGRVGGRQVVSLGSGCFSLGTI 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  187 VHELMHAVGFFHEQSRQDRDNYIDVVWQNVMNGADDQFEKYNLNVISHLDEPYDYSSIMHYGPYAFSGSGKKTLIPKKSG 266
Cdd:cd04280     79 VHELMHALGFYHEQSRPDRDDYVTINWENIQPGYEHNFDKYSPDTVTTYGVPYDYGSVMHYGPTAFSKNGKPTIVPKDPG 158

                          170       180
                   ....*....|....*....|..
gi 1832390731  267 AERMGQRVKFSDIDVRKINKLY 288
Cdd:cd04280    159 YQIIGQREGLSFLDIKKINKMY 180
ZnMc smart00235
Zinc-dependent metalloprotease; Neutral zinc metallopeptidases. This alignment represents a ...
 102-243 1.58e-46

Zinc-dependent metalloprotease; Neutral zinc metallopeptidases. This alignment represents a subset of known subfamilies. Highest similarity occurs in the HExxH zinc-binding site/ active site.


Pssm-ID: 214576 [Multi-domain]  Cd Length: 139  Bit Score: 164.06  E-value: 1.58e-46
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731   102 YRRWPNGEIPYTL-SSQYGAYARSVIANAMNEYHKKTCVRFVARDPArHHDYLWIHP-DEGC-YSLVGKTGGKQPVSLDS 178
Cdd:smart00235    2 SKKWPKGTVPYVIdSSSLSPEEREAIAKALAEWSDVTCIRFVERTGT-ADIYISFGSgDSGCtLSHAGRPGGDQHLSLGN 80

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1832390731   179 GCIQVGTIVHELMHAVGFFHEQSRQDRDNYIDVVWQNVMngaddqFEKYNLNVISHLDEPYDYSS 243
Cdd:smart00235   81 GCINTGVAAHELGHALGLYHEQSRSDRDNYMYINYTNID------TRNFDLSEDDSLGIPYDYGS 139
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1774-2033 5.93e-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: 68.22  E-value: 5.93e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1774 ESEEDLSKQLRGDPNSAILWIKYMSLFLQKADLAaarataeralESINYRETAELRNVWTAYLNMEVAF-----GDASTV 1848
Cdd:COG2956     26 KAIDLLEEALELDPETVEAHLALGNLYRRRGEYD----------RAIRIHQKLLERDPDRAEALLELAQdylkaGLLDRA 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1849 QKVFERACN-NVDSYTMHLQLAQIYQNSKKNQEAKQILETMVKKfRAQHIEVWVLLAEHLMKQKEHKAARDLLTRALSSV 1927
Cdd:COG2956     96 EELLEKLLElDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKL-GPENAHAYCELAELYLEQGDYDEAIEALEKALKLD 174

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1928 PKQQ--HTMLiskfAQLEFKYGDSERGTTLFEGLLTAHPKKTDLWLVYADAAVKHMGIEQARKIMDRACNSNNSLHKMRP 2005
Cdd:COG2956    175 PDCAraLLLL----AELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKALELDPSDDLLLA 250

                          250       260
                   ....*....|....*....|....*...
gi 1832390731 2006 LYKKwleIENRHGDSVSVELVRAKAEKY 2033
Cdd:COG2956    251 LADL---LERKEGLEAALALLERQLRRH 275
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
750-820 1.28e-10

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 59.15  E-value: 1.28e-10
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1832390731   750 GDIVEGKVVHVSPQGIHLNVCNFVRAFAPASMLSDKPIIgKLKSKFPLGSTVKCRIWQICKDRKKLIVSCK 820
Cdd:smart00316    3 GDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVK-DPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 750-820 2.28e-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: 46.84  E-value: 2.28e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1832390731  750 GDIVEGKVVHVSPQGIHLNVCNFVRAFAPASMLSDKPIIgKLKSKFPLGSTVKCRIWQICKDRKKLIVSCK 820
Cdd:cd05698      1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIK-DPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 483-546 4.50e-06

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: 46.09  E-value: 4.50e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1832390731  483 LVAGLVIHTCVTSLEEKGAVLDIGLDQMTGFLEKAQFP-PSGVFEGQPL--IVRVLSTTSRVVKVSA 546
Cdd:cd05694      2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGnFSKLKVGQLLlcVVEKVKDDGRVVSLSA 68
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 486-850 5.01e-06

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: 51.66  E-value: 5.01e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  486 GLVIHTCVTSLEEKGAVLDIGLdQMTGFLEKAQFP--PSGVFEGQPLIVRVLSTTSR----VVKVSALVEQDNLnmtscE 559
Cdd:TIGR00717   19 GSIVKGTVVAINKDTVFVDVGL-KSEGRIPKEEFLdaPLEIQVGDEVEVYLDRVEDRfgetVLSREKAQRHELW-----I 92

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  560 KLqLNHLMPGTILECEPTGDepVSNGVFVSIgNGLKGILPRRNLPPRLRENPEKL-GKAIRAVVM-FCQQNSKVLVlhAH 637
Cdd:TIGR00717   93 KL-EKAYEEGSIVEGKIVGK--VKGGFIVDL-NGVEAFLPGSQVDVKPIKDLDSLiGKTLKFKIIkLDQKRNNIVV--SR 166

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  638 PDIVAISKIEKR-TSFEGISIGDTVKCTVLDVIPSKctVFFSLPPTDGkkSLVTGLCSRGFLDNPDNIaenYNIGAEKLC 716
Cdd:TIGR00717  167 RAYLEEERSQAReELLENLKEGDVVKGVVKNITDFG--AFVDLGGVDG--LLHITDMSWKRVKHPSEY---VKVGQEVKV 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  717 RVIAYRYVERSIVVStrkdiLKQKITSYMDAV-----CGDIVEGKVVHVSPQGIHLNVCNFVRAFAPASMLSDKPIIGKL 791
Cdd:TIGR00717  240 KVIKFDKEKGRISLS-----LKQLGEDPWEAIekkfpVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHP 314

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1832390731  792 KSKFPLGSTVKCRIWQICKDRKKLIVS---CKERmlelktPLANTKEKLSVGDLLPCTVRKI 850
Cdd:TIGR00717  315 SKVVKKGDEVEVMILDIDPERRRLSLGlkqCKAN------PWEQFEEKHPVGDRVTGKIKKI 370
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 651-850 9.91e-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: 50.04  E-value: 9.91e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  651 SFEGISIGDTVKCTVLDVIPSkcTVFFSLpptdGKKSlvTGLCSRG-FLDNPDNIaeNYNIGAEKLCRVIAYRYVERSIV 729
Cdd:COG0539     12 SLKELKEGDIVKGTVVSIDDD--EVLVDI----GYKS--EGIIPLSeFSDEPGEL--EVKVGDEVEVYVEKVEDGEGEIV 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  730 VSTRK-DILK--QKITSYMDAvcGDIVEGKVVHVSPQGIHLNVCNfVRAFAPASMLSDKPIigKLKSKFpLGSTVKCRIW 806
Cdd:COG0539     82 LSKKKaDREKawEELEEAFEN--GEPVEGKVKGVVKGGLIVDIGG-VRAFLPASQVDVRPV--RDLDEY-VGKTLEFKII 155

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 1832390731  807 QICKDRKKLIVSckERML---ELKTPLANTKEKLSVGDLLPCTVRKI 850
Cdd:COG0539    156 KLDRKRNNVVVS--RRAVleeEREEKREELLEKLEEGDVVEGTVKNI 200
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1416-1675 5.07e-04

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 44.94  E-value: 5.07e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1416 NNFNVGDVVRcfgsaGTVES--DSEIRVEINGIWTGHIARENISDD----LKVETGIGGIIDVKLAPGQLREARVVAVDK 1489
Cdd:PRK00087   298 KQIRRGDIVK-----GTVVSvnENEVFVDVGYKSEGVIPLRELTLDeissLKESVKVGDEIEVKVLKLEDEDGYVVLSKK 372

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1490 KSNTLELSLNVEKnpKFEIGEKLTGRVFSepqKDNSVMLKLASGDQAILTATGITSIYesvDKKISEnfGKGEILDVica 1569
Cdd:PRK00087   373 EADREKAWKELEE--AFENGEPVKGKVKE---VVKGGLLVDYGGVRAFLPASHVELGY---VEDLSE--YKGQELEV--- 439

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1570 KVTQSKPRRYYVVTPSRYHDLKSCKNEKRKLILdpNNVTIGQNYDGIVVQASPSGVIVEIGpGIVGKIPVNE-------E 1642
Cdd:PRK00087   440 KIIEFNRKRRKKVVLSRKAILEEEKEKKKEETW--NSLEEGDVVEGEVKRLTDFGAFVDIG-GVDGLLHVSEiswgrveK 516

                          250       260       270
                   ....*....|....*....|....*....|....
gi 1832390731 1643 NSDIIDIGVK-SVVTVEIEKSTPKgFLLKLKEII 1675
Cdd:PRK00087   517 PSDVLKVGDEiKVYILDIDKENKK-LSLSLKKLL 549
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1833-1989 5.09e-04

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 45.07  E-value: 5.09e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1833 TAYLNMEVAFGDASTVQKVFERACN-NVDSYTMHLQLAQIYQNSKKNQEAKQILETMVKKFRAqHIEVWVLLAEHLMKQK 1911
Cdd:TIGR02917  537 LALAGLYLRTGNEEEAVAWLEKAAElNPQEIEPALALAQYYLGKGQLKKALAILNEAADAAPD-SPEAWLMLGRAQLAAG 615

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1832390731 1912 EHKAARDLLTRALSSVPKQQHTMLISKFAQLEFKygDSERGTTLFEGLLTAHPKKTDLWLVYADAAVKHMGIEQARKI 1989
Cdd:TIGR02917  616 DLNKAVSSFKKLLALQPDSALALLLLADAYAVMK--NYAKAITSLKRALELKPDNTEAQIGLAQLLLAAKRTESAKKI 691
TPR_19 pfam14559
Tetratricopeptide repeat;
1875-1930 7.29e-04

Tetratricopeptide repeat;


Pssm-ID: 434038 [Multi-domain]  Cd Length: 65  Bit Score: 39.49  E-value: 7.29e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1832390731 1875 SKKNQEAKQILETMVKKFRaQHIEVWVLLAEHLMKQKEHKAARDLLTRALSSVPKQ 1930
Cdd:pfam14559    1 EGDYAEALELLEQALAEDP-DNAEARLGLAEALLALGRLDEAEALLAALPAADPDD 55
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
569-634 8.12e-04

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 39.89  E-value: 8.12e-04
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1832390731   569 GTILECEPtgdepvsNGVFVSIGNGLKGILPRRNLPPRLRENPE---KLGKAIRAVVMFCQQNSKVLVL 634
Cdd:smart00316    8 GTVTEITP-------GGAFVDLGNGVEGLIPISELSDKRVKDPEevlKVGDEVKVKVLSVDEEKGRIIL 69
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 391-475 1.58e-03

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: 39.89  E-value: 1.58e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  391 EGLLGLGVVSDVFDDGIILHTAGNQNVRINVSEVANKFSQLINA------------EKIEMSDAFKIGQMVPFRVISK-K 457
Cdd:cd05693      3 EGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEEldeeseeeddeeELPDLEDLFSVGQLVRCKVVSLdK 82

                           90
                   ....*....|....*...
gi 1832390731  458 SKQDKGSVKGTCNPAKLN 475
Cdd:cd05693     83 SKSGKKRIELSLEPELVN 100
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 750-819 1.80e-03

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: 38.81  E-value: 1.80e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  750 GDIVEGKVVHVSPQGIHLNVCNFVRAFAPASMLSDKPIIGKLKsKFPLGSTVKCRIWQICKDRKKLIVSC 819
Cdd:pfam00575    4 GDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDE-VIKVGDEVKVKVLKVDKDRRRIILSI 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1609-1665 1.99e-03

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 38.74  E-value: 1.99e-03
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1832390731  1609 IGQNYDGIVVQASPSGVIVEIGPGIVGKIPVNE-------ENSDIIDIGvkSVVTVEIEKSTPK 1665
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISElsdkrvkDPEEVLKVG--DEVKVKVLSVDEE 63
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
583-854 2.22e-03

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 43.01  E-value: 2.22e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  583 SNGVFVSIGNGLKGILPRRNLPPRLRENPEKL---GKAIRAVVMFCQQNSKVLVLHA-HPD-IVAISKIEKrtSFEGisi 657
Cdd:PRK00087   315 ENEVFVDVGYKSEGVIPLRELTLDEISSLKESvkvGDEIEVKVLKLEDEDGYVVLSKkEADrEKAWKELEE--AFEN--- 389

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  658 GDTVKCTV-------LDVIPSKCTVFfsLPptdgkKSLVtglcSRGFLDNPDNIaenynIGAEKLCRVIAYRYVERSIVV 730
Cdd:PRK00087   390 GEPVKGKVkevvkggLLVDYGGVRAF--LP-----ASHV----ELGYVEDLSEY-----KGQELEVKIIEFNRKRRKKVV 453

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  731 STRKDILKQKITSYMDAVC-----GDIVEGKVVHVSPQGIHLNVcNFVRAFAPASMLSDKPIIgKLKSKFPLGSTVKCRI 805
Cdd:PRK00087   454 LSRKAILEEEKEKKKEETWnsleeGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWGRVE-KPSDVLKVGDEIKVYI 531

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*....
gi 1832390731  806 WQICKDRKKLIVSCKERMlelKTPLANTKEKLSVGDLLPCTVRKIFPTG 854
Cdd:PRK00087   532 LDIDKENKKLSLSLKKLL---PDPWENVEEKYPVGSIVLGKVVRIAPFG 577
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
397-462 6.98e-03

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 37.20  E-value: 6.98e-03
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1832390731   397 GVVSDVFDDGIILHTAGNQNVRINVSEVANKFsqlinaeKIEMSDAFKIGQMVPFRVISKKSKQDK 462
Cdd:smart00316    8 GTVTEITPGGAFVDLGNGVEGLIPISELSDKR-------VKDPEEVLKVGDEVKVKVLSVDEEKGR 66
PRK11788 PRK11788
tetratricopeptide repeat protein; Provisional
 1867-1942 9.25e-03

tetratricopeptide repeat protein; Provisional


Pssm-ID: 236983 [Multi-domain]  Cd Length: 389  Bit Score: 40.56  E-value: 9.25e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1832390731 1867 QLAQIYQNSKKNQEAKQILETMVKKFRAqhIEVWVLLAEHLMKQKEHKAARDLLTRALssvpkQQH-TMLIskFAQL 1942
Cdd:PRK11788   254 KLMECYQALGDEAEGLEFLRRALEEYPG--ADLLLALAQLLEEQEGPEAAQALLREQL-----RRHpSLRG--FHRL 321
 
Name Accession Description Interval E-value
Astacin pfam01400
Astacin (Peptidase family M12A); The members of this family are enzymes that cleave peptides. ...
 103-290 1.86e-100

Astacin (Peptidase family M12A); The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family contain two conserved disulphide bridges, these are joined 1-4 and 2-3. Members of this family have an amino terminal propeptide which is cleaved to give the active protease domain. All other linked domains are found to the carboxyl terminus of this domain. This family includes: Astacin, a digestive enzyme from Crayfish. Meprin, a multiple domain membrane component that is constructed from a homologous alpha and beta chain. Proteins involved in morphogenesis such as Swiss:P13497, and Tolloid from drosophila.


Pssm-ID: 426242 [Multi-domain]  Cd Length: 192  Bit Score: 320.77  E-value: 1.86e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  103 RRWPNGEIPYTLSSQYGAYARSVIANAMNEYHKKTCVRFVARDPARHHDYLWIHPDEGCYSLVGKTGGKQPVSLDSGCIQ 182
Cdd:pfam01400    1 KKWPNGPIPYVIDGSLTGLARALIRQAMRHWENKTCIRFVERTPAPDNNYLFFFKGDGCYSYVGRVGGRQPVSIGDGCDK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  183 VGTIVHELMHAVGFFHEQSRQDRDNYIDVVWQNVMNGADDQFEKYNLNVISHLDEPYDYSSIMHYGPYAFS-GSGKKTLI 261
Cdd:pfam01400   81 FGIIVHELGHALGFFHEQSRPDRDDYVSINWDNIDPGQEGNFDKYDPSEVDSYGVPYDYGSIMHYGPNAFSkNGSLPTIV 160

                          170       180       190
                   ....*....|....*....|....*....|
gi 1832390731  262 PKKSGAE-RMGQRVKFSDIDVRKINKLYNC 290
Cdd:pfam01400  161 PKDNDYQaTIGQRVKLSFYDIKKINKLYKC 190
ZnMc_astacin_like cd04280
Zinc-dependent metalloprotease, astacin_like subfamily or peptidase family M12A, a group of ...
 107-288 1.42e-93

Zinc-dependent metalloprotease, astacin_like subfamily or peptidase family M12A, a group of zinc-dependent proteolytic enzymes with a HExxH zinc-binding site/active site. Members of this family may have an amino terminal propeptide, which is cleaved to yield the active protease domain, which is consequently always found at the N-terminus in multi-domain architectures. This family includes: astacin, a digestive enzyme from Crayfish; meprin, a multiple domain membrane component that is constructed from a homologous alpha and beta chain, proteins involved in (bone) morphogenesis, tolloid from drosophila, and the sea urchin SPAN protein, which may also play a role in development.


Pssm-ID: 239807 [Multi-domain]  Cd Length: 180  Bit Score: 300.26  E-value: 1.42e-93
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  107 NGEIPYTLSSQYGAYARSVIANAMNEYHKKTCVRFVARDParHHDYLWIHPDEGCYSLVGKTGGKQPVSLDSGCIQVGTI 186
Cdd:cd04280      1 NGTVPYVIDGSFDESDRSLILRAMREIESNTCIRFVPRTT--EKDYIRIVKGSGCWSYVGRVGGRQVVSLGSGCFSLGTI 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  187 VHELMHAVGFFHEQSRQDRDNYIDVVWQNVMNGADDQFEKYNLNVISHLDEPYDYSSIMHYGPYAFSGSGKKTLIPKKSG 266
Cdd:cd04280     79 VHELMHALGFYHEQSRPDRDDYVTINWENIQPGYEHNFDKYSPDTVTTYGVPYDYGSVMHYGPTAFSKNGKPTIVPKDPG 158

                          170       180
                   ....*....|....*....|..
gi 1832390731  267 AERMGQRVKFSDIDVRKINKLY 288
Cdd:cd04280    159 YQIIGQREGLSFLDIKKINKMY 180
ZnMc_hatching_enzyme cd04283
Zinc-dependent metalloprotease, hatching enzyme-like subfamily. Hatching enzymes are secreted ...
 109-290 3.77e-75

Zinc-dependent metalloprotease, hatching enzyme-like subfamily. Hatching enzymes are secreted by teleost embryos to digest the egg envelope or chorion. In some teleosts, the hatching enzyme may be a system consisting of two evolutionary related metalloproteases, high choriolytic enzyme and low choriolytic enzyme (HCE and LCE), which may have different substrate specificities and cooperatively digest the chorion.


Pssm-ID: 239810 [Multi-domain]  Cd Length: 182  Bit Score: 247.56  E-value: 3.77e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  109 EIPYTLSSQYGAYARSVIANAMNEYHKKTCVRFVARdpARHHDYLWIHPDEGCYSLVGKTGGKQPVSLD-SGCIQVGTIV 187
Cdd:cd04283      5 YVPYVISPQYSENERAVIEKAMQEFETLTCVRFVPR--TTERDYLNIESRSGCWSYIGRQGGRQTVSLQkQGCMYKGIIQ 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  188 HELMHAVGFFHEQSRQDRDNYIDVVWQNVMNGADDQFEKYNLNvisHLDEPYDYSSIMHYGPYAFSGSGKKTLIPKKSGA 267
Cdd:cd04283     83 HELLHALGFYHEQTRSDRDKYVRINWENIIPDQLYNFDKQDTN---NLGTPYDYSSVMHYGRYAFSINGKPTIVPIPDPN 159

                          170       180
                   ....*....|....*....|...
gi 1832390731  268 ERMGQRVKFSDIDVRKINKLYNC 290
Cdd:cd04283    160 VPIGQRQGMSNLDILRINKLYNC 182
ZnMc_meprin cd04282
Zinc-dependent metalloprotease, meprin_like subfamily. Meprins are membrane-bound or secreted ...
 75-290 1.44e-51

Zinc-dependent metalloprotease, meprin_like subfamily. Meprins are membrane-bound or secreted extracellular proteases, which cleave a variety of targets, including peptides such as parathyroid hormone, gastrin, and cholecystokinin, cytokines such as osteopontin, and proteins such as collagen IV, fibronectin, casein and gelatin. Meprins may also be able to release proteins from the cell surface. Closely related meprin alpha- and beta-subunits form homo- and hetero-oligomers; these complexes are found on epithelial cells of the intestine, for example, and are also expressed in certain cancer cells.


Pssm-ID: 239809 [Multi-domain]  Cd Length: 230  Bit Score: 181.90  E-value: 1.44e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731   75 EGDIYLPSVKefvnennklGRNAIKQMYRRWPNgEIPYTLSSQYGAYARSVIANAMNEYHKKTCVRFvaRDPARHHDYLW 154
Cdd:cd04282     25 EGDILLDEGQ---------SRNGLIGDTYRWPF-PIPYILDDSLDLNAKGVILKAFEMYRLKSCVDF--KPYEGESNYIF 92

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  155 IHPDEGCYSLVGKTGGKQPVSLDSGCIQVGTIVHELMHAVGFFHEQSRQDRDNYIDVVWQNVMNGADDQFEKYNLNVISH 234
Cdd:cd04282     93 FFKGSGCWSMVGDQQGGQNLSIGAGCDYKATVEHEFLHALGFYHEQSRSDRDDYVKIWWDQILSGREHNFNKYDDSFSTD 172

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1832390731  235 LDEPYDYSSIMHYGPYAFS-GSGKKTLIPKKSGAER-MGQRVKFSDIDVRKINKLYNC 290
Cdd:cd04282    173 LNTPYDYESVMHYSPFSFNkGASEPTITTKIPEFNDiIGQRLDFSDIDLERLNRMYNC 230
ZnMc_BMP1_TLD cd04281
Zinc-dependent metalloprotease; BMP1/TLD-like subfamily. BMP1 (Bone morphogenetic protein 1) ...
 103-291 5.33e-51

Zinc-dependent metalloprotease; BMP1/TLD-like subfamily. BMP1 (Bone morphogenetic protein 1) and TLD (tolloid)-like metalloproteases play vital roles in extracellular matrix formation, by cleaving precursor proteins such as enzymes, structural proteins, and proteins involved in the mineralization of the extracellular matrix. The drosophila protein tolloid and its Xenopus homologue xolloid cleave and inactivate Sog and chordin, respectively, which are inhibitors of Dpp (the Drosophila decapentaplegic gene product) and its homologue BMP4, involved in dorso-ventral patterning.


Pssm-ID: 239808 [Multi-domain]  Cd Length: 200  Bit Score: 179.17  E-value: 5.33e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  103 RRWPNGEIPYTLSSQYGAYARSVIANAMNEYHKKTCVRFVARDParHHDYLWIHPDE-GCYSLVGKTG-GKQPVSLDSGC 180
Cdd:cd04281      8 RIWPGGVIPYVIDGNFTGSQRAMFKQAMRHWENFTCVTFVERTP--EENYIVFTYRPcGCCSYVGRRGnGPQAISIGKNC 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  181 IQVGTIVHELMHAVGFFHEQSRQDRDNYIDVVWQNVMNGADDQFEKYNLNVISHLDEPYDYSSIMHYGPYAFS-GSGKKT 259
Cdd:cd04281     86 DKFGIVVHELGHVIGFWHEHTRPDRDDHVTIIRENIQPGQEYNFLKMEPEEVDSLGEPYDFDSIMHYARNTFSrGMFLDT 165

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 1832390731  260 LIPKKSGA---ERMGQRVKFSDIDVRKINKLYNCA 291
Cdd:cd04281    166 ILPKRDPNgvrPEIGQRTRLSEGDIIQANKLYKCP 200
ZnMc smart00235
Zinc-dependent metalloprotease; Neutral zinc metallopeptidases. This alignment represents a ...
 102-243 1.58e-46

Zinc-dependent metalloprotease; Neutral zinc metallopeptidases. This alignment represents a subset of known subfamilies. Highest similarity occurs in the HExxH zinc-binding site/ active site.


Pssm-ID: 214576 [Multi-domain]  Cd Length: 139  Bit Score: 164.06  E-value: 1.58e-46
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731   102 YRRWPNGEIPYTL-SSQYGAYARSVIANAMNEYHKKTCVRFVARDPArHHDYLWIHP-DEGC-YSLVGKTGGKQPVSLDS 178
Cdd:smart00235    2 SKKWPKGTVPYVIdSSSLSPEEREAIAKALAEWSDVTCIRFVERTGT-ADIYISFGSgDSGCtLSHAGRPGGDQHLSLGN 80

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1832390731   179 GCIQVGTIVHELMHAVGFFHEQSRQDRDNYIDVVWQNVMngaddqFEKYNLNVISHLDEPYDYSS 243
Cdd:smart00235   81 GCINTGVAAHELGHALGLYHEQSRSDRDNYMYINYTNID------TRNFDLSEDDSLGIPYDYGS 139
ZnMc cd00203
Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major ...
 108-288 7.76e-22

Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease.


Pssm-ID: 238124 [Multi-domain]  Cd Length: 167  Bit Score: 94.51  E-value: 7.76e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  108 GEIPYTL--------SSQYGAYARSVIANAMNEYHKKTCVRFVARDPARHHDYLWI-------HPDEGCYSLVGKT--GG 170
Cdd:cd00203      1 KVIPYVVvaddrdveEENLSAQIQSLILIAMQIWRDYLNIRFVLVGVEIDKADIAIlvtrqdfDGGTGGWAYLGRVcdSL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  171 KQPVSLDSGCIQ----VGTIVHELMHAVGFFHEQSRQDRDNYIDVvwqnvmngaddqfekynlnVISHLDEPYDYSSIMH 246
Cdd:cd00203     81 RGVGVLQDNQSGtkegAQTIAHELGHALGFYHDHDRKDRDDYPTI-------------------DDTLNAEDDDYYSVMS 141

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 1832390731  247 YGPYAFSGsgkktlipkksgaermGQRVKFSDIDVRKINKLY 288
Cdd:cd00203    142 YTKGSFSD----------------GQRKDFSQCDIDQINKLY 167
ZnMc_MMP_like cd04268
Zinc-dependent metalloprotease, MMP_like subfamily. This group contains matrix ...
 107-288 1.66e-17

Zinc-dependent metalloprotease, MMP_like subfamily. This group contains matrix metalloproteinases (MMPs), serralysins, and the astacin_like family of proteases.


Pssm-ID: 239796 [Multi-domain]  Cd Length: 165  Bit Score: 81.77  E-value: 1.66e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  107 NGEIPYTLSSQYGAYARSVIANAMNEYHKKTCVRFVARDPARHHD-----YLWIHPDEGCYSLVGKTGG-------KQPV 174
Cdd:cd04268      1 KKPITYYIDDSVPDKLRAAILDAIEAWNKAFAIGFKNANDVDPADirysvIRWIPYNDGTWSYGPSQVDpltgeilLARV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  175 SLDSGCIQ------VGTIVHELMHAVGFFHEQSRQDRDNYIDVvwqnvmngaddqfekynlnvishLDEPYDYSSIMHYG 248
Cdd:cd04268     81 YLYSSFVEysgarlRNTAEHELGHALGLRHNFAASDRDDNVDL-----------------------LAEKGDTSSVMDYA 137

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 1832390731  249 PYAFSGSGKKtlipkksgaermGQRVKFSDIDVRKINKLY 288
Cdd:cd04268    138 PSNFSIQLGD------------GQKYTIGPYDIAAIKKLY 165
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1774-2033 5.93e-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: 68.22  E-value: 5.93e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1774 ESEEDLSKQLRGDPNSAILWIKYMSLFLQKADLAaarataeralESINYRETAELRNVWTAYLNMEVAF-----GDASTV 1848
Cdd:COG2956     26 KAIDLLEEALELDPETVEAHLALGNLYRRRGEYD----------RAIRIHQKLLERDPDRAEALLELAQdylkaGLLDRA 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1849 QKVFERACN-NVDSYTMHLQLAQIYQNSKKNQEAKQILETMVKKfRAQHIEVWVLLAEHLMKQKEHKAARDLLTRALSSV 1927
Cdd:COG2956     96 EELLEKLLElDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKL-GPENAHAYCELAELYLEQGDYDEAIEALEKALKLD 174

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1928 PKQQ--HTMLiskfAQLEFKYGDSERGTTLFEGLLTAHPKKTDLWLVYADAAVKHMGIEQARKIMDRACNSNNSLHKMRP 2005
Cdd:COG2956    175 PDCAraLLLL----AELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKALELDPSDDLLLA 250

                          250       260
                   ....*....|....*....|....*...
gi 1832390731 2006 LYKKwleIENRHGDSVSVELVRAKAEKY 2033
Cdd:COG2956    251 LADL---LERKEGLEAALALLERQLRRH 275
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
750-820 1.28e-10

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 59.15  E-value: 1.28e-10
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1832390731   750 GDIVEGKVVHVSPQGIHLNVCNFVRAFAPASMLSDKPIIgKLKSKFPLGSTVKCRIWQICKDRKKLIVSCK 820
Cdd:smart00316    3 GDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVK-DPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1865-1993 1.17e-08

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: 55.58  E-value: 1.17e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1865 HLQLAQIYQNSKKNQEAKQILETMVKKFRaQHIEVWVLLAEHLMKQKEHKAARDLLTRALSSVPKqqHTMLISKFAQLEF 1944
Cdd:COG4783      7 LYALAQALLLAGDYDEAEALLEKALELDP-DNPEAFALLGEILLQLGDLDEAIVLLHEALELDPD--EPEARLNLGLALL 83

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1832390731 1945 KYGDSERGTTLFEGLLTAHPKKTDLWLVYADAAVKHMGIEQARKIMDRA 1993
Cdd:COG4783     84 KAGDYDEALALLEKALKLDPEHPEAYLRLARAYRALGRPDEAIAALEKA 132
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1880-1993 5.12e-07

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: 50.77  E-value: 5.12e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1880 EAKQILETMVKKfRAQHIEVWVLLAEHLMKQKEHKAARDLLTRALSSVPKqqHTMLISKFAQLEFKYGDSERGTTLFEGL 1959
Cdd:COG4235      1 EAIARLRQALAA-NPNDAEGWLLLGRAYLRLGRYDEALAAYEKALRLDPD--NADALLDLAEALLAAGDTEEAEELLERA 77

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1832390731 1960 LTAHPKKTDLWLVYADAAVKHMGIEQARKIMDRA 1993
Cdd:COG4235     78 LALDPDNPEALYLLGLAAFQQGDYAEAIAAWQKL 111
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 750-820 2.28e-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: 46.84  E-value: 2.28e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1832390731  750 GDIVEGKVVHVSPQGIHLNVCNFVRAFAPASMLSDKPIIgKLKSKFPLGSTVKCRIWQICKDRKKLIVSCK 820
Cdd:cd05698      1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIK-DPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1834-1938 3.02e-06

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: 48.46  E-value: 3.02e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1834 AYLNMEvAFGDAstvQKVFERAC----NNVDsytMHLQLAQIYQNSKKNQEAKQILETMVKKfRAQHIEVWVLLAEHLMK 1909
Cdd:COG4235     26 AYLRLG-RYDEA---LAAYEKALrldpDNAD---ALLDLAEALLAAGDTEEAEELLERALAL-DPDNPEALYLLGLAAFQ 97

                           90       100
                   ....*....|....*....|....*....
gi 1832390731 1910 QKEHKAARDLLTRALSSVPKQQHTMLISK 1938
Cdd:COG4235     98 QGDYAEAIAAWQKLLALLPADAPARLLEA 126
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 483-546 4.50e-06

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: 46.09  E-value: 4.50e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1832390731  483 LVAGLVIHTCVTSLEEKGAVLDIGLDQMTGFLEKAQFP-PSGVFEGQPL--IVRVLSTTSRVVKVSA 546
Cdd:cd05694      2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGnFSKLKVGQLLlcVVEKVKDDGRVVSLSA 68
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 486-850 5.01e-06

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: 51.66  E-value: 5.01e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  486 GLVIHTCVTSLEEKGAVLDIGLdQMTGFLEKAQFP--PSGVFEGQPLIVRVLSTTSR----VVKVSALVEQDNLnmtscE 559
Cdd:TIGR00717   19 GSIVKGTVVAINKDTVFVDVGL-KSEGRIPKEEFLdaPLEIQVGDEVEVYLDRVEDRfgetVLSREKAQRHELW-----I 92

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  560 KLqLNHLMPGTILECEPTGDepVSNGVFVSIgNGLKGILPRRNLPPRLRENPEKL-GKAIRAVVM-FCQQNSKVLVlhAH 637
Cdd:TIGR00717   93 KL-EKAYEEGSIVEGKIVGK--VKGGFIVDL-NGVEAFLPGSQVDVKPIKDLDSLiGKTLKFKIIkLDQKRNNIVV--SR 166

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  638 PDIVAISKIEKR-TSFEGISIGDTVKCTVLDVIPSKctVFFSLPPTDGkkSLVTGLCSRGFLDNPDNIaenYNIGAEKLC 716
Cdd:TIGR00717  167 RAYLEEERSQAReELLENLKEGDVVKGVVKNITDFG--AFVDLGGVDG--LLHITDMSWKRVKHPSEY---VKVGQEVKV 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  717 RVIAYRYVERSIVVStrkdiLKQKITSYMDAV-----CGDIVEGKVVHVSPQGIHLNVCNFVRAFAPASMLSDKPIIGKL 791
Cdd:TIGR00717  240 KVIKFDKEKGRISLS-----LKQLGEDPWEAIekkfpVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHP 314

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1832390731  792 KSKFPLGSTVKCRIWQICKDRKKLIVS---CKERmlelktPLANTKEKLSVGDLLPCTVRKI 850
Cdd:TIGR00717  315 SKVVKKGDEVEVMILDIDPERRRLSLGlkqCKAN------PWEQFEEKHPVGDRVTGKIKKI 370
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 651-850 9.91e-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: 50.04  E-value: 9.91e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  651 SFEGISIGDTVKCTVLDVIPSkcTVFFSLpptdGKKSlvTGLCSRG-FLDNPDNIaeNYNIGAEKLCRVIAYRYVERSIV 729
Cdd:COG0539     12 SLKELKEGDIVKGTVVSIDDD--EVLVDI----GYKS--EGIIPLSeFSDEPGEL--EVKVGDEVEVYVEKVEDGEGEIV 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  730 VSTRK-DILK--QKITSYMDAvcGDIVEGKVVHVSPQGIHLNVCNfVRAFAPASMLSDKPIigKLKSKFpLGSTVKCRIW 806
Cdd:COG0539     82 LSKKKaDREKawEELEEAFEN--GEPVEGKVKGVVKGGLIVDIGG-VRAFLPASQVDVRPV--RDLDEY-VGKTLEFKII 155

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 1832390731  807 QICKDRKKLIVSckERML---ELKTPLANTKEKLSVGDLLPCTVRKI 850
Cdd:COG0539    156 KLDRKRNNVVVS--RRAVleeEREEKREELLEKLEEGDVVEGTVKNI 200
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 1865-1964 6.35e-05

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: 45.34  E-value: 6.35e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1865 HLQLAQIYQNSKKNQEAKQILETMVKKFrAQHIEVWVLLAEHLMKQKEHKAARDLLTRALSSVPkqQHTMLISKFAQLEF 1944
Cdd:COG5010     57 ESPSDNLYNKLGDFEESLALLEQALQLD-PNNPELYYNLALLYSRSGDKDEAKEYYEKALALSP--DNPNAYSNLAALLL 133

                           90       100
                   ....*....|....*....|
gi 1832390731 1945 KYGDSERGTTLFEGLLTAHP 1964
Cdd:COG5010    134 SLGQDDEAKAALQRALGTSP 153
ZnMc_MMP_like_3 cd04327
Zinc-dependent metalloprotease; MMP_like sub-family 3. A group of bacterial and fungal ...
 185-255 9.03e-05

Zinc-dependent metalloprotease; MMP_like sub-family 3. A group of bacterial and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.


Pssm-ID: 239819 [Multi-domain]  Cd Length: 198  Bit Score: 45.45  E-value: 9.03e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  185 TIVHELMHAVGFFHEQSRQDRDNYIDV--VWQNVMN--GADDQfEKYNLNVISHLDE------PYDYSSIMHygpYAFSG 254
Cdd:cd04327     95 VVLHEFGHALGFIHEHQSPAANIPWDKeaVYAYFSGppNWDRE-TVINHNVFAKLDDgdvaysPYDPDSIMH---YPFPG 170


                   .
gi 1832390731  255 S 255
Cdd:cd04327    171 S 171
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1860-1930 1.97e-04

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: 43.26  E-value: 1.97e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1832390731 1860 DSYTMHLQLAQIYQNSKKNQEAKQILETMVKKfRAQHIEVWVLLAEHLMKQKEHKAARDLLTRALSSVPKQ 1930
Cdd:COG4783     70 DEPEARLNLGLALLKAGDYDEALALLEKALKL-DPEHPEAYLRLARAYRALGRPDEAIAALEKALELDPDD 139
HemYx COG3071
Uncharacterized protein HemY, contains HemY_N domain and TPR repeats (unrelated to ...
 1895-1993 3.01e-04

Uncharacterized protein HemY, contains HemY_N domain and TPR repeats (unrelated to protoporphyrinogen oxidase HemY) [Function unknown];


Pssm-ID: 442305 [Multi-domain]  Cd Length: 323  Bit Score: 45.29  E-value: 3.01e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1895 QHIEVWVLLAEHLMKQKEHKAARDLLTRALSsvpKQQHTMLISKFAQLEFkyGDSERGTTLFEGLLTAHPKKTDLWLVYA 1974
Cdd:COG3071    191 RDPELAAAYARALIALGDHDEAERLLREALK---RQWDPRLVRLYGRLQG--GDPAKQLKRAEKWLKKHPNDPDLLLALG 265

                           90
                   ....*....|....*....
gi 1832390731 1975 DAAVKHMGIEQARKIMDRA 1993
Cdd:COG3071    266 RLCLRNQLWGKAREYLEAA 284
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 750-817 3.48e-04

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: 40.68  E-value: 3.48e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1832390731  750 GDIVEGKVVHVSPQGIHLNVCNFVRAFAPASMLSDKPIIGKLKsKFPLGSTVKCRIWQICKDRKKLIV 817
Cdd:cd05697      1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEK-KFKPGLKVKCRVLSVEPERKRLVL 67
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1416-1675 5.07e-04

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 44.94  E-value: 5.07e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1416 NNFNVGDVVRcfgsaGTVES--DSEIRVEINGIWTGHIARENISDD----LKVETGIGGIIDVKLAPGQLREARVVAVDK 1489
Cdd:PRK00087   298 KQIRRGDIVK-----GTVVSvnENEVFVDVGYKSEGVIPLRELTLDeissLKESVKVGDEIEVKVLKLEDEDGYVVLSKK 372

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1490 KSNTLELSLNVEKnpKFEIGEKLTGRVFSepqKDNSVMLKLASGDQAILTATGITSIYesvDKKISEnfGKGEILDVica 1569
Cdd:PRK00087   373 EADREKAWKELEE--AFENGEPVKGKVKE---VVKGGLLVDYGGVRAFLPASHVELGY---VEDLSE--YKGQELEV--- 439

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1570 KVTQSKPRRYYVVTPSRYHDLKSCKNEKRKLILdpNNVTIGQNYDGIVVQASPSGVIVEIGpGIVGKIPVNE-------E 1642
Cdd:PRK00087   440 KIIEFNRKRRKKVVLSRKAILEEEKEKKKEETW--NSLEEGDVVEGEVKRLTDFGAFVDIG-GVDGLLHVSEiswgrveK 516

                          250       260       270
                   ....*....|....*....|....*....|....
gi 1832390731 1643 NSDIIDIGVK-SVVTVEIEKSTPKgFLLKLKEII 1675
Cdd:PRK00087   517 PSDVLKVGDEiKVYILDIDKENKK-LSLSLKKLL 549
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1833-1989 5.09e-04

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 45.07  E-value: 5.09e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1833 TAYLNMEVAFGDASTVQKVFERACN-NVDSYTMHLQLAQIYQNSKKNQEAKQILETMVKKFRAqHIEVWVLLAEHLMKQK 1911
Cdd:TIGR02917  537 LALAGLYLRTGNEEEAVAWLEKAAElNPQEIEPALALAQYYLGKGQLKKALAILNEAADAAPD-SPEAWLMLGRAQLAAG 615

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1832390731 1912 EHKAARDLLTRALSSVPKQQHTMLISKFAQLEFKygDSERGTTLFEGLLTAHPKKTDLWLVYADAAVKHMGIEQARKI 1989
Cdd:TIGR02917  616 DLNKAVSSFKKLLALQPDSALALLLLADAYAVMK--NYAKAITSLKRALELKPDNTEAQIGLAQLLLAAKRTESAKKI 691
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 750-818 5.82e-04

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: 40.13  E-value: 5.82e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1832390731  750 GDIVEGKVVHVSPQGIHLNVcNFVRAFAPASMLSDKPIigKLKSKFpLGSTVKCRIWQICKDRKKLIVS 818
Cdd:cd04465      1 GEIVEGKVTEKVKGGLIVDI-EGVRAFLPASQVDLRPV--EDLDEY-VGKELKFKIIEIDRERNNIVLS 65
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
1860-1929 6.16e-04

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


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 40.92  E-value: 6.16e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1860 DSYTMHLQLAQIYQNSKKNQEAKQILETMvkKFRAQHIEVWVLLAEHLMKQKEHKAARDLLTRALSSVPK 1929
Cdd:COG3063     24 DNADALNNLGLLLLEQGRYDEAIALEKAL--KLDPNNAEALLNLAELLLELGDYDEALAYLERALELDPS 91
TPR_19 pfam14559
Tetratricopeptide repeat;
1875-1930 7.29e-04

Tetratricopeptide repeat;


Pssm-ID: 434038 [Multi-domain]  Cd Length: 65  Bit Score: 39.49  E-value: 7.29e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1832390731 1875 SKKNQEAKQILETMVKKFRaQHIEVWVLLAEHLMKQKEHKAARDLLTRALSSVPKQ 1930
Cdd:pfam14559    1 EGDYAEALELLEQALAEDP-DNAEARLGLAEALLALGRLDEAEALLAALPAADPDD 55
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
569-634 8.12e-04

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 39.89  E-value: 8.12e-04
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1832390731   569 GTILECEPtgdepvsNGVFVSIGNGLKGILPRRNLPPRLRENPE---KLGKAIRAVVMFCQQNSKVLVL 634
Cdd:smart00316    8 GTVTEITP-------GGAFVDLGNGVEGLIPISELSDKRVKDPEevlKVGDEVKVKVLSVDEEKGRIIL 69
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1894-1993 8.28e-04

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: 41.72  E-value: 8.28e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1894 AQHIEVWVLLAEHLMKQKEHKAARDLLTRALSSVPkqQHTMLISKFAQLEFKYGDSERGTTLFEGLLTAHPKKTDLWLVY 1973
Cdd:COG4783      1 AACAEALYALAQALLLAGDYDEAEALLEKALELDP--DNPEAFALLGEILLQLGDLDEAIVLLHEALELDPDEPEARLNL 78

                           90       100
                   ....*....|....*....|
gi 1832390731 1974 ADAAVKHMGIEQARKIMDRA 1993
Cdd:COG4783     79 GLALLKAGDYDEALALLEKA 98
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1858-1993 8.33e-04

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 43.46  E-value: 8.33e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1858 NVDSYTMHLQLAQIYQNSKKNQEAKQILETMVKKFRaQHIEVWVLLAEHLMKQKEHKAARDLLTRALSSVPKQQHTMLis 1937
Cdd:COG0457      4 DPDDAEAYNNLGLAYRRLGRYEEAIEDYEKALELDP-DDAEALYNLGLAYLRLGRYEEALADYEQALELDPDDAEALN-- 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1832390731 1938 KFAQLEFKYGDSERGTTLFEGLLTAHPKKTDLWLVYADAAVKhMG-IEQARKIMDRA 1993
Cdd:COG0457     81 NLGLALQALGRYEEALEDYDKALELDPDDAEALYNLGLALLE-LGrYDEAIEAYERA 136
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 738-818 1.06e-03

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: 39.88  E-value: 1.06e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  738 KQKITSYMDAVCGDIVEGKVVHVSPQGIHLNVCNFVRAFAPASMLSDKPIIgKLKSKFPLGSTVKCRIWQICKDRKKLIV 817
Cdd:cd04461      3 GTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVT-DPSFGFKKGQSVTAKVTSVDEEKQRFLL 81


                   .
gi 1832390731  818 S 818
Cdd:cd04461     82 S 82
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1840-2000 1.52e-03

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 43.53  E-value: 1.52e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1840 VAFGDASTVQKVFERACN-NVDSYTMHLQLAQIYQNSKKnqeAKQILETMVKKF---RAQHIEVWVLLAEHLMKQKEHKA 1915
Cdd:TIGR02917   67 LALGDYAAAEKELRKALSlGYPKNQVLPLLARAYLLQGK---FQQVLDELPGKTlldDEGAAELLALRGLAYLGLGQLEL 143

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731 1916 ARDLLTRALSSVPKQQHTMLISkfAQLEFKYGDSERGTTLFEGLLTAHPKKTDLWLVYADAAVKHMGIEQA----RKIMD 1991
Cdd:TIGR02917  144 AQKSYEQALAIDPRSLYAKLGL--AQLALAENRFDEARALIDEVLTADPGNVDALLLKGDLLLSLGNIELAlaayRKAIA 221


                   ....*....
gi 1832390731 1992 RACNSNNSL 2000
Cdd:TIGR02917  222 LRPNNIAVL 230
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 391-475 1.58e-03

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: 39.89  E-value: 1.58e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  391 EGLLGLGVVSDVFDDGIILHTAGNQNVRINVSEVANKFSQLINA------------EKIEMSDAFKIGQMVPFRVISK-K 457
Cdd:cd05693      3 EGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEEldeeseeeddeeELPDLEDLFSVGQLVRCKVVSLdK 82

                           90
                   ....*....|....*...
gi 1832390731  458 SKQDKGSVKGTCNPAKLN 475
Cdd:cd05693     83 SKSGKKRIELSLEPELVN 100
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 750-819 1.80e-03

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: 38.81  E-value: 1.80e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  750 GDIVEGKVVHVSPQGIHLNVCNFVRAFAPASMLSDKPIIGKLKsKFPLGSTVKCRIWQICKDRKKLIVSC 819
Cdd:pfam00575    4 GDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDE-VIKVGDEVKVKVLKVDKDRRRIILSI 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1609-1665 1.99e-03

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 38.74  E-value: 1.99e-03
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1832390731  1609 IGQNYDGIVVQASPSGVIVEIGPGIVGKIPVNE-------ENSDIIDIGvkSVVTVEIEKSTPK 1665
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISElsdkrvkDPEEVLKVG--DEVKVKVLSVDEE 63
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
583-854 2.22e-03

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 43.01  E-value: 2.22e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  583 SNGVFVSIGNGLKGILPRRNLPPRLRENPEKL---GKAIRAVVMFCQQNSKVLVLHA-HPD-IVAISKIEKrtSFEGisi 657
Cdd:PRK00087   315 ENEVFVDVGYKSEGVIPLRELTLDEISSLKESvkvGDEIEVKVLKLEDEDGYVVLSKkEADrEKAWKELEE--AFEN--- 389

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  658 GDTVKCTV-------LDVIPSKCTVFfsLPptdgkKSLVtglcSRGFLDNPDNIaenynIGAEKLCRVIAYRYVERSIVV 730
Cdd:PRK00087   390 GEPVKGKVkevvkggLLVDYGGVRAF--LP-----ASHV----ELGYVEDLSEY-----KGQELEVKIIEFNRKRRKKVV 453

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1832390731  731 STRKDILKQKITSYMDAVC-----GDIVEGKVVHVSPQGIHLNVcNFVRAFAPASMLSDKPIIgKLKSKFPLGSTVKCRI 805
Cdd:PRK00087   454 LSRKAILEEEKEKKKEETWnsleeGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWGRVE-KPSDVLKVGDEIKVYI 531

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*....
gi 1832390731  806 WQICKDRKKLIVSCKERMlelKTPLANTKEKLSVGDLLPCTVRKIFPTG 854
Cdd:PRK00087   532 LDIDKENKKLSLSLKKLL---PDPWENVEEKYPVGSIVLGKVVRIAPFG 577
CpoB COG1729
Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane ...
 1865-1929 3.30e-03

Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane constriction [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441335 [Multi-domain]  Cd Length: 113  Bit Score: 39.20  E-value: 3.30e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1832390731 1865 HLQLAQIYQNSKKNQEAKQILETMVKKF--RAQHIEVWVLLAEHLMKQKEHKAARDLLTRALSSVPK 1929
Cdd:COG1729     33 LYWLGEAYYALGDYDEAAEAFEKLLKRYpdSPKAPDALLKLGLSYLELGDYDKARATLEELIKKYPD 99
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
397-462 6.98e-03

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 37.20  E-value: 6.98e-03
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1832390731   397 GVVSDVFDDGIILHTAGNQNVRINVSEVANKFsqlinaeKIEMSDAFKIGQMVPFRVISKKSKQDK 462
Cdd:smart00316    8 GTVTEITPGGAFVDLGNGVEGLIPISELSDKR-------VKDPEEVLKVGDEVKVKVLSVDEEKGR 66
PRK11788 PRK11788
tetratricopeptide repeat protein; Provisional
 1867-1942 9.25e-03

tetratricopeptide repeat protein; Provisional


Pssm-ID: 236983 [Multi-domain]  Cd Length: 389  Bit Score: 40.56  E-value: 9.25e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1832390731 1867 QLAQIYQNSKKNQEAKQILETMVKKFRAqhIEVWVLLAEHLMKQKEHKAARDLLTRALssvpkQQH-TMLIskFAQL 1942
Cdd:PRK11788   254 KLMECYQALGDEAEGLEFLRRALEEYPG--ADLLLALAQLLEEQEGPEAAQALLREQL-----RRHpSLRG--FHRL 321
 
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.
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