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Conserved domains on  [gi|42570002|ref|NP_182244|]
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polyribonucleotide phosphorylase, putative (DOMAIN OF UNKNOWN FUNCTION 724 5) [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DUF724 pfam05266
Protein of unknown function (DUF724); This family contains several uncharacterized proteins ...
 285-469 6.33e-85

Protein of unknown function (DUF724); This family contains several uncharacterized proteins found in Arabidopsis thaliana and other plants. This region is often found associated with Agenet domains and may contain coiled-coil.


:

Pssm-ID: 428400 [Multi-domain]  Cd Length: 188  Bit Score: 259.13  E-value: 6.33e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002   285 VLPFVKKSPVWKIYESMEVFKRVPQSPHFSPLFEAKEDFREGFALGMMVTFSGVLEKVEDLKTDVPIRQLNSLKDSFTEL 364
Cdd:pfam05266   1 VLPFVKKSPLWKTIESMEVFKKVPQRPHFSPLLESKEELREGSALGMMVSFAGLLEKVKKLQVDDSRSVFESLMESFAEL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002   365 EKHGFTVTAPLSRIAKLLALKDRQLKILEELKVFDKEMKDESSKKHKAEQEFGEMERKIlevknkvLELQKQEAALEKQK 444
Cdd:pfam05266  81 EKHGFDVKAPQSRINKLLSLKDRQTKLLEELKKLEKKIAEEESEKRKLEEEIDELEKKI-------LELERQLALAKEKK 153

                         170       180
                  ....*....|....*....|....*
gi 42570002   445 DATYEKICKMESRARDLGVELEDVE 469
Cdd:pfam05266 154 EAADKEIARLKSEAEKLEQEIQDVE 178
PLN00207 super family cl33427
polyribonucleotide nucleotidyltransferase; Provisional
 7-108 3.15e-53

polyribonucleotide nucleotidyltransferase; Provisional


The actual alignment was detected with superfamily member PLN00207:

Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 192.03  E-value: 3.15e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002    7 TPSAMGLWLVPNHVSVKIPFGNREILVETGLMGRQASSAVTVTDGETIVFTSVCLADVPSEPSDFLPLYVHYQERFSAVG 86
Cdd:PLN00207  67 SSVGEGPGPFPQQFSVKIPVGDRHILVETGHIGRQASGSVTVTDGETIVYTSVCLADVPSEPSDFFPLSVHYQERFSAAG 146

                         90       100
                 ....*....|....*....|..
gi 42570002   87 RTSGGFFKREGRTKDHEVtFLC 108
Cdd:PLN00207 147 RTSGGFFKREGRTKDHEV-LIC 167
NADB_Rossmann super family cl21454
Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a ...
 106-176 3.00e-09

Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction.


The actual alignment was detected with superfamily member cd05329:

Pssm-ID: 473865 [Multi-domain]  Cd Length: 251  Bit Score: 57.46  E-value: 3.00e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 42570002 106 FLCLPAASYITG--QEELKACLNDWKSNGLVVSGLV-----RDQREKLIQEVSSTFSGKLNILSplaqgsgNNMGGSV 176
Cdd:cd05329  26 LAGLGAEVYTCArnQKELDECLTEWREKGFKVEGSVcdvssRSERQELMDTVASHFGGKLNILV-------NNAGTNI 96
 
Name Accession Description Interval E-value
DUF724 pfam05266
Protein of unknown function (DUF724); This family contains several uncharacterized proteins ...
 285-469 6.33e-85

Protein of unknown function (DUF724); This family contains several uncharacterized proteins found in Arabidopsis thaliana and other plants. This region is often found associated with Agenet domains and may contain coiled-coil.


Pssm-ID: 428400 [Multi-domain]  Cd Length: 188  Bit Score: 259.13  E-value: 6.33e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002   285 VLPFVKKSPVWKIYESMEVFKRVPQSPHFSPLFEAKEDFREGFALGMMVTFSGVLEKVEDLKTDVPIRQLNSLKDSFTEL 364
Cdd:pfam05266   1 VLPFVKKSPLWKTIESMEVFKKVPQRPHFSPLLESKEELREGSALGMMVSFAGLLEKVKKLQVDDSRSVFESLMESFAEL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002   365 EKHGFTVTAPLSRIAKLLALKDRQLKILEELKVFDKEMKDESSKKHKAEQEFGEMERKIlevknkvLELQKQEAALEKQK 444
Cdd:pfam05266  81 EKHGFDVKAPQSRINKLLSLKDRQTKLLEELKKLEKKIAEEESEKRKLEEEIDELEKKI-------LELERQLALAKEKK 153

                         170       180
                  ....*....|....*....|....*
gi 42570002   445 DATYEKICKMESRARDLGVELEDVE 469
Cdd:pfam05266 154 EAADKEIARLKSEAEKLEQEIQDVE 178
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 7-108 3.15e-53

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 192.03  E-value: 3.15e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002    7 TPSAMGLWLVPNHVSVKIPFGNREILVETGLMGRQASSAVTVTDGETIVFTSVCLADVPSEPSDFLPLYVHYQERFSAVG 86
Cdd:PLN00207  67 SSVGEGPGPFPQQFSVKIPVGDRHILVETGHIGRQASGSVTVTDGETIVYTSVCLADVPSEPSDFFPLSVHYQERFSAAG 146

                         90       100
                 ....*....|....*....|..
gi 42570002   87 RTSGGFFKREGRTKDHEVtFLC 108
Cdd:PLN00207 147 RTSGGFFKREGRTKDHEV-LIC 167
RNase_PH_PNPase_1 cd11363
Polyribonucleotide nucleotidyltransferase, repeat 1; Polyribonucleotide nucleotidyltransferase ...
 22-104 2.34e-30

Polyribonucleotide nucleotidyltransferase, repeat 1; Polyribonucleotide nucleotidyltransferase (PNPase) is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally, all members of this family form hexameric rings. In the case of PNPase the complex is a trimer, since each monomer contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction and in quality control of ribosomal RNA precursors. It is part of the RNA degradosome complex and binds to the scaffolding domain of the endoribonuclease RNase E.


Pssm-ID: 206768 [Multi-domain]  Cd Length: 229  Bit Score: 117.62  E-value: 2.34e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002  22 VKIPFGNREILVETGLMGRQASSAVTVTDGETIVFTSVCLADVPSEPSDFLPLYVHYQERFSAVGRTSGGFFKREGRTKD 101
Cdd:cd11363   3 FEVLVGGRTLTFETGKLAKQADGSVVVQYGDTVVLVTAVSSKKPKEGIDFFPLTVDYREKLYAAGKIPGGFFKREGRPSE 82


                ...
gi 42570002 102 HEV 104
Cdd:cd11363  83 KEI 85
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 21-104 5.19e-28

Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 117.41  E-value: 5.19e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002  21 SVKIPFGNREILVETGLMGRQASSAVTVTDGETIVFTSVCLADVPSEPSDFLPLYVHYQERFSAVGRTSGGFFKREGRTK 100
Cdd:COG1185   1 KKEFELGGRTLTLETGKLAKQADGAVLVRYGDTVVLVTVVASKEPREGIDFFPLTVDYQEKFYAAGKIPGGFFKREGRPS 80


                ....
gi 42570002 101 DHEV 104
Cdd:COG1185  81 EKEI 84
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 29-104 3.58e-10

3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria.


Pssm-ID: 426074 [Multi-domain]  Cd Length: 129  Bit Score: 57.60  E-value: 3.58e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 42570002    29 REILVETGLMgRQASSAVTVTDGETIVFTSVCLADVPSEPSDFLP--LYVHYQERFSAVGRtsggfFKREGRTKDHEV 104
Cdd:pfam01138   3 RPIEIETGVL-SQADGSALVELGDTKVLATVTGPIEPKEDRDFAPgrLTVEYELAPFASGE-----RPGEGRPSEREI 74
TR_SDR_c cd05329
tropinone reductase-I and II (TR-1, and TR-II)-like, classical (c) SDRs; This subgroup ...
 106-176 3.00e-09

tropinone reductase-I and II (TR-1, and TR-II)-like, classical (c) SDRs; This subgroup includes TR-I and TR-II; these proteins are members of the SDR family. TRs catalyze the NADPH-dependent reductions of the 3-carbonyl group of tropinone, to a beta-hydroxyl group. TR-I and TR-II produce different stereoisomers from tropinone, TR-I produces tropine (3alpha-hydroxytropane), and TR-II, produces pseudotropine (sigma-tropine, 3beta-hydroxytropane). SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction.


Pssm-ID: 187590 [Multi-domain]  Cd Length: 251  Bit Score: 57.46  E-value: 3.00e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 42570002 106 FLCLPAASYITG--QEELKACLNDWKSNGLVVSGLV-----RDQREKLIQEVSSTFSGKLNILSplaqgsgNNMGGSV 176
Cdd:cd05329  26 LAGLGAEVYTCArnQKELDECLTEWREKGFKVEGSVcdvssRSERQELMDTVASHFGGKLNILV-------NNAGTNI 96
CwlO1 COG3883
Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function ...
 354-464 1.10e-03

Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown];


Pssm-ID: 443091 [Multi-domain]  Cd Length: 379  Bit Score: 41.35  E-value: 1.10e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002 354 LNSlkDSFTELekhgftvtapLSRIAKLLALKDRQLKILEELKV-----------FDKEMKDESSKKHKAEQEFGEMERK 422
Cdd:COG3883 109 LGS--ESFSDF----------LDRLSALSKIADADADLLEELKAdkaeleakkaeLEAKLAELEALKAELEAAKAELEAQ 176

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 42570002 423 ILEVKNKVLELQKQEAALEKQKDATYEKICKMESRARDLGVE 464
Cdd:COG3883 177 QAEQEALLAQLSAEEAAAEAQLAELEAELAAAEAAAAAAAAA 218
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
353-469 1.23e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 41.59  E-value: 1.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002  353 QLNSLKDSFTELEKhgftVTAPLSRIAKLLALKDrQLKILEE-LKVFDKEMKDESSKKH-KAEQEFGEMERKILEVK--- 427
Cdd:PRK03918 474 KERKLRKELRELEK----VLKKESELIKLKELAE-QLKELEEkLKKYNLEELEKKAEEYeKLKEKLIKLKGEIKSLKkel 548

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 42570002  428 NKVLELQKQEAALEKQKDATYEKICKMESRARDLGVE-LEDVE 469
Cdd:PRK03918 549 EKLEELKKKLAELEKKLDELEEELAELLKELEELGFEsVEELE 591
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 339-469 3.39e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 40.04  E-value: 3.39e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002    339 LEKVEDLKTDVPiRQLNSLK------DSFTELEKHGFTVTAPLSrIAKLLALKDRQLKILEELKVFDKEMKDESSKKHKA 412
Cdd:TIGR02168  188 LDRLEDILNELE-RQLKSLErqaekaERYKELKAELRELELALL-VLRLEELREELEELQEELKEAEEELEELTAELQEL 265

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 42570002    413 EQ-------EFGEMERKILEVKNKVLELQKQEAALEKQKDATYEKICKMESRARDLGVELEDVE 469
Cdd:TIGR02168  266 EEkleelrlEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLEELE 329
 
Name Accession Description Interval E-value
DUF724 pfam05266
Protein of unknown function (DUF724); This family contains several uncharacterized proteins ...
 285-469 6.33e-85

Protein of unknown function (DUF724); This family contains several uncharacterized proteins found in Arabidopsis thaliana and other plants. This region is often found associated with Agenet domains and may contain coiled-coil.


Pssm-ID: 428400 [Multi-domain]  Cd Length: 188  Bit Score: 259.13  E-value: 6.33e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002   285 VLPFVKKSPVWKIYESMEVFKRVPQSPHFSPLFEAKEDFREGFALGMMVTFSGVLEKVEDLKTDVPIRQLNSLKDSFTEL 364
Cdd:pfam05266   1 VLPFVKKSPLWKTIESMEVFKKVPQRPHFSPLLESKEELREGSALGMMVSFAGLLEKVKKLQVDDSRSVFESLMESFAEL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002   365 EKHGFTVTAPLSRIAKLLALKDRQLKILEELKVFDKEMKDESSKKHKAEQEFGEMERKIlevknkvLELQKQEAALEKQK 444
Cdd:pfam05266  81 EKHGFDVKAPQSRINKLLSLKDRQTKLLEELKKLEKKIAEEESEKRKLEEEIDELEKKI-------LELERQLALAKEKK 153

                         170       180
                  ....*....|....*....|....*
gi 42570002   445 DATYEKICKMESRARDLGVELEDVE 469
Cdd:pfam05266 154 EAADKEIARLKSEAEKLEQEIQDVE 178
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 7-108 3.15e-53

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 192.03  E-value: 3.15e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002    7 TPSAMGLWLVPNHVSVKIPFGNREILVETGLMGRQASSAVTVTDGETIVFTSVCLADVPSEPSDFLPLYVHYQERFSAVG 86
Cdd:PLN00207  67 SSVGEGPGPFPQQFSVKIPVGDRHILVETGHIGRQASGSVTVTDGETIVYTSVCLADVPSEPSDFFPLSVHYQERFSAAG 146

                         90       100
                 ....*....|....*....|..
gi 42570002   87 RTSGGFFKREGRTKDHEVtFLC 108
Cdd:PLN00207 147 RTSGGFFKREGRTKDHEV-LIC 167
RNase_PH_PNPase_1 cd11363
Polyribonucleotide nucleotidyltransferase, repeat 1; Polyribonucleotide nucleotidyltransferase ...
 22-104 2.34e-30

Polyribonucleotide nucleotidyltransferase, repeat 1; Polyribonucleotide nucleotidyltransferase (PNPase) is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally, all members of this family form hexameric rings. In the case of PNPase the complex is a trimer, since each monomer contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction and in quality control of ribosomal RNA precursors. It is part of the RNA degradosome complex and binds to the scaffolding domain of the endoribonuclease RNase E.


Pssm-ID: 206768 [Multi-domain]  Cd Length: 229  Bit Score: 117.62  E-value: 2.34e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002  22 VKIPFGNREILVETGLMGRQASSAVTVTDGETIVFTSVCLADVPSEPSDFLPLYVHYQERFSAVGRTSGGFFKREGRTKD 101
Cdd:cd11363   3 FEVLVGGRTLTFETGKLAKQADGSVVVQYGDTVVLVTAVSSKKPKEGIDFFPLTVDYREKLYAAGKIPGGFFKREGRPSE 82


                ...
gi 42570002 102 HEV 104
Cdd:cd11363  83 KEI 85
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 17-104 1.50e-28

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 119.00  E-value: 1.50e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002   17 PNHVSVKIPFGNREILVETGLMGRQASSAVTVTDGETIVFTSVCLADVPSEPSDFLPLYVHYQERFSAVGRTSGGFFKRE 96
Cdd:PRK11824   2 FNKIVKSIEFGGRTLTLETGKLARQANGAVLVRYGDTVVLVTVVASKEPKEGQDFFPLTVDYEEKTYAAGKIPGGFFKRE 81


                 ....*...
gi 42570002   97 GRTKDHEV 104
Cdd:PRK11824  82 GRPSEKET 89
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 21-104 5.19e-28

Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 117.41  E-value: 5.19e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002  21 SVKIPFGNREILVETGLMGRQASSAVTVTDGETIVFTSVCLADVPSEPSDFLPLYVHYQERFSAVGRTSGGFFKREGRTK 100
Cdd:COG1185   1 KKEFELGGRTLTLETGKLAKQADGAVLVRYGDTVVLVTVVASKEPREGIDFFPLTVDYQEKFYAAGKIPGGFFKREGRPS 80


                ....
gi 42570002 101 DHEV 104
Cdd:COG1185  81 EKEI 84
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 29-104 3.58e-10

3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria.


Pssm-ID: 426074 [Multi-domain]  Cd Length: 129  Bit Score: 57.60  E-value: 3.58e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 42570002    29 REILVETGLMgRQASSAVTVTDGETIVFTSVCLADVPSEPSDFLP--LYVHYQERFSAVGRtsggfFKREGRTKDHEV 104
Cdd:pfam01138   3 RPIEIETGVL-SQADGSALVELGDTKVLATVTGPIEPKEDRDFAPgrLTVEYELAPFASGE-----RPGEGRPSEREI 74
TR_SDR_c cd05329
tropinone reductase-I and II (TR-1, and TR-II)-like, classical (c) SDRs; This subgroup ...
 106-176 3.00e-09

tropinone reductase-I and II (TR-1, and TR-II)-like, classical (c) SDRs; This subgroup includes TR-I and TR-II; these proteins are members of the SDR family. TRs catalyze the NADPH-dependent reductions of the 3-carbonyl group of tropinone, to a beta-hydroxyl group. TR-I and TR-II produce different stereoisomers from tropinone, TR-I produces tropine (3alpha-hydroxytropane), and TR-II, produces pseudotropine (sigma-tropine, 3beta-hydroxytropane). SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction.


Pssm-ID: 187590 [Multi-domain]  Cd Length: 251  Bit Score: 57.46  E-value: 3.00e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 42570002 106 FLCLPAASYITG--QEELKACLNDWKSNGLVVSGLV-----RDQREKLIQEVSSTFSGKLNILSplaqgsgNNMGGSV 176
Cdd:cd05329  26 LAGLGAEVYTCArnQKELDECLTEWREKGFKVEGSVcdvssRSERQELMDTVASHFGGKLNILV-------NNAGTNI 96
KELK pfam15796
KELK-motif containing domain of MRCK Ser/Thr protein kinase; KELK is a domain of eukaryotic ...
 391-436 2.13e-04

KELK-motif containing domain of MRCK Ser/Thr protein kinase; KELK is a domain of eukaryotic proteins found in serine/threonine-protein kinase MRCK-type proteins. The region is low-complexity, but it is not a predicted disordered-binding domain. The name comes from a highly conserved sequence motif within the domain. The function is not known.


Pssm-ID: 464876 [Multi-domain]  Cd Length: 80  Bit Score: 39.92  E-value: 2.13e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 42570002   391 ILEELKVFDKEMKDESSKKHKAEQEFGEMERKILEVKNKVLELQKQ 436
Cdd:pfam15796  26 SQERLKSQDKELKDAHSQRKLAMEEFSEVNEKLTELRSQKQKLSRQ 71
FAM76 pfam16046
FAM76 protein; This family of proteins is functionally uncharacterized. This family of ...
 380-444 3.88e-04

FAM76 protein; This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 233 and 341 amino acids in length.


Pssm-ID: 464993 [Multi-domain]  Cd Length: 303  Bit Score: 42.47  E-value: 3.88e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 42570002   380 KLLALKDRQL----KILEELKVFDKEMKDESSKKHKAEQEfgEMERKI--LEVKNKvlELQKQEAALEKQK 444
Cdd:pfam16046 236 KQLAQKDQQLlekdKQITELKAKHFTKERELRNKMKTMEK--EHEDKVeqLQIKIR--SLLKEVATLSKSK 302
CwlO1 COG3883
Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function ...
 354-464 1.10e-03

Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown];


Pssm-ID: 443091 [Multi-domain]  Cd Length: 379  Bit Score: 41.35  E-value: 1.10e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002 354 LNSlkDSFTELekhgftvtapLSRIAKLLALKDRQLKILEELKV-----------FDKEMKDESSKKHKAEQEFGEMERK 422
Cdd:COG3883 109 LGS--ESFSDF----------LDRLSALSKIADADADLLEELKAdkaeleakkaeLEAKLAELEALKAELEAAKAELEAQ 176

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 42570002 423 ILEVKNKVLELQKQEAALEKQKDATYEKICKMESRARDLGVE 464
Cdd:COG3883 177 QAEQEALLAQLSAEEAAAEAQLAELEAELAAAEAAAAAAAAA 218
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
353-469 1.23e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 41.59  E-value: 1.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002  353 QLNSLKDSFTELEKhgftVTAPLSRIAKLLALKDrQLKILEE-LKVFDKEMKDESSKKH-KAEQEFGEMERKILEVK--- 427
Cdd:PRK03918 474 KERKLRKELRELEK----VLKKESELIKLKELAE-QLKELEEkLKKYNLEELEKKAEEYeKLKEKLIKLKGEIKSLKkel 548

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 42570002  428 NKVLELQKQEAALEKQKDATYEKICKMESRARDLGVE-LEDVE 469
Cdd:PRK03918 549 EKLEELKKKLAELEKKLDELEEELAELLKELEELGFEsVEELE 591
DUF4200 pfam13863
Domain of unknown function (DUF4200); This family is found in eukaryotes. It is a coiled-coil ...
 383-451 1.79e-03

Domain of unknown function (DUF4200); This family is found in eukaryotes. It is a coiled-coil domain of unknwon function.


Pssm-ID: 464003 [Multi-domain]  Cd Length: 119  Bit Score: 38.32  E-value: 1.79e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 42570002   383 ALKDRQLKILEELKVFDKEMKDESSKKHKAEQEFGEMERKILEVKNKVLELQKQEAALEKQKDATYEKI 451
Cdd:pfam13863  35 ELEKKEQELKEDLIKFDKFLKENDAKRRRALKKAEEETKLKKEKEKEIKKLTAQIEELKSEISKLEEKL 103
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
383-469 2.11e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 40.82  E-value: 2.11e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002  383 ALKDRQLKILEELKVFDKEMKDESSKKHKAEQEFGEMErkilEVKNKVLELQKQEAALEKQKDATYEKICKMESRARDLG 462
Cdd:PRK03918 197 EKEKELEEVLREINEISSELPELREELEKLEKEVKELE----ELKEEIEELEKELESLEGSKRKLEEKIRELEERIEELK 272


                 ....*..
gi 42570002  463 VELEDVE 469
Cdd:PRK03918 273 KEIEELE 279
TR_SDR_c cd05329
tropinone reductase-I and II (TR-1, and TR-II)-like, classical (c) SDRs; This subgroup ...
 104-118 2.67e-03

tropinone reductase-I and II (TR-1, and TR-II)-like, classical (c) SDRs; This subgroup includes TR-I and TR-II; these proteins are members of the SDR family. TRs catalyze the NADPH-dependent reductions of the 3-carbonyl group of tropinone, to a beta-hydroxyl group. TR-I and TR-II produce different stereoisomers from tropinone, TR-I produces tropine (3alpha-hydroxytropane), and TR-II, produces pseudotropine (sigma-tropine, 3beta-hydroxytropane). SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction.


Pssm-ID: 187590 [Multi-domain]  Cd Length: 251  Bit Score: 39.35  E-value: 2.67e-03
                        10
                ....*....|....*
gi 42570002 104 VTFLCLPAASYITGQ 118
Cdd:cd05329 226 VAFLCMPAASYITGQ 240
EzrA pfam06160
Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like ...
 342-468 2.85e-03

Septation ring formation regulator, EzrA; During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation. The structure contains 5 spectrin like alpha helical repeats.


Pssm-ID: 428797 [Multi-domain]  Cd Length: 542  Bit Score: 40.22  E-value: 2.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002   342 VEDLKTDVPiRQLNSLKDSFTELEKHGFtvtaplsriakllALKDrqLKILEELKVFDKEMkdESSKKHKAEQEFGEMER 421
Cdd:pfam06160 202 YEELKTELP-DQLEELKEGYREMEEEGY-------------ALEH--LNVDKEIQQLEEQL--EENLALLENLELDEAEE 263

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 42570002   422 KILEVKNKVLELQKQ-------EAALEKQKDATYEKICKMESRARDLGVELEDV 468
Cdd:pfam06160 264 ALEEIEERIDQLYDLlekevdaKKYVEKNLPEIEDYLEHAEEQNKELKEELERV 317
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 339-469 3.39e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 40.04  E-value: 3.39e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002    339 LEKVEDLKTDVPiRQLNSLK------DSFTELEKHGFTVTAPLSrIAKLLALKDRQLKILEELKVFDKEMKDESSKKHKA 412
Cdd:TIGR02168  188 LDRLEDILNELE-RQLKSLErqaekaERYKELKAELRELELALL-VLRLEELREELEELQEELKEAEEELEELTAELQEL 265

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 42570002    413 EQ-------EFGEMERKILEVKNKVLELQKQEAALEKQKDATYEKICKMESRARDLGVELEDVE 469
Cdd:TIGR02168  266 EEkleelrlEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLEELE 329
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 340-466 4.06e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 39.65  E-value: 4.06e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42570002    340 EKVEDLKTDVPIRQlNSLKDSFTELEKHGFTVTAPLSRIAKLLALKDRQLKILEELKvfdKEMKDESSKKHKAEQEFGEM 419
Cdd:TIGR02168  295 NEISRLEQQKQILR-ERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELK---EELESLEAELEELEAELEEL 370

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 42570002    420 ERKILEVKNKVLELQKQEAALEKQKDATYEKICKMESRARDLGVELE 466
Cdd:TIGR02168  371 ESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEARLERLEDRRE 417
 
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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