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Conserved domains on  [gi|209490903|gb|ACI49572|]
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pp1ab, partial [Gill-associated virus genotype 2]

Protein Classification

NADAR family protein( domain architecture ID 20009833)

NADAR (NAD and ADP-ribose) family protein similar to Escherichia coli N-glycosidase YbiA, which catalyzes the hydrolysis of the N-glycosidic bond in the first two intermediates of riboflavin biosynthesis

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NADAR cd15457
Escherichia coli swarming motility protein YbiA and related proteins; This family of ...
 91-220 1.69e-19

Escherichia coli swarming motility protein YbiA and related proteins; This family of uncharacterized domains was initially classified as Domain of Unknown Function (DUF1768). It contains members such as the E. coli swarming motility protein YbiA. Mutations in YbiA cause defects in Escherichia coli swarming, but not necessarily in motility. More recently, this family has been predicted to be involved in NAD-utilizing pathways, likely to act on ADP-ribose derivatives, and has been named the NADAR (NAD and ADP-ribose) superfamily.


:

Pssm-ID: 271319  Cd Length: 148  Bit Score: 81.12  E-value: 1.69e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209490903  91 IYFEKSTtviaynGPNNKLSNMY--TDNLKPFPYHTLENRYQSEKAKYLG----KKLILH-NNPFETLKEAKKVfTREDN 163
Cdd:cd15457    3 IFFYGHT------DPYGCLSNFYpsPFEVDGVTYPTAEHYMQAQKALLFGdpeiAEKILAaKTPKEAKKLGRKV-RGFDR 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 209490903 164 KIWAKVSAEVMTRLLFEKF-NNPELSKHLINTGKSHLVENTQH-PIWG-------GKGRGENLHGK 220
Cdd:cd15457   76 PDWEEVRLDVMREALRAKFsQNPELRELLLSTGDRELVEASPRdRIWGigldadpRKWRGQNLLGK 141
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 3-71 4.71e-06

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd18786:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 89  Bit Score: 43.58  E-value: 4.71e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 209490903   3 AILVTHHEAFSIIRQYFT------DIDIQIPIYTVHTSQGRTFDrgIVVSYRNTAFTRDPNIVNVAVSRFRFQCI 71
Cdd:cd18786   14 VVLTPYHRDRAYLNQYLQglsldeFDLQLVGAITIDSSQGLTFD--VVTLYLPTANSLTPRRLYVALTRARKRLV 86
 
Name Accession Description Interval E-value
NADAR cd15457
Escherichia coli swarming motility protein YbiA and related proteins; This family of ...
 91-220 1.69e-19

Escherichia coli swarming motility protein YbiA and related proteins; This family of uncharacterized domains was initially classified as Domain of Unknown Function (DUF1768). It contains members such as the E. coli swarming motility protein YbiA. Mutations in YbiA cause defects in Escherichia coli swarming, but not necessarily in motility. More recently, this family has been predicted to be involved in NAD-utilizing pathways, likely to act on ADP-ribose derivatives, and has been named the NADAR (NAD and ADP-ribose) superfamily.


Pssm-ID: 271319  Cd Length: 148  Bit Score: 81.12  E-value: 1.69e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209490903  91 IYFEKSTtviaynGPNNKLSNMY--TDNLKPFPYHTLENRYQSEKAKYLG----KKLILH-NNPFETLKEAKKVfTREDN 163
Cdd:cd15457    3 IFFYGHT------DPYGCLSNFYpsPFEVDGVTYPTAEHYMQAQKALLFGdpeiAEKILAaKTPKEAKKLGRKV-RGFDR 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 209490903 164 KIWAKVSAEVMTRLLFEKF-NNPELSKHLINTGKSHLVENTQH-PIWG-------GKGRGENLHGK 220
Cdd:cd15457   76 PDWEEVRLDVMREALRAKFsQNPELRELLLSTGDRELVEASPRdRIWGigldadpRKWRGQNLLGK 141
NADAR pfam08719
NADAR domain; This is a domain of unknown function, it has been named been named the NADAR ...
 92-220 4.42e-15

NADAR domain; This is a domain of unknown function, it has been named been named the NADAR (NAD and ADP-ribose) domain.


Pssm-ID: 462576  Cd Length: 156  Bit Score: 69.56  E-value: 4.42e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209490903   92 YFEKSTtviayNGPNNKLSNMYT----------DNLKPFPYHTLENRYQSEKAKYLG-----KKLILHNNPFETLKEAKK 156
Cdd:pfam08719   1 YFYGPT-----EDPYGCFSNFYPspftvdgvphPVLEGKTYPTAEHYMMAQKALLFGdtppaEKILAAASPREAKALGRR 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 209490903  157 VfTREDNKIWAKVSAEVMTRLLFEKFN-NPELSKHLINTGKSHLVENTQH-PIWG------GKGRGENLHGK 220
Cdd:pfam08719  76 V-RGFDEADWDEVKVDVMREGNLAKFTqNEDLRELLLSTGDRELVEASPRdRIWGiglgadEKWRGKNLLGK 146
ribofla_fusion TIGR02464
conserved hypothetical protein, ribA/ribD-fused; This model describes a sequence region that ...
 122-220 6.15e-09

conserved hypothetical protein, ribA/ribD-fused; This model describes a sequence region that occurs in at least three different polypeptide contexts. It is found fused to GTP cyclohydrolase II, the RibA of riboflavin biosynthesis (TIGR00505), as in Vibrio vulnificus. It is found fused to riboflavin biosynthesis protein RibD (TIGR00326) in rice and Arabidopsis. It occurs as a standalone protein in a number of bacterial species in varied contexts, including single gene operons and bacteriophage genomes. The member from E. coli currently is named YbiA. The function(s) of members of this family is unknown.


Pssm-ID: 274144  Cd Length: 153  Bit Score: 53.15  E-value: 6.15e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209490903  122 YHTLENRYQSEKAKYLGKKLILH-----NNPFETLKEAKKVfTREDNKIWAKVSAEVMTRLLFEKF-NNPELSKHLINTG 195
Cdd:TIGR02464  28 FPTSEHYYMAQKARLFGDEEIAEeileaKTPEEAKRLGRKV-RGFLEKQWDQVKYEVMRRALLAKFsTHADLREILLSTG 106

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 209490903  196 KSHLVENTQH-PIWGGKG-----------RGENLHGK 220
Cdd:TIGR02464 107 GKKLVEASPNdKIWGIGLdaqdariprnwKGKNLLGK 143
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 3-71 4.71e-06

C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Similar to SF2 helicases, they do not form toroidal, predominantly hexameric structures like SF3-6. SF1 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350173 [Multi-domain]  Cd Length: 89  Bit Score: 43.58  E-value: 4.71e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 209490903   3 AILVTHHEAFSIIRQYFT------DIDIQIPIYTVHTSQGRTFDrgIVVSYRNTAFTRDPNIVNVAVSRFRFQCI 71
Cdd:cd18786   14 VVLTPYHRDRAYLNQYLQglsldeFDLQLVGAITIDSSQGLTFD--VVTLYLPTANSLTPRRLYVALTRARKRLV 86
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
15-71 3.57e-05

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 44.35  E-value: 3.57e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 209490903  15 IRQYFTDIDIQIPIYTVHTSQGRTFDRgIVVS---------YRNTAF-TRDPNIVNVAVSRFRFQCI 71
Cdd:COG1112  727 LREALGDGLEPVFVGTVDRFQGDERDV-IIFSlvysndedvPRNFGFlNGGPRRLNVAVSRARRKLI 792
 
Name Accession Description Interval E-value
NADAR cd15457
Escherichia coli swarming motility protein YbiA and related proteins; This family of ...
 91-220 1.69e-19

Escherichia coli swarming motility protein YbiA and related proteins; This family of uncharacterized domains was initially classified as Domain of Unknown Function (DUF1768). It contains members such as the E. coli swarming motility protein YbiA. Mutations in YbiA cause defects in Escherichia coli swarming, but not necessarily in motility. More recently, this family has been predicted to be involved in NAD-utilizing pathways, likely to act on ADP-ribose derivatives, and has been named the NADAR (NAD and ADP-ribose) superfamily.


Pssm-ID: 271319  Cd Length: 148  Bit Score: 81.12  E-value: 1.69e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209490903  91 IYFEKSTtviaynGPNNKLSNMY--TDNLKPFPYHTLENRYQSEKAKYLG----KKLILH-NNPFETLKEAKKVfTREDN 163
Cdd:cd15457    3 IFFYGHT------DPYGCLSNFYpsPFEVDGVTYPTAEHYMQAQKALLFGdpeiAEKILAaKTPKEAKKLGRKV-RGFDR 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 209490903 164 KIWAKVSAEVMTRLLFEKF-NNPELSKHLINTGKSHLVENTQH-PIWG-------GKGRGENLHGK 220
Cdd:cd15457   76 PDWEEVRLDVMREALRAKFsQNPELRELLLSTGDRELVEASPRdRIWGigldadpRKWRGQNLLGK 141
NADAR pfam08719
NADAR domain; This is a domain of unknown function, it has been named been named the NADAR ...
 92-220 4.42e-15

NADAR domain; This is a domain of unknown function, it has been named been named the NADAR (NAD and ADP-ribose) domain.


Pssm-ID: 462576  Cd Length: 156  Bit Score: 69.56  E-value: 4.42e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209490903   92 YFEKSTtviayNGPNNKLSNMYT----------DNLKPFPYHTLENRYQSEKAKYLG-----KKLILHNNPFETLKEAKK 156
Cdd:pfam08719   1 YFYGPT-----EDPYGCFSNFYPspftvdgvphPVLEGKTYPTAEHYMMAQKALLFGdtppaEKILAAASPREAKALGRR 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 209490903  157 VfTREDNKIWAKVSAEVMTRLLFEKFN-NPELSKHLINTGKSHLVENTQH-PIWG------GKGRGENLHGK 220
Cdd:pfam08719  76 V-RGFDEADWDEVKVDVMREGNLAKFTqNEDLRELLLSTGDRELVEASPRdRIWGiglgadEKWRGKNLLGK 146
ribofla_fusion TIGR02464
conserved hypothetical protein, ribA/ribD-fused; This model describes a sequence region that ...
 122-220 6.15e-09

conserved hypothetical protein, ribA/ribD-fused; This model describes a sequence region that occurs in at least three different polypeptide contexts. It is found fused to GTP cyclohydrolase II, the RibA of riboflavin biosynthesis (TIGR00505), as in Vibrio vulnificus. It is found fused to riboflavin biosynthesis protein RibD (TIGR00326) in rice and Arabidopsis. It occurs as a standalone protein in a number of bacterial species in varied contexts, including single gene operons and bacteriophage genomes. The member from E. coli currently is named YbiA. The function(s) of members of this family is unknown.


Pssm-ID: 274144  Cd Length: 153  Bit Score: 53.15  E-value: 6.15e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209490903  122 YHTLENRYQSEKAKYLGKKLILH-----NNPFETLKEAKKVfTREDNKIWAKVSAEVMTRLLFEKF-NNPELSKHLINTG 195
Cdd:TIGR02464  28 FPTSEHYYMAQKARLFGDEEIAEeileaKTPEEAKRLGRKV-RGFLEKQWDQVKYEVMRRALLAKFsTHADLREILLSTG 106

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 209490903  196 KSHLVENTQH-PIWGGKG-----------RGENLHGK 220
Cdd:TIGR02464 107 GKKLVEASPNdKIWGIGLdaqdariprnwKGKNLLGK 143
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 3-71 4.71e-06

C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Similar to SF2 helicases, they do not form toroidal, predominantly hexameric structures like SF3-6. SF1 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350173 [Multi-domain]  Cd Length: 89  Bit Score: 43.58  E-value: 4.71e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 209490903   3 AILVTHHEAFSIIRQYFT------DIDIQIPIYTVHTSQGRTFDrgIVVSYRNTAFTRDPNIVNVAVSRFRFQCI 71
Cdd:cd18786   14 VVLTPYHRDRAYLNQYLQglsldeFDLQLVGAITIDSSQGLTFD--VVTLYLPTANSLTPRRLYVALTRARKRLV 86
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
15-71 3.57e-05

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 44.35  E-value: 3.57e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 209490903  15 IRQYFTDIDIQIPIYTVHTSQGRTFDRgIVVS---------YRNTAF-TRDPNIVNVAVSRFRFQCI 71
Cdd:COG1112  727 LREALGDGLEPVFVGTVDRFQGDERDV-IIFSlvysndedvPRNFGFlNGGPRRLNVAVSRARRKLI 792
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 30-71 2.07e-03

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 38.42  E-value: 2.07e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 209490903  30 TVHTSQGRTFDRGIVV--SYRNTAFTRdpNIVNVAVSRFRFQCI 71
Cdd:COG0507  446 TVHKSQGSTFDRVILVlpSEHSPLLSR--ELLYTALTRARELLT 487
SF1_C_RecD cd18809
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ...
 30-71 4.13e-03

C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350196 [Multi-domain]  Cd Length: 80  Bit Score: 35.23  E-value: 4.13e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 209490903  30 TVHTSQGRTFDRGIVV-SYRNTAFTRdpNIVNVAVSRFRFQCI 71
Cdd:cd18809   37 TIHKSQGSEFDRVIVVlPTSHPMLSR--GLLYTALTRARKLLT 77
 
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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