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Conserved domains on  [gi|1728380121|dbj|GEQ70694|]
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hypothetical protein JCM33374_g4373 [Metschnikowia sp. JCM 33374]

Protein Classification

oligonucleotide/oligosaccharide-binding-fold domain-containing protein( domain architecture ID 10543240)

oligonucleotide/oligosaccharide-binding (OB)-fold domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 79-156 1.18e-32

Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself -. The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins.


:

Pssm-ID: 400182 [Multi-domain]  Cd Length: 82  Bit Score: 111.96  E-value: 1.18e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1728380121  79 IRKALVAGFFMQVAKKKSGNKGFLTVKDNQDVLIHPSTVLSKE----NEWVIYNEFVLTSKNYIRTVTNVRPEWLVELAP 154
Cdd:pfam07717   1 LRAALAAGLYPNVARRDPKGKGYTTLSDNQRVFIHPSSVLFNEktfpPEWVVYQELVETTKVYIRTVTAISPEWLLLFAP 80


                  ..
gi 1728380121 155 KY 156
Cdd:pfam07717  81 HI 82
PRK11131 super family cl32644
ATP-dependent RNA helicase HrpA; Provisional
 3-164 2.92e-09

ATP-dependent RNA helicase HrpA; Provisional


The actual alignment was detected with superfamily member PRK11131:

Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 55.45  E-value: 2.92e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1728380121    3 FAHPDGDHLTLLNVYE-------AFNSDDahnvgLHQWCRDNFLSYRSLLSARSVRSQLRRIMErhELELVSTdySSPKY 75
Cdd:PRK11131   544 FADKESDFLAFVNLWNylqeqqkALSSNQ-----FRRLCRTDYLNYLRVREWQDIYTQLRQVVK--ELGIPVN--SEPAE 614

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1728380121   76 WDNIRKALVAGFFMQVAKKKSGNKGFLTVKdNQDVLIHPSTVL-SKENEWVIYNEFVLTSKNYIRTVTNVRPEWLVELAP 154
Cdd:PRK11131   615 YREIHTALLTGLLSHIGMKDAEKQEYTGAR-NARFSIFPGSGLfKKPPKWVMVAELVETSRLWGRIAARIEPEWIEPLAQ 693

                          170
                   ....*....|....
gi 1728380121  155 ----KYYNLDHFAK 164
Cdd:PRK11131   694 hlikRSYSEPHWEK 707
 
Name Accession Description Interval E-value
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 79-156 1.18e-32

Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself -. The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins.


Pssm-ID: 400182 [Multi-domain]  Cd Length: 82  Bit Score: 111.96  E-value: 1.18e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1728380121  79 IRKALVAGFFMQVAKKKSGNKGFLTVKDNQDVLIHPSTVLSKE----NEWVIYNEFVLTSKNYIRTVTNVRPEWLVELAP 154
Cdd:pfam07717   1 LRAALAAGLYPNVARRDPKGKGYTTLSDNQRVFIHPSSVLFNEktfpPEWVVYQELVETTKVYIRTVTAISPEWLLLFAP 80


                  ..
gi 1728380121 155 KY 156
Cdd:pfam07717  81 HI 82
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 3-164 2.92e-09

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 55.45  E-value: 2.92e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1728380121    3 FAHPDGDHLTLLNVYE-------AFNSDDahnvgLHQWCRDNFLSYRSLLSARSVRSQLRRIMErhELELVSTdySSPKY 75
Cdd:PRK11131   544 FADKESDFLAFVNLWNylqeqqkALSSNQ-----FRRLCRTDYLNYLRVREWQDIYTQLRQVVK--ELGIPVN--SEPAE 614

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1728380121   76 WDNIRKALVAGFFMQVAKKKSGNKGFLTVKdNQDVLIHPSTVL-SKENEWVIYNEFVLTSKNYIRTVTNVRPEWLVELAP 154
Cdd:PRK11131   615 YREIHTALLTGLLSHIGMKDAEKQEYTGAR-NARFSIFPGSGLfKKPPKWVMVAELVETSRLWGRIAARIEPEWIEPLAQ 693

                          170
                   ....*....|....
gi 1728380121  155 ----KYYNLDHFAK 164
Cdd:PRK11131   694 hlikRSYSEPHWEK 707
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
35-154 4.03e-05

HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 43.15  E-value: 4.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1728380121  35 RDNFLSYRSLLSARSVRSQLRRIMERHELELVSTDysspkywDNIRKALVAGFFMQVAKKKSGNKGFLTVKdNQDVLIHP 114
Cdd:COG1643   480 QREFLSYLRLREWRDLARQLRRLLGEGANEEPADY-------EAIGLLLALAYPDRIARRRGEGGRYLLAR-GRGAALFP 551

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1728380121 115 STVLSKEnEWVIYNEFVLTSKNY-IRTVTNVRPEWLVELAP 154
Cdd:COG1643   552 GSPLAKK-EWLVAAELVGGAAEArIRLAAPIDPEWLEELAA 591
 
Name Accession Description Interval E-value
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 79-156 1.18e-32

Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself -. The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins.


Pssm-ID: 400182 [Multi-domain]  Cd Length: 82  Bit Score: 111.96  E-value: 1.18e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1728380121  79 IRKALVAGFFMQVAKKKSGNKGFLTVKDNQDVLIHPSTVLSKE----NEWVIYNEFVLTSKNYIRTVTNVRPEWLVELAP 154
Cdd:pfam07717   1 LRAALAAGLYPNVARRDPKGKGYTTLSDNQRVFIHPSSVLFNEktfpPEWVVYQELVETTKVYIRTVTAISPEWLLLFAP 80


                  ..
gi 1728380121 155 KY 156
Cdd:pfam07717  81 HI 82
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 3-164 2.92e-09

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 55.45  E-value: 2.92e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1728380121    3 FAHPDGDHLTLLNVYE-------AFNSDDahnvgLHQWCRDNFLSYRSLLSARSVRSQLRRIMErhELELVSTdySSPKY 75
Cdd:PRK11131   544 FADKESDFLAFVNLWNylqeqqkALSSNQ-----FRRLCRTDYLNYLRVREWQDIYTQLRQVVK--ELGIPVN--SEPAE 614

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1728380121   76 WDNIRKALVAGFFMQVAKKKSGNKGFLTVKdNQDVLIHPSTVL-SKENEWVIYNEFVLTSKNYIRTVTNVRPEWLVELAP 154
Cdd:PRK11131   615 YREIHTALLTGLLSHIGMKDAEKQEYTGAR-NARFSIFPGSGLfKKPPKWVMVAELVETSRLWGRIAARIEPEWIEPLAQ 693

                          170
                   ....*....|....
gi 1728380121  155 ----KYYNLDHFAK 164
Cdd:PRK11131   694 hlikRSYSEPHWEK 707
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
35-154 4.03e-05

HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 43.15  E-value: 4.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1728380121  35 RDNFLSYRSLLSARSVRSQLRRIMERHELELVSTDysspkywDNIRKALVAGFFMQVAKKKSGNKGFLTVKdNQDVLIHP 114
Cdd:COG1643   480 QREFLSYLRLREWRDLARQLRRLLGEGANEEPADY-------EAIGLLLALAYPDRIARRRGEGGRYLLAR-GRGAALFP 551

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1728380121 115 STVLSKEnEWVIYNEFVLTSKNY-IRTVTNVRPEWLVELAP 154
Cdd:COG1643   552 GSPLAKK-EWLVAAELVGGAAEArIRLAAPIDPEWLEELAA 591
 
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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