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Conserved domains on  [gi|767957355|ref|XP_011516950|]
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DNA excision repair protein ERCC-6-like 2 isoform X2 [Homo sapiens]

Protein Classification

SF2_C_SNF and VIGSSK domain-containing protein( domain architecture ID 13039337)

SF2_C_SNF and VIGSSK domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 4-88 1.32e-39

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 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: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 143.00  E-value: 1.32e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767957355    4 GLDYRRLDGSTKSEERLKIVKEFNSTQDVNICLVSTMAGGLGLNFVGANVVVLFDPTWNPANDLQAIDRAYRIGQCRDVK 83
Cdd:cd18793    51 GIKYLRLDGSTSSKERQKLVDRFNEDPDIRVFLLSTKAGGVGLNLTAANRVILYDPWWNPAVEEQAIDRAHRIGQKKPVV 130


                  ....*
gi 767957355   84 VLRLI 88
Cdd:cd18793   131 VYRLI 135
VIGSSK super family cl20696
Helicase-associated putative binding domain, C-terminal; The function of this short, ...
 574-598 1.81e-03

Helicase-associated putative binding domain, C-terminal; The function of this short, serine-rich C-terminal region is not known. However, as it is frequently found at the very C-terminus of P-loop containing nucleoside triphosphate hydrolases, it might possibly be a binding domain.


The actual alignment was detected with superfamily member pfam14773:

Pssm-ID: 464308  Cd Length: 62  Bit Score: 37.59  E-value: 1.81e-03
                           10        20
                   ....*....|....*....|....*
gi 767957355   574 VAYIHSNQNVIGSSKAENHMSRWAA 598
Cdd:pfam14773   38 VEYTHENSEVIGTSKVEEQLSRRAE 62
 
Name Accession Description Interval E-value
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 4-88 1.32e-39

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 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: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 143.00  E-value: 1.32e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767957355    4 GLDYRRLDGSTKSEERLKIVKEFNSTQDVNICLVSTMAGGLGLNFVGANVVVLFDPTWNPANDLQAIDRAYRIGQCRDVK 83
Cdd:cd18793    51 GIKYLRLDGSTSSKERQKLVDRFNEDPDIRVFLLSTKAGGVGLNLTAANRVILYDPWWNPAVEEQAIDRAHRIGQKKPVV 130


                  ....*
gi 767957355   84 VLRLI 88
Cdd:cd18793   131 VYRLI 135
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 4-107 2.98e-33

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 137.66  E-value: 2.98e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767957355    4 GLDYRRLDGSTKSEERLKIVKEFNSTQDVNICLVSTMAGGLGLNFVGANVVVLFDPTWNPANDLQAIDRAYRIGQCRDVK 83
Cdd:COG0553   573 GIEYAYLHGGTSAEERDELVDRFQEGPEAPVFLISLKAGGEGLNLTAADHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQ 652

                          90       100
                  ....*....|....*....|....
gi 767957355   84 VLRLISLGTVEEIMYLRQIYKQQL 107
Cdd:COG0553   653 VYKLVAEGTIEEKILELLEEKRAL 676
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 4-77 2.00e-21

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 90.35  E-value: 2.00e-21
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767957355     4 GLDYRRLDGSTKSEERLKIVKEFNStQDVNIcLVSTMAGGLGLNFVGANVVVLFDPTWNPANDLQAIDRAYRIG 77
Cdd:pfam00271   38 GIKVARLHGDLSQEEREEILEDFRK-GKIDV-LVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
HELICc smart00490
helicase superfamily c-terminal domain;
4-77 6.65e-21

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 87.65  E-value: 6.65e-21
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767957355      4 GLDYRRLDGSTKSEERLKIVKEFNStqDVNICLVSTMAGGLGLNFVGANVVVLFDPTWNPANDLQAIDRAYRIG 77
Cdd:smart00490   11 GIKVARLHGGLSQEEREEILDKFNN--GKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
 1-112 5.41e-20

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 96.02  E-value: 5.41e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767957355    1 MASGLDYRRLDGSTKSEERLKIVKEFNSTQDVNIC-LVSTMAGGLGLNFVGANVVVLFDPTWNPANDLQAIDRAYRIGQC 79
Cdd:PLN03142  508 MYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVfLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQK 587

                          90       100       110
                  ....*....|....*....|....*....|...
gi 767957355   80 RDVKVLRLISLGTVEEIMYLRQIYKQQLHCVVV 112
Cdd:PLN03142  588 KEVQVFRFCTEYTIEEKVIERAYKKLALDALVI 620
VIGSSK pfam14773
Helicase-associated putative binding domain, C-terminal; The function of this short, ...
 574-598 1.81e-03

Helicase-associated putative binding domain, C-terminal; The function of this short, serine-rich C-terminal region is not known. However, as it is frequently found at the very C-terminus of P-loop containing nucleoside triphosphate hydrolases, it might possibly be a binding domain.


Pssm-ID: 464308  Cd Length: 62  Bit Score: 37.59  E-value: 1.81e-03
                           10        20
                   ....*....|....*....|....*
gi 767957355   574 VAYIHSNQNVIGSSKAENHMSRWAA 598
Cdd:pfam14773   38 VEYTHENSEVIGTSKVEEQLSRRAE 62
 
Name Accession Description Interval E-value
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 4-88 1.32e-39

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 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: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 143.00  E-value: 1.32e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767957355    4 GLDYRRLDGSTKSEERLKIVKEFNSTQDVNICLVSTMAGGLGLNFVGANVVVLFDPTWNPANDLQAIDRAYRIGQCRDVK 83
Cdd:cd18793    51 GIKYLRLDGSTSSKERQKLVDRFNEDPDIRVFLLSTKAGGVGLNLTAANRVILYDPWWNPAVEEQAIDRAHRIGQKKPVV 130


                  ....*
gi 767957355   84 VLRLI 88
Cdd:cd18793   131 VYRLI 135
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 4-107 2.98e-33

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 137.66  E-value: 2.98e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767957355    4 GLDYRRLDGSTKSEERLKIVKEFNSTQDVNICLVSTMAGGLGLNFVGANVVVLFDPTWNPANDLQAIDRAYRIGQCRDVK 83
Cdd:COG0553   573 GIEYAYLHGGTSAEERDELVDRFQEGPEAPVFLISLKAGGEGLNLTAADHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQ 652

                          90       100
                  ....*....|....*....|....
gi 767957355   84 VLRLISLGTVEEIMYLRQIYKQQL 107
Cdd:COG0553   653 VYKLVAEGTIEEKILELLEEKRAL 676
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 4-77 2.00e-21

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 90.35  E-value: 2.00e-21
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767957355     4 GLDYRRLDGSTKSEERLKIVKEFNStQDVNIcLVSTMAGGLGLNFVGANVVVLFDPTWNPANDLQAIDRAYRIG 77
Cdd:pfam00271   38 GIKVARLHGDLSQEEREEILEDFRK-GKIDV-LVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
HELICc smart00490
helicase superfamily c-terminal domain;
4-77 6.65e-21

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 87.65  E-value: 6.65e-21
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767957355      4 GLDYRRLDGSTKSEERLKIVKEFNStqDVNICLVSTMAGGLGLNFVGANVVVLFDPTWNPANDLQAIDRAYRIG 77
Cdd:smart00490   11 GIKVARLHGGLSQEEREEILDKFNN--GKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
 1-112 5.41e-20

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 96.02  E-value: 5.41e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767957355    1 MASGLDYRRLDGSTKSEERLKIVKEFNSTQDVNIC-LVSTMAGGLGLNFVGANVVVLFDPTWNPANDLQAIDRAYRIGQC 79
Cdd:PLN03142  508 MYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVfLLSTRAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHRIGQK 587

                          90       100       110
                  ....*....|....*....|....*....|...
gi 767957355   80 RDVKVLRLISLGTVEEIMYLRQIYKQQLHCVVV 112
Cdd:PLN03142  588 KEVQVFRFCTEYTIEEKVIERAYKKLALDALVI 620
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 36-78 4.29e-05

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 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: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 42.69  E-value: 4.29e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 767957355   36 LVSTMAGGLGLNFVGANVVVLFDPTWNPANDLQAIDRAYRIGQ 78
Cdd:cd18785    26 LVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRGGK 68
VIGSSK pfam14773
Helicase-associated putative binding domain, C-terminal; The function of this short, ...
 574-598 1.81e-03

Helicase-associated putative binding domain, C-terminal; The function of this short, serine-rich C-terminal region is not known. However, as it is frequently found at the very C-terminus of P-loop containing nucleoside triphosphate hydrolases, it might possibly be a binding domain.


Pssm-ID: 464308  Cd Length: 62  Bit Score: 37.59  E-value: 1.81e-03
                           10        20
                   ....*....|....*....|....*
gi 767957355   574 VAYIHSNQNVIGSSKAENHMSRWAA 598
Cdd:pfam14773   38 VEYTHENSEVIGTSKVEEQLSRRAE 62
 
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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