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Conserved domains on  [gi|71987152|ref|NP_001022624|]
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Eukaryotic initiation factor 4A [Caenorhabditis elegans]

Protein Classification

DEAD/DEAH box helicase family protein( domain architecture ID 1000205)

DEAD/DEAH box helicase family protein such as a DEAD/DEAH box-containing ATP-dependent helicase, which catalyzes the unwinding of DNA or RNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 1-115 1.54e-67

N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.


The actual alignment was detected with superfamily member PTZ00424:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 401  Bit Score: 208.14  E-value: 1.54e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152    1 MTENQFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGV 80
Cdd:PTZ00424 287 MHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGV 366

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 71987152   81 AINFVTENDARQLKEIESYYTTQIEEMPESIADLI 115
Cdd:PTZ00424 367 AINFVTPDDIEQLKEIERHYNTQIEEMPMEVADYL 401
 
Name Accession Description Interval E-value
PTZ00424 PTZ00424
helicase 45; Provisional
 1-115 1.54e-67

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 208.14  E-value: 1.54e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152    1 MTENQFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGV 80
Cdd:PTZ00424 287 MHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGV 366

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 71987152   81 AINFVTENDARQLKEIESYYTTQIEEMPESIADLI 115
Cdd:PTZ00424 367 AINFVTPDDIEQLKEIERHYNTQIEEMPMEVADYL 401
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
1-108 3.01e-49

Superfamily II DNA and RNA helicase [Replication, recombination and repair];


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 161.47  E-value: 3.01e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152   1 MTENQFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGV 80
Cdd:COG0513 261 LQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYVHRIGRTGRAGAEGT 340

                        90       100
                ....*....|....*....|....*...
gi 71987152  81 AINFVTENDARQLKEIESYYTTQIEEMP 108
Cdd:COG0513 341 AISLVTPDERRLLRAIEKLIGQKIEEEE 368
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 1-85 7.85e-49

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 151.89  E-value: 7.85e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152   1 MTENQFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGV 80
Cdd:cd18787  47 LEELGIKVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAGRKGT 126


                ....*
gi 71987152  81 AINFV 85
Cdd:cd18787 127 AITFV 131
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 1-76 2.96e-32

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: 109.22  E-value: 2.96e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 71987152     1 MTENQFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFG 76
Cdd:pfam00271  34 LEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
HELICc smart00490
helicase superfamily c-terminal domain;
1-76 2.18e-30

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 103.45  E-value: 2.18e-30
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 71987152      1 MTENQFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFG 76
Cdd:smart00490   7 LKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82
 
Name Accession Description Interval E-value
PTZ00424 PTZ00424
helicase 45; Provisional
 1-115 1.54e-67

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 208.14  E-value: 1.54e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152    1 MTENQFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGV 80
Cdd:PTZ00424 287 MHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGV 366

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 71987152   81 AINFVTENDARQLKEIESYYTTQIEEMPESIADLI 115
Cdd:PTZ00424 367 AINFVTPDDIEQLKEIERHYNTQIEEMPMEVADYL 401
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
1-108 3.01e-49

Superfamily II DNA and RNA helicase [Replication, recombination and repair];


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 161.47  E-value: 3.01e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152   1 MTENQFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGV 80
Cdd:COG0513 261 LQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYVHRIGRTGRAGAEGT 340

                        90       100
                ....*....|....*....|....*...
gi 71987152  81 AINFVTENDARQLKEIESYYTTQIEEMP 108
Cdd:COG0513 341 AISLVTPDERRLLRAIEKLIGQKIEEEE 368
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 1-85 7.85e-49

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 151.89  E-value: 7.85e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152   1 MTENQFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGV 80
Cdd:cd18787  47 LEELGIKVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAGRKGT 126


                ....*
gi 71987152  81 AINFV 85
Cdd:cd18787 127 AITFV 131
PRK11776 PRK11776
ATP-dependent RNA helicase DbpA; Provisional
 2-105 3.55e-36

ATP-dependent RNA helicase DbpA; Provisional


Pssm-ID: 236977 [Multi-domain]  Cd Length: 460  Bit Score: 127.61  E-value: 3.55e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152    2 TENQFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGVA 81
Cdd:PRK11776 263 NAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLA 342

                         90       100
                 ....*....|....*....|....
gi 71987152   82 INFVTENDARQLKEIESYYTTQIE 105
Cdd:PRK11776 343 LSLVAPEEMQRANAIEDYLGRKLN 366
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 1-76 2.96e-32

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: 109.22  E-value: 2.96e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 71987152     1 MTENQFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFG 76
Cdd:pfam00271  34 LEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 11-99 1.56e-31

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 115.04  E-value: 1.56e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152   11 LHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGVAINFVTENDA 90
Cdd:PRK11192 275 LEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDH 354


                 ....*....
gi 71987152   91 RQLKEIESY 99
Cdd:PRK11192 355 LLLGKIERY 363
HELICc smart00490
helicase superfamily c-terminal domain;
1-76 2.18e-30

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 103.45  E-value: 2.18e-30
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 71987152      1 MTENQFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFG 76
Cdd:smart00490   7 LKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82
PTZ00110 PTZ00110
helicase; Provisional
 10-96 1.04e-27

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 105.24  E-value: 1.04e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152   10 CLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGVAINFVTEND 89
Cdd:PTZ00110 406 CIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDK 485


                 ....*..
gi 71987152   90 ARQLKEI 96
Cdd:PTZ00110 486 YRLARDL 492
PRK04837 PRK04837
ATP-dependent RNA helicase RhlB; Provisional
 8-104 2.35e-27

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235314 [Multi-domain]  Cd Length: 423  Bit Score: 103.51  E-value: 2.35e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152    8 VSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGVAINFVTE 87
Cdd:PRK04837 282 VGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACE 361

                         90
                 ....*....|....*..
gi 71987152   88 NDARQLKEIESYYTTQI 104
Cdd:PRK04837 362 EYALNLPAIETYIGHSI 378
PRK01297 PRK01297
ATP-dependent RNA helicase RhlB; Provisional
 1-108 6.76e-27

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 234938 [Multi-domain]  Cd Length: 475  Bit Score: 102.68  E-value: 6.76e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152    1 MTENQFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGV 80
Cdd:PRK01297 355 LVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGV 434

                         90       100
                 ....*....|....*....|....*....
gi 71987152   81 AINFVTENDARQLKEIESYYTTQIE-EMP 108
Cdd:PRK01297 435 SISFAGEDDAFQLPEIEELLGRKIScEMP 463
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 4-115 1.40e-26

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 102.23  E-value: 1.40e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152    4 NQFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGVAIN 83
Cdd:PRK11634 268 NGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALL 347

                         90       100       110
                 ....*....|....*....|....*....|..
gi 71987152   84 FVTENDARQLKEIESYYTTQIEEMPESIADLI 115
Cdd:PRK11634 348 FVENRERRLLRNIERTMKLTIPEVELPNAELL 379
PRK04537 PRK04537
ATP-dependent RNA helicase RhlB; Provisional
 1-108 5.94e-26

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235307 [Multi-domain]  Cd Length: 572  Bit Score: 100.41  E-value: 5.94e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152    1 MTENQFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGV 80
Cdd:PRK04537 277 LERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGD 356

                         90       100
                 ....*....|....*....|....*...
gi 71987152   81 AINFVTENDARQLKEIESYYTTQIEEMP 108
Cdd:PRK04537 357 AISFACERYAMSLPDIEAYIEQKIPVEP 384
PRK10590 PRK10590
ATP-dependent RNA helicase RhlE; Provisional
 7-107 1.24e-22

ATP-dependent RNA helicase RhlE; Provisional


Pssm-ID: 236722 [Multi-domain]  Cd Length: 456  Bit Score: 90.64  E-value: 1.24e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152    7 TVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGVAINFVT 86
Cdd:PRK10590 271 RSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVC 350

                         90       100
                 ....*....|....*....|.
gi 71987152   87 ENDARQLKEIESYYTTQIEEM 107
Cdd:PRK10590 351 VDEHKLLRDIEKLLKKEIPRI 371
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 11-96 5.51e-19

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 80.60  E-value: 5.51e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152   11 LHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGVAINFVTENDA 90
Cdd:PLN00206 398 IHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDR 477


                 ....*.
gi 71987152   91 RQLKEI 96
Cdd:PLN00206 478 NLFPEL 483
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 1-88 1.01e-12

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 62.94  E-value: 1.01e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152   1 MTENQFTVSCLHGDMDQAERDTIMREFRSGSS--RVLITTDILARGIDVQQVSLVINYDLPSN--RENyiHRIGRSGRFG 76
Cdd:COG0553 569 LEERGIEYAYLHGGTSAEERDELVDRFQEGPEapVFLISLKAGGEGLNLTAADHVIHYDLWWNpaVEE--QAIDRAHRIG 646

                        90
                ....*....|....
gi 71987152  77 -RKGV-AINFVTEN 88
Cdd:COG0553 647 qTRDVqVYKLVAEG 660
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 14-71 1.53e-12

C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains 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: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 59.53  E-value: 1.53e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 71987152  14 DMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGR 71
Cdd:cd18802  73 LMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGR 130
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 1-70 1.28e-11

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: 57.10  E-value: 1.28e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 71987152   1 MTENQFTVSCLHGDMDQAERDTIMREFRSGSS--RVLITTDILARGIDVQQVSLVINYDLPSN------RENYIHRIG 70
Cdd:cd18793  47 LRERGIKYLRLDGSTSSKERQKLVDRFNEDPDirVFLLSTKAGGVGLNLTAANRVILYDPWWNpaveeqAIDRAHRIG 124
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
2-94 1.65e-09

Superfamily II DNA helicase RecQ [Replication, recombination and repair];


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 53.61  E-value: 1.65e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152   2 TENQFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGVA 81
Cdd:COG0514 251 REAGIRAAAYHAGLDAEEREANQDRFLRDEVDVIVATIAFGMGIDKPDVRFVIHYDLPKSIEAYYQEIGRAGRDGLPAEA 330

                        90
                ....*....|...
gi 71987152  82 INFVTENDARQLK 94
Cdd:COG0514 331 LLLYGPEDVAIQR 343
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 19-100 1.89e-09

ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, recombination and repair];


Pssm-ID: 440818 [Multi-domain]  Cd Length: 758  Bit Score: 53.30  E-value: 1.89e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152  19 ERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGVAInFVTENDArqlkeIES 98
Cdd:COG1205 332 ERREIERGLRSGELLGVVSTNALELGIDIGGLDAVVLAGYPGTRASFWQQAGRAGRRGQDSLVV-LVAGDDP-----LDQ 405


                ..
gi 71987152  99 YY 100
Cdd:COG1205 406 YY 407
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
15-88 2.97e-09

ERCC4-related helicase [Replication, recombination and repair];


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 52.81  E-value: 2.97e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 71987152  15 MDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGVAInFVTEN 88
Cdd:COG1111 395 LTQKEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRKREGRVVV-LIAKG 467
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 34-85 3.61e-09

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: 49.24  E-value: 3.61e-09
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 71987152  34 VLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFG-RKGVAINFV 85
Cdd:cd18785  25 ILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRGGkDEGEVILFV 77
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 12-74 4.72e-09

C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR family helicases 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: 350183 [Multi-domain]  Cd Length: 150  Bit Score: 50.73  E-value: 4.72e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 71987152  12 HGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGR 74
Cdd:cd18796  75 HGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDVDLVIQIGSPKSVARLLQRLGRSGH 137
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
3-71 1.00e-08

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 51.56  E-value: 1.00e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 71987152   3 ENQFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGR 71
Cdd:COG1061 327 EAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLRPTGSPREFIQRLGR 395
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 5-81 5.70e-08

C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It is a DEAD-like helicase 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: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 48.11  E-value: 5.70e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152   5 QFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDlpsnrenyIHRIGRS------GRFGRK 78
Cdd:cd18811  61 ELNVGLLHGRLKSDEKDAVMAEFREGEVDILVSTTVIEVGVDVPNATVMVIED--------AERFGLSqlhqlrGRVGRG 132


                ...
gi 71987152  79 GVA 81
Cdd:cd18811 133 DHQ 135
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 15-79 9.22e-08

C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef 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: 350188 [Multi-domain]  Cd Length: 143  Bit Score: 47.35  E-value: 9.22e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 71987152  15 MDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRfGRKG 79
Cdd:cd18801  74 MSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMIQRMGRTGR-KRQG 137
SF2_C_Hrq cd18797
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...
 19-82 5.83e-07

C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases 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: 350184 [Multi-domain]  Cd Length: 146  Bit Score: 44.94  E-value: 5.83e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 71987152  19 ERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGVAI 82
Cdd:cd18797  80 DRREIEAELFNGELLGVVATNALELGIDIGGLDAVVLAGYPGSLASLWQQAGRAGRRGKDSLVI 143
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 12-84 7.36e-07

C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. 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: 350181 [Multi-domain]  Cd Length: 134  Bit Score: 44.51  E-value: 7.36e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 71987152  12 HGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGVAINF 84
Cdd:cd18794  61 HAGLEPSDRRDVQRKWLRDKIQVIVATVAFGMGIDKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECILF 133
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 4-99 1.23e-06

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 45.47  E-value: 1.23e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152    4 NQFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRKGVAIN 83
Cdd:PRK11057 259 RGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAML 338

                         90       100
                 ....*....|....*....|....*...
gi 71987152   84 F------------VTENDARQLKEIESY 99
Cdd:PRK11057 339 FydpadmawlrrcLEEKPAGQQQDIERH 366
RecG COG1200
RecG-like helicase [Replication, recombination and repair];
5-38 4.28e-06

RecG-like helicase [Replication, recombination and repair];


Pssm-ID: 440813 [Multi-domain]  Cd Length: 684  Bit Score: 43.89  E-value: 4.28e-06
                        10        20        30
                ....*....|....*....|....*....|....
gi 71987152   5 QFTVSCLHGDMDQAERDTIMREFRSGSSRVLITT 38
Cdd:COG1200 503 GLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVAT 536
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
 5-80 5.70e-06

C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. 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: 350179 [Multi-domain]  Cd Length: 160  Bit Score: 42.64  E-value: 5.70e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152   5 QFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDlpsnrenyIHRIGRS------GRFGRK 78
Cdd:cd18792  60 EARVALLHGKMTEDEKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIIED--------ADRFGLSqlhqlrGRVGRG 131


                ..
gi 71987152  79 GV 80
Cdd:cd18792 132 KH 133
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
 11-105 6.73e-06

C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II), and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA. Its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a DEAD-like helicase 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: 350177 [Multi-domain]  Cd Length: 171  Bit Score: 42.62  E-value: 6.73e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152  11 LHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYD-----LPSNRENYIHRIGRSGRfGRKGVAI--- 82
Cdd:cd18790  57 LHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDadkegFLRSETSLIQTIGRAAR-NVNGKVIlya 135

                        90       100
                ....*....|....*....|...
gi 71987152  83 NFVTENDARQLKEIESYYTTQIE 105
Cdd:cd18790 136 DKITDSMQKAIEETERRREIQME 158
PRK09751 PRK09751
putative ATP-dependent helicase Lhr; Provisional
 12-73 8.26e-06

putative ATP-dependent helicase Lhr; Provisional


Pssm-ID: 137505 [Multi-domain]  Cd Length: 1490  Bit Score: 43.37  E-value: 8.26e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 71987152    12 HGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSG 73
Cdd:PRK09751  308 HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAG 369
PRK13766 PRK13766
Hef nuclease; Provisional
 15-100 1.44e-05

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 42.55  E-value: 1.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152   15 MDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYD-LPSN-RenYIHRIGRSGRfGRKGVAINFVTEnDARQ 92
Cdd:PRK13766 407 MSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEpVPSEiR--SIQRKGRTGR-QEEGRVVVLIAK-GTRD 482


                 ....*...
gi 71987152   93 lkeiESYY 100
Cdd:PRK13766 483 ----EAYY 486
PLN03137 PLN03137
ATP-dependent DNA helicase; Q4-like; Provisional
 12-78 2.74e-05

ATP-dependent DNA helicase; Q4-like; Provisional


Pssm-ID: 215597 [Multi-domain]  Cd Length: 1195  Bit Score: 41.81  E-value: 2.74e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 71987152    12 HGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRIGRSGRFGRK 78
Cdd:PLN03137  711 HGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQR 777
SF2_C_priA cd18804
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ...
 19-109 7.13e-05

C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a DEAD-like helicase 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: 350191 [Multi-domain]  Cd Length: 238  Bit Score: 40.31  E-value: 7.13e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152  19 ERDTIMREFRSGSSRVLITTDILARGIDVQQVSLV--INYDLPSNRENY---------IHRI-GRSGRFGRKGVAI--NF 84
Cdd:cd18804 132 ALEKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVgiLNADSGLNSPDFraserafqlLTQVsGRAGRGDKPGKVIiqTY 211

                        90       100
                ....*....|....*....|....*
gi 71987152  85 VTENDARQLKEIESYYTTQIEEMPE 109
Cdd:cd18804 212 NPEHPLIQAAKEEDYEAFYEEELAE 236
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 12-82 7.15e-05

C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. This family includes spliceosomal Brr2 RNA helicase, ASCC3 (involved in the repair of N-alkylated nucleotides), Mtr4 (involved in processing of structured RNAs), DDX60 (involved in viral RNA degradation), and other proteins. Ski2-like RNA helicases 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: 350182 [Multi-domain]  Cd Length: 154  Bit Score: 39.46  E-value: 7.15e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152  12 HGDMDQAERDTIMREFRSGSSRVLITTDILARGI----------DVQQVSLVINYDLPSNreNYIHRIGRSGR--FGRKG 79
Cdd:cd18795  70 HAGLTREDRELVEELFREGLIKVLVATSTLAAGVnlpartviikGTQRYDGKGYRELSPL--EYLQMIGRAGRpgFDTRG 147


                ...
gi 71987152  80 VAI 82
Cdd:cd18795 148 EAI 150
PRK10917 PRK10917
ATP-dependent DNA helicase RecG; Provisional
 11-47 9.37e-05

ATP-dependent DNA helicase RecG; Provisional


Pssm-ID: 236794 [Multi-domain]  Cd Length: 681  Bit Score: 40.13  E-value: 9.37e-05
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 71987152   11 LHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDV 47
Cdd:PRK10917 511 LHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDV 547
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
 11-71 1.32e-04

C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase 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: 350176 [Multi-domain]  Cd Length: 153  Bit Score: 38.77  E-value: 1.32e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 71987152  11 LHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQ--VSLVINYDLPSNREnYIHRIGR 71
Cdd:cd18789  74 ITGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEanVAIQISGHGGSRRQ-EAQRLGR 135
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
 8-81 2.04e-04

C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a DEAD-like helicase 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: 350197 [Multi-domain]  Cd Length: 151  Bit Score: 38.48  E-value: 2.04e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 71987152   8 VSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLVINYDLPSNRENYIHRI-GRSGRFGRKGVA 81
Cdd:cd18810  54 IAIAHGQMTENELEEVMLEFAKGEYDILVCTTIIESGIDIPNANTIIIERADKFGLAQLYQLrGRVGRSKERAYA 128
PRK05580 PRK05580
primosome assembly protein PriA; Validated
 20-82 4.97e-04

primosome assembly protein PriA; Validated


Pssm-ID: 235514 [Multi-domain]  Cd Length: 679  Bit Score: 37.83  E-value: 4.97e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71987152   20 RDTIMR---------EFRSGSSRVLITTDILARGIDVQQVSLV--INYDLPSNRENY---------IHRI-GRSGRFGRK 78
Cdd:PRK05580 460 RDTTRRkgaleqllaQFARGEADILIGTQMLAKGHDFPNVTLVgvLDADLGLFSPDFrasertfqlLTQVaGRAGRAEKP 539


                 ....
gi 71987152   79 GVAI 82
Cdd:PRK05580 540 GEVL 543
Cas3_I cd09639
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ...
 4-78 1.36e-03

CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I


Pssm-ID: 187770 [Multi-domain]  Cd Length: 353  Bit Score: 36.64  E-value: 1.36e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 71987152   4 NQFTVSCLHG---DMDQAERDT-IMREFRSGSSRVLITTDILARGIDVqQVSLVINYDLPSNRenYIHRIGRSGRFGRK 78
Cdd:cd09639 243 PEEEIMLIHSrftEKDRAKKEAeLLLEFKKSEKFVIVATQVIEASLDI-SVDVMITELAPIDS--LIQRLGRLHRYGEK 318
PRK05298 PRK05298
excinuclease ABC subunit UvrB;
1-53 2.32e-03

excinuclease ABC subunit UvrB;


Pssm-ID: 235395 [Multi-domain]  Cd Length: 652  Bit Score: 36.18  E-value: 2.32e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 71987152    1 MTENQFTVSCLHGDMDQAERDTIMREFRSGSSRVLITTDILARGIDVQQVSLV 53
Cdd:PRK05298 466 LKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDIPEVSLV 518
ComFA COG4098
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ...
 19-74 8.41e-03

Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, recombination and repair];


Pssm-ID: 443274 [Multi-domain]  Cd Length: 451  Bit Score: 34.47  E-value: 8.41e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 71987152  19 ERDTIMREFRSGSSRVLITTDILARGIDVQQVS-LVINYDlpsnrenyiHRI----------GRSGR 74
Cdd:COG4098 357 ERKEKVQAFRDGEIPILVTTTILERGVTFPNVDvAVLGAD---------HPVfteaalvqiaGRVGR 414
 
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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