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Conserved domains on  [gi|698409689|ref|XP_009708936|]
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PREDICTED: probable ATP-dependent RNA helicase DDX28, partial [Cariama cristata]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 13209184)

DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA

CATH:  3.40.50.300
EC:  3.6.4.-
Gene Ontology:  GO:0016887|GO:0003676|GO:0004386|GO:0005524
PubMed:  20206133|20225155

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 44-177 1.14e-45

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: 147.65  E-value: 1.14e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  44 VLQKFVRLKGRDKLPELLHLLKDHPaSSGAVLIFCNSASTVNWLGYILDDHKIKHLRLQGQMSAAARAGIFTSFQKGDVP 123
Cdd:cd18787    1 IKQLYVVVEEEEKKLLLLLLLLEKL-KPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKVR 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 698409689 124 VLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGSKapGAVVSFV 177
Cdd:cd18787   80 VLVATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAGRK--GTAITFV 131
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 3-50 1.98e-13

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 cd17948:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 231  Bit Score: 66.62  E-value: 1.98e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 698409689   3 TQVVVVGATFPVGLSQMLGKFTDVGRFVTLTTQSLHRLPPHVLQKFVR 50
Cdd:cd17948  184 TQLVLVSATMPSGVGEVLSKVIDVDSIETVTSDKLHRLMPHVKQKFLR 231
 
Name Accession Description Interval E-value
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 44-177 1.14e-45

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: 147.65  E-value: 1.14e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  44 VLQKFVRLKGRDKLPELLHLLKDHPaSSGAVLIFCNSASTVNWLGYILDDHKIKHLRLQGQMSAAARAGIFTSFQKGDVP 123
Cdd:cd18787    1 IKQLYVVVEEEEKKLLLLLLLLEKL-KPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKVR 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 698409689 124 VLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGSKapGAVVSFV 177
Cdd:cd18787   80 VLVATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAGRK--GTAITFV 131
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
10-196 1.24e-40

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 142.98  E-value: 1.24e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  10 ATFPVGLSQMLGKFTDVGRFVTLTTQSLHrlPPHVLQKFVRLKGRDKLPELLHLLKDHPASSgaVLIFCNSASTVNWLGY 89
Cdd:COG0513  184 ATMPPEIRKLAKRYLKNPVRIEVAPENAT--AETIEQRYYLVDKRDKLELLRRLLRDEDPER--AIVFCNTKRGADRLAE 259

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  90 ILDDHKIKHLRLQGQMSAAARAGIFTSFQKGDVPVLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGSKa 169
Cdd:COG0513  260 KLQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYVHRIGRTGRAGAE- 338

                        170       180
                 ....*....|....*....|....*..
gi 698409689 170 pGAVVSFVTHQwDVDLVRKIETAARKR 196
Cdd:COG0513  339 -GTAISLVTPD-ERRLLRAIEKLIGQK 363
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 55-166 1.81e-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: 113.46  E-value: 1.81e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689   55 DKLPELLHLLKDHPasSGAVLIFCNSASTVNwLGYILDDHKIKHLRLQGQMSAAARAGIFTSFQKGDVPVLVCTDLASRG 134
Cdd:pfam00271   1 EKLEALLELLKKER--GGKVLIFSQTKKTLE-AELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERG 77

                          90       100       110
                  ....*....|....*....|....*....|..
gi 698409689  135 LDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVG 166
Cdd:pfam00271  78 LDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
HELICc smart00490
helicase superfamily c-terminal domain;
86-166 6.70e-24

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 90.35  E-value: 6.70e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689    86 WLGYILDDHKIKHLRLQGQMSAAARAGIFTSFQKGDVPVLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRV 165
Cdd:smart00490   2 ELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRA 81


                   .
gi 698409689   166 G 166
Cdd:smart00490  82 G 82
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 56-190 2.51e-22

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 93.47  E-value: 2.51e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  56 KLPELLHLLKDHPASSGAVliFCNSASTVNWLGYILDDHKIKHLRLQGQMSAAARAGIFTSFQKGDVPVLVCTDLASRGL 135
Cdd:PRK11192 232 KTALLCHLLKQPEVTRSIV--FVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGI 309

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 698409689 136 DTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGSKapGAVVSFV-THqwDVDLVRKIE 190
Cdd:PRK11192 310 DIDDVSHVINFDMPRSADTYLHRIGRTGRAGRK--GTAISLVeAH--DHLLLGKIE 361
DEADc_DDX28 cd17948
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box ...
 3-50 1.98e-13

DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box polypeptide 28) plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function. DDX28 is a member of the DEAD-box helicases, 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. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350706 [Multi-domain]  Cd Length: 231  Bit Score: 66.62  E-value: 1.98e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 698409689   3 TQVVVVGATFPVGLSQMLGKFTDVGRFVTLTTQSLHRLPPHVLQKFVR 50
Cdd:cd17948  184 TQLVLVSATMPSGVGEVLSKVIDVDSIETVTSDKLHRLMPHVKQKFLR 231
 
Name Accession Description Interval E-value
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 44-177 1.14e-45

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: 147.65  E-value: 1.14e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  44 VLQKFVRLKGRDKLPELLHLLKDHPaSSGAVLIFCNSASTVNWLGYILDDHKIKHLRLQGQMSAAARAGIFTSFQKGDVP 123
Cdd:cd18787    1 IKQLYVVVEEEEKKLLLLLLLLEKL-KPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKVR 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 698409689 124 VLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGSKapGAVVSFV 177
Cdd:cd18787   80 VLVATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAGRK--GTAITFV 131
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
10-196 1.24e-40

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 142.98  E-value: 1.24e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  10 ATFPVGLSQMLGKFTDVGRFVTLTTQSLHrlPPHVLQKFVRLKGRDKLPELLHLLKDHPASSgaVLIFCNSASTVNWLGY 89
Cdd:COG0513  184 ATMPPEIRKLAKRYLKNPVRIEVAPENAT--AETIEQRYYLVDKRDKLELLRRLLRDEDPER--AIVFCNTKRGADRLAE 259

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  90 ILDDHKIKHLRLQGQMSAAARAGIFTSFQKGDVPVLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGSKa 169
Cdd:COG0513  260 KLQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYVHRIGRTGRAGAE- 338

                        170       180
                 ....*....|....*....|....*..
gi 698409689 170 pGAVVSFVTHQwDVDLVRKIETAARKR 196
Cdd:COG0513  339 -GTAISLVTPD-ERRLLRAIEKLIGQK 363
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 55-166 1.81e-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: 113.46  E-value: 1.81e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689   55 DKLPELLHLLKDHPasSGAVLIFCNSASTVNwLGYILDDHKIKHLRLQGQMSAAARAGIFTSFQKGDVPVLVCTDLASRG 134
Cdd:pfam00271   1 EKLEALLELLKKER--GGKVLIFSQTKKTLE-AELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERG 77

                          90       100       110
                  ....*....|....*....|....*....|..
gi 698409689  135 LDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVG 166
Cdd:pfam00271  78 LDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
HELICc smart00490
helicase superfamily c-terminal domain;
86-166 6.70e-24

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 90.35  E-value: 6.70e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689    86 WLGYILDDHKIKHLRLQGQMSAAARAGIFTSFQKGDVPVLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRV 165
Cdd:smart00490   2 ELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRA 81


                   .
gi 698409689   166 G 166
Cdd:smart00490  82 G 82
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 56-190 2.51e-22

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 93.47  E-value: 2.51e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  56 KLPELLHLLKDHPASSGAVliFCNSASTVNWLGYILDDHKIKHLRLQGQMSAAARAGIFTSFQKGDVPVLVCTDLASRGL 135
Cdd:PRK11192 232 KTALLCHLLKQPEVTRSIV--FVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGI 309

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 698409689 136 DTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGSKapGAVVSFV-THqwDVDLVRKIE 190
Cdd:PRK11192 310 DIDDVSHVINFDMPRSADTYLHRIGRTGRAGRK--GTAISLVeAH--DHLLLGKIE 361
PTZ00424 PTZ00424
helicase 45; Provisional
 75-190 1.71e-21

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 91.04  E-value: 1.71e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  75 LIFCNSASTVNWLGYILDDHKIKHLRLQGQMSAAARAGIFTSFQKGDVPVLVCTDLASRGLDTSSVQLVVNYDFPDTLQD 154
Cdd:PTZ00424 271 IIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPEN 350

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 698409689 155 YLHRVGRVGRVGSKapGAVVSFVTHQwDVDLVRKIE 190
Cdd:PTZ00424 351 YIHRIGRSGRFGRK--GVAINFVTPD-DIEQLKEIE 383
PRK11776 PRK11776
ATP-dependent RNA helicase DbpA; Provisional
 1-180 2.15e-21

ATP-dependent RNA helicase DbpA; Provisional


Pssm-ID: 236977 [Multi-domain]  Cd Length: 460  Bit Score: 91.02  E-value: 2.15e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689   1 ARTQVVVVGATFPVGLSQMLGKFTDvgRFVTLTTQSLHRLPpHVLQKFVRLKGRDKLPELLHLLKDH-PASSgavLIFCN 79
Cdd:PRK11776 177 ARRQTLLFSATYPEGIAAISQRFQR--DPVEVKVESTHDLP-AIEQRFYEVSPDERLPALQRLLLHHqPESC---VVFCN 250

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  80 SASTVNWLGYILDDHKIKHLRLQGQMSAAARAGIFTSFQKGDVPVLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRV 159
Cdd:PRK11776 251 TKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRI 330

                        170       180
                 ....*....|....*....|.
gi 698409689 160 GRVGRVGSKapGAVVSFVTHQ 180
Cdd:PRK11776 331 GRTGRAGSK--GLALSLVAPE 349
PTZ00110 PTZ00110
helicase; Provisional
 31-178 3.45e-21

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 90.99  E-value: 3.45e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  31 TLTTQSLHRLPPHVlqkFVrLKGRDKLPELLHLLKDHPASSGAVLIFCNSASTVNWLGYILDDHKIKHLRLQGQMSAAAR 110
Cdd:PTZ00110 341 SLDLTACHNIKQEV---FV-VEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEER 416

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 698409689 111 AGIFTSFQKGDVPVLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGSKapGAVVSFVT 178
Cdd:PTZ00110 417 TWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAK--GASYTFLT 482
PRK04537 PRK04537
ATP-dependent RNA helicase RhlB; Provisional
 55-185 1.95e-18

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235307 [Multi-domain]  Cd Length: 572  Bit Score: 83.08  E-value: 1.95e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  55 DKLPELLHLLKdhpASSGA-VLIFCNSASTVNWLGYILDDHKIKHLRLQGQMSAAARAGIFTSFQKGDVPVLVCTDLASR 133
Cdd:PRK04537 243 EKQTLLLGLLS---RSEGArTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAAR 319

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 698409689 134 GLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGskAPGAVVSFVTHQWDVDL 185
Cdd:PRK04537 320 GLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLG--EEGDAISFACERYAMSL 369
PRK10590 PRK10590
ATP-dependent RNA helicase RhlE; Provisional
 74-214 2.87e-18

ATP-dependent RNA helicase RhlE; Provisional


Pssm-ID: 236722 [Multi-domain]  Cd Length: 456  Bit Score: 82.16  E-value: 2.87e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  74 VLIFCNSASTVNWLGYILDDHKIKHLRLQGQMSAAARAGIFTSFQKGDVPVLVCTDLASRGLDTSSVQLVVNYDFPDTLQ 153
Cdd:PRK10590 248 VLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPE 327

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 698409689 154 DYLHRVGRVGRvgSKAPGAVVSFVThqwdVD---LVRKIETAARK---RTGLPGM--DSSINMPPPKGG 214
Cdd:PRK10590 328 DYVHRIGRTGR--AAATGEALSLVC----VDehkLLRDIEKLLKKeipRIAIPGYepDPSIKAEPIQNG 390
PRK04837 PRK04837
ATP-dependent RNA helicase RhlB; Provisional
 101-185 1.76e-17

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235314 [Multi-domain]  Cd Length: 423  Bit Score: 79.63  E-value: 1.76e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689 101 LQGQMSAAARAGIFTSFQKGDVPVLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGSKapGAVVSFVTHQ 180
Cdd:PRK04837 285 LTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGAS--GHSISLACEE 362


                 ....*
gi 698409689 181 WDVDL 185
Cdd:PRK04837 363 YALNL 367
PRK01297 PRK01297
ATP-dependent RNA helicase RhlB; Provisional
 44-176 3.19e-15

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 234938 [Multi-domain]  Cd Length: 475  Bit Score: 73.41  E-value: 3.19e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  44 VLQKFVRLKGRDKLPELLHLLKDHPASSgaVLIFCNSASTVNWLGYILDDHKIKHLRLQGQMSAAARAGIFTSFQKGDVP 123
Cdd:PRK01297 310 VEQHVYAVAGSDKYKLLYNLVTQNPWER--VMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIR 387

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 698409689 124 VLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGSKapGAVVSF 176
Cdd:PRK01297 388 VLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGAS--GVSISF 438
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 56-170 1.69e-14

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: 67.50  E-value: 1.69e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  56 KLPELLHLLKDHPASSGAVLIFCNSASTVNWLGYILDDHKIKHLRLQGQMSAAARAGIFTSFQKG-DVPV-LVCTDLASR 133
Cdd:cd18793   12 KLEALLELLEELREPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDpDIRVfLLSTKAGGV 91

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 698409689 134 GLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGSKAP 170
Cdd:cd18793   92 GLNLTAANRVILYDPWWNPAVEEQAIDRAHRIGQKKP 128
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 101-190 2.18e-14

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 71.03  E-value: 2.18e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689 101 LQGQMSAAARAGIFTSFQKGDVPVLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGSKapGAVVSFVTHQ 180
Cdd:PRK11634 275 LNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRA--GRALLFVENR 352

                         90
                 ....*....|
gi 698409689 181 wDVDLVRKIE 190
Cdd:PRK11634 353 -ERRLLRNIE 361
DEADc_DDX28 cd17948
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box ...
 3-50 1.98e-13

DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box polypeptide 28) plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function. DDX28 is a member of the DEAD-box helicases, 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. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350706 [Multi-domain]  Cd Length: 231  Bit Score: 66.62  E-value: 1.98e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 698409689   3 TQVVVVGATFPVGLSQMLGKFTDVGRFVTLTTQSLHRLPPHVLQKFVR 50
Cdd:cd17948  184 TQLVLVSATMPSGVGEVLSKVIDVDSIETVTSDKLHRLMPHVKQKFLR 231
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 35-178 2.65e-13

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 67.94  E-value: 2.65e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  35 QSLHRL------PPHVLQKFVRLKGRD-KLPELLHLLKDHPASSGAVLIFCNSASTVNWLGYILDDHKIKHLRLQGQMSA 107
Cdd:COG0553  506 AALTRLrqicshPALLLEEGAELSGRSaKLEALLELLEELLAEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSA 585

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 698409689 108 AARAGIFTSFQKG-DVPV-LVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGSKAPGAVVSFVT 178
Cdd:COG0553  586 EERDELVDRFQEGpEAPVfLISLKAGGEGLNLTAADHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVA 658
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 95-177 6.10e-13

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 66.74  E-value: 6.10e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  95 KIKHLRLQGQMSAAARAGIFTSFQKGDVPVLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGSkaPGAVV 174
Cdd:PLN00206 392 GLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGE--KGTAI 469


                 ...
gi 698409689 175 SFV 177
Cdd:PLN00206 470 VFV 472
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
49-188 5.59e-12

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 64.01  E-value: 5.59e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  49 VRLKGRDKLPELLHLLKDHPASSGavLIFCNSASTVNWLGYILDDHKIKHLRLQGQMSAAARAGIFTSFQKGDVPVLVCT 128
Cdd:COG0514  210 VPKPPDDKLAQLLDFLKEHPGGSG--IVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEREANQDRFLRDEVDVIVAT 287

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 698409689 129 dlaSR---GLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGskAPGAVVSFVTHQwDVDLVRK 188
Cdd:COG0514  288 ---IAfgmGIDKPDVRFVIHYDLPKSIEAYYQEIGRAGRDG--LPAEALLLYGPE-DVAIQRF 344
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
19-198 1.05e-10

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 60.42  E-value: 1.05e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  19 MLGKFTDVGRFVTLTT-QSLHRLPPHVLQKFVRLKGRDKLPELLHLLKDHPaSSGAVLIFCNSASTVNWLGYILDDHKIK 97
Cdd:COG1061  253 YLAPPEYYGIRVDLTDeRAEYDALSERLREALAADAERKDKILRELLREHP-DDRKTLVFCSSVDHAEALAELLNEAGIR 331

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  98 HLRLQGQMSAAARAGIFTSFQKGDVPVLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRvgsKAPG---AVV 174
Cdd:COG1061  332 AAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLRPTGSPREFIQRLGRGLR---PAPGkedALV 408

                        170       180
                 ....*....|....*....|....*
gi 698409689 175 -SFVTHqwDVDLVRKIETAARKRTG 198
Cdd:COG1061  409 yDFVGN--DVPVLEELAKDLRDLAG 431
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 56-174 1.08e-09

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: 54.67  E-value: 1.08e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  56 KLPELLHLLKDH-----PASSGAVLIFCNSASTVNWLGYILDDHK--IKHLRLQGQMSAAARAG--------IFTSFQKG 120
Cdd:cd18801   10 KLEKLEEIVKEHfkkkqEGSDTRVIIFSEFRDSAEEIVNFLSKIRpgIRATRFIGQASGKSSKGmsqkeqkeVIEQFRKG 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 698409689 121 DVPVLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRvgsKAPGAVV 174
Cdd:cd18801   90 GYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMIQRMGRTGR---KRQGRVV 140
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
56-178 3.54e-09

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 55.89  E-value: 3.54e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  56 KLPELLHLLKD----HPASSgaVLIFCNSASTVNWLGYILDDHKIKHLRLQGQ--------MSAAARAGIFTSFQKGDVP 123
Cdd:COG1111  336 KLSKLREILKEqlgtNPDSR--IIVFTQYRDTAEMIVEFLSEPGIKAGRFVGQaskegdkgLTQKEQIEILERFRAGEFN 413

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689 124 VLVCTDLASRGLDTSSVQLVVNYDfP-----DTLQdylhRVGRVGRvgsKAPGAVVSFVT 178
Cdd:COG1111  414 VLVATSVAEEGLDIPEVDLVIFYE-PvpseiRSIQ----RKGRTGR---KREGRVVVLIA 465
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 56-168 5.76e-09

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: 52.59  E-value: 5.76e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  56 KLPELLHLLKDHPASSGAV--LIFCNSASTVNWLGYILDDH--KIKHLRLQ-------------GQMSAAARAGIFTSFQ 118
Cdd:cd18802    8 KLQKLIEILREYFPKTPDFrgIIFVERRATAVVLSRLLKEHpsTLAFIRCGfligrgnssqrkrSLMTQRKQKETLDKFR 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 698409689 119 KGDVPVLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGSK 168
Cdd:cd18802   88 DGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSK 137
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 57-169 2.69e-08

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 53.18  E-value: 2.69e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  57 LPELLHLLKDHPASSGavLIFCNSASTVNWLGYILDDHKIKHLRLQGQMSAAARAGIFTSFQKGDVPVLVCTDLASRGLD 136
Cdd:PRK11057 224 LDQLMRYVQEQRGKSG--IIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGIN 301

                         90       100       110
                 ....*....|....*....|....*....|...
gi 698409689 137 TSSVQLVVNYDFPDTLQDYLHRVGRVGRVGSKA 169
Cdd:PRK11057 302 KPNVRFVVHFDIPRNIESYYQETGRAGRDGLPA 334
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 124-177 1.17e-07

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: 47.70  E-value: 1.17e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 698409689 124 VLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRvGSKAPGAVVSFV 177
Cdd:cd18785   25 ILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGR-GGKDEGEVILFV 77
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 45-169 3.29e-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: 47.59  E-value: 3.29e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  45 LQKFVRLKG--RDKLPELLHLLKDHPASSGavLIFCNSASTVNWLGYILDDHKIKHLRLQGQMSAAARAGIFTSFQKGDV 122
Cdd:cd18794    4 LFYSVRPKDkkDEKLDLLKRIKVEHLGGSG--IIYCLSRKECEQVAARLQSKGISAAAYHAGLEPSDRRDVQRKWLRDKI 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 698409689 123 PVLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGSKA 169
Cdd:cd18794   82 QVIVATVAFGMGIDKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPS 128
PRK13766 PRK13766
Hef nuclease; Provisional
 55-178 1.35e-06

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 48.33  E-value: 1.35e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  55 DKLPELL-HLLKDHPASSgaVLIFCNSASTVNWLGYILDDHKIKHLRLQGQMSAAARAG--------IFTSFQKGDVPVL 125
Cdd:PRK13766 350 EKLREIVkEQLGKNPDSR--IIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGmsqkeqieILDKFRAGEFNVL 427

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 698409689 126 VCTDLASRGLDTSSVQLVVNYD-FPD---TLQdylhRVGRVGRvgsKAPGAVVSFVT 178
Cdd:PRK13766 428 VSTSVAEEGLDIPSVDLVIFYEpVPSeirSIQ----RKGRTGR---QEEGRVVVLIA 477
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 53-164 3.63e-06

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: 44.95  E-value: 3.63e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  53 GRDKLPELLHLLKDHpassGAVLIFCNSASTVNWLGYIL--------DDHKIKHLrlQGQMSAAARAGIFTSFQKGDVPV 124
Cdd:cd18796   24 GADAYAEVIFLLERH----KSTLVFTNTRSQAERLAQRLrelcpdrvPPDFIALH--HGSLSRELREEVEAALKRGDLKV 97

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 698409689 125 LVCT---DLasrGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGR 164
Cdd:cd18796   98 VVATsslEL---GIDIGDVDLVIQIGSPKSVARLLQRLGRSGH 137
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 42-169 1.76e-03

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: 38.66  E-value: 1.76e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689  42 PHVLQKFVRlkgRDKLPELLHLLKDHpASSGA-VLIFCNSASTVNWLGYILDDHKIKHlRLQGQMsAAARAG-------- 112
Cdd:COG1205  262 PPLVDDGIR---RSALAEAARLLADL-VREGLrTLVFTRSRRGAELLARYARRALREP-DLADRV-AAYRAGylpeerre 335

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 698409689 113 IFTSFQKGDVPVLVCT---DLasrGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGSKA 169
Cdd:COG1205  336 IERGLRSGELLGVVSTnalEL---GIDIGGLDAVVLAGYPGTRASFWQQAGRAGRRGQDS 392
SF2_C_Hrq cd18797
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...
 107-174 2.63e-03

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: 36.85  E-value: 2.63e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 698409689 107 AAARAG--------IFTSFQKGDVPVLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVGRVGSKAPGAVV 174
Cdd:cd18797   70 ASYRAGylaedrreIEAELFNGELLGVVATNALELGIDIGGLDAVVLAGYPGSLASLWQQAGRAGRRGKDSLVILV 145
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
 101-164 5.40e-03

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: 36.09  E-value: 5.40e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 698409689 101 LQGQMSAAARAGIFTSFQKGDVPVLVCTDLASRGLDTSSVQLVVNYDfPDTL---QdyLHRV-GRVGR 164
Cdd:cd18792   66 LHGKMTEDEKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIIED-ADRFglsQ--LHQLrGRVGR 130
PRK09751 PRK09751
putative ATP-dependent helicase Lhr; Provisional
 102-173 8.45e-03

putative ATP-dependent helicase Lhr; Provisional


Pssm-ID: 137505 [Multi-domain]  Cd Length: 1490  Bit Score: 36.83  E-value: 8.45e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 698409689  102 QGQMSAAARAGIFTSFQKGDVPVLVCTDLASRGLDTSSVQLVVNYDFPDTLQDYLHRVGRVG-RVGSKAPGAV 173
Cdd:PRK09751  308 HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGhQVGGVSKGLF 380
 
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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