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Conserved domains on  [gi|1937369939|ref|NP_113774|]
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DNA-binding protein SMUBP-2 [Rattus norvegicus]

Protein Classification

AN1-type zinc finger protein( domain architecture ID 13510947)

AN1-type zinc finger protein similar to plant zinc finger AN1 domain-containing stress-associated proteins that may be involved in environmental stress response

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TIGR00376 super family cl36628
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 19-640 0e+00

DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair]


The actual alignment was detected with superfamily member TIGR00376:

Pssm-ID: 273041 [Multi-domain]  Cd Length: 636  Bit Score: 799.41  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939  19 LERDAEVEERRSWQEHSSLKELQSRGVCLLKLQVSgQRTGLYGQRLVTFEPRKfgpavvlPSNS-FTSGDIVGLYDTNES 97
Cdd:TIGR00376   1 LERDAEISAMMNEIRRLSLKQRERRGRAILNLQGK-IRGGLLGFLLVRFGRRK-------AIATeISVGDIVLVSRGNPL 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939  98 SQLATGVLTRITQKSVIVAFDEShDFQLNLDRentYRLLKLANDVTYKRLKKALLTLKKYHSgpasSLIDVLLGGSTPSP 177
Cdd:TIGR00376  73 QSDLTGVVTRVGKRFITVALEES-VPQWSLKR---VRIDLYANDVTFKRMKEALRALTENHS----RLLEFLLGREAPSK 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 178 ATEIPPLTFYNTTLDPSQKEAVSFALAQKEVAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNLVERLALC 257
Cdd:TIGR00376 145 ASEIHDFQFFDPNLNESQKEAVLFALSSKDLFLIHGPPGTGKTRTVVELIRQLVKRGLRVLVTAPSNIAVDNLLERLALC 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 258 KKQILRLGHPARLLESVQQHSLDAVLARSDNAQIVADIRRDIDQVFGK-NKKTQDKREKSNFRNEIKLLRKELKEReEAA 336
Cdd:TIGR00376 225 DQKIVRLGHPARLLKSNKQHSLDYLIENHPKYQIVADIREKIDELIEErNKKTKPSPQKRRGLSDIKILRKALKKR-EAR 303

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 337 IVQSLSAADVVLATNTGASTDGPLKLLPED---------------------------YFDVVVVDECAQALEASCWIPLL 389
Cdd:TIGR00376 304 GIESLKIASMAEWIETNKSIDRLLKLLPESeerimneilaesdatnsmagseilngqYFDVAVIDEASQAMEPSCLIPLL 383

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 390 KAPKCILAGDHKQLPPTTVSHKAalAGLSRSLMERLAEKHGAAvVRMLAVQYRMHQAITRWASEAMYHGQLTAHPSVAGH 469
Cdd:TIGR00376 384 KARKLILAGDHKQLPPTILSHDA--EELSLTLFERLIKEYPER-SRTLNVQYRMNQKIMEFPSREFYNGKLTAHESVANI 460

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 470 LLKDLPGVADTE-----ETSVPLLLIDTAGCGLLELEEEDSQSKGNPGEVRLVTLHIQALVDAGVQAGDIAVIAPYNLQV 544
Cdd:TIGR00376 461 LLRDLPKVEATEseddlETGIPLLFIDTSGCELFELKEADSTSKYNPGEAELVSEIIQALVKMGVPANDIGVITPYDAQV 540

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 545 DLLRQSLSNKHPELEIKSVDGFQGREKEAVILTFVRSNRKGEVGFLAEDRRINVAVTRARRHVAVICDSHTVNNHAFLKT 624
Cdd:TIGR00376 541 DLLRQLLEHRHIDIEVSSVDGFQGREKEVIIISFVRSNRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKR 620

                         650
                  ....*....|....*.
gi 1937369939 625 LVDYFTEHGEVRTAFE 640
Cdd:TIGR00376 621 LIEWCKQHGEVREAFK 636
R3H_Smubp-2_like cd02641
R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and ...
 724-782 1.27e-23

R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.


:

Pssm-ID: 100070  Cd Length: 60  Bit Score: 94.73  E-value: 1.27e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 724 TEHFRAMIEEFVASKEA-QLEFPTSLSSHDRLRVHQLAEEFGLKHDSTGEGKARHITVSR 782
Cdd:cd02641     1 VKHLKAMVKAFMKDPKAtELEFPPTLSSHDRLLVHELAEELGLRHESTGEGSDRVITVSK 60
ZnF_AN1 smart00154
AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in ...
 890-930 1.83e-11

AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.


:

Pssm-ID: 197545  Cd Length: 39  Bit Score: 59.33  E-value: 1.83e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1937369939  890 CSFtkCSASTTTLGQFCMHCSRRYCLSHHLPEIHGCGEKAR 930
Cdd:smart00154   1 CHF--CRKKVGLTGFKCRHCGNLFCGEHRLPEDHDCPGDYK 39
 
Name Accession Description Interval E-value
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 19-640 0e+00

DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273041 [Multi-domain]  Cd Length: 636  Bit Score: 799.41  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939  19 LERDAEVEERRSWQEHSSLKELQSRGVCLLKLQVSgQRTGLYGQRLVTFEPRKfgpavvlPSNS-FTSGDIVGLYDTNES 97
Cdd:TIGR00376   1 LERDAEISAMMNEIRRLSLKQRERRGRAILNLQGK-IRGGLLGFLLVRFGRRK-------AIATeISVGDIVLVSRGNPL 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939  98 SQLATGVLTRITQKSVIVAFDEShDFQLNLDRentYRLLKLANDVTYKRLKKALLTLKKYHSgpasSLIDVLLGGSTPSP 177
Cdd:TIGR00376  73 QSDLTGVVTRVGKRFITVALEES-VPQWSLKR---VRIDLYANDVTFKRMKEALRALTENHS----RLLEFLLGREAPSK 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 178 ATEIPPLTFYNTTLDPSQKEAVSFALAQKEVAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNLVERLALC 257
Cdd:TIGR00376 145 ASEIHDFQFFDPNLNESQKEAVLFALSSKDLFLIHGPPGTGKTRTVVELIRQLVKRGLRVLVTAPSNIAVDNLLERLALC 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 258 KKQILRLGHPARLLESVQQHSLDAVLARSDNAQIVADIRRDIDQVFGK-NKKTQDKREKSNFRNEIKLLRKELKEReEAA 336
Cdd:TIGR00376 225 DQKIVRLGHPARLLKSNKQHSLDYLIENHPKYQIVADIREKIDELIEErNKKTKPSPQKRRGLSDIKILRKALKKR-EAR 303

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 337 IVQSLSAADVVLATNTGASTDGPLKLLPED---------------------------YFDVVVVDECAQALEASCWIPLL 389
Cdd:TIGR00376 304 GIESLKIASMAEWIETNKSIDRLLKLLPESeerimneilaesdatnsmagseilngqYFDVAVIDEASQAMEPSCLIPLL 383

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 390 KAPKCILAGDHKQLPPTTVSHKAalAGLSRSLMERLAEKHGAAvVRMLAVQYRMHQAITRWASEAMYHGQLTAHPSVAGH 469
Cdd:TIGR00376 384 KARKLILAGDHKQLPPTILSHDA--EELSLTLFERLIKEYPER-SRTLNVQYRMNQKIMEFPSREFYNGKLTAHESVANI 460

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 470 LLKDLPGVADTE-----ETSVPLLLIDTAGCGLLELEEEDSQSKGNPGEVRLVTLHIQALVDAGVQAGDIAVIAPYNLQV 544
Cdd:TIGR00376 461 LLRDLPKVEATEseddlETGIPLLFIDTSGCELFELKEADSTSKYNPGEAELVSEIIQALVKMGVPANDIGVITPYDAQV 540

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 545 DLLRQSLSNKHPELEIKSVDGFQGREKEAVILTFVRSNRKGEVGFLAEDRRINVAVTRARRHVAVICDSHTVNNHAFLKT 624
Cdd:TIGR00376 541 DLLRQLLEHRHIDIEVSSVDGFQGREKEVIIISFVRSNRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKR 620

                         650
                  ....*....|....*.
gi 1937369939 625 LVDYFTEHGEVRTAFE 640
Cdd:TIGR00376 621 LIEWCKQHGEVREAFK 636
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 191-442 2.37e-111

DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, or IGHMBP2) is a 5' to 3' helicase that unwinds RNA and DNA duplexes in an ATP-dependent reaction. It is a DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence (5'-GGGCT-3') related to the immunoglobulin mu chain switch region. The IGHMBP2 gene is responsible for Charcot-Marie-Tooth disease (CMT) type 2S and spinal muscular atrophy with respiratory distress type 1 (SMARD1). It is also thought to play a role in frontotemporal dementia (FTD) with amyotrophic lateral sclerosis (ALS) and major depressive disorder (MDD). SMUBP2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350802 [Multi-domain]  Cd Length: 191  Bit Score: 341.51  E-value: 2.37e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 191 LDPSQKEAVSFALAQKEVAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNLVERLALCKKQILRLGHPARL 270
Cdd:cd18044     2 LNDSQKEAVKFALSQKDVALIHGPPGTGKTTTVVEIILQAVKRGEKVLACAPSNIAVDNLVERLVALKVKVVRIGHPARL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 271 LESVQQHSLDAvlarsdnaqivadirrdidqvfgknkktqdkreksnfrneikllrkelkereeaaivqsLSAADVVLAT 350
Cdd:cd18044    82 LESVLDHSLDA-----------------------------------------------------------LVAAQVVLAT 102

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 351 NTGASTDGplkLLPEDYFDVVVVDECAQALEASCWIPLLKAPKCILAGDHKQLPPTTVSHKAALAGLSRSLMERLAEKHG 430
Cdd:cd18044   103 NTGAGSRQ---LLPNELFDVVVIDEAAQALEASCWIPLLKARRCILAGDHKQLPPTILSDKAARGGLGVTLFERLVNLYG 179

                         250
                  ....*....|..
gi 1937369939 431 AAVVRMLAVQYR 442
Cdd:cd18044   180 ESVVRMLTVQYR 191
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 417-613 5.75e-75

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.


Pssm-ID: 463780 [Multi-domain]  Cd Length: 196  Bit Score: 244.76  E-value: 5.75e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 417 LSRSLMERLAEKHGAAVVrMLAVQYRMHQAITRWASEAMYHGQLTAHPSVAGHLLkdlPGVADTEETSVPLLLIDTAGCg 496
Cdd:pfam13087   1 LDRSLFERLQELGPSAVV-MLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPL---PDDFHLPDPLGPLVFIDVDGS- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 497 lLELEEEDSQSKGNPGEVRLVTLHIQALVDAGVQAG-DIAVIAPYNLQVDLLRQSLSNKH---PELEIKSVDGFQGREKE 572
Cdd:pfam13087  76 -EEEESDGGTSYSNEAEAELVVQLVEKLIKSGPEEPsDIGVITPYRAQVRLIRKLLKRKLggkLEIEVNTVDGFQGREKD 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1937369939 573 AVILTFVRSNRKGEVGFLAEDRRINVAVTRARRHVAVICDS 613
Cdd:pfam13087 155 VIIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNA 195
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
306-632 1.80e-72

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 256.59  E-value: 1.80e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 306 NKKTQDKREKSNFRNEIKLLRKELKEREEAAIVQSLSAADVVLATNTGASTDGPLKllpEDYFDVVVVDECAQALEASCW 385
Cdd:COG1112   497 EKLIAELREAARLRRALRRELKKRRELRKLLWDALLELAPVVGMTPASVARLLPLG---EGSFDLVIIDEASQATLAEAL 573

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 386 IPLLKAPKCILAGDHKQLPPTTVS---HKAALAGLSRSLMERLAEKHGAAVVrMLAVQYRMHQAITRWASEAMYHGQLTA 462
Cdd:COG1112   574 GALARAKRVVLVGDPKQLPPVVFGeeaEEVAEEGLDESLLDRLLARLPERGV-MLREHYRMHPEIIAFSNRLFYDGKLVP 652

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 463 HPSVAGHLLkdlpgvadtEETSVPLLLIDTAGCGlleleEEDSQSKGNPGEVRLVTLHIQALVDAGVQAGDIAVIAPYNL 542
Cdd:COG1112   653 LPSPKARRL---------ADPDSPLVFIDVDGVY-----ERRGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRA 718

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 543 QVDLLRQSL----SNKHPELEIKSVDGFQGREKEAVILTFVRSNRK---GEVGFLAED-RRINVAVTRARRHVAVICDSH 614
Cdd:COG1112   719 QVALIRELLrealGDGLEPVFVGTVDRFQGDERDVIIFSLVYSNDEdvpRNFGFLNGGpRRLNVAVSRARRKLIVVGSRE 798

                         330       340
                  ....*....|....*....|.
gi 1937369939 615 TV---NNHAFLKTLVDYFTEH 632
Cdd:COG1112   799 LLdsdPSTPALKRLLEYLERA 819
R3H_Smubp-2_like cd02641
R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and ...
 724-782 1.27e-23

R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.


Pssm-ID: 100070  Cd Length: 60  Bit Score: 94.73  E-value: 1.27e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 724 TEHFRAMIEEFVASKEA-QLEFPTSLSSHDRLRVHQLAEEFGLKHDSTGEGKARHITVSR 782
Cdd:cd02641     1 VKHLKAMVKAFMKDPKAtELEFPPTLSSHDRLLVHELAEELGLRHESTGEGSDRVITVSK 60
R3H smart00393
Putative single-stranded nucleic acids-binding domain;
707-783 9.94e-17

Putative single-stranded nucleic acids-binding domain;


Pssm-ID: 214647  Cd Length: 79  Bit Score: 75.80  E-value: 9.94e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1937369939  707 QHSSKANGSDRTGGTDRTEHFRAMIEEFVASKEAQLEFPTsLSSHDRLRVHQLAEEFGLKHDSTGEGKARHITVSRR 783
Cdd:smart00393   4 LPVTLDALSYRPRRREELIELELEIARFVKSTKESVELPP-MNSYERKIVHELAEKYGLESESFGEGPKRRVVISKK 79
ZnF_AN1 smart00154
AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in ...
 890-930 1.83e-11

AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.


Pssm-ID: 197545  Cd Length: 39  Bit Score: 59.33  E-value: 1.83e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1937369939  890 CSFtkCSASTTTLGQFCMHCSRRYCLSHHLPEIHGCGEKAR 930
Cdd:smart00154   1 CHF--CRKKVGLTGFKCRHCGNLFCGEHRLPEDHDCPGDYK 39
R3H pfam01424
R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most ...
 731-782 4.59e-11

R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA.


Pssm-ID: 460206  Cd Length: 60  Bit Score: 59.04  E-value: 4.59e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1937369939 731 IEEFVASKEAQLEFPtSLSSHDRLRVHQLAEEFGLKHDSTGEGKARHITVSR 782
Cdd:pfam01424  10 LAEFVKDTGKSLELP-PMSSYERRIIHELAQKYGLESESEGEEPNRRVVVYK 60
DEXDc smart00487
DEAD-like helicases superfamily;
186-255 1.43e-09

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 58.66  E-value: 1.43e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1937369939  186 FYNTTLDPSQKEAVSFALAQKEVAIIHGPPGTGKTTTVVEIILQAVKQGL--KVLCCAPSNIAVDNLVERLA 255
Cdd:smart00487   4 FGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKggRVLVLVPTRELAEQWAEELK 75
zf-AN1 pfam01428
AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in ...
 890-927 5.26e-09

AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis. The following pattern describes the zinc finger. C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C Where X can be any amino acid, and numbers in brackets indicate the number of residues.


Pssm-ID: 460208  Cd Length: 37  Bit Score: 52.31  E-value: 5.26e-09
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1937369939 890 CSFTKCSASTTTLGQfCMHCSRRYCLSHHLPEIHGCGE 927
Cdd:pfam01428   1 CSFKGCKKKDFLPFK-CRFCGKNFCLKHRLPEDHDCSG 37
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was ...
 203-260 7.49e-04

IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was built to hit full-length AAA+ ATPases of IS21 family IS (insertion sequence) elements.


Pssm-ID: 439516  Cd Length: 232  Bit Score: 42.07  E-value: 7.49e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1937369939 203 LAQKEVAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCcapsnIAVDNLVERLALCKKQ 260
Cdd:NF038214   87 IERAENVLLLGPPGTGKTHLAIALGYAACRQGYRVRF-----TTAADLVEQLAQARAD 139
 
Name Accession Description Interval E-value
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 19-640 0e+00

DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273041 [Multi-domain]  Cd Length: 636  Bit Score: 799.41  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939  19 LERDAEVEERRSWQEHSSLKELQSRGVCLLKLQVSgQRTGLYGQRLVTFEPRKfgpavvlPSNS-FTSGDIVGLYDTNES 97
Cdd:TIGR00376   1 LERDAEISAMMNEIRRLSLKQRERRGRAILNLQGK-IRGGLLGFLLVRFGRRK-------AIATeISVGDIVLVSRGNPL 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939  98 SQLATGVLTRITQKSVIVAFDEShDFQLNLDRentYRLLKLANDVTYKRLKKALLTLKKYHSgpasSLIDVLLGGSTPSP 177
Cdd:TIGR00376  73 QSDLTGVVTRVGKRFITVALEES-VPQWSLKR---VRIDLYANDVTFKRMKEALRALTENHS----RLLEFLLGREAPSK 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 178 ATEIPPLTFYNTTLDPSQKEAVSFALAQKEVAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNLVERLALC 257
Cdd:TIGR00376 145 ASEIHDFQFFDPNLNESQKEAVLFALSSKDLFLIHGPPGTGKTRTVVELIRQLVKRGLRVLVTAPSNIAVDNLLERLALC 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 258 KKQILRLGHPARLLESVQQHSLDAVLARSDNAQIVADIRRDIDQVFGK-NKKTQDKREKSNFRNEIKLLRKELKEReEAA 336
Cdd:TIGR00376 225 DQKIVRLGHPARLLKSNKQHSLDYLIENHPKYQIVADIREKIDELIEErNKKTKPSPQKRRGLSDIKILRKALKKR-EAR 303

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 337 IVQSLSAADVVLATNTGASTDGPLKLLPED---------------------------YFDVVVVDECAQALEASCWIPLL 389
Cdd:TIGR00376 304 GIESLKIASMAEWIETNKSIDRLLKLLPESeerimneilaesdatnsmagseilngqYFDVAVIDEASQAMEPSCLIPLL 383

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 390 KAPKCILAGDHKQLPPTTVSHKAalAGLSRSLMERLAEKHGAAvVRMLAVQYRMHQAITRWASEAMYHGQLTAHPSVAGH 469
Cdd:TIGR00376 384 KARKLILAGDHKQLPPTILSHDA--EELSLTLFERLIKEYPER-SRTLNVQYRMNQKIMEFPSREFYNGKLTAHESVANI 460

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 470 LLKDLPGVADTE-----ETSVPLLLIDTAGCGLLELEEEDSQSKGNPGEVRLVTLHIQALVDAGVQAGDIAVIAPYNLQV 544
Cdd:TIGR00376 461 LLRDLPKVEATEseddlETGIPLLFIDTSGCELFELKEADSTSKYNPGEAELVSEIIQALVKMGVPANDIGVITPYDAQV 540

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 545 DLLRQSLSNKHPELEIKSVDGFQGREKEAVILTFVRSNRKGEVGFLAEDRRINVAVTRARRHVAVICDSHTVNNHAFLKT 624
Cdd:TIGR00376 541 DLLRQLLEHRHIDIEVSSVDGFQGREKEVIIISFVRSNRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKR 620

                         650
                  ....*....|....*.
gi 1937369939 625 LVDYFTEHGEVRTAFE 640
Cdd:TIGR00376 621 LIEWCKQHGEVREAFK 636
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 191-442 2.37e-111

DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, or IGHMBP2) is a 5' to 3' helicase that unwinds RNA and DNA duplexes in an ATP-dependent reaction. It is a DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence (5'-GGGCT-3') related to the immunoglobulin mu chain switch region. The IGHMBP2 gene is responsible for Charcot-Marie-Tooth disease (CMT) type 2S and spinal muscular atrophy with respiratory distress type 1 (SMARD1). It is also thought to play a role in frontotemporal dementia (FTD) with amyotrophic lateral sclerosis (ALS) and major depressive disorder (MDD). SMUBP2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350802 [Multi-domain]  Cd Length: 191  Bit Score: 341.51  E-value: 2.37e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 191 LDPSQKEAVSFALAQKEVAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNLVERLALCKKQILRLGHPARL 270
Cdd:cd18044     2 LNDSQKEAVKFALSQKDVALIHGPPGTGKTTTVVEIILQAVKRGEKVLACAPSNIAVDNLVERLVALKVKVVRIGHPARL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 271 LESVQQHSLDAvlarsdnaqivadirrdidqvfgknkktqdkreksnfrneikllrkelkereeaaivqsLSAADVVLAT 350
Cdd:cd18044    82 LESVLDHSLDA-----------------------------------------------------------LVAAQVVLAT 102

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 351 NTGASTDGplkLLPEDYFDVVVVDECAQALEASCWIPLLKAPKCILAGDHKQLPPTTVSHKAALAGLSRSLMERLAEKHG 430
Cdd:cd18044   103 NTGAGSRQ---LLPNELFDVVVIDEAAQALEASCWIPLLKARRCILAGDHKQLPPTILSDKAARGGLGVTLFERLVNLYG 179

                         250
                  ....*....|..
gi 1937369939 431 AAVVRMLAVQYR 442
Cdd:cd18044   180 ESVVRMLTVQYR 191
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 417-613 5.75e-75

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.


Pssm-ID: 463780 [Multi-domain]  Cd Length: 196  Bit Score: 244.76  E-value: 5.75e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 417 LSRSLMERLAEKHGAAVVrMLAVQYRMHQAITRWASEAMYHGQLTAHPSVAGHLLkdlPGVADTEETSVPLLLIDTAGCg 496
Cdd:pfam13087   1 LDRSLFERLQELGPSAVV-MLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPL---PDDFHLPDPLGPLVFIDVDGS- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 497 lLELEEEDSQSKGNPGEVRLVTLHIQALVDAGVQAG-DIAVIAPYNLQVDLLRQSLSNKH---PELEIKSVDGFQGREKE 572
Cdd:pfam13087  76 -EEEESDGGTSYSNEAEAELVVQLVEKLIKSGPEEPsDIGVITPYRAQVRLIRKLLKRKLggkLEIEVNTVDGFQGREKD 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1937369939 573 AVILTFVRSNRKGEVGFLAEDRRINVAVTRARRHVAVICDS 613
Cdd:pfam13087 155 VIIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNA 195
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
306-632 1.80e-72

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 256.59  E-value: 1.80e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 306 NKKTQDKREKSNFRNEIKLLRKELKEREEAAIVQSLSAADVVLATNTGASTDGPLKllpEDYFDVVVVDECAQALEASCW 385
Cdd:COG1112   497 EKLIAELREAARLRRALRRELKKRRELRKLLWDALLELAPVVGMTPASVARLLPLG---EGSFDLVIIDEASQATLAEAL 573

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 386 IPLLKAPKCILAGDHKQLPPTTVS---HKAALAGLSRSLMERLAEKHGAAVVrMLAVQYRMHQAITRWASEAMYHGQLTA 462
Cdd:COG1112   574 GALARAKRVVLVGDPKQLPPVVFGeeaEEVAEEGLDESLLDRLLARLPERGV-MLREHYRMHPEIIAFSNRLFYDGKLVP 652

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 463 HPSVAGHLLkdlpgvadtEETSVPLLLIDTAGCGlleleEEDSQSKGNPGEVRLVTLHIQALVDAGVQAGDIAVIAPYNL 542
Cdd:COG1112   653 LPSPKARRL---------ADPDSPLVFIDVDGVY-----ERRGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRA 718

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 543 QVDLLRQSL----SNKHPELEIKSVDGFQGREKEAVILTFVRSNRK---GEVGFLAED-RRINVAVTRARRHVAVICDSH 614
Cdd:COG1112   719 QVALIRELLrealGDGLEPVFVGTVDRFQGDERDVIIFSLVYSNDEdvpRNFGFLNGGpRRLNVAVSRARRKLIVVGSRE 798

                         330       340
                  ....*....|....*....|.
gi 1937369939 615 TV---NNHAFLKTLVDYFTEH 632
Cdd:COG1112   799 LLdsdPSTPALKRLLEYLERA 819
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 194-409 6.68e-67

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.


Pssm-ID: 404072 [Multi-domain]  Cd Length: 248  Bit Score: 224.53  E-value: 6.68e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 194 SQKEAVSFALAQKEVAIIHGPPGTGKTTTVVEIILQAVKQGL-------KVLCCAPSNIAVDNLVERLALCKKQ----IL 262
Cdd:pfam13086   1 SQREAIRSALSSSHFTLIQGPPGTGKTTTIVELIRQLLSYPAtsaaagpRILVCAPSNAAVDNILERLLRKGQKygpkIV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 263 RLGHPARLLESVQQHSLDAVLARSDN----AQIVADIRR------------------DIDQVFGKNKKTQDKREKSNFRN 320
Cdd:pfam13086  81 RIGHPAAISEAVLPVSLDYLVESKLNneedAQIVKDISKeleklakalrafekeiivEKLLKSRNKDKSKLEQERRKLRS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 321 EIKLLRKELKEREEAAIVQSLSAADVVLATNTGASTDgplKLLPEDYFDVVVVDECAQALEASCWIPLLKAP-KCILAGD 399
Cdd:pfam13086 161 ERKELRKELRRREQSLEREILDEAQIVCSTLSGAGSR---LLSSLANFDVVIIDEAAQALEPSTLIPLLRGPkKVVLVGD 237

                         250
                  ....*....|
gi 1937369939 400 HKQLPPTTVS 409
Cdd:pfam13086 238 PKQLPPTVIS 247
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 443-629 3.23e-59

C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), and similar proteins. They are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350195 [Multi-domain]  Cd Length: 184  Bit Score: 200.54  E-value: 3.23e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 443 MHQAITRWASEAMYHGQLTAHPSVAGHLLKDlpgvaDTEETSVPLLLIDTAGCgllELEEEDSQSKGNPGEVRLVTLHIQ 522
Cdd:cd18808     1 MHPEISEFPSKLFYEGKLKAGVSVAARLNPP-----PLPGPSKPLVFVDVSGG---EEREESGTSKSNEAEAELVVELVK 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 523 ALVDAGVQAGDIAVIAPYNLQVDLLRQSLSNKH---PELEIKSVDGFQGREKEAVILTFVRSNRKGE-VGFLAEDRRINV 598
Cdd:cd18808    73 YLLKSGVKPSSIGVITPYRAQVALIRELLRKRGgllEDVEVGTVDNFQGREKDVIILSLVRSNESGGsIGFLSDPRRLNV 152

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1937369939 599 AVTRARRHVAVICDSHTVNNHAFLKTLVDYF 629
Cdd:cd18808   153 ALTRAKRGLIIVGNPDTLSKDPLWKKLLEYL 183
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
 191-442 1.57e-44

DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of Nonsense Transcripts, or ATP-Dependent Helicase RENT1) is an RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. It is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. It is recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) located downstream from the termination codon through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Diseases associated with UPF1 include juvenile amyotrophic lateral sclerosis and epidermolysis bullosa, junctional, non-Herlitz type. UPF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350797 [Multi-domain]  Cd Length: 234  Bit Score: 160.88  E-value: 1.57e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 191 LDPSQKEAVSFALaQKEVAIIHGPPGTGKTTTVVEIILQAVKQGL-KVLCCAPSNIAVDNLVERLALCKKQILRLghpar 269
Cdd:cd18039     2 LNHSQVDAVKTAL-QRPLSLIQGPPGTGKTVTSATIVYHLVKQGNgPVLVCAPSNVAVDQLTEKIHQTGLKVVRL----- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 270 llesvqqhsldAVLARSDNAQIVADIrrdidqVFGKNKKTQDKREKSNFRNEIKLLRKELKEREEAAIVQS--------L 341
Cdd:cd18039    76 -----------CAKSREAVESPVSFL------ALHNQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLkrkaerelL 138

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 342 SAADVVLATNTGASTdgplKLLPEDYFDVVVVDECAQALEASCWIPLLKAPK-CILAGDHKQLPPTTVSHKAALAGLSRS 420
Cdd:cd18039   139 RNADVICCTCVGAGD----PRLSKMKFRTVLIDEATQATEPECLIPLVHGAKqVILVGDHCQLGPVVMCKKAAKAGLSQS 214

                         250       260
                  ....*....|....*....|..
gi 1937369939 421 LMERLAeKHGAAVVRmLAVQYR 442
Cdd:cd18039   215 LFERLV-QLGIRPIR-LQVQYR 234
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 195-442 3.42e-44

DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses different enzymatic activities, such as single-stranded DNA (ssDNA)-dependent ATPase, 5-3 helicase, and endonuclease activities, and is involved in DNA replication and DNA repair in the nucleus and mitochondrion. It is involved in Okazaki fragment processing by cleaving long flaps that escape FEN1: flaps that are longer than 27 nucleotides are coated by replication protein A complex (RPA), leading to recruit DNA2 which cleaves the flap until it is too short to bind RPA and becomes a substrate for FEN1. It is also involved in 5-end resection of DNA during double-strand break (DSB) repair; it is recruited by BLM and mediates the cleavage of 5-ssDNA, while the 3-ssDNA cleavage is prevented by the presence of RPA. DNA2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350799 [Multi-domain]  Cd Length: 203  Bit Score: 158.94  E-value: 3.42e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 195 QKEAVSFALAQKEVAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNLVERLALCKKQILRLGHPARLLESV 274
Cdd:cd18041     6 QRQAIKKVLNAKDYALILGMPGTGKTTTIAALVRILVALGKSVLLTSYTHSAVDNILLKLKKFGVNFLRLGRLKKIHPDV 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 275 QQHSLDAVLARSDNAQivadirrdidqvfgknkktqdkreksnfrneikllrkELKEreeaaivqSLSAADVVLATNTGA 354
Cdd:cd18041    86 QEFTLEAILKSCKSVE-------------------------------------ELES--------KYESVSVVATTCLGI 120

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 355 STDgplkLLPEDYFDVVVVDECAQALEASCWIPLLKAPKCILAGDHKQLPPTTVSHKAALAGLSRSLMERLAEKHGAAVV 434
Cdd:cd18041   121 NHP----IFRRRTFDYCIVDEASQITLPICLGPLRLAKKFVLVGDHYQLPPLVKSREARELGMDESLFKRLSEAHPDAVV 196


                  ....*...
gi 1937369939 435 rMLAVQYR 442
Cdd:cd18041   197 -QLTIQYR 203
DEXXQc_Helz-like cd18038
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ...
 191-425 3.99e-40

DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and similar proteins. Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. All are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350796 [Multi-domain]  Cd Length: 229  Bit Score: 148.15  E-value: 3.99e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 191 LDPSQKEAVSFALAQKEVA---IIHGPPGTGKTTTVVEIILQAVKQ--GLKVLCCAPSNIAVDNLVERLA---LCKKQIL 262
Cdd:cd18038     2 LNDEQKLAVRNIVTGTSRPppyIIFGPPGTGKTVTLVEAILQVLRQppEARILVCAPSNSAADLLAERLLnalVTKREIL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 263 RLGHPARLLESVqqhsldavlarsdnaqivadirrdidqvfgknkktqDKREKSnFRNEIKLLRKELKEREEaaivqsLS 342
Cdd:cd18038    82 RLNAPSRDRASV------------------------------------PPELLP-YCNSKAEGTFRLPSLEE------LK 118

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 343 AADVVLATNTGAS--TDGPlklLPEDYFDVVVVDECAQALEASCWIPL----LKAPKCILAGDHKQLPPTTVSHKAALAG 416
Cdd:cd18038   119 KYRIVVCTLMTAGrlVQAG---VPNGHFTHIFIDEAGQATEPEALIPLselaSKNTQIVLAGDPKQLGPVVRSPLARKYG 195


                  ....*....
gi 1937369939 417 LSRSLMERL 425
Cdd:cd18038   196 LGKSLLERL 204
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 191-442 6.38e-40

DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in transcription, neurogenesis, and antiviral response. SEXT is an R-loop-associated protein that is thought to function as an RNA/DNA helicase. R-loops consist of RNA/DNA hybrids, formed during transcription when nascent RNA hybridizes to the DNA template strand, displacing the non-template DNA strand. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). S. cerevisiae homolog splicing endonuclease 1 (Sen1) is an exclusively nuclear protein, important for nucleolar organization. S. cerevisiae Sen1 and its ortholog, the Schizosaccharomyces pombe Sen1, share conserved domains and belong to the family I class of helicases. Both proteins translocate 5' to 3' and unwind both DNA and RNA duplexes and also RNA/DNA hybrids in vitro. SETX is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438712 [Multi-domain]  Cd Length: 218  Bit Score: 146.97  E-value: 6.38e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 191 LDPSQKEAV-SFALAQKEVAIIHGPPGTGKTTTVVEII-------------------------LQAVKQGLKVLCCAPSN 244
Cdd:cd18042     1 LNESQLEAIaSALQNSPGITLIQGPPGTGKTKTIVGILsvllagkyrkyyekvkkklrklqrnLNNKKKKNRILVCAPSN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 245 IAVDNLVERLalckkqilrlghparllesvqqhsldavlarsdnaqivadirrdidqvfgKNKKTQDKREKSNFRNEIKL 324
Cdd:cd18042    81 AAVDEIVLRL--------------------------------------------------LSEGFLDGDGRSYKPNVVRV 110

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 325 LRKELKereeAAIVQSlsaADVVLATNTGASTDgPLKLLPEDyFDVVVVDECAQALEASCWIPL-LKAPKCILAGDHKQL 403
Cdd:cd18042   111 GRQELR----ASILNE---ADIVCTTLSSSGSD-LLESLPRG-FDTVIIDEAAQAVELSTLIPLrLGCKRLILVGDPKQL 181

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1937369939 404 PPTTVSHKAALAGLSRSLMERLaEKHGAAVVrMLAVQYR 442
Cdd:cd18042   182 PATVFSKVAQKLGYDRSLFERL-QLAGYPVL-MLTTQYR 218
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 208-442 1.48e-28

DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438708 [Multi-domain]  Cd Length: 121  Bit Score: 110.79  E-value: 1.48e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 208 VAIIHGPPGTGKTTTVVEIILQAVKQ--GLKVLCCAPSNIAVDNLverlalckkqilrlghparllesvqqhsldavlar 285
Cdd:cd17934     1 ISLIQGPPGTGKTTTIAAIVLQLLKGlrGKRVLVTAQSNVAVDNV----------------------------------- 45

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 286 sdnaqivadirrdidqvfgknkktqdkreksnfrneikllrkelkereeaaivqslsaadvvlatntgastdgplkllpe 365
Cdd:cd17934       --------------------------------------------------------------------------------

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1937369939 366 dyfDVVVVDECAQALEASCWIPLLKAPKCILAGDHKQLPPTTVSHKAALAGLS--RSLMERLAEKHGAAVVRMLAVQYR 442
Cdd:cd17934    46 ---DVVIIDEASQITEPELLIALIRAKKVVLVGDPKQLPPVVQEDHAALLGLSfiLSLLLLFRLLLPGSPKVMLDTQYR 121
DEXXQc_Mov10L1 cd18078
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ...
 191-425 2.52e-25

DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. Mov10L1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350836 [Multi-domain]  Cd Length: 230  Bit Score: 105.53  E-value: 2.52e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 191 LDPSQKEAVSFAL---AQKEVAIIHGPPGTGKTTTVVEIILQAVKQ--GLKVLCCAPSNIAVDNLVERLALCKkqILRLG 265
Cdd:cd18078     2 LNELQKEAVKRILggeCRPLPYILFGPPGTGKTVTIIEAILQVVYNlpRSRILVCAPSNSAADLVTSRLHESK--VLKPG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 266 HPARllesvqqhsLDAVLARSDnaqIVADIRRDIDqvfgknKKTQDKREKSNFRneikllrkelkereeaaivqslsaad 345
Cdd:cd18078    80 DMVR---------LNAVNRFES---TVIDARKLYC------RLGEDLSKASRHR-------------------------- 115

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 346 VVLATNTGASTDGPLKlLPEDYFDVVVVDECAQALEASCWIPL----LKAPKCILAGDHKQLPPTTVSHKAALAGLSRSL 421
Cdd:cd18078   116 IVISTCSTAGLLYQMG-LPVGHFTHVFVDEAGQATEPESLIPLglisSRDGQIILAGDPMQLGPVIKSRLASAYGLGVSF 194


                  ....
gi 1937369939 422 MERL 425
Cdd:cd18078   195 LERL 198
R3H_Smubp-2_like cd02641
R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and ...
 724-782 1.27e-23

R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.


Pssm-ID: 100070  Cd Length: 60  Bit Score: 94.73  E-value: 1.27e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 724 TEHFRAMIEEFVASKEA-QLEFPTSLSSHDRLRVHQLAEEFGLKHDSTGEGKARHITVSR 782
Cdd:cd02641     1 VKHLKAMVKAFMKDPKAtELEFPPTLSSHDRLLVHELAEELGLRHESTGEGSDRVITVSK 60
DEXXc_HELZ2-C cd18040
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 191-442 1.09e-21

C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known as PPAR-alpha-interacting complex protein 285 or PRIC285 and PPAR-gamma DBD-interacting protein 1 or PDIP1) acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB and RXRA. It belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350798 [Multi-domain]  Cd Length: 271  Bit Score: 96.05  E-value: 1.09e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 191 LDPSQKEAVSFALAqKEVAIIHGPPGTGKTTTVVEIILQAVKQ-------------GLKVLCCAPSNIAVDNLVERL-AL 256
Cdd:cd18040     2 LNPSQNHAVRTALT-KPFTLIQGPPGTGKTVTGVHIAYWFAKQnreiqsvsgegdgGPCVLYCGPSNKSVDVVAELLlKV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 257 CKKQILRL-GHPARLLE----SVQQHSLDAVLARSDNAQIVADI--RRDIDQvfGKNKKTQDKREksnFRNEIKLLRKEL 329
Cdd:cd18040    81 PGLKILRVySEQIETTEypipNEPRHPNKKSERESKPNSELSSItlHHRIRQ--PSNPHSQQIKA---FEARFERTQEKI 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 330 KEREE--------AAIVQSLSAADVVLATNTGASTDgplKLLPEDYFDVVVVDECAQALEASCWIPLLKAPKC---ILAG 398
Cdd:cd18040   156 TEEDIktykiliwEARFEELETVDVILCTCSEAASQ---KMRTHANVKQCIVDECGMCTEPESLIPIVSAPRAeqvVLIG 232

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 1937369939 399 DHKQLPPTTVSHKAALAGLSRSLMERLAEKhgaavVRMLAVQYR 442
Cdd:cd18040   233 DHKQLRPVVQNKEAQKLGLGRSLFERYAEK-----ACMLDTQYR 271
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 190-441 9.20e-21

EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that represses class II MHC (major histocompatibility complex) gene expression. NFX1 binds a conserved cis-acting element, termed the X-box, in promoters of human class II MHC genes. The Cys-rich region contains several NFX1-type zinc finger domains. Frequently, a R3H domain is present in the C-terminus, and a RING finger domain and a PAM2 motif are present in the N-terminus. The lack of R3H and PAM2 motifs in the plant proteins indicates functional differences. Plant NFX1-like proteins are proposed to modulate growth and survival by coordinating reactive oxygen species, salicylic acid, further biotic stress and abscisic acid responses. A common feature of all members may be E3 ubiquitin ligase, due to the presence of a RING finger domain, as well as DNA binding. NFX1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350694 [Multi-domain]  Cd Length: 178  Bit Score: 90.68  E-value: 9.20e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 190 TLDPSQKEAVSFALaQKEVAIIHGPPGTGKTTT---VVEIILQAVKQGLK--VLCCAPSNIAVDNLVER-LALCKKQILR 263
Cdd:cd17936     1 TLDPSQLEALKHAL-TSELALIQGPPGTGKTFLgvkLVRALLQNQDLSITgpILVVCYTNHALDQFLEGlLDFGPTKIVR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 264 LGhparllesvqqhsldavlarsdnaqivadirrdidqvfgknkktqdkreksnfrneikllrkelkereeaaivqslsa 343
Cdd:cd17936    80 LG------------------------------------------------------------------------------ 81

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 344 ADVVLATNTGASTDGPL--KLLPEdyfdVVVVDECAQALEA---SCWIPLLKapKCILAGDHKQLPPTTVSHKAALAG-- 416
Cdd:cd17936    82 ARVIGMTTTGAAKYRELlqALGPK----VVIVEEAAEVLEAhilAALTPSTE--HLILIGDHKQLRPKVNVYELTAKKyn 155

                         250       260
                  ....*....|....*....|....*
gi 1937369939 417 LSRSLMERLAEKhGAAVVrMLAVQY 441
Cdd:cd17936   156 LDVSLFERLVKN-GLPFV-TLNVQR 178
R3H smart00393
Putative single-stranded nucleic acids-binding domain;
707-783 9.94e-17

Putative single-stranded nucleic acids-binding domain;


Pssm-ID: 214647  Cd Length: 79  Bit Score: 75.80  E-value: 9.94e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1937369939  707 QHSSKANGSDRTGGTDRTEHFRAMIEEFVASKEAQLEFPTsLSSHDRLRVHQLAEEFGLKHDSTGEGKARHITVSRR 783
Cdd:smart00393   4 LPVTLDALSYRPRRREELIELELEIARFVKSTKESVELPP-MNSYERKIVHELAEKYGLESESFGEGPKRRVVISKK 79
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 188-427 1.40e-13

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


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 74.63  E-value: 1.40e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 188 NTTLDPSQKEAVSFALAQKEVAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNLVErlalckkqilRLGHP 267
Cdd:COG0507   122 GITLSDEQREAVALALTTRRVSVLTGGAGTGKTTTLRALLAALEALGLRVALAAPTGKAAKRLSE----------STGIE 191

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 268 ARLLesvqqHSLdavlarsdnaqivadirrdidqvFGKNKKTQDKReksnfRNEIKLLRKelkereeaaivqslsaadvv 347
Cdd:COG0507   192 ARTI-----HRL-----------------------LGLRPDSGRFR-----HNRDNPLTP-------------------- 218

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 348 latntgastdgplkllpedyFDVVVVDEC--------AQALEAscwiplLKAPKC--ILAGDHKQLPPttVSHKAALAGL 417
Cdd:COG0507   219 --------------------ADLLVVDEAsmvdtrlmAALLEA------LPRAGArlILVGDPDQLPS--VGAGAVLRDL 270

                         250
                  ....*....|
gi 1937369939 418 SRSLMERLAE 427
Cdd:COG0507   271 IESGTVPVVE 280
R3H cd02325
R3H domain. The name of the R3H domain comes from the characteristic spacing of the most ...
 725-782 1.06e-11

R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100064  Cd Length: 59  Bit Score: 60.71  E-value: 1.06e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1937369939 725 EHFRAMIEEFVASKEAQ-LEFPtSLSSHDRLRVHQLAEEFGLKHDSTGEGKARHITVSR 782
Cdd:cd02325     2 EEREEELEAFAKDAAGKsLELP-PMNSYERKLIHDLAEYYGLKSESEGEGPNRRVVITK 59
ZnF_AN1 smart00154
AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in ...
 890-930 1.83e-11

AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.


Pssm-ID: 197545  Cd Length: 39  Bit Score: 59.33  E-value: 1.83e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1937369939  890 CSFtkCSASTTTLGQFCMHCSRRYCLSHHLPEIHGCGEKAR 930
Cdd:smart00154   1 CHF--CRKKVGLTGFKCRHCGNLFCGEHRLPEDHDCPGDYK 39
DEXXQc_HELZ cd18077
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ...
 190-427 1.95e-11

DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. HELZ is a member of the family I class of RNA helicases of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350835 [Multi-domain]  Cd Length: 226  Bit Score: 64.81  E-value: 1.95e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 190 TLDPSQKEAVSFALAQKEVAI----IHGPPGTGKTTTVVEIILQAVKQ-GLKVLCCAPSNIAVDnlverlaLCKKQILrl 264
Cdd:cd18077     1 RLNAKQKEAVLAITTPLSIQLppvlLIGPFGTGKTFTLAQAVKHILQQpETRILICTHSNSAAD-------LYIKEYL-- 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 265 gHParlleSVQQHSLDAVLARsdnaqiVADIRRDIDQVFGKNKKTQDKREKSNFRNEIKllrkelkereeaaivQSLSAA 344
Cdd:cd18077    72 -HP-----YVETGNPRARPLR------VYYRNRWVKTVHPVVQKYCLIDEHGTFRMPTR---------------EDVMRH 124

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 345 DVVLATNTGASTDGPLKLLPeDYFDVVVVDECAQALEASCWIPLLKAPK---CILAGDHKQLPPTTVSHKAALAGLSRSL 421
Cdd:cd18077   125 RVVVVTLSTSQYLCQLDLEP-GFFTHILLDEAAQAMECEAIMPLALATKstrIVLAGDHMQLSPEVYSEFARERNLHISL 203


                  ....*.
gi 1937369939 422 MERLAE 427
Cdd:cd18077   204 LERLYE 209
R3H pfam01424
R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most ...
 731-782 4.59e-11

R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA.


Pssm-ID: 460206  Cd Length: 60  Bit Score: 59.04  E-value: 4.59e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1937369939 731 IEEFVASKEAQLEFPtSLSSHDRLRVHQLAEEFGLKHDSTGEGKARHITVSR 782
Cdd:pfam01424  10 LAEFVKDTGKSLELP-PMSSYERRIIHELAQKYGLESESEGEEPNRRVVVYK 60
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 192-405 2.38e-10

DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. This is central to many aspects of cellular DNA and RNA metabolism and accordingly, they are implicated in a wide range of nucleic acid processing events including DNA replication, recombination, and repair as well as many aspects of RNA metabolism. Superfamily 1 helicases are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350801 [Multi-domain]  Cd Length: 127  Bit Score: 59.13  E-value: 2.38e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 192 DPSQKEAVSFALAQKEVaIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDnlverlalckkqilrlghparll 271
Cdd:cd18043     1 DSSQEAAIISARNGKNV-VIQGPPGTGKSQTIANIIANALARGKRVLFVSEKKAALD----------------------- 56

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 272 esvqqhsldaVLARSdnaqivadirrdidqvfgknkktqdkreksnfrneikllrkelkereeAAIVQSLSAADVVLATN 351
Cdd:cd18043    57 ----------VVRFP------------------------------------------------CWIMSPLSVSQYLPLNR 78

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1937369939 352 tgastdgplkllpeDYFDVVVVDECAQALEASCwIPLL-KAPKCILAGDHKQLPP 405
Cdd:cd18043    79 --------------NLFDLVIFDEASQIPIEEA-LPALfRGKQVVVVGDDKQLPP 118
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 195-252 1.17e-09

DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350691 [Multi-domain]  Cd Length: 155  Bit Score: 57.95  E-value: 1.17e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1937369939 195 QKEAVSFALAQKeVAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNLVE 252
Cdd:cd17933     2 QKAAVRLVLRNR-VSVLTGGAGTGKTTTLKALLAALEAEGKRVVLAAPTGKAAKRLSE 58
DEXDc smart00487
DEAD-like helicases superfamily;
186-255 1.43e-09

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 58.66  E-value: 1.43e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1937369939  186 FYNTTLDPSQKEAVSFALAQKEVAIIHGPPGTGKTTTVVEIILQAVKQGL--KVLCCAPSNIAVDNLVERLA 255
Cdd:smart00487   4 FGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKggRVLVLVPTRELAEQWAEELK 75
AAA_19 pfam13245
AAA domain;
195-264 1.45e-09

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 57.23  E-value: 1.45e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1937369939 195 QKEAVSFALAQKeVAIIHGPPGTGKTTTVVEIILQAVKQG---LKVLCCAPSNIAVDNLVERLALCKKQILRL 264
Cdd:pfam13245   1 QREAVRTALPSK-VVLLTGGPGTGKTTTIRHIVALLVALGgvsFPILLAAPTGRAAKRLSERTGLPASTIHRL 72
EEXXQc_AQR cd17935
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ...
 188-449 1.92e-09

EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds precursor-mRNA introns at a defined position and is part of a pentameric intron-binding complex (IBC). It is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350693 [Multi-domain]  Cd Length: 207  Bit Score: 58.59  E-value: 1.92e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 188 NTTLDPSQKEAVSFALaQKEVAIIHGPPGTGKTTTVVEII--LQAVKQGLKVLCCAPSNIAVDNLVERLA---LCKKQIL 262
Cdd:cd17935     3 TVKFTPTQIEAIRSGM-QPGLTMVVGPPGTGKTDVAVQIIsnLYHNFPNQRTLIVTHSNQALNQLFEKIMaldIDERHLL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 263 RLGHPARLLESVQQHsldAVLARSDnaqivadirrdidqvfgknkktqdkreksnfrneikLLRKELKereeaaivqsls 342
Cdd:cd17935    82 RLGHGAKIIAMTCTH---AALKRGE------------------------------------LVELGFK------------ 110

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 343 aadvvlatntgastdgplkllpedyFDVVVVDECAQALEASCWIPL-LKAPKC--------ILAGDHKQLPPttVSHKAA 413
Cdd:cd17935   111 -------------------------YDNILMEEAAQILEIETFIPLlLQNPEDgpnrlkrlIMIGDHHQLPP--VIKNMA 163

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1937369939 414 LAGLS---RSLMERLAeKHGAAVVRmLAVQYRMHQAITR 449
Cdd:cd17935   164 FQKYSnmeQSLFTRLV-RLGVPTVD-LDAQGRARASISS 200
R3H_DEXH_helicase cd06007
R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may ...
 730-782 2.20e-09

R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100077  Cd Length: 59  Bit Score: 54.24  E-value: 2.20e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1937369939 730 MIEEFVASKEAQLEFPTSLSSHDRLRVHQLAEEFGLKHDSTGEGKARHITVSR 782
Cdd:cd06007     7 ALEDFRASDNEEYEFPSSLTNHERAVIHRLCRKLGLKSKSKGKGSNRRLSVYK 59
zf-AN1 pfam01428
AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in ...
 890-927 5.26e-09

AN1-like Zinc finger; Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis. The following pattern describes the zinc finger. C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C Where X can be any amino acid, and numbers in brackets indicate the number of residues.


Pssm-ID: 460208  Cd Length: 37  Bit Score: 52.31  E-value: 5.26e-09
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1937369939 890 CSFTKCSASTTTLGQfCMHCSRRYCLSHHLPEIHGCGE 927
Cdd:pfam01428   1 CSFKGCKKKDFLPFK-CRFCGKNFCLKHRLPEDHDCSG 37
R3H_G-patch cd02646
R3H domain of a group of fungal and plant proteins with unknown function, who also contain a ...
 731-782 1.53e-08

R3H domain of a group of fungal and plant proteins with unknown function, who also contain a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the R3H domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100075  Cd Length: 58  Bit Score: 51.80  E-value: 1.53e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1937369939 731 IEEFVASKEAQLEFPTsLSSHDRLRVHQLAEEFGLKHDSTGEGKARHITVSR 782
Cdd:cd02646     8 IEAFLLDSRDSLSFPP-MDKHGRKTIHKLANCYNLKSKSRGKGKKRFVTVTK 58
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 533-607 2.78e-08

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


Pssm-ID: 350173 [Multi-domain]  Cd Length: 89  Bit Score: 52.05  E-value: 2.78e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 533 DIAVIAPYNLQVDLLRQSLSNKH------PELEIKSVDGFQGREKEAVILTFVRSNrkgevgfLAEDRRINVAVTRARRH 606
Cdd:cd18786    12 KGVVLTPYHRDRAYLNQYLQGLSldefdlQLVGAITIDSSQGLTFDVVTLYLPTAN-------SLTPRRLYVALTRARKR 84


                  .
gi 1937369939 607 V 607
Cdd:cd18786    85 L 85
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 366-441 7.18e-08

DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. 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. SF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438706 [Multi-domain]  Cd Length: 121  Bit Score: 51.72  E-value: 7.18e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1937369939 366 DYFDVVVVDECAQALEASCWIPLLKAPKC---ILAGDHKQLPPTTVSHKAALAGLSRSLMERLAeKHGAAVVRmLAVQY 441
Cdd:cd17914    45 AQLDNILVDEAAQILEPETSRLIDLALDQgrvILVGDHDQLGPVWRGAVLAKICNEQSLFTRLV-RLGVSLIR-LQVQY 121
R3H_NRF cd02640
R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB ...
 728-782 8.22e-08

R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB proteins that can silence the IFNbeta promoter via binding to a negative regulatory element (NRE). Beside R3H NRF also contains a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100069  Cd Length: 60  Bit Score: 49.70  E-value: 8.22e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1937369939 728 RAMIEEFVASKEAQ-LEFPTSLSSHDRLRVHQLAEEFGLKHDSTGEGKARHITVSR 782
Cdd:cd02640     5 RQIIQNYAHSDDIRdMVFSPEFSKEERALIHQIAQKYGLKSRSYGSGNDRYLVISK 60
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 190-256 2.88e-07

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.


Pssm-ID: 433343 [Multi-domain]  Cd Length: 191  Bit Score: 51.80  E-value: 2.88e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1937369939 190 TLDPSQKEAVSFALA-QKEVAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNLVERLAL 256
Cdd:pfam13604   1 TLNAEQAAAVRALLTsGDRVAVLVGPAGTGKTTALKALREAWEAAGYRVIGLAPTGRAAKVLGEELGI 68
DEXXQc_HELZ2-N cd18076
N-terminal DEXXQ-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 195-433 1.09e-06

N-terminal DEXXQ-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known as PPAR-alpha-interacting complex protein 285 or PRIC285 and PPAR-gamma DBD-interacting protein 1 or PDIP1) acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB, and RXRA. It belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350834 [Multi-domain]  Cd Length: 230  Bit Score: 50.66  E-value: 1.09e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 195 QKEAVSFALAQ----KEVA--IIHGPPGTGKTTTVVEIILQAVKQ-GLKVLCCAPSNIAVDNLVERLAlckKQILRLGHP 267
Cdd:cd18076     6 QQLAFNFIAGKpseaRFVPplLIYGPFGTGKTFTLAMAALEVIREpGTKVLICTHTNSAADIYIREYF---HPYVDKGHP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 268 ArlLESVQQHSLDAVLARSDNAQIVADIRRDIDQVFgknkktqdkreksnfrneikllrkELKEREEaaivqsLSAADVV 347
Cdd:cd18076    83 E--ARPLRIKATDRPNAITDPDTITYCCLTKDRQCF------------------------RLPTRDE------LDFHNIV 130

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 348 LATNTGASTdgpLKLLPeDYFDVVVVDECAQALEASCWIPLLKA---PKCILAGDHKQLPPTTVSHKAALAGlSRSLMER 424
Cdd:cd18076   131 ITTTAMAFN---LHVLS-GFFTHIFIDEAAQMLECEALIPLSYAgpkTRVVLAGDHMQMTPKLFSVADYNRA-NHTLLNR 205

                         250
                  ....*....|....
gi 1937369939 425 L-----AEKHGAAV 433
Cdd:cd18076   206 LfhyyqGEKHEVAV 219
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 209-250 1.49e-05

DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. 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. SF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438706 [Multi-domain]  Cd Length: 121  Bit Score: 45.17  E-value: 1.49e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1937369939 209 AIIHGPPGTGKTTTVVEIIL----QAVKQGLKVLCCAPSNIAVDNL 250
Cdd:cd17914     2 SLIQGPPGTGKTRVLVKIVAalmqNKNGEPGRILLVTPTNKAAAQL 47
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 170-273 2.29e-05

exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273631 [Multi-domain]  Cd Length: 582  Bit Score: 48.22  E-value: 2.29e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 170 LGGSTPSPAtEIPPLTFYNTTLDPSQKEAVSFALA-QKEVAIIHGPPGTGKTTTVVEIIL----QAVKQG-LKVLCCAPS 243
Cdd:TIGR01447 123 LLEARKRTA-PSAILENLFPLLNEQNWRKTAVALAlKSNFSLITGGPGTGKTTTVARLLLalvkQSPKQGkLRIALAAPT 201

                          90       100       110
                  ....*....|....*....|....*....|
gi 1937369939 244 NIAVDNLVERLalcKKQILRLGHPARLLES 273
Cdd:TIGR01447 202 GKAAARLAESL---RKAVKNLAAAEALIAA 228
SF1_C_UvrD cd18807
C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase ...
 513-611 4.92e-05

C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. This family also includes ATP-dependent helicase/nuclease AddA and helicase/nuclease RecBCD subunit RecB, among others. UvrD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350194 [Multi-domain]  Cd Length: 150  Bit Score: 44.53  E-value: 4.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 513 EVRLVTLHIQALVDAG-VQAGDIAVIAPYNLQVDLLRQSLsnkhpELEIKSVDGFQGREKEAVILTFVRSNRKGEVGF-- 589
Cdd:cd18807    45 EAKAIADEIKRLIESGpVQYSDIAILVRTNRQARVIEEAL-----RVTLMTIHASKGLEFPVVFIVGLGEGFIPSDASyh 119

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1937369939 590 --------LAEDRRI-NVAVTRARRHVAVIC 611
Cdd:cd18807   120 aakedeerLEEERRLlYVALTRAKKELYLVG 150
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 206-254 1.82e-04

DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350689 [Multi-domain]  Cd Length: 151  Bit Score: 42.92  E-value: 1.82e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1937369939 206 KEVAIIHGPPGTGKTTTVV-EIILQAVKQGLKVLCCAPSNIAVDNLVERL 254
Cdd:cd17931     1 GQLTVLDLHPGAGKTTRVLpQIIREAIKKRLRTLVLAPTRVVAAEMYEAL 50
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 205-292 6.95e-04

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 41.20  E-value: 6.95e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939  205 QKEVAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNLVERLALCKKQILRLGHPARLLESVQQhsldavLA 284
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALA------LA 74


                   ....*...
gi 1937369939  285 RSDNAQIV 292
Cdd:smart00382  75 RKLKPDVL 82
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was ...
 203-260 7.49e-04

IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was built to hit full-length AAA+ ATPases of IS21 family IS (insertion sequence) elements.


Pssm-ID: 439516  Cd Length: 232  Bit Score: 42.07  E-value: 7.49e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1937369939 203 LAQKEVAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCcapsnIAVDNLVERLALCKKQ 260
Cdd:NF038214   87 IERAENVLLLGPPGTGKTHLAIALGYAACRQGYRVRF-----TTAADLVEQLAQARAD 139
R3H_encore_like cd02642
R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the ...
 731-783 1.36e-03

R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H domain is a potential regulator of DBF1 activity in stress responses. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100071  Cd Length: 63  Bit Score: 37.97  E-value: 1.36e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1937369939 731 IEEFVASKEAQ-LEFPtSLSSHDRLRVHQLAEEFGLKHDSTGEGKaRHITVSRR 783
Cdd:cd02642    12 LLAFIKDSTRQsLELP-PMNSYYRLLAHRVAQYYGLDHNVDNSGG-KCVIVNKT 63
DnaC COG1484
DNA replication protein DnaC [Replication, recombination and repair];
203-260 1.39e-03

DNA replication protein DnaC [Replication, recombination and repair];


Pssm-ID: 441093 [Multi-domain]  Cd Length: 242  Bit Score: 41.30  E-value: 1.39e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1937369939 203 LAQKEVAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCcapsnIAVDNLVERLALCKKQ 260
Cdd:COG1484    96 IERGENLILLGPPGTGKTHLAIALGHEACRAGYRVRF-----TTAPDLVNELKEARAD 148
DEXQc_UvrD cd17932
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ...
 192-255 1.97e-03

DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. UvrD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350690 [Multi-domain]  Cd Length: 189  Bit Score: 40.58  E-value: 1.97e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1937369939 192 DPSQKEAVSfaLAQKEVAIIHGPpGTGKTTTVVEIILQAVKQGlkvlCCAPSNI--------AVDNLVERLA 255
Cdd:cd17932     1 NPEQREAVT--HPDGPLLVLAGA-GSGKTRVLTHRIAYLILEG----GVPPERIlavtftnkAAKEMRERLR 65
DEXHc_RHA-like cd17917
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ...
 207-255 2.33e-03

DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438707 [Multi-domain]  Cd Length: 159  Bit Score: 39.75  E-value: 2.33e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1937369939 207 EVAIIHGPPGTGKTTTVVEIILQA---VKQGLKVLCCAPSNIAVDNLVERLA 255
Cdd:cd17917     2 QVVVIVGETGSGKTTQVPQFLLEDglaKGGKGRIVCTQPRRIAAISVAERVA 53
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 202-255 3.09e-03

DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA two-partner secretion (TPS) system, a secretion pathway important to the secretion of large virulence-associated proteins. HrpB belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438711 [Multi-domain]  Cd Length: 174  Bit Score: 39.62  E-value: 3.09e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1937369939 202 ALAQKEVAIIHGPPGTGKTTTVVEIILQAV-KQGLKVLCCAPSNIAVDNLVERLA 255
Cdd:cd17990    13 ALDAGGQVVLEAPPGAGKTTRVPLALLAELwIAGGKIIVLEPRRVAARAAARRLA 67
UvrD COG0210
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
191-551 6.20e-03

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


Pssm-ID: 439980 [Multi-domain]  Cd Length: 721  Bit Score: 40.30  E-value: 6.20e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 191 LDPSQKEAVSFalaqkevaiIHGP------PGTGKTTTVVEIILQAVKQGL----KVLCCAPSNIAVDNLVERLAlckkq 260
Cdd:COG0210     7 LNPEQRAAVEH---------PEGPllvlagAGSGKTRVLTHRIAYLIAEGGvdpeQILAVTFTNKAAREMRERIE----- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 261 iLRLGHPARLLES----------VQQHSLDA-------VLARSDNAQIVADIRRDIDQvfgknkkTQDKREKSNFRNEIK 323
Cdd:COG0210    73 -ALLGRLARGLWVgtfhslalriLRRHAELLglppnftILDGDDQLRLIKELLKELGL-------DEKRFPPRELLSLIS 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 324 LLRKEL-------------KEREEAAIV-----------QSLSAADVVLATNTGASTDGPLKLLPEDYFDVVVVDEC--- 376
Cdd:COG0210   145 RAKNEGltpeelaellaadPEWRAAAELyeayqerlranNALDFDDLLLLAVRLLEENPEVLEKYQNRFRYILVDEYqdt 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 377 --AQALeascwipLLKApkciLAGDHKQL-----------------PpttvshkaalaglsrSLMERLAEKHGAAVVRML 437
Cdd:COG0210   225 npAQYE-------LLRL----LAGDGRNLcvvgdddqsiygfrgadP---------------ENILRFEKDFPDAKVIKL 278

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 438 AVQYRMHQAITRWASeamyhgQLTAHpsVAGHLLKDLpgVADTEETSVPLllidtagcgLLELEEEDSqskgnpgEVRLV 517
Cdd:COG0210   279 EQNYRSTQNILDAAN------AVIAN--NPGRLGKNL--WTDNGEGEKVR---------LYVAPDEEE-------EARFV 332

                         410       420       430
                  ....*....|....*....|....*....|....
gi 1937369939 518 TLHIQALVDAGVQAGDIAVIAPYNLQVDLLRQSL 551
Cdd:COG0210   333 ADEIRELHEEGVPLSDIAVLYRTNAQSRALEEAL 366
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
210-373 7.33e-03

RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 39.13  E-value: 7.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 210 IIHGPPGTGKTTTVVEIILQAVKQGLKVLCcapsnIAVDNLVERLalcKKQILRLGHP-ARLLES--VQQHSLDAVLARS 286
Cdd:COG0467    24 LLSGPPGTGKTTLALQFLAEGLRRGEKGLY-----VSFEESPEQL---LRRAESLGLDlEEYIESglLRIIDLSPEELGL 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1937369939 287 DNAQIVADIRRDIDqvfgknkKTQDKR--------------EKSNFRNEIKLLRKELKEREeaaivqslsaaDVVLATNT 352
Cdd:COG0467    96 DLEELLARLREAVE-------EFGAKRvvidslsglllalpDPERLREFLHRLLRYLKKRG-----------VTTLLTSE 157

                         170       180
                  ....*....|....*....|..
gi 1937369939 353 GASTDGPLKLLPEDY-FDVVVV 373
Cdd:COG0467   158 TGGLEDEATEGGLSYlADGVIL 179
DEXHc_DHX16 cd17974
DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably ...
 196-266 9.32e-03

DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably involved in pre-mRNA splicing. DHX16 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350732 [Multi-domain]  Cd Length: 174  Bit Score: 38.25  E-value: 9.32e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1937369939 196 KEAVSFALAQKEVAIIHGPPGTGKTTTVVEIILQA--VKQGLKVLCCAPSNIAVDNLVERLAlcKKQILRLGH 266
Cdd:cd17974     7 RDDLLAAVKEHQVLIIVGETGSGKTTQIPQYLHEAgyTKGGGKIGCTQPRRVAAMSVAARVA--EEMGVKLGN 77
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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