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Conserved domains on  [gi|116268057|ref|NP_001070800|]
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probable ATP-dependent RNA helicase DDX28 [Danio rerio]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 13028675)

DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA; such as Bacillus cereus ATP-dependent RNA helicase DbpA that is involved in the assembly of the 50S ribosomal subunit

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEADc_DDX28 cd17948
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box ...
 162-390 5.05e-110

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: 327.79  E-value: 5.05e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 162 LVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLL--AGSERSIRAVVIVPSRELAEQ 239
Cdd:cd17948    1 LVEILQRQGITKPTTVQKQGIPSILRGRNTLCAAETGSGKTLTYLLPIIQRLLRYKLlaEGPFNAPRGLVITPSRELAEQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 240 VNSVARSVSERFGLVVKVVGGGRGVGTIKaAFARGQPDILVSTPGALLKALWKRFISLSELYFLVIDEADTMFDDSFAGM 319
Cdd:cd17948   81 IGSVAQSLTEGLGLKVKVITGGRTKRQIR-NPHFEEVDILVATPGALSKLLTSRIYSLEQLRHLVLDEADTLLDDSFNEK 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 116268057 320 LEKILSHTQVASRLSE-TIGLARKAQLVVVGATFPGGVGDVLSKATDLASISTVKSRMLHHLMPHIKQTFLR 390
Cdd:cd17948  160 LSHFLRRFPLASRRSEnTDGLDPGTQLVLVSATMPSGVGEVLSKVIDVDSIETVTSDKLHRLMPHVKQKFLR 231
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 384-517 2.91e-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: 155.74  E-value: 2.91e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 384 IKQTFLRVKGADKILELHQALKRAEQEQKgVLVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQRGKTN 463
Cdd:cd18787    1 IKQLYVVVEEEEKKLLLLLLLLEKLKPGK-AIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKVR 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 116268057 464 VLVCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAGgsEGGEVLSFV 517
Cdd:cd18787   80 VLVATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAG--RKGTAITFV 131
 
Name Accession Description Interval E-value
DEADc_DDX28 cd17948
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box ...
 162-390 5.05e-110

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: 327.79  E-value: 5.05e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 162 LVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLL--AGSERSIRAVVIVPSRELAEQ 239
Cdd:cd17948    1 LVEILQRQGITKPTTVQKQGIPSILRGRNTLCAAETGSGKTLTYLLPIIQRLLRYKLlaEGPFNAPRGLVITPSRELAEQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 240 VNSVARSVSERFGLVVKVVGGGRGVGTIKaAFARGQPDILVSTPGALLKALWKRFISLSELYFLVIDEADTMFDDSFAGM 319
Cdd:cd17948   81 IGSVAQSLTEGLGLKVKVITGGRTKRQIR-NPHFEEVDILVATPGALSKLLTSRIYSLEQLRHLVLDEADTLLDDSFNEK 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 116268057 320 LEKILSHTQVASRLSE-TIGLARKAQLVVVGATFPGGVGDVLSKATDLASISTVKSRMLHHLMPHIKQTFLR 390
Cdd:cd17948  160 LSHFLRRFPLASRRSEnTDGLDPGTQLVLVSATMPSGVGEVLSKVIDVDSIETVTSDKLHRLMPHVKQKFLR 231
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
152-556 4.66e-91

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 285.89  E-value: 4.66e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 152 TFHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLqedlLAGSERSIRAVVIV 231
Cdd:COG0513    3 SFADLGLSPPLLKALAELGYTTPTPIQAQAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQRL----DPSRPRAPQALILA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 232 PSRELAEQVNSVARSVSErfglvvkvvGGGRGVGTI---------KAAFARGqPDILVSTPGALLKALWKRFISLSELYF 302
Cdd:COG0513   79 PTRELALQVAEELRKLAK---------YLGLRVATVyggvsigrqIRALKRG-VDIVVATPGRLLDLIERGALDLSGVET 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 303 LVIDEADTMFDDSFAGMLEKILSHTqvasrlsetiglARKAQLVVVGATFPGGVGDVLSK-ATDLASISTVKSRMLHhlm 381
Cdd:COG0513  149 LVLDEADRMLDMGFIEDIERILKLL------------PKERQTLLFSATMPPEIRKLAKRyLKNPVRIEVAPENATA--- 213

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 382 PHIKQTFLRVKGADKILELHQALKRAEQEQkgVLVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQRGK 461
Cdd:COG0513  214 ETIEQRYYLVDKRDKLELLRRLLRDEDPER--AIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGQRERALDAFRNGK 291

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 462 TNVLVCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAGGSegGEVLSFVTqPWDVELVQKIETAARR---RTS 538
Cdd:COG0513  292 IRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYVHRIGRTGRAGAE--GTAISLVT-PDERRLLRAIEKLIGQkieEEE 368

                        410
                 ....*....|....*...
gi 116268057 539 LPGMETDIQKPSQTTDAK 556
Cdd:COG0513  369 LPGFEPVEEKRLERLKPK 386
PTZ00110 PTZ00110
helicase; Provisional
 162-518 9.68e-47

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 171.88  E-value: 9.68e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 162 LVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLP-IIHRLQEDLLAGSERSIrAVVIVPSRELAEQV 240
Cdd:PTZ00110 141 ILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPaIVHINAQPLLRYGDGPI-VLVLAPTRELAEQI 219

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 241 NSVARSVSERFGLVVKVVGGGRGVGTIKAAFARGQpDILVSTPGALLKALWKRFISLSELYFLVIDEADTMFDDSFAGML 320
Cdd:PTZ00110 220 REQCNKFGASSKIRNTVAYGGVPKRGQIYALRRGV-EILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGFEPQI 298

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 321 EKILSHtqvasrlsetIGLARkaQLVVVGATFPGgvgDVLSKATDLAS-------ISTVKSRMLHHlmphIKQTFLRVKG 393
Cdd:PTZ00110 299 RKIVSQ----------IRPDR--QTLMWSATWPK---EVQSLARDLCKeepvhvnVGSLDLTACHN----IKQEVFVVEE 359

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 394 ADKILELHQALKRAEQEQKGVLVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQRGKTNVLVCTDIASR 473
Cdd:PTZ00110 360 HEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASR 439

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*
gi 116268057 474 GLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAGGSegGEVLSFVT 518
Cdd:PTZ00110 440 GLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAK--GASYTFLT 482
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 384-517 2.91e-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: 155.74  E-value: 2.91e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 384 IKQTFLRVKGADKILELHQALKRAEQEQKgVLVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQRGKTN 463
Cdd:cd18787    1 IKQLYVVVEEEEKKLLLLLLLLEKLKPGK-AIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKVR 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 116268057 464 VLVCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAGgsEGGEVLSFV 517
Cdd:cd18787   80 VLVATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAG--RKGTAITFV 131
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 175-359 2.12e-34

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 127.74  E-value: 2.12e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057  175 TTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLlagseRSIRAVVIVPSRELAEQvnsVARSVSERFGLV 254
Cdd:pfam00270   1 TPIQAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALEALDKLD-----NGPQALVLAPTRELAEQ---IYEELKKLGKGL 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057  255 VKVVGGGRGVGTIKAAFAR-GQPDILVSTPGALLKALWKRFiSLSELYFLVIDEADTMFDDSFAGMLEKILSHtqvasrl 333
Cdd:pfam00270  73 GLKVASLLGGDSRKEQLEKlKGPDILVGTPGRLLDLLQERK-LLKNLKLLVLDEAHRLLDMGFGPDLEEILRR------- 144

                         170       180
                  ....*....|....*....|....*.
gi 116268057  334 setigLARKAQLVVVGATFPGGVGDV 359
Cdd:pfam00270 145 -----LPKKRQILLLSATLPRNLEDL 165
DEXDc smart00487
DEAD-like helicases superfamily;
166-356 4.23e-32

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 122.60  E-value: 4.23e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057   166 LQRQNIIHPTTVQLQTIPKILKG-RNILCAAETGSGKTLTYLLPIIHRLQEdllagsERSIRAVVIVPSRELAEQVNSVA 244
Cdd:smart00487   1 IEKFGFEPLRPYQKEAIEALLSGlRDVILAAPTGSGKTLAALLPALEALKR------GKGGRVLVLVPTRELAEQWAEEL 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057   245 RSVSERFGLVVKVVGGGRGVGTIKAAFARGQPDILVSTPGALLKALWKRFISLSELYFLVIDEADTMFDDSFAGMLEKIL 324
Cdd:smart00487  75 KKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLL 154

                          170       180       190
                   ....*....|....*....|....*....|..
gi 116268057   325 SHtqvasrlsetigLARKAQLVVVGATFPGGV 356
Cdd:smart00487 155 KL------------LPKNVQLLLLSATPPEEI 174
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 395-506 1.12e-28

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


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 109.61  E-value: 1.12e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057  395 DKILELHQALKRAEQEQkgVLVFCNSASTVNwLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQRGKTNVLVCTDIASRG 474
Cdd:pfam00271   1 EKLEALLELLKKERGGK--VLIFSQTKKTLE-AELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERG 77

                          90       100       110
                  ....*....|....*....|....*....|..
gi 116268057  475 LDTQRVGLIVNYDFPESQTDYIHRAGRVGRAG 506
Cdd:pfam00271  78 LDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
HELICc smart00490
helicase superfamily c-terminal domain;
431-506 2.73e-23

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 93.82  E-value: 2.73e-23
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 116268057   431 LEEMGVGHMRLQGEMPAAMREGVFRDFQRGKTNVLVCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAG 506
Cdd:smart00490   7 LKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 396-500 9.20e-11

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 64.48  E-value: 9.20e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 396 KILELHQALKRAEQEQKGVLVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQRGKTN--VLVCTDIASR 473
Cdd:COG0553  534 KLEALLELLEELLAEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQEGPEApvFLISLKAGGE 613

                         90       100       110
                 ....*....|....*....|....*....|...
gi 116268057 474 GLDTQRVGLIVNYDFP-----ESQ-TDYIHRAG 500
Cdd:COG0553  614 GLNLTAADHVIHYDLWwnpavEEQaIDRAHRIG 646
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 382-506 5.54e-04

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 42.78  E-value: 5.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 382 PHIKQTFLrvkgaDKILELHQaLKRAEQEQKGV--LVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQR 459
Cdd:PRK11057 211 PNIRYTLV-----EKFKPLDQ-LMRYVQEQRGKsgIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQR 284

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 116268057 460 GKTNVLVCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAG 506
Cdd:PRK11057 285 DDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDG 331
 
Name Accession Description Interval E-value
DEADc_DDX28 cd17948
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box ...
 162-390 5.05e-110

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: 327.79  E-value: 5.05e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 162 LVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLL--AGSERSIRAVVIVPSRELAEQ 239
Cdd:cd17948    1 LVEILQRQGITKPTTVQKQGIPSILRGRNTLCAAETGSGKTLTYLLPIIQRLLRYKLlaEGPFNAPRGLVITPSRELAEQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 240 VNSVARSVSERFGLVVKVVGGGRGVGTIKaAFARGQPDILVSTPGALLKALWKRFISLSELYFLVIDEADTMFDDSFAGM 319
Cdd:cd17948   81 IGSVAQSLTEGLGLKVKVITGGRTKRQIR-NPHFEEVDILVATPGALSKLLTSRIYSLEQLRHLVLDEADTLLDDSFNEK 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 116268057 320 LEKILSHTQVASRLSE-TIGLARKAQLVVVGATFPGGVGDVLSKATDLASISTVKSRMLHHLMPHIKQTFLR 390
Cdd:cd17948  160 LSHFLRRFPLASRRSEnTDGLDPGTQLVLVSATMPSGVGEVLSKVIDVDSIETVTSDKLHRLMPHVKQKFLR 231
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
152-556 4.66e-91

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 285.89  E-value: 4.66e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 152 TFHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLqedlLAGSERSIRAVVIV 231
Cdd:COG0513    3 SFADLGLSPPLLKALAELGYTTPTPIQAQAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQRL----DPSRPRAPQALILA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 232 PSRELAEQVNSVARSVSErfglvvkvvGGGRGVGTI---------KAAFARGqPDILVSTPGALLKALWKRFISLSELYF 302
Cdd:COG0513   79 PTRELALQVAEELRKLAK---------YLGLRVATVyggvsigrqIRALKRG-VDIVVATPGRLLDLIERGALDLSGVET 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 303 LVIDEADTMFDDSFAGMLEKILSHTqvasrlsetiglARKAQLVVVGATFPGGVGDVLSK-ATDLASISTVKSRMLHhlm 381
Cdd:COG0513  149 LVLDEADRMLDMGFIEDIERILKLL------------PKERQTLLFSATMPPEIRKLAKRyLKNPVRIEVAPENATA--- 213

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 382 PHIKQTFLRVKGADKILELHQALKRAEQEQkgVLVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQRGK 461
Cdd:COG0513  214 ETIEQRYYLVDKRDKLELLRRLLRDEDPER--AIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGQRERALDAFRNGK 291

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 462 TNVLVCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAGGSegGEVLSFVTqPWDVELVQKIETAARR---RTS 538
Cdd:COG0513  292 IRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYVHRIGRTGRAGAE--GTAISLVT-PDERRLLRAIEKLIGQkieEEE 368

                        410
                 ....*....|....*...
gi 116268057 539 LPGMETDIQKPSQTTDAK 556
Cdd:COG0513  369 LPGFEPVEEKRLERLKPK 386
DEADc cd00268
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ...
 162-362 8.25e-55

DEAD-box helicase domain of 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. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350669 [Multi-domain]  Cd Length: 196  Bit Score: 183.41  E-value: 8.25e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 162 LVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDlLAGSERSIRAVVIVPSRELAEQVN 241
Cdd:cd00268    1 LLKALKKLGFEKPTPIQAQAIPLILSGRDVIGQAQTGSGKTLAFLLPILEKLLPE-PKKKGRGPQALVLAPTRELAMQIA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 242 SVARSVSERFGLVVKVVGGGRGVGTIKAAFARGqPDILVSTPGALLKALWKRFISLSELYFLVIDEADTMFDDSFAGMLE 321
Cdd:cd00268   80 EVARKLGKGTGLKVAAIYGGAPIKKQIEALKKG-PDIVVGTPGRLLDLIERGKLDLSNVKYLVLDEADRMLDMGFEEDVE 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 116268057 322 KILSHTQvasrlsetiglaRKAQLVVVGATFPGGVGDVLSK 362
Cdd:cd00268  159 KILSALP------------KDRQTLLFSATLPEEVKELAKK 187
PTZ00110 PTZ00110
helicase; Provisional
 162-518 9.68e-47

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 171.88  E-value: 9.68e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 162 LVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLP-IIHRLQEDLLAGSERSIrAVVIVPSRELAEQV 240
Cdd:PTZ00110 141 ILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPaIVHINAQPLLRYGDGPI-VLVLAPTRELAEQI 219

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 241 NSVARSVSERFGLVVKVVGGGRGVGTIKAAFARGQpDILVSTPGALLKALWKRFISLSELYFLVIDEADTMFDDSFAGML 320
Cdd:PTZ00110 220 REQCNKFGASSKIRNTVAYGGVPKRGQIYALRRGV-EILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGFEPQI 298

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 321 EKILSHtqvasrlsetIGLARkaQLVVVGATFPGgvgDVLSKATDLAS-------ISTVKSRMLHHlmphIKQTFLRVKG 393
Cdd:PTZ00110 299 RKIVSQ----------IRPDR--QTLMWSATWPK---EVQSLARDLCKeepvhvnVGSLDLTACHN----IKQEVFVVEE 359

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 394 ADKILELHQALKRAEQEQKGVLVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQRGKTNVLVCTDIASR 473
Cdd:PTZ00110 360 HEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASR 439

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*
gi 116268057 474 GLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAGGSegGEVLSFVT 518
Cdd:PTZ00110 440 GLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAK--GASYTFLT 482
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 151-530 1.29e-46

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 168.97  E-value: 1.29e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 151 KTFHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQeDLLAGSERSIRAVVI 230
Cdd:PRK11192   1 TTFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLL-DFPRRKSGPPRILIL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 231 VPSRELAEQVNSVARSVSERFGLVVKVVGGGRGVGTIKAAFARGQpDILVSTPGALLKALWKRFISLSELYFLVIDEADT 310
Cdd:PRK11192  80 TPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSENQ-DIVVATPGRLLQYIKEENFDCRAVETLILDEADR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 311 MFDDSFAGMLEKILSHTQvasrlsetiglARKaQLVVVGATFPG-GVGD----VLSKATDLASISTVKSRmlhhlmPHIK 385
Cdd:PRK11192 159 MLDMGFAQDIETIAAETR-----------WRK-QTLLFSATLEGdAVQDfaerLLNDPVEVEAEPSRRER------KKIH 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 386 QTFLRVKGADKILELHQALKRAEQEQKGVlVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQRGKTNVL 465
Cdd:PRK11192 221 QWYYRADDLEHKTALLCHLLKQPEVTRSI-VFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVL 299

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 116268057 466 VCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAGgsEGGEVLSFVtQPWDVELVQKIE 530
Cdd:PRK11192 300 VATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAG--RKGTAISLV-EAHDHLLLGKIE 361
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 384-517 2.91e-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: 155.74  E-value: 2.91e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 384 IKQTFLRVKGADKILELHQALKRAEQEQKgVLVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQRGKTN 463
Cdd:cd18787    1 IKQLYVVVEEEEKKLLLLLLLLEKLKPGK-AIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKVR 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 116268057 464 VLVCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAGgsEGGEVLSFV 517
Cdd:cd18787   80 VLVATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAG--RKGTAITFV 131
PRK10590 PRK10590
ATP-dependent RNA helicase RhlE; Provisional
 152-545 6.28e-44

ATP-dependent RNA helicase RhlE; Provisional


Pssm-ID: 236722 [Multi-domain]  Cd Length: 456  Bit Score: 162.28  E-value: 6.28e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 152 TFHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRL-QEDLLAGSERSIRAVVI 230
Cdd:PRK10590   2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLiTRQPHAKGRRPVRALIL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 231 VPSRELAEQVNSVARSVSeRFGLVVKVVGGGRGVGTIKAAFARGQPDILVSTPGALLKALWKRFISLSELYFLVIDEADT 310
Cdd:PRK10590  82 TPTRELAAQIGENVRDYS-KYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADR 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 311 MFDDSFAGMLEKILSHtqvasrlsetigLARKAQLVVVGATFpggvgdvlskaTDlaSISTVKSRMLHHlmPHIKQTFLR 390
Cdd:PRK10590 161 MLDMGFIHDIRRVLAK------------LPAKRQNLLFSATF-----------SD--DIKALAEKLLHN--PLEIEVARR 213

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 391 VKGADKILE-LHQALKRAEQE----------QKGVLVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQR 459
Cdd:PRK10590 214 NTASEQVTQhVHFVDKKRKREllsqmigkgnWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKS 293

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 460 GKTNVLVCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAGGSegGEVLSFVTQPwDVELVQKIETAARR---R 536
Cdd:PRK10590 294 GDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAAT--GEALSLVCVD-EHKLLRDIEKLLKKeipR 370


                 ....*....
gi 116268057 537 TSLPGMETD 545
Cdd:PRK10590 371 IAIPGYEPD 379
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 152-517 4.02e-43

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 163.10  E-value: 4.02e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 152 TFHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLlagseRSIRAVVIV 231
Cdd:PRK11634   7 TFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPEL-----KAPQILVLA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 232 PSRELAEQVNSVARSVSERFGLVVKVVGGGRGVGTIKAAFARGQPDILVSTPGALLKALWKRFISLSELYFLVIDEADTM 311
Cdd:PRK11634  82 PTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEM 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 312 FDDSFAGMLEKILSHtqvasrlsetigLARKAQLVVVGATFPGGVGDV----LSKATDLASISTVKSRmlhhlmPHIKQT 387
Cdd:PRK11634 162 LRMGFIEDVETIMAQ------------IPEGHQTALFSATMPEAIRRItrrfMKEPQEVRIQSSVTTR------PDISQS 223

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 388 FLRVKGADKilelHQALKR-AEQEQ-KGVLVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQRGKTNVL 465
Cdd:PRK11634 224 YWTVWGMRK----NEALVRfLEAEDfDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDIL 299

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|..
gi 116268057 466 VCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAGgsEGGEVLSFV 517
Cdd:PRK11634 300 IATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAG--RAGRALLFV 349
PRK01297 PRK01297
ATP-dependent RNA helicase RhlB; Provisional
 150-549 6.17e-43

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 234938 [Multi-domain]  Cd Length: 475  Bit Score: 159.69  E-value: 6.17e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 150 KKTFHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLLAgSERSI---R 226
Cdd:PRK01297  86 KTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPP-KERYMgepR 164

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 227 AVVIVPSRELAEQVNSVARSVSERFGLVVKVVGGGRGVGTIKAAFARGQPDILVSTPGALLKALWKRFISLSELYFLVID 306
Cdd:PRK01297 165 ALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLD 244

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 307 EADTMFDDSFAGMLEKILSHTQVASrlsetiglarKAQLVVVGATFpggVGDVLSKATD-LASISTVKSRMLHHLMPHIK 385
Cdd:PRK01297 245 EADRMLDMGFIPQVRQIIRQTPRKE----------ERQTLLFSATF---TDDVMNLAKQwTTDPAIVEIEPENVASDTVE 311

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 386 QTFLRVKGADKILELHQALKRAEQEQkgVLVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQRGKTNVL 465
Cdd:PRK01297 312 QHVYAVAGSDKYKLLYNLVTQNPWER--VMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVL 389

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 466 VCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAGGSegGEVLSFVTQPwDVELVQKIETAARRRTSLPGMETD 545
Cdd:PRK01297 390 VATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGAS--GVSISFAGED-DAFQLPEIEELLGRKISCEMPPAE 466


                 ....
gi 116268057 546 IQKP 549
Cdd:PRK01297 467 LLKP 470
PRK11776 PRK11776
ATP-dependent RNA helicase DbpA; Provisional
 149-530 1.51e-41

ATP-dependent RNA helicase DbpA; Provisional


Pssm-ID: 236977 [Multi-domain]  Cd Length: 460  Bit Score: 155.73  E-value: 1.51e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 149 SKKTFHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLLAgsersIRAV 228
Cdd:PRK11776   2 SMTAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFR-----VQAL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 229 VIVPSRELAEQVNSVARSVSeRFGLvvkvvgggrgvgTIKA-AFARGQP------------DILVSTPGALLKALWKRFI 295
Cdd:PRK11776  77 VLCPTRELADQVAKEIRRLA-RFIP------------NIKVlTLCGGVPmgpqidslehgaHIIVGTPGRILDHLRKGTL 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 296 SLSELYFLVIDEADTMFDDSFAGMLEKILSHTqvasrlsetiglARKAQLVVVGATFPGGVgdvlskatdlASIS----- 370
Cdd:PRK11776 144 DLDALNTLVLDEADRMLDMGFQDAIDAIIRQA------------PARRQTLLFSATYPEGI----------AAISqrfqr 201

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 371 ---TVKSRMLHHLmPHIKQTFLRVKGADKILELHQALKRAEQEQkgVLVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPA 447
Cdd:PRK11776 202 dpvEVKVESTHDL-PAIEQRFYEVSPDERLPALQRLLLHHQPES--CVVFCNTKKECQEVADALNAQGFSALALHGDLEQ 278

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 448 AMREGVFRDFQRGKTNVLVCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAGgsEGGEVLSFVTqPWDVELVQ 527
Cdd:PRK11776 279 RDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAG--SKGLALSLVA-PEEMQRAN 355


                 ...
gi 116268057 528 KIE 530
Cdd:PRK11776 356 AIE 358
DEADc_DDX52 cd17957
DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ...
 162-338 8.05e-39

DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ubiquitously expressed in testis, endometrium, and other tissues in humans. DDX52 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: 350715 [Multi-domain]  Cd Length: 198  Bit Score: 140.80  E-value: 8.05e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 162 LVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDllaGSERSIRAVVIVPSRELAEQVN 241
Cdd:cd17957    1 LLNNLEESGYREPTPIQMQAIPILLHGRDLLACAPTGSGKTLAFLIPILQKLGKP---RKKKGLRALILAPTRELASQIY 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 242 SVARSVSERFGLVVKVVGGGRGVGTIKAAFARGQPDILVSTPGALLKALWKRFISLSELYFLVIDEADTMFDDSFAGMLE 321
Cdd:cd17957   78 RELLKLSKGTGLRIVLLSKSLEAKAKDGPKSITKYDILVSTPLRLVFLLKQGPIDLSSVEYLVLDEADKLFEPGFREQTD 157

                        170       180
                 ....*....|....*....|.
gi 116268057 322 KIL---SHTQV-ASRLSETIG 338
Cdd:cd17957  158 EILaacTNPNLqRSLFSATIP 178
DEADc_DDX56 cd17961
DEAD-box helicase domain of DEAD box protein 56; DDX56 is a helicase required for assembly of ...
 158-326 6.29e-35

DEAD-box helicase domain of DEAD box protein 56; DDX56 is a helicase required for assembly of infectious West Nile virus particles. New research suggests that DDX56 relocalizes to the site of virus assembly during WNV infection and that its interaction with WNV capsid in the cytoplasm may occur transiently during virion morphogenesis. DDX56 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: 350719 [Multi-domain]  Cd Length: 206  Bit Score: 130.40  E-value: 6.29e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 158 LCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHR-LQEDLLAGSERSIRAVVIVPSREL 236
Cdd:cd17961    1 LDPRLLKAIAKLGWEKPTLIQSKAIPLALEGKDILARARTGSGKTAAYALPIIQKiLKAKAESGEEQGTRALILVPTREL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 237 AEQVNSVARSVSER-FGLVVKVVGGGRGVGTIKAAFARGQPDILVSTPGALLKALW-KRFISLSELYFLVIDEADTMFDD 314
Cdd:cd17961   81 AQQVSKVLEQLTAYcRKDVRVVNLSASSSDSVQRALLAEKPDIVVSTPARLLSHLEsGSLLLLSTLKYLVIDEADLVLSY 160

                        170
                 ....*....|..
gi 116268057 315 SFAGMLEKILSH 326
Cdd:cd17961  161 GYEEDLKSLLSY 172
PRK04537 PRK04537
ATP-dependent RNA helicase RhlB; Provisional
 152-533 7.37e-35

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235307 [Multi-domain]  Cd Length: 572  Bit Score: 138.54  E-value: 7.37e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 152 TFHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRL--QEDLLAGSERSIRAVV 229
Cdd:PRK04537  10 TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLlsRPALADRKPEDPRALI 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 230 IVPSRELAEQVNSVA----RSVSERFGLVVKVVGGGRGVGTIKAAFargqpDILVSTPGALLKALWK-RFISLSELYFLV 304
Cdd:PRK04537  90 LAPTRELAIQIHKDAvkfgADLGLRFALVYGGVDYDKQRELLQQGV-----DVIIATPGRLIDYVKQhKVVSLHACEICV 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 305 IDEADTMFDDSFAGMLEKILshtqvaSRLSETIglarKAQLVVVGATFPGGVGDVLSKATDLASISTVKSRMLhhLMPHI 384
Cdd:PRK04537 165 LDEADRMFDLGFIKDIRFLL------RRMPERG----TRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETI--TAARV 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 385 KQTFLRVKGADKILELHQALKRAEQEQkgVLVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQRGKTNV 464
Cdd:PRK04537 233 RQRIYFPADEEKQTLLLGLLSRSEGAR--TMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEI 310

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 116268057 465 LVCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAGgsEGGEVLSFVTQPW-----DVE--LVQKIETAA 533
Cdd:PRK04537 311 LVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLG--EEGDAISFACERYamslpDIEayIEQKIPVEP 384
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 175-359 2.12e-34

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 127.74  E-value: 2.12e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057  175 TTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLlagseRSIRAVVIVPSRELAEQvnsVARSVSERFGLV 254
Cdd:pfam00270   1 TPIQAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALEALDKLD-----NGPQALVLAPTRELAEQ---IYEELKKLGKGL 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057  255 VKVVGGGRGVGTIKAAFAR-GQPDILVSTPGALLKALWKRFiSLSELYFLVIDEADTMFDDSFAGMLEKILSHtqvasrl 333
Cdd:pfam00270  73 GLKVASLLGGDSRKEQLEKlKGPDILVGTPGRLLDLLQERK-LLKNLKLLVLDEAHRLLDMGFGPDLEEILRR------- 144

                         170       180
                  ....*....|....*....|....*.
gi 116268057  334 setigLARKAQLVVVGATFPGGVGDV 359
Cdd:pfam00270 145 -----LPKKRQILLLSATLPRNLEDL 165
PTZ00424 PTZ00424
helicase 45; Provisional
 152-530 4.13e-34

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 133.41  E-value: 4.13e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 152 TFHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLlagseRSIRAVVIV 231
Cdd:PTZ00424  29 SFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDL-----NACQALILA 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 232 PSRELAEQVNSVARSVSERFGLVVKVVGGGRGVGTIKAAFARGQpDILVSTPGALLKALWKRFISLSELYFLVIDEADTM 311
Cdd:PTZ00424 104 PTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGV-HMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEM 182

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 312 FDDSFAGMLEKILSHtqvasrlsetigLARKAQLVVVGATFPGGVGDVLSKATDLASISTVKSRMLhhLMPHIKQTFLRV 391
Cdd:PTZ00424 183 LSRGFKGQIYDVFKK------------LPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDEL--TLEGIRQFYVAV 248

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 392 KGA----DKILELHQALKRAEqeqkgVLVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQRGKTNVLVC 467
Cdd:PTZ00424 249 EKEewkfDTLCDLYETLTITQ-----AIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLIT 323

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 116268057 468 TDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAGgsEGGEVLSFVTqPWDVELVQKIE 530
Cdd:PTZ00424 324 TDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFG--RKGVAINFVT-PDDIEQLKEIE 383
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 152-517 1.17e-33

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 134.15  E-value: 1.17e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 152 TFHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLLAGS--ERSIRAVV 229
Cdd:PLN00206 122 SFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPseQRNPLAMV 201

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 230 IVPSRELAEQVNSVARSVSERFglvvkvvgggrgvgTIKAAFARGQP-------------DILVSTPGALLKALWKRFIS 296
Cdd:PLN00206 202 LTPTRELCVQVEDQAKVLGKGL--------------PFKTALVVGGDampqqlyriqqgvELIVGTPGRLIDLLSKHDIE 267

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 297 LSELYFLVIDEADTMFDDSFAgmlEKILshtQVASRLSEtiglarkAQLVVVGATFPGGVGDVLSK-ATDLASISTVKSR 375
Cdd:PLN00206 268 LDNVSVLVLDEVDCMLERGFR---DQVM---QIFQALSQ-------PQVLLFSATVSPEVEKFASSlAKDIILISIGNPN 334

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 376 mlhhlMPH--IKQTFLRVKGADKILELHQALKRAEQEQKGVLVFCNSASTVNWLGYSLEEM-GVGHMRLQGEMPAAMREG 452
Cdd:PLN00206 335 -----RPNkaVKQLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVtGLKALSIHGEKSMKERRE 409

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 116268057 453 VFRDFQRGKTNVLVCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAGgsEGGEVLSFV 517
Cdd:PLN00206 410 VMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMG--EKGTAIVFV 472
DEADc_DDX27 cd17947
DEAD-box helicase domain of DEAD box protein 27; DDX27 (also called RHLP, deficiency of ...
 162-373 1.31e-32

DEAD-box helicase domain of DEAD box protein 27; DDX27 (also called RHLP, deficiency of ribosomal subunits protein 1 homolog, and probable ATP-dependent RNA helicase DDX27) is involved in the processing of 5.8S and 28S ribosomal RNAs. More specifically, the encoded protein localizes to the nucleolus, where it interacts with the PeBoW complex to ensure proper 3' end formation of 47S rRNA. DDX27 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: 350705 [Multi-domain]  Cd Length: 196  Bit Score: 123.90  E-value: 1.31e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 162 LVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQedLLAGSERSIRAVVIVPSRELAEQVN 241
Cdd:cd17947    1 LLRALSSLGFTKPTPIQAAAIPLALLGKDICASAVTGSGKTAAFLLPILERLL--YRPKKKAATRVLVLVPTRELAMQCF 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 242 SVARSVSeRFGLVVKVVGGGRGVGTIKAAFARGQPDILVSTPGALLKALWKRF-ISLSELYFLVIDEADTMFDDSFAGML 320
Cdd:cd17947   79 SVLQQLA-QFTDITFALAVGGLSLKAQEAALRARPDIVIATPGRLIDHLRNSPsFDLDSIEILVLDEADRMLEEGFADEL 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 116268057 321 EKILSHtqvasrlsetigLARKAQLVVVGATFPggvgdvlSKATDLASISTVK 373
Cdd:cd17947  158 KEILRL------------CPRTRQTMLFSATMT-------DEVKDLAKLSLNK 191
DEXDc smart00487
DEAD-like helicases superfamily;
166-356 4.23e-32

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 122.60  E-value: 4.23e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057   166 LQRQNIIHPTTVQLQTIPKILKG-RNILCAAETGSGKTLTYLLPIIHRLQEdllagsERSIRAVVIVPSRELAEQVNSVA 244
Cdd:smart00487   1 IEKFGFEPLRPYQKEAIEALLSGlRDVILAAPTGSGKTLAALLPALEALKR------GKGGRVLVLVPTRELAEQWAEEL 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057   245 RSVSERFGLVVKVVGGGRGVGTIKAAFARGQPDILVSTPGALLKALWKRFISLSELYFLVIDEADTMFDDSFAGMLEKIL 324
Cdd:smart00487  75 KKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLL 154

                          170       180       190
                   ....*....|....*....|....*....|..
gi 116268057   325 SHtqvasrlsetigLARKAQLVVVGATFPGGV 356
Cdd:smart00487 155 KL------------LPKNVQLLLLSATPPEEI 174
DEADc_DDX51 cd17956
DEAD-box helicase domain of DEAD box protein 51; DDX51 aids cell cancer proliferation by ...
 162-351 7.13e-31

DEAD-box helicase domain of DEAD box protein 51; DDX51 aids cell cancer proliferation by regulating multiple signalling pathways. Mammalian DEAD box protein Ddx51 acts in 3' end maturation of 28S rRNA by promoting the release of U8 snoRNA.It 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: 350714 [Multi-domain]  Cd Length: 231  Bit Score: 120.04  E-value: 7.13e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 162 LVETLQRQNIIHPTTVQLQTIPKILKG---------RNILCAAETGSGKTLTYLLPIIhrlqEDLLAGSERSIRAVVIVP 232
Cdd:cd17956    1 LLKNLQNNGITSAFPVQAAVIPWLLPSskstppyrpGDLCVSAPTGSGKTLAYVLPIV----QALSKRVVPRLRALIVVP 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 233 SRELAEQVNSVARSVSERFglvvkvvgggrgvgTIKAAFARGQ---------------------PDILVSTPGALLKAL- 290
Cdd:cd17956   77 TKELVQQVYKVFESLCKGT--------------GLKVVSLSGQksfkkeqklllvdtsgrylsrVDILVATPGRLVDHLn 142

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 116268057 291 WKRFISLSELYFLVIDEADTMFDDSFAGMLEKILSHTQVASRLSETIGLARKA--------QLVVVGAT 351
Cdd:cd17956  143 STPGFTLKHLRFLVIDEADRLLNQSFQDWLETVMKALGRPTAPDLGSFGDANLlersvrplQKLLFSAT 211
PRK04837 PRK04837
ATP-dependent RNA helicase RhlB; Provisional
 149-516 2.08e-30

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235314 [Multi-domain]  Cd Length: 423  Bit Score: 123.54  E-value: 2.08e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 149 SKKTFHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLlAGSERSI--- 225
Cdd:PRK04837   6 TEQKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHP-APEDRKVnqp 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 226 RAVVIVPSRELAEQVNSVARSVSErfglvvkvvgggrgVGTIKAAFARG-------------QPDILVSTPGALLKALWK 292
Cdd:PRK04837  85 RALIMAPTRELAVQIHADAEPLAQ--------------ATGLKLGLAYGgdgydkqlkvlesGVDILIGTTGRLIDYAKQ 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 293 RFISLSELYFLVIDEADTMFDDSFAG----MLEKILSHTQvasRLSetiglarkaqlVVVGATfpggvgdvLS-KATDLA 367
Cdd:PRK04837 151 NHINLGAIQVVVLDEADRMFDLGFIKdirwLFRRMPPANQ---RLN-----------MLFSAT--------LSyRVRELA 208

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 368 --------SISTVKSRMLHHlmpHIKQTFLRVKGADKILeLHQALKRAEQEQKGVlVFCNSAstvnwlgYSLEEM----- 434
Cdd:PRK04837 209 fehmnnpeYVEVEPEQKTGH---RIKEELFYPSNEEKMR-LLQTLIEEEWPDRAI-IFANTK-------HRCEEIwghla 276

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 435 GVGHmR---LQGEMPAAMREGVFRDFQRGKTNVLVCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAGGSegG 511
Cdd:PRK04837 277 ADGH-RvglLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGAS--G 353


                 ....*
gi 116268057 512 EVLSF 516
Cdd:PRK04837 354 HSISL 358
DEADc_DDX31 cd17949
DEAD-box helicase domain of DEAD box protein 31; DDX31 (also called helicain or G2 helicase) ...
 162-373 3.14e-30

DEAD-box helicase domain of DEAD box protein 31; DDX31 (also called helicain or G2 helicase) plays a role in ribosome biogenesis and TP53/p53 regulation through its interaction with NPM1. DDX31 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: 350707 [Multi-domain]  Cd Length: 214  Bit Score: 117.69  E-value: 3.14e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 162 LVETL-QRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQedllaGSERSIR------AVVIVPSR 234
Cdd:cd17949    1 LVSHLkSKMGIEKPTAIQKLAIPVLLQGRDVLVRSQTGSGKTLAYLLPIIQRLL-----SLEPRVDrsdgtlALVLVPTR 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 235 ELAEQVNSVARSV-------------------SErfglvvkvvgggrgvgtiKAAFARGQPdILVSTPGALLKALWK-RF 294
Cdd:cd17949   76 ELALQIYEVLEKLlkpfhwivpgyliggekrkSE------------------KARLRKGVN-ILIATPGRLLDHLKNtQS 136

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 295 ISLSELYFLVIDEADTMFDDSFAGMLEKILSHTQVASRLSETIG-LARKAQLVVVGATFPGGVgdvlskaTDLASISTVK 373
Cdd:cd17949  137 FDVSNLRWLVLDEADRLLDMGFEKDITKILELLDDKRSKAGGEKsKPSRRQTVLVSATLTDGV-------KRLAGLSLKD 209
DEADc_DDX49 cd17955
DEAD-box helicase domain of DEAD box protein 49; DDX49 (also called Dbp8) is a member of the ...
 153-326 8.29e-30

DEAD-box helicase domain of DEAD box protein 49; DDX49 (also called Dbp8) 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: 350713 [Multi-domain]  Cd Length: 204  Bit Score: 116.17  E-value: 8.29e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 153 FHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDllagsERSIRAVVIVP 232
Cdd:cd17955    1 FEDLGLSSWLVKQCASLGIKEPTPIQKLCIPEILAGRDVIGGAKTGSGKTAAFALPILQRLSED-----PYGIFALVLTP 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 233 SRELAEQvnsvarsVSERFGLVVKVVGGGRGVGT-----IKAAFA-RGQPDILVSTPG---ALLKALWKRFISLSELYFL 303
Cdd:cd17955   76 TRELAYQ-------IAEQFRALGAPLGLRCCVIVggmdmVKQALElSKRPHIVVATPGrlaDHLRSSDDTTKVLSRVKFL 148

                        170       180
                 ....*....|....*....|...
gi 116268057 304 VIDEADTMFDDSFAGMLEKILSH 326
Cdd:cd17955  149 VLDEADRLLTGSFEDDLATILSA 171
DEADc_DDX54 cd17959
DEAD-box helicase domain of DEAD box protein 54; DDX54 interacts in a hormone-dependent manner ...
 152-353 1.87e-29

DEAD-box helicase domain of DEAD box protein 54; DDX54 interacts in a hormone-dependent manner with nuclear receptors, and represses their transcriptional activity. DDX54 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: 350717 [Multi-domain]  Cd Length: 205  Bit Score: 115.09  E-value: 1.87e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 152 TFHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLlagSERSIRAVVIV 231
Cdd:cd17959    2 GFQSMGLSPPLLRAIKKKGYKVPTPIQRKTIPLILDGRDVVAMARTGSGKTAAFLIPMIEKLKAHS---PTVGARALILS 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 232 PSRELAEQVNSVARSVSeRFGLVVKVVGGGRGVGTIKAAFARGQPDILVSTPGALLKALWKRFISLSELYFLVIDEADTM 311
Cdd:cd17959   79 PTRELALQTLKVTKELG-KFTDLRTALLVGGDSLEEQFEALASNPDIIIATPGRLLHLLVEMNLKLSSVEYVVFDEADRL 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 116268057 312 FDDSFAGMLEKILshtqvaSRLSETiglarkAQLVVVGATFP 353
Cdd:cd17959  158 FEMGFAEQLHEIL------SRLPEN------RQTLLFSATLP 187
DEADc_DDX6 cd17940
DEAD-box helicase domain of DEAD box protein 6; DEAD box protein 6 (DDX6, also known as Rck or ...
 153-380 7.52e-29

DEAD-box helicase domain of DEAD box protein 6; DEAD box protein 6 (DDX6, also known as Rck or p54) participates in mRNA regulation mediated by miRNA-mediated silencing. It also plays a role in global and transcript-specific messenger RNA (mRNA) storage, translational repression, and decay. It is a member of the DEAD-box helicase family, 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: 350698 [Multi-domain]  Cd Length: 201  Bit Score: 113.55  E-value: 7.52e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 153 FHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEdllagSERSIRAVVIVP 232
Cdd:cd17940    1 FEDYGLKRELLMGIFEKGFEKPSPIQEESIPIALSGRDILARAKNGTGKTGAYLIPILEKIDP-----KKDVIQALILVP 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 233 SRELAEQVNSVARSVSErfgLVVKVVGGGRGVGTIKAAFARGQPD--ILVSTPGALLKALWKRFISLSELYFLVIDEADT 310
Cdd:cd17940   76 TRELALQTSQVCKELGK---HMGVKVMVTTGGTSLRDDIMRLYQTvhVLVGTPGRILDLAKKGVADLSHCKTLVLDEADK 152

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 311 MFDDSFAGMLEKILSHtqvasrlsetigLARKAQLVVVGATFPggvgdvlskatdlasiSTVKSRMLHHL 380
Cdd:cd17940  153 LLSQDFQPIIEKILNF------------LPKERQILLFSATFP----------------LTVKNFMDRHM 194
DEADc_DDX3_DDX4 cd17967
DEAD-box helicase domain of ATP-dependent RNA helicases DDX3 and DDX4; This subfamily includes ...
 157-353 8.36e-29

DEAD-box helicase domain of ATP-dependent RNA helicases DDX3 and DDX4; This subfamily includes Drosophila melanogaster Vasa, which is essential for development. DEAD box protein 3 (DDX3) has been reported to display a high level of RNA-independent ATPase activity stimulated by both RNA and DNA. DEAD box protein 4 (DDX4, also known as VASA homolog) is an ATP-dependent RNA helicase required during spermatogenesis and is essential for the germline integrity. DDX3 and DDX4 are members 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: 350725 [Multi-domain]  Cd Length: 221  Bit Score: 113.74  E-value: 8.36e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 157 NLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLLAGSERSIR-----AVVIV 231
Cdd:cd17967    6 GLRELLLENIKRAGYTKPTPVQKYAIPIILAGRDLMACAQTGSGKTAAFLLPIISKLLEDGPPSVGRGRRkaypsALILA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 232 PSRELAEQVNSVARSVSERfglvvkvvgggrgvGTIKAAFA------RGQP-------DILVSTPGALLKALWKRFISLS 298
Cdd:cd17967   86 PTRELAIQIYEEARKFSYR--------------SGVRSVVVyggadvVHQQlqllrgcDILVATPGRLVDFIERGRISLS 151

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 116268057 299 ELYFLVIDEADTMFDDSFAGMLEKILSHTQ---VASRlsetiglarkaQLVVVGATFP 353
Cdd:cd17967  152 SIKFLVLDEADRMLDMGFEPQIRKIVEHPDmppKGER-----------QTLMFSATFP 198
DEADc_DDX4 cd18052
DEAD-box helicase domain of DEAD box protein 4; DEAD box protein 4 (DDX4, also known as VASA ...
 152-353 1.11e-28

DEAD-box helicase domain of DEAD box protein 4; DEAD box protein 4 (DDX4, also known as VASA homolog) is an ATP-dependent RNA helicase required during spermatogenesis and is essential for the germline integrity. DEAD-box helicases are 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: 350810 [Multi-domain]  Cd Length: 264  Bit Score: 114.68  E-value: 1.11e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 152 TFHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLLAGSE----RSIRA 227
Cdd:cd18052   44 TFEEANLCETLLKNIRKAGYEKPTPVQKYAIPIILAGRDLMACAQTGSGKTAAFLLPVLTGMMKEGLTASSfsevQEPQA 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 228 VVIVPSRELAEQVNSVARSVSERfglvvkvvgggrgvGTIKAAFARG------QPD-------ILVSTPGALLKALWKRF 294
Cdd:cd18052  124 LIVAPTRELANQIFLEARKFSYG--------------TCIRPVVVYGgvsvghQIRqiekgchILVATPGRLLDFIGRGK 189

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 116268057 295 ISLSELYFLVIDEADTMFDDSFAGMLEKILSH---TQVASRlsetiglarkaQLVVVGATFP 353
Cdd:cd18052  190 ISLSKLKYLILDEADRMLDMGFGPEIRKLVSEpgmPSKEDR-----------QTLMFSATFP 240
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 395-506 1.12e-28

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


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 109.61  E-value: 1.12e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057  395 DKILELHQALKRAEQEQkgVLVFCNSASTVNwLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQRGKTNVLVCTDIASRG 474
Cdd:pfam00271   1 EKLEALLELLKKERGGK--VLIFSQTKKTLE-AELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERG 77

                          90       100       110
                  ....*....|....*....|....*....|..
gi 116268057  475 LDTQRVGLIVNYDFPESQTDYIHRAGRVGRAG 506
Cdd:pfam00271  78 LDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
DEADc_MSS116 cd17964
DEAD-box helicase domain of DEAD-box helicase Mss116; Mss116 is an RNA chaperone important for ...
 160-326 2.91e-28

DEAD-box helicase domain of DEAD-box helicase Mss116; Mss116 is an RNA chaperone important for mitochondrial group I and II intron splicing, translational activation, and RNA end processing. Mss116 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: 350722 [Multi-domain]  Cd Length: 211  Bit Score: 111.91  E-value: 2.91e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 160 PELVETLQRQNIIHPTTVQLQTIPKIL-KGRNILCAAETGSGKTLTYLLPIIHRLQEDLLAGSERSIRAVVIVPSRELAE 238
Cdd:cd17964    3 PSLLKALTRMGFETMTPVQQKTLKPILsTGDDVLARAKTGTGKTLAFLLPAIQSLLNTKPAGRRSGVSALIISPTRELAL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 239 QVNSVARSVSERFGLVVKVVGG--GRGVGTIKaAFARGQPDILVSTPGALLKAL----WKRFisLSELYFLVIDEADTMF 312
Cdd:cd17964   83 QIAAEAKKLLQGLRKLRVQSAVggTSRRAELN-RLRRGRPDILVATPGRLIDHLenpgVAKA--FTDLDYLVLDEADRLL 159

                        170
                 ....*....|....
gi 116268057 313 DDSFAGMLEKILSH 326
Cdd:cd17964  160 DMGFRPDLEQILRH 173
DEADc_MRH4 cd17965
DEAD-box helicase domain of ATP-dependent RNA helicase MRH4; Mitochondrial RNA helicase 4 ...
 172-353 8.24e-28

DEAD-box helicase domain of ATP-dependent RNA helicase MRH4; Mitochondrial RNA helicase 4 (MRH4) plays an essential role during the late stages of mitochondrial ribosome or mitoribosome assembly by promoting remodeling of the 21S rRNA-protein interactions. MRH4 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: 350723 [Multi-domain]  Cd Length: 251  Bit Score: 112.08  E-value: 8.24e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 172 IHPTTVQLQTIPKILKGRNI----------------LCAAETGSGKTLTYLLPIIHRLQEDLLAGSERS----------- 224
Cdd:cd17965   29 IKPSPIQTLAIKKLLKTLMRkvtkqtsneepklevfLLAAETGSGKTLAYLAPLLDYLKRQEQEPFEEAeeeyesakdtg 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 225 -IRAVVIVPSRELAEQVNSVARSVSErfglvvkvvGGGRGVGTIKAAFA----------RGQPDILVSTPGALLKALWKR 293
Cdd:cd17965  109 rPRSVILVPTHELVEQVYSVLKKLSH---------TVKLGIKTFSSGFGpsyqrlqlafKGRIDILVTTPGKLASLAKSR 179

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 294 FISLSELYFLVIDEADTMFDDSFagmlekILSHTQVASRLSETiglarkAQLVVVGATFP 353
Cdd:cd17965  180 PKILSRVTHLVVDEADTLFDRSF------LQDTTSIIKRAPKL------KHLILCSATIP 227
DEADc_DDX55 cd17960
DEAD-box helicase domain of DEAD box protein 55; DDX55 is a member of the DEAD-box helicases, ...
 162-326 9.59e-28

DEAD-box helicase domain of DEAD box protein 55; DDX55 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: 350718 [Multi-domain]  Cd Length: 202  Bit Score: 110.36  E-value: 9.59e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 162 LVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLLAGSERSIRAVVIVPSRELAEQVN 241
Cdd:cd17960    1 ILDVVAELGFTSMTPVQAATIPLFLSNKDVVVEAVTGSGKTLAFLIPVLEILLKRKANLKKGQVGALIISPTRELATQIY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 242 SVARSVSERFGLVVKVVGGGRGVGTIK--AAFARGQPDILVSTPGALLKaLWKRF---ISLSELYFLVIDEADTMFDDSF 316
Cdd:cd17960   81 EVLQSFLEHHLPKLKCQLLIGGTNVEEdvKKFKRNGPNILVGTPGRLEE-LLSRKadkVKVKSLEVLVLDEADRLLDLGF 159

                        170
                 ....*....|
gi 116268057 317 AGMLEKILSH 326
Cdd:cd17960  160 EADLNRILSK 169
DEADc_DDX23 cd17945
DEAD-box helicase domain of DEAD box protein 23; DDX23 (also called U5 snRNP 100kD protein and ...
 162-326 9.60e-28

DEAD-box helicase domain of DEAD box protein 23; DDX23 (also called U5 snRNP 100kD protein and PRP28 homolog) is involved in pre-mRNA splicing and its phosphorylated form (by SRPK2) is required for spliceosomal B complex formation. Diseases associated with DDX23 include distal hereditary motor neuropathy, type II. DDX23 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: 350703 [Multi-domain]  Cd Length: 220  Bit Score: 110.87  E-value: 9.60e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 162 LVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEdLLAGSERSI----RAVVIVPSRELA 237
Cdd:cd17945    1 LLRVIRKLGYKEPTPIQRQAIPIGLQNRDIIGIAETGSGKTAAFLIPLLVYISR-LPPLDEETKddgpYALILAPTRELA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 238 EQVNSVARSVSERFGLVVKVVGGGRGVGTIKAAFARGqPDILVSTPGALLKALWKRFISLSELYFLVIDEADTMFDDSFA 317
Cdd:cd17945   80 QQIEEETQKFAKPLGIRVVSIVGGHSIEEQAFSLRNG-CEILIATPGRLLDCLERRLLVLNQCTYVVLDEADRMIDMGFE 158


                 ....*....
gi 116268057 318 GMLEKILSH 326
Cdd:cd17945  159 PQVTKILDA 167
DEADc_DDX47 cd17954
DEAD-box helicase domain of DEAD box protein 47; DDX47 (also called E4-DEAD box protein) can ...
 152-326 2.48e-27

DEAD-box helicase domain of DEAD box protein 47; DDX47 (also called E4-DEAD box protein) can shuttle between the nucleus and the cytoplasm, and has an RNA-independent ATPase activity. DX47 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: 350712 [Multi-domain]  Cd Length: 203  Bit Score: 109.33  E-value: 2.48e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 152 TFHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDllagsERSIRAVVIV 231
Cdd:cd17954    1 TFKELGVCEELCEACEKLGWKKPTKIQEEAIPVALQGRDIIGLAETGSGKTAAFALPILQALLEN-----PQRFFALVLA 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 232 PSRELAEQVNSVARSVSERFGLVVKVVGGGRGVGTIKAAFARgQPDILVSTPGALLKAL--WKRFiSLSELYFLVIDEAD 309
Cdd:cd17954   76 PTRELAQQISEQFEALGSSIGLKSAVLVGGMDMMAQAIALAK-KPHVIVATPGRLVDHLenTKGF-SLKSLKFLVMDEAD 153

                        170
                 ....*....|....*..
gi 116268057 310 TMFDDSFAGMLEKILSH 326
Cdd:cd17954  154 RLLNMDFEPEIDKILKV 170
DEADc_DDX42 cd17952
DEAD-box helicase domain of DEAD box protein 42; DDX42 (also called Splicing Factor ...
 162-328 8.59e-27

DEAD-box helicase domain of DEAD box protein 42; DDX42 (also called Splicing Factor 3B-Associated 125 kDa Protein, RHELP, or RNAHP) is an NTPase with a preference for ATP, the hydrolysis of which is enhanced by various RNA substrates. It acts as a non-processive RNA helicase with protein displacement and RNA annealing activities. DDX42 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: 350710 [Multi-domain]  Cd Length: 197  Bit Score: 107.50  E-value: 8.59e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 162 LVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLP-IIHRLQEDLLAGSERSIrAVVIVPSRELAEQV 240
Cdd:cd17952    1 LLNAIRKQEYEQPTPIQAQALPVALSGRDMIGIAKTGSGKTAAFIWPmLVHIMDQRELEKGEGPI-AVIVAPTRELAQQI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 241 NSVARSVSERFGLVVKVVGGGRGVGTIKAAFARGqPDILVSTPGALLKALWKRFISLSELYFLVIDEADTMFDDSFAGML 320
Cdd:cd17952   80 YLEAKKFGKAYNLRVVAVYGGGSKWEQAKALQEG-AEIVVATPGRLIDMVKKKATNLQRVTYLVLDEADRMFDMGFEYQV 158


                 ....*...
gi 116268057 321 EKILSHTQ 328
Cdd:cd17952  159 RSIVGHVR 166
DEADc_DDX1 cd17938
DEAD-box helicase domain of DEAD box protein 1; DEAD box protein 1 (DDX1) acts as an ...
 153-351 5.46e-26

DEAD-box helicase domain of DEAD box protein 1; DEAD box protein 1 (DDX1) acts as an ATP-dependent RNA helicase, able to unwind both RNA-RNA and RNA-DNA duplexes. It possesses 5' single-stranded RNA overhang nuclease activity as well as ATPase activity on various RNA, but not DNA polynucleotides. DDX1 may play a role in RNA clearance at DNA double-strand breaks (DSBs), thereby facilitating the template-guided repair of transcriptionally active regions of the genome. It may also be involved in 3'-end cleavage and polyadenylation of pre-mRNAs. DDX1 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: 350696 [Multi-domain]  Cd Length: 204  Bit Score: 105.48  E-value: 5.46e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 153 FHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIhrlqedllagseRSIRAVVIVP 232
Cdd:cd17938    1 FEELGVMPELIKAVEELDWLLPTDIQAEAIPLILGGGDVLMAAETGSGKTGAFCLPVL------------QIVVALILEP 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 233 SRELAEQVNSVARSVSERFGLVVKVVGGGRGVGTIKAAFAR--GQPDILVSTPGALLKALWKRFISLSELYFLVIDEADT 310
Cdd:cd17938   69 SRELAEQTYNCIENFKKYLDNPKLRVALLIGGVKAREQLKRleSGVDIVVGTPGRLEDLIKTGKLDLSSVRFFVLDEADR 148

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 116268057 311 MFDDSFAGMLEKILS----HTQVASRLsetiglarkaQLVVVGAT 351
Cdd:cd17938  149 LLSQGNLETINRIYNripkITSDGKRL----------QVIVCSAT 183
DEADc_DDX24 cd17946
DEAD-box helicase domain of DEAD box protein 24; The human DDX24 gene encodes a DEAD box ...
 162-381 8.57e-26

DEAD-box helicase domain of DEAD box protein 24; The human DDX24 gene encodes a DEAD box protein, which shows little similarity to any of the other known human DEAD box proteins, but shows a high similarity to mouse Ddx24 at the amino acid level. MDM2 mediates nonproteolytic polyubiquitylation of the DEAD-Box RNA helicase DDX24. DDX24 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: 350704 [Multi-domain]  Cd Length: 235  Bit Score: 105.78  E-value: 8.57e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 162 LVETLQRQNIIHPTTVQLQTIPKILK-GRNILCAAETGSGKTLTYLLPIIHRL----QEDLLAGSERSIRAVVIVPSREL 236
Cdd:cd17946    1 ILRALADLGFSEPTPIQALALPAAIRdGKDVIGAAETGSGKTLAFGIPILERLlsqkSSNGVGGKQKPLRALILTPTREL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 237 AEQV----NSVARSVSerfglvvkvvgggrgvgtIKAAFARG-------------QPDILVSTPG---ALLKALWKRFIS 296
Cdd:cd17946   81 AVQVkdhlKAIAKYTN------------------IKIASIVGglavqkqerllkkRPEIVVATPGrlwELIQEGNEHLAN 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 297 LSELYFLVIDEADTMFDDSFAGMLEKILSHTQVASRLSetiglARKAQLVVVGATFPGGVGDVLSKATDLASISTVKSRM 376
Cdd:cd17946  143 LKSLRFLVLDEADRMLEKGHFAELEKILELLNKDRAGK-----KRKRQTFVFSATLTLDHQLPLKLNSKKKKKKKEKKQK 217


                 ....*
gi 116268057 377 LHHLM 381
Cdd:cd17946  218 LELLI 222
DEADc_DDX5_DDX17 cd17966
DEAD-box helicase domain of ATP-dependent RNA helicases DDX5 and DDX17; DDX5 and DDX17 are ...
 162-327 9.15e-25

DEAD-box helicase domain of ATP-dependent RNA helicases DDX5 and DDX17; DDX5 and DDX17 are members 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: 350724 [Multi-domain]  Cd Length: 197  Bit Score: 101.68  E-value: 9.15e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 162 LVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLP-IIHRLQEDLLAGSERSIrAVVIVPSRELAEQV 240
Cdd:cd17966    1 VMDELKRQGFTEPTAIQAQGWPMALSGRDMVGIAQTGSGKTLAFLLPaIVHINAQPPLERGDGPI-VLVLAPTRELAQQI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 241 NSVARSVSERFGLVVKVVGGGRGVGTIKAAFARGqPDILVSTPGALLKALWKRFISLSELYFLVIDEADTMFDDSFAGML 320
Cdd:cd17966   80 QQEANKFGGSSRLRNTCVYGGAPKGPQIRDLRRG-VEICIATPGRLIDFLDQGKTNLRRVTYLVLDEADRMLDMGFEPQI 158


                 ....*..
gi 116268057 321 EKILSHT 327
Cdd:cd17966  159 RKIVDQI 165
DEADc_DDX46 cd17953
DEAD-box helicase domain of DEAD box protein 46; DDX46 (also called Prp5-like DEAD-box protein) ...
 165-353 5.13e-24

DEAD-box helicase domain of DEAD box protein 46; DDX46 (also called Prp5-like DEAD-box protein) is a component of the 17S U2 snRNP complex. It plays an important role in pre-mRNA splicing and has a role in antiviral innate immunity. DDX46 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: 350711 [Multi-domain]  Cd Length: 222  Bit Score: 100.53  E-value: 5.13e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 165 TLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPII-HRLQEDLLAGSERSIrAVVIVPSRELAEQVNSV 243
Cdd:cd17953   26 LIKKLGYEKPTPIQAQALPAIMSGRDVIGIAKTGSGKTLAFLLPMFrHIKDQRPVKPGEGPI-GLIMAPTRELALQIYVE 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 244 ARSVSERFGLVVKVVGGGRGVGTIKAAFARGQpDILVSTPGAL---LKALWKRFISLSELYFLVIDEADTMFDDSFAGML 320
Cdd:cd17953  105 CKKFSKALGLRVVCVYGGSGISEQIAELKRGA-EIVVCTPGRMidiLTANNGRVTNLRRVTYVVLDEADRMFDMGFEPQI 183

                        170       180       190
                 ....*....|....*....|....*....|...
gi 116268057 321 EKILshtqvasrlsETIGLARkaQLVVVGATFP 353
Cdd:cd17953  184 MKIV----------NNIRPDR--QTVLFSATFP 204
DEADc_DDX10 cd17941
DEAD-box helicase domain of DEAD box protein 10; Fusion of the DDX10 gene and the nucleoporin ...
 166-326 1.77e-23

DEAD-box helicase domain of DEAD box protein 10; Fusion of the DDX10 gene and the nucleoporin gene, NUP98, by inversion 11 (p15q22) chromosome translocation is found in the patients with de novo or therapy-related myeloid malignancies. Diseases associated with DDX10 (also known as DDX10-NUP98 Fusion Protein Type 2) include myelodysplastic syndrome and leukemia, acute myeloid. DDX10 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: 350699 [Multi-domain]  Cd Length: 198  Bit Score: 98.13  E-value: 1.77e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 166 LQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEdLLAGSERSIRAVVIVPSRELAEQVNSVAR 245
Cdd:cd17941    5 LKEAGFIKMTEIQRDSIPHALQGRDILGAAKTGSGKTLAFLVPLLEKLYR-ERWTPEDGLGALIISPTRELAMQIFEVLR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 246 SVSerfglvvkvvgggrGVGTIKAAFARG------------QPDILVSTPGALLKALWKR-FISLSELYFLVIDEADTMF 312
Cdd:cd17941   84 KVG--------------KYHSFSAGLIIGgkdvkeekerinRMNILVCTPGRLLQHMDETpGFDTSNLQMLVLDEADRIL 149

                        170
                 ....*....|....
gi 116268057 313 DDSFAGMLEKILSH 326
Cdd:cd17941  150 DMGFKETLDAIVEN 163
HELICc smart00490
helicase superfamily c-terminal domain;
431-506 2.73e-23

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 93.82  E-value: 2.73e-23
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 116268057   431 LEEMGVGHMRLQGEMPAAMREGVFRDFQRGKTNVLVCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAG 506
Cdd:smart00490   7 LKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82
DEADc_DDX43_DDX53 cd17958
DEAD-box helicase domain of DEAD box proteins 43 and 53; DDX43 (also called cancer/testis ...
 162-356 8.59e-23

DEAD-box helicase domain of DEAD box proteins 43 and 53; DDX43 (also called cancer/testis antigen 13 or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 is also called cancer/testis antigen 26 or DEAD-Box Protein CAGE. Both DDX46 and DDX53 are members 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: 350716 [Multi-domain]  Cd Length: 197  Bit Score: 95.99  E-value: 8.59e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 162 LVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLP-IIHRLQEDLLAGSERSIRAVVIVPSRELAEQV 240
Cdd:cd17958    1 IMKEIKKQGFEKPSPIQSQAWPIILQGIDLIGVAQTGTGKTLAYLLPgFIHLDLQPIPREQRNGPGVLVLTPTRELALQI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 241 NSVARSVSERFGLVVKVVGGGRGVGTIKAafARGQPDILVSTPGALLKALWKRFISLSELYFLVIDEADTMFDDSFAGML 320
Cdd:cd17958   81 EAECSKYSYKGLKSVCVYGGGNRNEQIED--LSKGVDIIIATPGRLNDLQMNNVINLKSITYLVLDEADRMLDMGFEPQI 158

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 116268057 321 EKILSHTQvasrlsetiglaRKAQLVVVGATFPGGV 356
Cdd:cd17958  159 RKILLDIR------------PDRQTIMTSATWPDGV 182
DEADc_DDX41 cd17951
DEAD-box helicase domain of DEAD box protein 41; DDX41 (also called ABS and MPLPF) interacts ...
 162-326 2.38e-22

DEAD-box helicase domain of DEAD box protein 41; DDX41 (also called ABS and MPLPF) interacts with several spliceosomal proteins and may recognize the bacterial second messengers cyclic di-GMP and cyclic di-AMP, resulting in the induction of genes involved in the innate immune response. Diseases associated with DDX41 include "myeloproliferative/lymphoproliferative neoplasms, familial" and "Ddx41-related susceptibility to familial myeloproliferative/lymphoproliferative neoplasms". DDX41 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: 350709 [Multi-domain]  Cd Length: 206  Bit Score: 95.10  E-value: 2.38e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 162 LVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPII-HRLQEDL---LAGSERSIrAVVIVPSRELA 237
Cdd:cd17951    1 ILKGLKKKGIKKPTPIQMQGLPTILSGRDMIGIAFTGSGKTLVFTLPLImFALEQEKklpFIKGEGPY-GLIVCPSRELA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 238 EQVNSVARSVSERFGLVVKVVGGGRGVgtIKAAFARGQPD-------ILVSTPGALLKALWKRFISLSELYFLVIDEADT 310
Cdd:cd17951   80 RQTHEVIEYYCKALQEGGYPQLRCLLC--IGGMSVKEQLEvirkgvhIVVATPGRLMDMLNKKKINLDICRYLCLDEADR 157

                        170
                 ....*....|....*.
gi 116268057 311 MFDDSFAGMLEKILSH 326
Cdd:cd17951  158 MIDMGFEEDIRTIFSY 173
DEADc_DDX5 cd18049
DEAD-box helicase domain of DEAD box protein 5; DDX5 (also called RNA helicase P68, HLR1, ...
 153-324 2.30e-21

DEAD-box helicase domain of DEAD box protein 5; DDX5 (also called RNA helicase P68, HLR1, G17P1, or HUMP68) is involved in pathways that include the alteration of RNA structures, plays a role as a coregulator of transcription, a regulator of splicing, and in the processing of small noncoding RNAs. It synergizes with DDX17 and SRA1 RNA to activate MYOD1 transcriptional activity and is involved in skeletal muscle differentiation. Dysregulation of this gene may play a role in cancer development. DDX5 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: 350807 [Multi-domain]  Cd Length: 234  Bit Score: 93.15  E-value: 2.30e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 153 FHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLP-IIHRLQEDLLAGSERSIrAVVIV 231
Cdd:cd18049   26 FYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPaIVHINHQPFLERGDGPI-CLVLA 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 232 PSRELAEQVNSVARSVSERFGLVVKVVGGGRGVGTIKAAFARGQpDILVSTPGALLKALWKRFISLSELYFLVIDEADTM 311
Cdd:cd18049  105 PTRELAQQVQQVAAEYGRACRLKSTCIYGGAPKGPQIRDLERGV-EICIATPGRLIDFLEAGKTNLRRCTYLVLDEADRM 183

                        170
                 ....*....|...
gi 116268057 312 FDDSFAGMLEKIL 324
Cdd:cd18049  184 LDMGFEPQIRKIV 196
DEADc_DDX20 cd17943
DEAD-box helicase domain of DEAD box protein 20; DDX20 (also called DEAD Box Protein DP 103, ...
 162-362 4.13e-20

DEAD-box helicase domain of DEAD box protein 20; DDX20 (also called DEAD Box Protein DP 103, Component Of Gems 3, Gemin-3, and SMN-Interacting Protein) interacts directly with SMN (survival of motor neurons), the spinal muscular atrophy gene product, and may play a catalytic role in the function of the SMN complex on ribonucleoproteins. Diseases associated with DDX20 include spinal muscular atrophy and muscular atrophy. DDX20 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: 350701 [Multi-domain]  Cd Length: 192  Bit Score: 88.48  E-value: 4.13e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 162 LVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLqeDLLAgseRSIRAVVIVPSRELAEQVN 241
Cdd:cd17943    1 VLEGLKAAGFQRPSPIQLAAIPLGLAGHDLIVQAKSGTGKTLVFVVIALESL--DLER---RHPQVLILAPTREIAVQIH 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 242 SVARSVSERFGLVVKVVGGGRGVGTIKAAFARGqPDILVSTPGALLKALWKRFISLSELYFLVIDEADTMFDDSFAGMLE 321
Cdd:cd17943   76 DVFKKIGKKLEGLKCEVFIGGTPVKEDKKKLKG-CHIAVGTPGRIKQLIELGALNVSHVRLFVLDEADKLMEGSFQKDVN 154

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 116268057 322 KILSHtqvasrlsetigLARKAQLVVVGATFPGGVGDVLSK 362
Cdd:cd17943  155 WIFSS------------LPKNKQVIAFSATYPKNLDNLLAR 183
DEADc_DDX59 cd17962
DEAD-box helicase domain of DEAD box protein 59; DDX59 plays an important role in lung cancer ...
 174-356 1.03e-19

DEAD-box helicase domain of DEAD box protein 59; DDX59 plays an important role in lung cancer development by promoting DNA replication. DDX59 knockdown mice showed reduced cell proliferation, anchorage-independent cell growth, and reduction of tumor formation. Recent work shows that EGFR and Ras regulate DDX59 during lung cancer development. Diseases associated with DDX59 (also called zinc finger HIT domain-containing protein 5) include orofaciodigital syndrome V and orofaciodigital syndrome. DDX59 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: 350720 [Multi-domain]  Cd Length: 193  Bit Score: 87.22  E-value: 1.03e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 174 PTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDllagsERSIRAVVIVPSRELAEQVNSVARSVSERFGL 253
Cdd:cd17962   13 PTPIQMQMIPVGLLGRDILASADTGSGKTAAFLLPVIIRCLTE-----HRNPSALILTPTRELAVQIEDQAKELMKGLPP 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 254 VVKVVGGGRGVGTIKAAFARGQPDILVSTPGALLKALWKRFISLSELYFLVIDEADTMFDDSFAGMLEKILSHtqvasrl 333
Cdd:cd17962   88 MKTALLVGGLPLPPQLYRLQQGVKVIIATPGRLLDILKQSSVELDNIKIVVVDEADTMLKMGFQQQVLDILEN------- 160

                        170       180
                 ....*....|....*....|...
gi 116268057 334 setigLARKAQLVVVGATFPGGV 356
Cdd:cd17962  161 -----ISHDHQTILVSATIPRGI 178
DEADc_DDX17 cd18050
DEAD-box helicase domain of DEAD box protein 17; DDX17 (also called DEAD Box Protein P72 or ...
 153-328 1.24e-19

DEAD-box helicase domain of DEAD box protein 17; DDX17 (also called DEAD Box Protein P72 or DEAD Box Protein P82) has a wide variety of functions including regulating the alternative splicing of exons exhibiting specific features such as the inclusion of AC-rich alternative exons in CD44 transcripts, playing a role in innate immunity, and promoting mRNA degradation mediated by the antiviral zinc-finger protein ZC3HAV1 in an ATPase-dependent manner. DDX17 synergizes with DDX5 and SRA1 RNA to activate MYOD1 transcriptional activity and is involved in skeletal muscle differentiation. DDX17 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: 350808 [Multi-domain]  Cd Length: 271  Bit Score: 88.91  E-value: 1.24e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 153 FHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLP-IIHRLQEDLLAGSERSIrAVVIV 231
Cdd:cd18050   64 FHQANFPQYVMDVLLDQNFKEPTPIQCQGFPLALSGRDMVGIAQTGSGKTLAYLLPaIVHINHQPYLERGDGPI-CLVLA 142

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 232 PSRELAEQVNSVARSVSERFGLVVKVVGGGRGVGTIKAAFARGQpDILVSTPGALLKALWKRFISLSELYFLVIDEADTM 311
Cdd:cd18050  143 PTRELAQQVQQVADDYGKSSRLKSTCIYGGAPKGPQIRDLERGV-EICIATPGRLIDFLEAGKTNLRRCTYLVLDEADRM 221

                        170
                 ....*....|....*..
gi 116268057 312 FDDSFAGMLEKILSHTQ 328
Cdd:cd18050  222 LDMGFEPQIRKIVDQIR 238
DEADc_DDX3 cd18051
DEAD-box helicase domain of DEAD box protein 3; DDX3 (also called helicase-like protein, DEAD ...
 159-323 6.87e-19

DEAD-box helicase domain of DEAD box protein 3; DDX3 (also called helicase-like protein, DEAD box, X isoform, or DDX14) has been reported to display a high level of RNA-independent ATPase activity stimulated by both RNA and DNA. This protein has multiple conserved domains and is thought to play roles in both the nucleus and cytoplasm. Nuclear roles include transcriptional regulation, mRNP assembly, pre-mRNA splicing, and mRNA export. In the cytoplasm, this protein is thought to be involved in translation, cellular signaling, and viral replication. Misregulation of this gene has been implicated in tumorigenesis. Diseases associated with DDX3 include mental retardation, X-linked 102 and agenesis of the corpus callosum, with facial anomalies and robin sequence. DDX3 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: 350809 [Multi-domain]  Cd Length: 249  Bit Score: 86.25  E-value: 6.87e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 159 CPELVET---LQRQNIIH----------PTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQED-----LLAG 220
Cdd:cd18051   16 CPPHIETfsdLDLGEIIRnnielarytkPTPVQKHAIPIIKSKRDLMACAQTGSGKTAAFLLPILSQIYEQgpgesLPSE 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 221 SERSIR------AVVIVPSRELAEQVNSVARSVSERfglvvkvvgggrgvGTIKAAFARGQPDI-------------LVS 281
Cdd:cd18051   96 SGYYGRrkqyplALVLAPTRELASQIYDEARKFAYR--------------SRVRPCVVYGGADIgqqmrdlergchlLVA 161

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 116268057 282 TPGALLKALWKRFISLSELYFLVIDEADTMFDDSFAGMLEKI 323
Cdd:cd18051  162 TPGRLVDMLERGKIGLDYCKYLVLDEADRMLDMGFEPQIRRI 203
DEADc_DDX18 cd17942
DEAD-box helicase domain of DEAD box protein 18; This DDX18 gene encodes a DEAD box protein ...
 166-325 1.84e-18

DEAD-box helicase domain of DEAD box protein 18; This DDX18 gene encodes a DEAD box protein and is activated by Myc protein. DDX18 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: 350700 [Multi-domain]  Cd Length: 198  Bit Score: 83.56  E-value: 1.84e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 166 LQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEdLLAGSERSIRAVVIVPSRELAEQVNSVAR 245
Cdd:cd17942    5 IEEMGFTKMTEIQAKSIPPLLEGRDVLGAAKTGSGKTLAFLIPAIELLYK-LKFKPRNGTGVIIISPTRELALQIYGVAK 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 246 SVSERFGLVVKVVGGGRGVGTIKAAFARGQPdILVSTPGALLKALW--KRFIsLSELYFLVIDEADTMFDDSFAGMLEKI 323
Cdd:cd17942   84 ELLKYHSQTFGIVIGGANRKAEAEKLGKGVN-ILVATPGRLLDHLQntKGFL-YKNLQCLIIDEADRILEIGFEEEMRQI 161


                 ..
gi 116268057 324 LS 325
Cdd:cd17942  162 IK 163
DEADc_DDX19_DDX25 cd17963
DEAD-box helicase domain of ATP-dependent RNA helicases DDX19 and DDX25; DDX19 (also called ...
 158-356 5.06e-18

DEAD-box helicase domain of ATP-dependent RNA helicases DDX19 and DDX25; DDX19 (also called DEAD box RNA helicase DEAD5) and DDX25 (also called gonadotropin-regulated testicular RNA helicase (GRTH)) are members 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: 350721 [Multi-domain]  Cd Length: 196  Bit Score: 82.24  E-value: 5.06e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 158 LCPELVETLQRQNIIHPTTVQLQTIPKILKG--RNILCAAETGSGKTLTYLLPIIHRLQEDLlagseRSIRAVVIVPSRE 235
Cdd:cd17963    1 LKPELLKGLYAMGFNKPSKIQETALPLILSDppENLIAQSQSGTGKTAAFVLAMLSRVDPTL-----KSPQALCLAPTRE 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 236 LAEQVNSVARSVSeRFGlvvkvvgggrgvgTIKAAFARGQPD----------ILVSTPGALLKALWKRFISLSELYFLVI 305
Cdd:cd17963   76 LARQIGEVVEKMG-KFT-------------GVKVALAVPGNDvprgkkitaqIVIGTPGTVLDWLKKRQLDLKKIKILVL 141

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 116268057 306 DEADTMFD-DSFAGMLEKILSHtqvasrlsetigLARKAQLVVVGATFPGGV 356
Cdd:cd17963  142 DEADVMLDtQGHGDQSIRIKRM------------LPRNCQILLFSATFPDSV 181
DEADc_DDX21_DDX50 cd17944
DEAD-box helicase domain of DEAD box proteins 21 and 50; DDX21 (also called Gu-Alpha and ...
 163-362 5.76e-18

DEAD-box helicase domain of DEAD box proteins 21 and 50; DDX21 (also called Gu-Alpha and nucleolar RNA helicase 2) is an RNA helicase that acts as a sensor of the transcriptional status of both RNA polymerase (Pol) I and II. It promotes ribosomal RNA (rRNA) processing and transcription from polymerase II (Pol II) and binds various RNAs, such as rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs. DDX50 (also called Gu-Beta, Nucleolar Protein Gu2, and malignant cell derived RNA helicase). DDX21 and DDX50 have similar genomic structures and are in tandem orientation on chromosome 10, suggesting that the two genes arose by gene duplication in evolution. Diseases associated with DDX21 include stomach disease and cerebral creatine deficiency syndrome 3. Diseases associated with DDX50 include rectal disease. Both are members 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. Their name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.


Pssm-ID: 350702 [Multi-domain]  Cd Length: 202  Bit Score: 82.59  E-value: 5.76e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 163 VETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLLAGSE-RSIRAVVIVPSRELAEQVN 241
Cdd:cd17944    2 IKLLQARGVTYLFPIQVKTFHPVYSGKDLIAQARTGTGKTFSFAIPLIEKLQEDQQPRKRgRAPKVLVLAPTRELANQVT 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 242 SVARSVSERFGLvvkvvgggrgvgtikAAFARGQP------------DILVSTPGALLKALWKRFISLSELYFLVIDEAD 309
Cdd:cd17944   82 KDFKDITRKLSV---------------ACFYGGTPyqqqifairngiDILVGTPGRIKDHLQNGRLDLTKLKHVVLDEVD 146

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 116268057 310 TMFDDSFAGMLEKILSHTQVASrlSEtiglaRKAQLVVVGATFPGGVGDVLSK 362
Cdd:cd17944  147 QMLDMGFAEQVEEILSVSYKKD--SE-----DNPQTLLFSATCPDWVYNVAKK 192
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 157-507 2.47e-17

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: 85.66  E-value: 2.47e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 157 NLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDllagseRSIRAVVIVPSREL 236
Cdd:COG1205   40 WLPPELRAALKKRGIERLYSHQAEAIEAARAGKNVVIATPTASGKSLAYLLPVLEALLED------PGATALYLYPTKAL 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 237 A-EQVNSVARSVSErfglvvkvvgggrGVGTIKAA------------FARGQPDILVSTP----GALL--KALWKRFisL 297
Cdd:COG1205  114 ArDQLRRLRELAEA-------------LGLGVRVAtydgdtppeerrWIREHPDIVLTNPdmlhYGLLphHTRWARF--F 178

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 298 SELYFLVIDEAdtmfddsfagmlekilsHT-------QVA------SRLSETIGlarkAQLVVVGATfpggvgdvlskAT 364
Cdd:COG1205  179 RNLRYVVIDEA-----------------HTyrgvfgsHVAnvlrrlRRICRHYG----SDPQFILAS-----------AT 226

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 365 -----DLAS---------ISTVKSR--MLHHLM--PHIKQTFLRvkgADKILELHQALKRAEQEQKGVLVFCNSASTV-- 424
Cdd:COG1205  227 ignpaEHAErltgrpvtvVDEDGSPrgERTFVLwnPPLVDDGIR---RSALAEAARLLADLVREGLRTLVFTRSRRGAel 303

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 425 --NWLGYSLEEMGVGHmRLQ---GEMPAAMREGVFRDFQRGKTNVLVCT-------DIAsrGLDtqrvgLIVNYDFPESQ 492
Cdd:COG1205  304 laRYARRALREPDLAD-RVAayrAGYLPEERREIERGLRSGELLGVVSTnalelgiDIG--GLD-----AVVLAGYPGTR 375

                        410
                 ....*....|....*
gi 116268057 493 TDYIHRAGRVGRAGG 507
Cdd:COG1205  376 ASFWQQAGRAGRRGQ 390
DEADc_DDX39 cd17950
DEAD-box helicase domain of DEAD box protein 39; DDX39A is involved in pre-mRNA splicing and ...
 153-314 1.06e-16

DEAD-box helicase domain of DEAD box protein 39; DDX39A is involved in pre-mRNA splicing and is required for the export of mRNA out of the nucleus. DDX39B is an essential splicing factor required for association of U2 small nuclear ribonucleoprotein with pre-mRNA, and it also plays an important role in mRNA export from the nucleus to the cytoplasm. Diseases associated with DDX39A (also called UAP56-Related Helicase, 49 kDa) include gastrointestinal stromal tumor and inflammatory bowel disease 6, while diseases associated with DDX39B (also called 56 kDa U2AF65-Associated Protein) include Plasmodium vivax malaria. DDX39 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: 350708 [Multi-domain]  Cd Length: 208  Bit Score: 78.93  E-value: 1.06e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 153 FHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDllagsERSIRAVVIVP 232
Cdd:cd17950    4 FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLSTLQQLEPV-----DGQVSVLVICH 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 233 SRELAEQVnsvaRSVSERFGLVVKVVGGGRGVGTI-----KAAFARGQPDILVSTPGALLKALWKRFISLSELYFLVIDE 307
Cdd:cd17950   79 TRELAFQI----SNEYERFSKYMPNVKTAVFFGGVpikkdIEVLKNKCPHIVVGTPGRILALVREKKLKLSHVKHFVLDE 154


                 ....*..
gi 116268057 308 ADTMFDD 314
Cdd:cd17950  155 CDKMLEQ 161
DEADc_EIF4A cd17939
DEAD-box helicase domain of eukaryotic initiation factor 4A; The eukaryotic initiation ...
 174-353 1.07e-16

DEAD-box helicase domain of eukaryotic initiation factor 4A; The eukaryotic initiation factor-4A (eIF4A) family consists of 3 proteins EIF4A1, EIF4A2, and EIF4A3. These factors are required for the binding of mRNA to 40S ribosomal subunits. In addition these proteins are helicases that function to unwind double-stranded RNA. EIF4A proteins are members 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: 350697 [Multi-domain]  Cd Length: 199  Bit Score: 78.52  E-value: 1.07e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 174 PTTVQLQTIPKILKGRNILCAAETGSGKTLTYllpIIHRLQEdlLAGSERSIRAVVIVPSRELAEQVNSVARSVSERFGL 253
Cdd:cd17939   20 PSAIQQRAIVPIIKGRDVIAQAQSGTGKTATF---SIGALQR--IDTTVRETQALVLAPTRELAQQIQKVVKALGDYMGV 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 254 VVKVVGGGRGVGTIKAAFARGqPDILVSTPGALLKALWKRFISLSELYFLVIDEADTMFDDSFAGMLEKILSHtqvasrl 333
Cdd:cd17939   95 KVHACIGGTSVREDRRKLQYG-PHIVVGTPGRVFDMLQRRSLRTDKIKMFVLDEADEMLSRGFKDQIYDIFQF------- 166

                        170       180
                 ....*....|....*....|
gi 116268057 334 setigLARKAQLVVVGATFP 353
Cdd:cd17939  167 -----LPPETQVVLFSATMP 181
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 188-339 5.48e-14

N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 69.35  E-value: 5.48e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 188 GRNILCAAETGSGKTLTYLLPIIHRLqedllagSERSIRAVVIVPSRELAEQvnsVARSVSERFGLVVKVVGGG-RGVGT 266
Cdd:cd00046    1 GENVLITAPTGSGKTLAALLAALLLL-------LKKGKKVLVLVPTKALALQ---TAERLRELFGPGIRVAVLVgGSSAE 70

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 116268057 267 IKAAFARGQPDILVSTPGALLKAL---WKRFisLSELYFLVIDEADtMFDDSFAGMLEKILSHTQVASRLSETIGL 339
Cdd:cd00046   71 EREKNKLGDADIIIATPDMLLNLLlreDRLF--LKDLKLIIVDEAH-ALLIDSRGALILDLAVRKAGLKNAQVILL 143
DEADc_EIF4AII_EIF4AI_DDX2 cd18046
DEAD-box helicase domain of eukaryotic initiation factor 4A-I and 4-II; Eukaryotic initiation ...
 153-362 5.69e-14

DEAD-box helicase domain of eukaryotic initiation factor 4A-I and 4-II; Eukaryotic initiation factor 4A-I (DDX2A) and eukaryotic initiation factor 4A-II (DDX2B) are involved in cap recognition and are required for mRNA binding to ribosome. They are 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: 350804 [Multi-domain]  Cd Length: 201  Bit Score: 70.94  E-value: 5.69e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 153 FHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLlagseRSIRAVVIVP 232
Cdd:cd18046    1 FDDMNLKESLLRGIYAYGFEKPSAIQQRAIMPCIKGYDVIAQAQSGTGKTATFSISILQQIDTSL-----KATQALVLAP 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 233 SRELAEQVNSVARSVSERFGLVVKV----VGGGRGVGTIKAAfargqPDILVSTPGALLKALWKRFISLSELYFLVIDEA 308
Cdd:cd18046   76 TRELAQQIQKVVMALGDYMGIKCHAciggTSVRDDAQKLQAG-----PHIVVGTPGRVFDMINRRYLRTDYIKMFVLDEA 150

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 116268057 309 DTMFDDSFAGMLEKILSHtqvasrlsetigLARKAQLVVVGATFPGGVGDVLSK 362
Cdd:cd18046  151 DEMLSRGFKDQIYDIFQK------------LPPDTQVVLLSATMPNDVLEVTTK 192
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
187-536 5.71e-14

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 74.68  E-value: 5.71e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 187 KGRNILCAAeTGSGKTLTYLLpIIHRLQEDLlagsersiRAVVIVPSRELAEQVnsvarsvSERFGLVVKVVGGGRGVGT 266
Cdd:COG1061  100 GGRGLVVAP-TGTGKTVLALA-LAAELLRGK--------RVLVLVPRRELLEQW-------AEELRRFLGDPLAGGGKKD 162

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 267 IKAafargqpDILVSTPGALLKALwkRFISLSELY-FLVIDEADTMFDDSFagmlEKILSHTQVASRLsetiGL----AR 341
Cdd:COG1061  163 SDA-------PITVATYQSLARRA--HLDELGDRFgLVIIDEAHHAGAPSY----RRILEAFPAAYRL----GLtatpFR 225

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 342 KAQLVVVGATFPGGVGDV-LSKATD---LASISTV-------KSRMLHHLMPHIKQTFLRVKGADKILELHQALKRAEQE 410
Cdd:COG1061  226 SDGREILLFLFDGIVYEYsLKEAIEdgyLAPPEYYgirvdltDERAEYDALSERLREALAADAERKDKILRELLREHPDD 305

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 411 QKgVLVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQRGKTNVLVCTDIASRGLDTQRVGLIVNYDFPE 490
Cdd:COG1061  306 RK-TLVFCSSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLRPTG 384

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*....
gi 116268057 491 SQTDYIHRAGRVGRAggSEGGE---VLSFVTQpwDVELVQKIETAARRR 536
Cdd:COG1061  385 SPREFIQRLGRGLRP--APGKEdalVYDFVGN--DVPVLEELAKDLRDL 429
DEADc_EIF4AIII_DDX48 cd18045
DEAD-box helicase domain of eukaryotic initiation factor 4A-III; Eukaryotic initiation factor ...
 153-362 7.25e-14

DEAD-box helicase domain of eukaryotic initiation factor 4A-III; Eukaryotic initiation factor 4A-III (EIF4AIII, also known as DDX48) is part of the exon junction complex (EJC) that plays a major role in posttranscriptional regulation of mRNA. EJC consists of four proteins (eIF4AIII, Barentsz [Btz], Mago, and Y14), mRNA, and ATP. DDX48 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: 350803 [Multi-domain]  Cd Length: 201  Bit Score: 70.57  E-value: 7.25e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 153 FHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLlagseRSIRAVVIVP 232
Cdd:cd18045    1 FETMGLREDLLRGIYAYGFEKPSAIQQRAIKPIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV-----RETQALILSP 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 233 SRELAEQVNSVARSVSERFGLVVKVVGGGRGVGTIKAAFARGQpDILVSTPGALLKALWKRFISLSELYFLVIDEADTMF 312
Cdd:cd18045   76 TRELAVQIQKVLLALGDYMNVQCHACIGGTSVGDDIRKLDYGQ-HIVSGTPGRVFDMIRRRSLRTRHIKMLVLDEADEML 154

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 116268057 313 DDSFAGMLEKILSHtqvasrlsetigLARKAQLVVVGATFPGGVGDVLSK 362
Cdd:cd18045  155 NKGFKEQIYDVYRY------------LPPATQVVLVSATLPQDILEMTNK 192
DEXHc_Hrq1-like cd17923
DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a ...
 178-310 3.21e-13

DEAH-box helicase domain of Hrq1 and similar proteins; 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. Hrq1 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350681 [Multi-domain]  Cd Length: 182  Bit Score: 68.00  E-value: 3.21e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 178 QLQTIPKILKGRNILCAAETGSGKTLTYLLPIIhrlqEDLLagSERSIRAVVIVPSRELAeqvNSVARSVSERFGLVVKV 257
Cdd:cd17923    5 QAEAIEAARAGRSVVVTTGTASGKSLCYQLPIL----EALL--RDPGSRALYLYPTKALA---QDQLRSLRELLEQLGLG 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 116268057 258 VGGGR----GVGTIKAAFARGQPDILVSTPG----ALLK--ALWKRFisLSELYFLVIDEADT 310
Cdd:cd17923   76 IRVATydgdTPREERRAIIRNPPRILLTNPDmlhyALLPhhDRWARF--LRNLRYVVLDEAHT 136
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 178-353 1.98e-12

DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350679 [Multi-domain]  Cd Length: 181  Bit Score: 65.75  E-value: 1.98e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 178 QLQTIPKI-LKGRNILCAAETGSGKTLTYLLPIIHRlqedlLAGSERsiRAVVIVPSRELAEQvnsVARSVSERFGLVVK 256
Cdd:cd17921    6 QREALRALyLSGDSVLVSAPTSSGKTLIAELAILRA-----LATSGG--KAVYIAPTRALVNQ---KEADLRERFGPLGK 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 257 VVGGGRGVGTIKAAFArGQPDILVSTP---GALLKALWKRFISLSELyfLVIDEADTMFDDSFAGMLEKILSHtqvasrl 333
Cdd:cd17921   76 NVGLLTGDPSVNKLLL-AEADILVATPeklDLLLRNGGERLIQDVRL--VVVDEAHLIGDGERGVVLELLLSR------- 145

                        170       180
                 ....*....|....*....|
gi 116268057 334 seTIGLARKAQLVVVGATFP 353
Cdd:cd17921  146 --LLRINKNARFVGLSATLP 163
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 189-308 8.01e-12

DEXH-box helicase domain of 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. Dicers exist throughout eukaryotes, and a subset have 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 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: 350792 [Multi-domain]  Cd Length: 200  Bit Score: 64.60  E-value: 8.01e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 189 RNILCAAETGSGKTLTYLLpIIHRLQEDLLAGSERSIRAVVIVPSRELAEQVNSVARSVS--ERFGLVVKVVGGGRGVGT 266
Cdd:cd18034   17 RNTIVVLPTGSGKTLIAVM-LIKEMGELNRKEKNPKKRAVFLVPTVPLVAQQAEAIRSHTdlKVGEYSGEMGVDKWTKER 95

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 116268057 267 IKAAFArgQPDILVSTPGALLKALWKRFISLSELYFLVIDEA 308
Cdd:cd18034   96 WKEELE--KYDVLVMTAQILLDALRHGFLSLSDINLLIFDEC 135
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 396-500 1.80e-11

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 61.72  E-value: 1.80e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 396 KILELHQALKRAEQEQKGVLVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQRGKTN--VLVCTDIASR 473
Cdd:cd18793   12 KLEALLELLEELREPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDPDIrvFLLSTKAGGV 91

                         90       100       110
                 ....*....|....*....|....*....|...
gi 116268057 474 GLDTQRVGLIVNYDFP-----ESQ-TDYIHRAG 500
Cdd:cd18793   92 GLNLTAANRVILYDPWwnpavEEQaIDRAHRIG 124
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 396-500 9.20e-11

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


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 64.48  E-value: 9.20e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 396 KILELHQALKRAEQEQKGVLVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQRGKTN--VLVCTDIASR 473
Cdd:COG0553  534 KLEALLELLEELLAEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQEGPEApvFLISLKAGGE 613

                         90       100       110
                 ....*....|....*....|....*....|...
gi 116268057 474 GLDTQRVGLIVNYDFP-----ESQ-TDYIHRAG 500
Cdd:COG0553  614 GLNLTAADHVIHYDLWwnpavEEQaIDRAHRIG 646
Lhr COG1201
Lhr-like helicase [Replication, recombination and repair];
173-283 4.60e-10

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


Pssm-ID: 440814 [Multi-domain]  Cd Length: 850  Bit Score: 62.43  E-value: 4.60e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 173 HPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRL-QEDLLAGSERSIRAVVIVPSRELAeqvNSVARSVSERF 251
Cdd:COG1201   24 APTPPQREAWPAIAAGESTLLIAPTGSGKTLAAFLPALDELaRRPRPGELPDGLRVLYISPLKALA---NDIERNLRAPL 100

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 116268057 252 GLVVKVVGGGRGVGTI-----------KAAFARGQPDILVSTP 283
Cdd:COG1201  101 EEIGEAAGLPLPEIRVgvrtgdtpaseRQRQRRRPPHILITTP 143
DEADc_DDX25 cd18048
DEAD-box helicase domain of DEAD box protein 25; DDX25 (also called gonadotropin-regulated ...
 149-356 5.60e-09

DEAD-box helicase domain of DEAD box protein 25; DDX25 (also called gonadotropin-regulated testicular RNA helicase (GRTH) is a testis-specific protein essential for completion of spermatogenesis. DDX25 is also a novel negative regulator of IFN pathway and facilitates RNA virus infection. Diseases associated with DDX25 include hydrolethalus syndrome, an autosomal recessive lethal malformation syndrome characterized by multiple developmental defects of fetus.. DDX25 (also called gonadotropin-regulated testicular RNA helicase) 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: 350806 [Multi-domain]  Cd Length: 229  Bit Score: 56.57  E-value: 5.60e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 149 SKKTFHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKG--RNILCAAETGSGKTLTYLLPIIHRLQedllaGSERSIR 226
Cdd:cd18048   16 SVKSFEELHLKEELLRGIYAMGFNRPSKIQENALPMMLADppQNLIAQSQSGTGKTAAFVLAMLSRVD-----ALKLYPQ 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 227 AVVIVPSRELAEQVNSVARSVSeRFGLVVKVVGGGRGVGTIKAAFARGQpdILVSTPGALLKALWK-RFISLSELYFLVI 305
Cdd:cd18048   91 CLCLSPTFELALQTGKVVEEMG-KFCVGIQVIYAIRGNRPGKGTDIEAQ--IVIGTPGTVLDWCFKlRLIDVTNISVFVL 167

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 116268057 306 DEADTMFDdsfagmlekILSHTQVASRLSETigLARKAQLVVVGATFPGGV 356
Cdd:cd18048  168 DEADVMIN---------VQGHSDHSVRVKRS--MPKECQMLLFSATFEDSV 207
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 444-508 7.71e-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: 54.52  E-value: 7.71e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 116268057 444 EMPAAMREGVFRDFQRGKTNVLVCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRvGRAGGS 508
Cdd:cd18802   73 LMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGR-ARAPNS 136
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 463-510 9.42e-09

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 52.32  E-value: 9.42e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 116268057 463 NVLVCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAGGSEG 510
Cdd:cd18785   24 EILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRGGKDEG 71
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
160-506 1.70e-08

Replicative superfamily II helicase [Replication, recombination and repair];


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 57.21  E-value: 1.70e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 160 PELVETLQRQNIIHPTTVQLQTIPK-ILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLlagsersiRAVVIVPSRELAE 238
Cdd:COG1204    9 EKVIEFLKERGIEELYPPQAEALEAgLLEGKNLVVSAPTASGKTLIAELAILKALLNGG--------KALYIVPLRALAS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 239 QvnsVARSVSERFGLVVKVVGGGRGVGTIKAAFArGQPDILVSTP---GALL--KALWKRFISLselyfLVIDEADtMFD 313
Cdd:COG1204   81 E---KYREFKRDFEELGIKVGVSTGDYDSDDEWL-GRYDILVATPeklDSLLrnGPSWLRDVDL-----VVVDEAH-LID 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 314 DSFAGM-LEKILshtqvaSRLSEtigLARKAQLVVVGATFpGGVGDVLS--KATDLAS-ISTVKSRMLHHLmpHIKQTFL 389
Cdd:COG1204  151 DESRGPtLEVLL------ARLRR---LNPEAQIVALSATI-GNAEEIAEwlDAELVKSdWRPVPLNEGVLY--DGVLRFD 218

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 390 RV--KGADKILEL-HQALKRAEQeqkgVLVFCNS-ASTVNW-----------------------------------LGYS 430
Cdd:COG1204  219 DGsrRSKDPTLALaLDLLEEGGQ----VLVFVSSrRDAESLakkladelkrrltpeereeleelaeellevseethTNEK 294

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 431 LEEM---GVG--HmrlqGEMPAAMREGVFRDFQRGKTNVLVCTDIASRGL----------DTQRVGlivNYDFPESqtDY 495
Cdd:COG1204  295 LADClekGVAfhH----AGLPSELRRLVEDAFREGLIKVLVATPTLAAGVnlparrviirDTKRGG---MVPIPVL--EF 365

                        410
                 ....*....|.
gi 116268057 496 IHRAGRVGRAG 506
Cdd:COG1204  366 KQMAGRAGRPG 376
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
382-513 3.62e-08

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 56.28  E-value: 3.62e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 382 PHIKQTFLRVKGAD----KILELHQALKRAEQEQKG--VLVFCNSASTVNWLGYSLEEMGVGHMRLQGEmpaAMREG--- 452
Cdd:COG1111  318 PRFRKAMRLAEEADiehpKLSKLREILKEQLGTNPDsrIIVFTQYRDTAEMIVEFLSEPGIKAGRFVGQ---ASKEGdkg 394

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 116268057 453 --------VFRDFQRGKTNVLVCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAGgseGGEV 513
Cdd:COG1111  395 ltqkeqieILERFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRKR---EGRV 460
DEXHc_LHR-like cd17922
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ...
 188-307 5.91e-08

DEXH-box helicase domain of LHR; 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 from 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: 350680 [Multi-domain]  Cd Length: 166  Bit Score: 52.59  E-value: 5.91e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 188 GRNILCAAETGSGKTLTYLLPIIHrlqeDLLAGSERSIRAVVIVPSRELAeqvNSVARSVSERFGLVVKVVGGGR----G 263
Cdd:cd17922    1 GRNVLIAAPTGSGKTEAAFLPALS----SLADEPEKGVQVLYISPLKALI---NDQERRLEEPLDEIDLEIPVAVrhgdT 73

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 116268057 264 VGTIKAAFARGQPDILVSTP---GALL--KALWKRFislSELYFLVIDE 307
Cdd:cd17922   74 SQSEKAKQLKNPPGILITTPeslELLLvnKKLRELF---AGLRYVVVDE 119
DEXHc_HFM1 cd18023
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ...
 177-353 2.91e-07

DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box helicase, required for crossover formation and complete synapsis of homologous chromosomes during meiosis. HFM1 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350781 [Multi-domain]  Cd Length: 206  Bit Score: 51.20  E-value: 2.91e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 177 VQLQTIPKILKG-RNILCAAETGSGKTLTYLLPIIHRLQEdLLAGSERSIRAVVIVPSRELAEQvnsVARSVSERFGLVV 255
Cdd:cd18023    5 IQSEVFPDLLYSdKNFVVSAPTGSGKTVLFELAILRLLKE-RNPLPWGNRKVVYIAPIKALCSE---KYDDWKEKFGPLG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 256 KVVGGGRGVGTIKAAFARGQPDILVSTPGA--LLKALWKRFISLSELYFLV-IDEADTMfDDSFAGMLEKILSHTQVASR 332
Cdd:cd18023   81 LSCAELTGDTEMDDTFEIQDADIILTTPEKwdSMTRRWRDNGNLVQLVALVlIDEVHII-KENRGATLEVVVSRMKTLSS 159

                        170       180
                 ....*....|....*....|..
gi 116268057 333 LSETIGL-ARKAQLVVVGATFP 353
Cdd:cd18023  160 SSELRGStVRPMRFVAVSATIP 181
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 453-504 4.52e-07

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: 49.28  E-value: 4.52e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 116268057 453 VFRDFQRGKTNVLVCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGR 504
Cdd:cd18801   82 VIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMIQRMGRTGR 133
DEXHc_RecQ cd17920
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ...
 178-308 4.82e-07

DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box helicase superfamily is a family of highly conserved DNA repair helicases. This domain contains the ATP-binding region.


Pssm-ID: 350678 [Multi-domain]  Cd Length: 200  Bit Score: 50.61  E-value: 4.82e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 178 QLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHR------------LQEDLLAG-SERSIRAVVIvpsrelaeqvNSvA 244
Cdd:cd17920   17 QLEAINAVLAGRDVLVVMPTGGGKSLCYQLPALLLdgvtlvvsplisLMQDQVDRlQQLGIRAAAL----------NS-T 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 116268057 245 RSVSERfglvvkvvgggrgvGTIKAAFARGQPDILVSTPGALLKALWKRFI----SLSELYFLVIDEA 308
Cdd:cd17920   86 LSPEEK--------------REVLLRIKNGQYKLLYVTPERLLSPDFLELLqrlpERKRLALIVVDEA 139
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 178-308 4.97e-07

DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex 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. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part 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: 350685 [Multi-domain]  Cd Length: 201  Bit Score: 50.51  E-value: 4.97e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 178 QLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEdllAGSERSIRAVVIVPSRELAEQVNSVARSVSERfGLVVKV 257
Cdd:cd17927    7 QLELAQPALKGKNTIICLPTGSGKTFVAVLICEHHLKK---FPAGRKGKVVFLANKVPLVEQQKEVFRKHFER-PGYKVT 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 116268057 258 VGGGRGVGTIKAAFARGQPDILVSTPGALLKALWK-RFISLSELYFLVIDEA 308
Cdd:cd17927   83 GLSGDTSENVSVEQIVESSDVIIVTPQILVNDLKSgTIVSLSDFSLLVFDEC 134
PRK13767 PRK13767
ATP-dependent helicase; Provisional
 175-237 5.21e-07

ATP-dependent helicase; Provisional


Pssm-ID: 237497 [Multi-domain]  Cd Length: 876  Bit Score: 52.58  E-value: 5.21e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 116268057 175 TTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRL----QEDLLagsERSIRAVVIVPSRELA 237
Cdd:PRK13767  34 TPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELfrlgREGEL---EDKVYCLYVSPLRALN 97
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 388-506 6.64e-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: 48.74  E-value: 6.64e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 388 FLRVKGADKILELHQALKRAEQEQKG--VLVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQRGKTNVL 465
Cdd:cd18794    5 FYSVRPKDKKDEKLDLLKRIKVEHLGgsGIIYCLSRKECEQVAARLQSKGISAAAYHAGLEPSDRRDVQRKWLRDKIQVI 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 116268057 466 VCTdIA-SRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAG 506
Cdd:cd18794   85 VAT-VAfGMGIDKPDVRFVIHYSLPKSMESYYQESGRAGRDG 125
ResIII pfam04851
Type III restriction enzyme, res subunit;
181-308 3.27e-06

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 47.28  E-value: 3.27e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057  181 TIPKILKG-RNILCAAETGSGKTLTYLLpIIHRLQEdllagSERSIRAVVIVPSRELAEQvnsvARsvsERFGLVVKVVG 259
Cdd:pfam04851  15 LLESIKNGqKRGLIVMATGSGKTLTAAK-LIARLFK-----KGPIKKVLFLVPRKDLLEQ----AL---EEFKKFLPNYV 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 116268057  260 GGRGVGT-IKAAFARGQPDILVSTPGALLKALWKRFISLSELYFLVI--DEA 308
Cdd:pfam04851  82 EIGEIISgDKKDESVDDNKIVVTTIQSLYKALELASLELLPDFFDVIiiDEA 133
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
178-506 3.86e-06

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 49.37  E-value: 3.86e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 178 QLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHR------------LQEDLLAG-SERSIRAVVIvpsrelaeqvNSvA 244
Cdd:COG0514   22 QEEIIEAVLAGRDALVVMPTGGGKSLCYQLPALLLpgltlvvspliaLMKDQVDAlRAAGIRAAFL----------NS-S 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 245 RSVSERfglvvkvvgggrgvGTIKAAFARGQPDIL-VStPGALLKALWKRFISLSELYFLVIDEAdtmfddsfagmleki 323
Cdd:COG0514   91 LSAEER--------------REVLRALRAGELKLLyVA-PERLLNPRFLELLRRLKISLFAIDEA--------------- 140

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 324 lsHTqvasrLSE----------TIGLARKA--QLVVVG--ATfpggvgdvlskATDlasisTVKSRMLHHL-MPHIKQ-- 386
Cdd:COG0514  141 --HC-----ISQwghdfrpdyrRLGELRERlpNVPVLAltAT-----------ATP-----RVRADIAEQLgLEDPRVfv 197

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 387 ----------TFLRVKGADKILELHQALKraEQEQKGVLVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRD 456
Cdd:COG0514  198 gsfdrpnlrlEVVPKPPDDKLAQLLDFLK--EHPGGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEREANQDR 275

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|.
gi 116268057 457 FQRGKTNVLVCTdIA-SRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAG 506
Cdd:COG0514  276 FLRDEVDVIVAT-IAfGMGIDKPDVRFVIHYDLPKSIEAYYQEIGRAGRDG 325
DEADc_DDX19 cd18047
DEAD-box helicase domain of DEAD box protein 19; DDX19 is an RNA helicase involved in both ...
 151-356 1.38e-05

DEAD-box helicase domain of DEAD box protein 19; DDX19 is an RNA helicase involved in both mRNA (mRNA) export from the nucleus into the cytoplasm and in mRNA translation. DDX19 functions in the nucleus in resolving RNA:DNA hybrids (R-loops). Activation of a DNA damage response pathway dependent upon the ATR kinase, a major regulator of replication fork progression, stimulates translocation of DDX19 from the cytoplasm into the nucleus. Only nuclear Ddx19 is competent to resolve R-loops. DDX19 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: 350805 [Multi-domain]  Cd Length: 205  Bit Score: 46.25  E-value: 1.38e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 151 KTFHCFNLCPELVETLQRQNIIHPTTVQLQTIPKILKG--RNILCAAETGSGKTLTYLLPIIHRLQEdllagSERSIRAV 228
Cdd:cd18047    1 KSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEppQNLIAQSQSGTGKTAAFVLAMLSQVEP-----ANKYPQCL 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 229 VIVPSRELAEQVNSVARSVSeRFGLVVKVVGGGRGVGTIKAAFARGQpdILVSTPGALLKALWK-RFISLSELYFLVIDE 307
Cdd:cd18047   76 CLSPTYELALQTGKVIEQMG-KFYPELKLAYAVRGNKLERGQKISEQ--IVIGTPGTVLDWCSKlKFIDPKKIKVFVLDE 152

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 116268057 308 ADTMFDDSfagmlekilSHTQVASRLSETigLARKAQLVVVGATFPGGV 356
Cdd:cd18047  153 ADVMIATQ---------GHQDQSIRIQRM--LPRNCQMLLFSATFEDSV 190
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
 185-239 1.20e-04

DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350786 [Multi-domain]  Cd Length: 177  Bit Score: 43.09  E-value: 1.20e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 116268057 185 ILKGRNILCAAETGSGKTLTYLLPIIHRlqedLLAGSersiRAVVIVPSRELAEQ 239
Cdd:cd18028   14 LLKGENLLISIPTASGKTLIAEMAMVNT----LLEGG----KALYLVPLRALASE 60
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 412-508 2.98e-04

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: 41.48  E-value: 2.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 412 KGVLVFCNSASTVNWLGYSL----------EEMGVGHmrlqGEMPAAMREGVFRDFQRGKTNVLVCTDIASRGLDTQRVG 481
Cdd:cd18796   39 KSTLVFTNTRSQAERLAQRLrelcpdrvppDFIALHH----GSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDVD 114

                         90       100
                 ....*....|....*....|....*..
gi 116268057 482 LIVNYDFPESQTDYIHRAGRVGRAGGS 508
Cdd:cd18796  115 LVIQIGSPKSVARLLQRLGRSGHRPGA 141
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 441-516 4.16e-04

C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 41.18  E-value: 4.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 441 LQGEMPAAMREGVFRDFQRGKTNVLVCTDIASRGLDTQRVGLIVNYD---FPESQtdyIHR-AGRVGRaggsegGEVLSF 516
Cdd:cd18811   67 LHGRLKSDEKDAVMAEFREGEVDILVSTTVIEVGVDVPNATVMVIEDaerFGLSQ---LHQlRGRVGR------GDHQSY 137
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 172-239 4.81e-04

DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) 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: 350794 [Multi-domain]  Cd Length: 204  Bit Score: 41.69  E-value: 4.81e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 116268057 172 IHPTTVQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQEDLLAGSERsiRAVVIVPSRELAEQ 239
Cdd:cd18036    1 LELRNYQLELVLPALRGKNTIICAPTGSGKTRVAVYICRHHLEKRRSAGEKG--RVVVLVNKVPLVEQ 66
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 382-506 5.54e-04

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 42.78  E-value: 5.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 382 PHIKQTFLrvkgaDKILELHQaLKRAEQEQKGV--LVFCNSASTVNWLGYSLEEMGVGHMRLQGEMPAAMREGVFRDFQR 459
Cdd:PRK11057 211 PNIRYTLV-----EKFKPLDQ-LMRYVQEQRGKsgIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQR 284

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 116268057 460 GKTNVLVCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRAG 506
Cdd:PRK11057 285 DDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDG 331
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
 441-504 6.38e-04

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: 40.71  E-value: 6.38e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 116268057 441 LQGEMPAAMREGVFRDFQRGKTNVLVCTDIASRGLDTQRVGLIVNYD---FPESQtdyIHR-AGRVGR 504
Cdd:cd18792   66 LHGKMTEDEKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIIEDadrFGLSQ---LHQlRGRVGR 130
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
 435-506 7.26e-04

C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350197 [Multi-domain]  Cd Length: 151  Bit Score: 40.40  E-value: 7.26e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 435 GVGHmrlqGEMPAAMREGVFRDFQRGKTNVLVCTDIASRGLdtqrvglivnyDFPESQTDYIHRA------------GRV 502
Cdd:cd18810   55 AIAH----GQMTENELEEVMLEFAKGEYDILVCTTIIESGI-----------DIPNANTIIIERAdkfglaqlyqlrGRV 119


                 ....
gi 116268057 503 GRAG 506
Cdd:cd18810  120 GRSK 123
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 178-308 8.85e-04

DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part 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: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 39.98  E-value: 8.85e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 178 QLQTIPKILKGRN----ILCAAeTGSGKTLTYLLPIIHRLQEdllagsersiRAVVIVPSRELAEQvnsvarsVSERFGL 253
Cdd:cd17926    5 QEEALEAWLAHKNnrrgILVLP-TGSGKTLTALALIAYLKEL----------RTLIVVPTDALLDQ-------WKERFED 66

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 116268057 254 VVKVVGGGRGVGTIKAAFARGqpDILVSTPGALLKALwKRFISLSELY-FLVIDEA 308
Cdd:cd17926   67 FLGDSSIGLIGGGKKKDFDDA--NVVVATYQSLSNLA-EEEKDLFDQFgLLIVDEA 119
DEXHc_RecQ4-like cd18018
DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) ...
 178-308 8.95e-04

DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Mutations cause Rothmund-Thomson/RAPADILINO/Baller-Gerold syndrome.


Pssm-ID: 350776 [Multi-domain]  Cd Length: 201  Bit Score: 40.70  E-value: 8.95e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 178 QLQTIPKILKGRNILCAAETGSGKTLTYLLPIIhrlqedLLAGSERSIrAVVIVPSREL-AEQVNSVARSVSerfGLVVK 256
Cdd:cd18018   17 QEEAIARLLSGRSTLVVLPTGAGKSLCYQLPAL------LLRRRGPGL-TLVVSPLIALmKDQVDALPRAIK---AAALN 86

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 116268057 257 VVGGGRGVGTIKAAFARGQPDILVSTPGALLKALWKRFISLSE-LYFLVIDEA 308
Cdd:cd18018   87 SSLTREERRRILEKLRAGEVKILYVSPERLVNESFRELLRQTPpISLLVVDEA 139
PRK00254 PRK00254
ski2-like helicase; Provisional
 185-239 9.51e-04

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 42.11  E-value: 9.51e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 116268057 185 ILKGRNILCAAETGSGKTLTYLLPIIHRLQEDllAGsersiRAVVIVPSRELAEQ 239
Cdd:PRK00254  36 VLEGKNLVLAIPTASGKTLVAEIVMVNKLLRE--GG-----KAVYLVPLKALAEE 83
PRK13766 PRK13766
Hef nuclease; Provisional
 395-519 2.36e-03

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 41.01  E-value: 2.36e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 395 DKILELhqaLKRAEQEQKG--VLVFCNSASTVNWLGYSLEEMGVGHMRLQGEmpaAMREG-----------VFRDFQRGK 461
Cdd:PRK13766 350 EKLREI---VKEQLGKNPDsrIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQ---ASKDGdkgmsqkeqieILDKFRAGE 423

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 116268057 462 TNVLVCTDIASRGLDTQRVGLIVNYDFPESQTDYIHRAGRVGRaggSEGGEVLSFVTQ 519
Cdd:PRK13766 424 FNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGR---QEEGRVVVLIAK 478
DEXHc_RecQ1 cd18015
DEXH-box helicase domain of RecQ1; ATP-dependent DNA helicase Q1 (RecQ1) is part of the RecQ ...
 178-208 4.39e-03

DEXH-box helicase domain of RecQ1; ATP-dependent DNA helicase Q1 (RecQ1) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350773 [Multi-domain]  Cd Length: 209  Bit Score: 38.89  E-value: 4.39e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 116268057 178 QLQTIPKILKGRNILCAAETGSGKTLTYLLP 208
Cdd:cd18015   23 QLETINATMAGRDVFLVMPTGGGKSLCYQLP 53
DEXHc_RecG cd17918
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ...
 174-307 5.92e-03

DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase RecG family is part of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350676 [Multi-domain]  Cd Length: 180  Bit Score: 38.17  E-value: 5.92e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 174 PTTVQLQTIPKILKG------RNILCAAETGSGKTLTYLLPIihrlqedlLAGSERSIRAVVIVPSRELAEQVNSVARsv 247
Cdd:cd17918   16 LTKDQAQAIKDIEKDlhspepMDRLLSGDVGSGKTLVALGAA--------LLAYKNGKQVAILVPTEILAHQHYEEAR-- 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 248 sERFGLVVKVVGGGRGVGTIKAafargQPDILVSTpGALLKALWKRfislSELYFLVIDE 307
Cdd:cd17918   86 -KFLPFINVELVTGGTKAQILS-----GISLLVGT-HALLHLDVKF----KNLDLVIVDE 134
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 177-308 6.18e-03

DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef 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: 350793 [Multi-domain]  Cd Length: 181  Bit Score: 37.88  E-value: 6.18e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116268057 177 VQLQTIPKILKGRNILCAAETGSGKTLTYLLPIIHRLQedllagsERSIRAVVIVPSRELAEQVNSVARSVserFGLVVK 256
Cdd:cd18035    5 LYQVLIAAVALNGNTLIVLPTGLGKTIIAILVAADRLT-------KKGGKVLILAPSRPLVEQHAENLKRV---LNIPDK 74

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 116268057 257 VVGGGRGVGTIKAAFARGQPDILVSTPGALLKALWKRFISLSELYFLVIDEA 308
Cdd:cd18035   75 ITSLTGEVKPEERAERWDASKIIVATPQVIENDLLAGRITLDDVSLLIFDEA 126
SF2_C_priA cd18804
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ...
 455-514 7.68e-03

C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350191 [Multi-domain]  Cd Length: 238  Bit Score: 38.38  E-value: 7.68e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 116268057 455 RDFQRGKTNVLVCTDIASRGLDTQRVGL--IVNYDFPESQTDYihRAG-RV--------GRAG-GSEGGEVL 514
Cdd:cd18804  138 DQFERGEIDILIGTQMIAKGLDFPNVTLvgILNADSGLNSPDF--RASeRAfqlltqvsGRAGrGDKPGKVI 207
 
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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