Psyllid ID: psy7789

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------
Protein Sequence
MGIPFISALPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLEN
Secondary Structure (PSIPRED)
ccccccccccccccEEEEEccccHHHHHHHHHccccEEEccccHHHHHHHcccEEcccEEEEEccccccccccccHHHHHHHHcccccccEEEEEEccccHHHHHHHHHHHcccEEEEEcccccccccEEEEEEEEcccHHHHHHHHHHccccccEEEEEcccccHHHHHHHHHHccccEEEEccccccHHHHHccc
Secondary Structure Prediction (SSPRO)
ccHHHHcccccccEEEEEEccccccHHHHHHHcccEEEEEcccHHHHHHHcccccHcHEEEEEEcHHHHHHHcccHHHHHHHHHHccHHHcEEEEEccccHHHHHHHHHHHcccEEEEEEccccccccEEEEEEEccHHHHHHHHHHHHHcccccEEEEEEccccHHHHHHHHHHccccEEEEcccccHHHHHHHcc
Coil and Loop (DISEMBL)
mgipfisalpiplrtclaiggvpmnqslDVIKKgchmmvatpgrlMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSalvkpitinvgragaasMNVVQEVEYVKQEAKIVYLLEClqkteppvliFAEKKQDVDAIHEYLLlkgkpfftlkslkedqnnqtlen
Flexible Loop (DISEMBL)
mgipfisalpiPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKgkpfftlkslkedqnnqtlen
Low Complexity Region (SEG)
MGIPFISALPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLEN
Disordered region (IsUnstruct)
**IPFISALPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLK*************
Disordered Region (DISOPRED)
**IPF**ALPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKE*********
Disordered Region (DISEMBL)
MGIPFISALPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKED********
Disordered Region (DISPRO)
MGIPFISALPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLK**********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGIPFISALPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLEN
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

No hits with e-value below 0.001 by BLAST

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	197
FB|FBgn0015331	619	abs "abstrakt" [Drosophila mel	0.873	0.277	0.809	4e-74
UNIPROTKB|F1NAH6	607	LOC100859810 "Uncharacterized	0.939	0.304	0.759	6.1e-71
UNIPROTKB|A3KN07	622	DDX41 "Uncharacterized protein	0.918	0.290	0.747	2.4e-69
UNIPROTKB|E2R052	622	DDX41 "Uncharacterized protein	0.918	0.290	0.747	2.4e-69
UNIPROTKB|J9NZF6	649	DDX41 "Uncharacterized protein	0.918	0.278	0.747	2.4e-69
UNIPROTKB|J3KNN5	640	DDX41 "Probable ATP-dependent	0.918	0.282	0.747	2.4e-69
UNIPROTKB|Q9UJV9	622	DDX41 "Probable ATP-dependent	0.918	0.290	0.747	2.4e-69
MGI|MGI:1920185	622	Ddx41 "DEAD (Asp-Glu-Ala-Asp)	0.918	0.290	0.747	2.4e-69
RGD|1311758	622	Ddx41 "DEAD (Asp-Glu-Ala-Asp)	0.918	0.290	0.747	2.4e-69
RGD|1559513	621	RGD1559513 "similar to DEAD (A	0.923	0.293	0.733	1.7e-68

FB|FBgn0015331 abs "abstrakt" [Drosophila melanogaster (taxid:7227)]

 Score = 748 (268.4 bits), Expect = 4.0e-74, P = 4.0e-74
 Identities = 140/173 (80%), Positives = 164/173 (94%)

Query:     6 ISALPIP-LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCL 64
             + A  +P +R+CLA+GG+P++++LDVI +G H++VATPGRLMDMLDKK+++LD+CRYLC+
Sbjct:   280 LQACGMPEIRSCLAMGGLPVSEALDVISRGVHIVVATPGRLMDMLDKKILTLDMCRYLCM 339

Query:    65 DEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGA 124
             DEADRM+DMGFEEDVRTIFSFF+GQRQTLLFSATMPKKIQNFARSALVKP+TINVGRAGA
Sbjct:   340 DEADRMIDMGFEEDVRTIFSFFKGQRQTLLFSATMPKKIQNFARSALVKPVTINVGRAGA 399

Query:   125 ASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKG 177
             ASMNV Q+VEYVKQEAK+VYLL+CLQKT PPVLIFAEKKQDVD IHEYLLLKG
Sbjct:   400 ASMNVTQQVEYVKQEAKVVYLLDCLQKTAPPVLIFAEKKQDVDCIHEYLLLKG 452

GO:0008026 "ATP-dependent helicase activity" evidence=ISS

GO:0004004 "ATP-dependent RNA helicase activity" evidence=NAS

GO:0004386 "helicase activity" evidence=ISS

GO:0030010 "establishment of cell polarity" evidence=NAS

GO:0007399 "nervous system development" evidence=NAS

GO:0005634 "nucleus" evidence=NAS

GO:0009653 "anatomical structure morphogenesis" evidence=NAS

GO:0006915 "apoptotic process" evidence=NAS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC

GO:0071011 "precatalytic spliceosome" evidence=IDA

UNIPROTKB|F1NAH6 LOC100859810 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 718 (257.8 bits), Expect = 6.1e-71, P = 6.1e-71
 Identities = 142/187 (75%), Positives = 161/187 (86%)

Query:     8 ALPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEA 67
             +LP PLR  L IGG+ + + ++ IK G HMMVATPGRLMD+L KKMVSLD+CRYL LDEA
Sbjct:   284 SLP-PLRCALCIGGMSVKEQMETIKHGVHMMVATPGRLMDLLQKKMVSLDICRYLALDEA 342

Query:    68 DRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASM 127
             DRM+DMGFE D+RTIFS+F+GQRQTLLFSATMPKKIQNFA+SALVKPITINVGRAGAAS+
Sbjct:   343 DRMIDMGFEGDIRTIFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPITINVGRAGAASL 402

Query:   128 NVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLK 187
             +VVQEVEYVK+EAK+VYLLECLQKT PPVLIFAEKK DVDAIHEYLLLKG     +   K
Sbjct:   403 DVVQEVEYVKEEAKMVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGK 462

Query:   188 EDQNNQT 194
              DQ  +T
Sbjct:   463 -DQEERT 468

GO:0008026 "ATP-dependent helicase activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0035458 "cellular response to interferon-beta" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0051607 "defense response to virus" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

UNIPROTKB|A3KN07 DDX41 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 703 (252.5 bits), Expect = 2.4e-69, P = 2.4e-69
 Identities = 136/182 (74%), Positives = 157/182 (86%)

Query:    13 LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
             LR  L IGG+ + + ++ I+ G HMMVATPGRLMD+L KKMVSLD+CRYL LDEADRM+D
Sbjct:   292 LRCALCIGGMSVKEQMETIRHGVHMMVATPGRLMDLLQKKMVSLDICRYLALDEADRMID 351

Query:    73 MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQE 132
             MGFE D+RTIFS+F+GQRQTLLFSATMPKKIQNFA+SALVKP+TINVGRAGAAS++V+QE
Sbjct:   352 MGFEGDIRTIFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINVGRAGAASLDVIQE 411

Query:   133 VEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNN 192
             VEYVK+EAK+VYLLECLQKT PPVLIFAEKK DVDAIHEYLLLKG     +   K DQ  
Sbjct:   412 VEYVKEEAKMVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGK-DQEE 470

Query:   193 QT 194
             +T
Sbjct:   471 RT 472

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008026 "ATP-dependent helicase activity" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0051607 "defense response to virus" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0035458 "cellular response to interferon-beta" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

UNIPROTKB|E2R052 DDX41 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 703 (252.5 bits), Expect = 2.4e-69, P = 2.4e-69
 Identities = 136/182 (74%), Positives = 157/182 (86%)

Query:    13 LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
             LR  L IGG+ + + ++ I+ G HMMVATPGRLMD+L KKMVSLD+CRYL LDEADRM+D
Sbjct:   292 LRCALCIGGMSVKEQMETIRHGVHMMVATPGRLMDLLQKKMVSLDICRYLALDEADRMID 351

Query:    73 MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQE 132
             MGFE D+RTIFS+F+GQRQTLLFSATMPKKIQNFA+SALVKP+TINVGRAGAAS++V+QE
Sbjct:   352 MGFEGDIRTIFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINVGRAGAASLDVIQE 411

Query:   133 VEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNN 192
             VEYVK+EAK+VYLLECLQKT PPVLIFAEKK DVDAIHEYLLLKG     +   K DQ  
Sbjct:   412 VEYVKEEAKMVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGK-DQEE 470

Query:   193 QT 194
             +T
Sbjct:   471 RT 472

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0051607 "defense response to virus" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0035458 "cellular response to interferon-beta" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008026 "ATP-dependent helicase activity" evidence=IEA

UNIPROTKB|J9NZF6 DDX41 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 703 (252.5 bits), Expect = 2.4e-69, P = 2.4e-69
 Identities = 136/182 (74%), Positives = 157/182 (86%)

Query:    13 LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
             LR  L IGG+ + + ++ I+ G HMMVATPGRLMD+L KKMVSLD+CRYL LDEADRM+D
Sbjct:   319 LRCALCIGGMSVKEQMETIRHGVHMMVATPGRLMDLLQKKMVSLDICRYLALDEADRMID 378

Query:    73 MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQE 132
             MGFE D+RTIFS+F+GQRQTLLFSATMPKKIQNFA+SALVKP+TINVGRAGAAS++V+QE
Sbjct:   379 MGFEGDIRTIFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINVGRAGAASLDVIQE 438

Query:   133 VEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNN 192
             VEYVK+EAK+VYLLECLQKT PPVLIFAEKK DVDAIHEYLLLKG     +   K DQ  
Sbjct:   439 VEYVKEEAKMVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGK-DQEE 497

Query:   193 QT 194
             +T
Sbjct:   498 RT 499

GO:0005524 "ATP binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008026 "ATP-dependent helicase activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|J3KNN5 DDX41 "Probable ATP-dependent RNA helicase DDX41" [Homo sapiens (taxid:9606)]

 Score = 703 (252.5 bits), Expect = 2.4e-69, P = 2.4e-69
 Identities = 136/182 (74%), Positives = 157/182 (86%)

Query:    13 LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
             LR  L IGG+ + + ++ I+ G HMMVATPGRLMD+L KKMVSLD+CRYL LDEADRM+D
Sbjct:   310 LRCALCIGGMSVKEQMETIRHGVHMMVATPGRLMDLLQKKMVSLDICRYLALDEADRMID 369

Query:    73 MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQE 132
             MGFE D+RTIFS+F+GQRQTLLFSATMPKKIQNFA+SALVKP+TINVGRAGAAS++V+QE
Sbjct:   370 MGFEGDIRTIFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINVGRAGAASLDVIQE 429

Query:   133 VEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNN 192
             VEYVK+EAK+VYLLECLQKT PPVLIFAEKK DVDAIHEYLLLKG     +   K DQ  
Sbjct:   430 VEYVKEEAKMVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGK-DQEE 488

Query:   193 QT 194
             +T
Sbjct:   489 RT 490

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008026 "ATP-dependent helicase activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|Q9UJV9 DDX41 "Probable ATP-dependent RNA helicase DDX41" [Homo sapiens (taxid:9606)]

 Score = 703 (252.5 bits), Expect = 2.4e-69, P = 2.4e-69
 Identities = 136/182 (74%), Positives = 157/182 (86%)

Query:    13 LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
             LR  L IGG+ + + ++ I+ G HMMVATPGRLMD+L KKMVSLD+CRYL LDEADRM+D
Sbjct:   292 LRCALCIGGMSVKEQMETIRHGVHMMVATPGRLMDLLQKKMVSLDICRYLALDEADRMID 351

Query:    73 MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQE 132
             MGFE D+RTIFS+F+GQRQTLLFSATMPKKIQNFA+SALVKP+TINVGRAGAAS++V+QE
Sbjct:   352 MGFEGDIRTIFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINVGRAGAASLDVIQE 411

Query:   133 VEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNN 192
             VEYVK+EAK+VYLLECLQKT PPVLIFAEKK DVDAIHEYLLLKG     +   K DQ  
Sbjct:   412 VEYVKEEAKMVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGK-DQEE 470

Query:   193 QT 194
             +T
Sbjct:   471 RT 472

GO:0008026 "ATP-dependent helicase activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0035458 "cellular response to interferon-beta" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0051607 "defense response to virus" evidence=IEA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0007275 "multicellular organismal development" evidence=TAS

GO:0006396 "RNA processing" evidence=TAS

GO:0006915 "apoptotic process" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

MGI|MGI:1920185 Ddx41 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 41" [Mus musculus (taxid:10090)]

 Score = 703 (252.5 bits), Expect = 2.4e-69, P = 2.4e-69
 Identities = 136/182 (74%), Positives = 157/182 (86%)

Query:    13 LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
             LR  L IGG+ + + ++ I+ G HMMVATPGRLMD+L KKMVSLD+CRYL LDEADRM+D
Sbjct:   292 LRCALCIGGMSVKEQMETIRHGVHMMVATPGRLMDLLQKKMVSLDICRYLALDEADRMID 351

Query:    73 MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQE 132
             MGFE D+RTIFS+F+GQRQTLLFSATMPKKIQNFA+SALVKP+TINVGRAGAAS++V+QE
Sbjct:   352 MGFEGDIRTIFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINVGRAGAASLDVIQE 411

Query:   133 VEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNN 192
             VEYVK+EAK+VYLLECLQKT PPVLIFAEKK DVDAIHEYLLLKG     +   K DQ  
Sbjct:   412 VEYVKEEAKMVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGK-DQEE 470

Query:   193 QT 194
             +T
Sbjct:   471 RT 472

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IDA

GO:0003723 "RNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IDA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008026 "ATP-dependent helicase activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0035458 "cellular response to interferon-beta" evidence=IMP

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0046872 "metal ion binding" evidence=IEA

GO:0051607 "defense response to virus" evidence=IMP

GO:0071013 "catalytic step 2 spliceosome" evidence=ISO

RGD|1311758 Ddx41 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 41" [Rattus norvegicus (taxid:10116)]

 Score = 703 (252.5 bits), Expect = 2.4e-69, P = 2.4e-69
 Identities = 136/182 (74%), Positives = 157/182 (86%)

Query:    13 LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
             LR  L IGG+ + + ++ I+ G HMMVATPGRLMD+L KKMVSLD+CRYL LDEADRM+D
Sbjct:   292 LRCALCIGGMSVKEQMETIRHGVHMMVATPGRLMDLLQKKMVSLDICRYLALDEADRMID 351

Query:    73 MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQE 132
             MGFE D+RTIFS+F+GQRQTLLFSATMPKKIQNFA+SALVKP+TINVGRAGAAS++V+QE
Sbjct:   352 MGFEGDIRTIFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINVGRAGAASLDVIQE 411

Query:   133 VEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNN 192
             VEYVK+EAK+VYLLECLQKT PPVLIFAEKK DVDAIHEYLLLKG     +   K DQ  
Sbjct:   412 VEYVKEEAKMVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGK-DQEE 470

Query:   193 QT 194
             +T
Sbjct:   471 RT 472

GO:0003677 "DNA binding" evidence=IEA;ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005783 "endoplasmic reticulum" evidence=IEA;ISO

GO:0008026 "ATP-dependent helicase activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0035458 "cellular response to interferon-beta" evidence=IEA;ISO

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA;ISO

GO:0051607 "defense response to virus" evidence=IEA;ISO

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=ISO

RGD|1559513 RGD1559513 "similar to DEAD (Asp-Glu-Ala-Asp) box polypeptide 41" [Rattus norvegicus (taxid:10116)]

 Score = 695 (249.7 bits), Expect = 1.7e-68, P = 1.7e-68
 Identities = 135/184 (73%), Positives = 158/184 (85%)

Query:    12 PLRTC-LAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRM 70
             PL  C L IGGV + + ++ ++ G H+MVATPGRLMD+L KKMVSLD+CRYL LDEADRM
Sbjct:   289 PLLHCALCIGGVSLKEQMETMRHGVHIMVATPGRLMDLLQKKMVSLDICRYLALDEADRM 348

Query:    71 VDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVV 130
             +DMGFE D+RTIFS+F+GQRQTLLFSATMPKKIQNFA+SALVKP+TINVGRAGAAS++V+
Sbjct:   349 IDMGFEGDIRTIFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINVGRAGAASLDVI 408

Query:   131 QEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQ 190
             QEVEYVK+EAK+VYLLECLQKT PPVLIFA+KK DVDAIHEYLLLKG     +   K DQ
Sbjct:   409 QEVEYVKEEAKMVYLLECLQKTPPPVLIFAKKKADVDAIHEYLLLKGVEAVAIHGGK-DQ 467

Query:   191 NNQT 194
               +T
Sbjct:   468 EERT 471

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0008026 "ATP-dependent helicase activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4	0.691

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	197
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	1e-46
cd00268	203	cd00268, DEADc, DEAD-box helicases	2e-44
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	1e-40
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	1e-33
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	4e-28
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	3e-27
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	1e-25
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	3e-25
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	4e-25
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	6e-24
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-22
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	4e-18
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	5e-18
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	9e-18
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	1e-17

>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]

 Score =  159 bits (405), Expect = 1e-46
 Identities = 63/182 (34%), Positives = 96/182 (52%), Gaps = 4/182 (2%)

Query: 6   ISALPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLD 65
           +      LR  +  GGV + + ++ +K+G  ++VATPGRL+D++ +  + L     L LD
Sbjct: 122 LGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLD 181

Query: 66  EADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAG-- 123
           EADRM+DMGF +D+  I       RQTLLFSATMP  I+  AR  L  P+ I V      
Sbjct: 182 EADRMLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLE 241

Query: 124 AASMNVVQEVEYVK-QEAKIVYLLECLQKTEPP-VLIFAEKKQDVDAIHEYLLLKGKPFF 181
                + Q    V+ +E K+  LL+ L+  +   V++F   K+ V+ + E L  +G    
Sbjct: 242 RTLKKIKQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVA 301

Query: 182 TL 183
            L
Sbjct: 302 AL 303

Length = 513

>gnl|CDD|238167 cd00268, DEADc, DEAD-box helicases

 Score =  146 bits (371), Expect = 2e-44
 Identities = 49/106 (46%), Positives = 73/106 (68%)

Query: 13  LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
           L+  +  GG  +++ +  +K+G H++VATPGRL+D+L++  + L   +YL LDEADRM+D
Sbjct: 98  LKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLD 157

Query: 73  MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITIN 118
           MGFE+ +R I       RQTLLFSATMPK++++ AR  L  P+ I 
Sbjct: 158 MGFEDQIREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRIL 203

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. Length = 203

>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional

 Score =  144 bits (364), Expect = 1e-40
 Identities = 71/173 (41%), Positives = 101/173 (58%), Gaps = 7/173 (4%)

Query: 13  LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
           +R  +A GGVP    +  +++G  +++A PGRL+D L+  + +L    YL LDEADRM+D
Sbjct: 232 IRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLD 291

Query: 73  MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVK--PITINVGRAG-AASMNV 129
           MGFE  +R I S  R  RQTL++SAT PK++Q+ AR  L K  P+ +NVG     A  N+
Sbjct: 292 MGFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSLARD-LCKEEPVHVNVGSLDLTACHNI 350

Query: 130 VQEVEYVKQEAKIVYLLECLQKTEPP---VLIFAEKKQDVDAIHEYLLLKGKP 179
            QEV  V++  K   L   LQ+       +LIF E K+  D + + L L G P
Sbjct: 351 KQEVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWP 403

Length = 545

>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional

 Score =  123 bits (312), Expect = 1e-33
 Identities = 52/156 (33%), Positives = 83/156 (53%), Gaps = 4/156 (2%)

Query: 20  GGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDV 79
           GGVPM   +D ++ G H++V TPGR++D L K  + LD    L LDEADRM+DMGF++ +
Sbjct: 109 GGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAI 168

Query: 80  RTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEY-VKQ 138
             I      +RQTLLFSAT P+ I   ++     P+ + V          +++  Y V  
Sbjct: 169 DAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTHDLP--AIEQRFYEVSP 226

Query: 139 EAKIVYLLECLQKTEP-PVLIFAEKKQDVDAIHEYL 173
           + ++  L   L   +P   ++F   K++   + + L
Sbjct: 227 DERLPALQRLLLHHQPESCVVFCNTKKECQEVADAL 262

Length = 460

>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional

 Score =  109 bits (273), Expect = 4e-28
 Identities = 53/131 (40%), Positives = 76/131 (58%)

Query: 11  IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRM 70
           + +R+ +  GGV +N  +  ++ G  ++VATPGRL+D+  +  V LD    L LDEADRM
Sbjct: 102 LNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRM 161

Query: 71  VDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVV 130
           +DMGF  D+R + +    +RQ LLFSAT    I+  A   L  P+ I V R   AS  V 
Sbjct: 162 LDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVT 221

Query: 131 QEVEYVKQEAK 141
           Q V +V ++ K
Sbjct: 222 QHVHFVDKKRK 232

Length = 456

>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional

 Score =  106 bits (267), Expect = 3e-27
 Identities = 61/164 (37%), Positives = 87/164 (53%), Gaps = 6/164 (3%)

Query: 19  IGGVPMNQSLDVIK-KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEE 77
           +GG+  ++ L  ++ + C ++VATPGRL+D   +  V LD+   + LDEADRM+DMGF  
Sbjct: 197 VGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFIP 256

Query: 78  DVRTI--FSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEY 135
            VR I   +  + +RQTLLFSAT    + N A+     P  + +     AS  V Q V  
Sbjct: 257 QVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYA 316

Query: 136 VKQEAKIVYLLECLQKTEP--PVLIFAEKKQDVDAIHEYLLLKG 177
           V    K   LL  L    P   V++FA +K +V  I E L+  G
Sbjct: 317 VAGSDK-YKLLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDG 359

Length = 475

>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase; Provisional

 Score =  102 bits (255), Expect = 1e-25
 Identities = 64/185 (34%), Positives = 96/185 (51%), Gaps = 8/185 (4%)

Query: 11  IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRM 70
           +P +T L +GG  M Q L  I++G  ++V TPGRL+D+L K  + LD    L LDE D M
Sbjct: 223 LPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCM 282

Query: 71  VDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVV 130
           ++ GF + V  IF     Q Q LLFSAT+  +++ FA S     I I++G     +  V 
Sbjct: 283 LERGFRDQVMQIFQAL-SQPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVK 341

Query: 131 QEVEYV---KQEAKIVYLLECLQKTEPPVLIFAEKKQDVD----AIHEYLLLKGKPFFTL 183
           Q   +V   +++ K+  +L+  Q  +PP ++F   +   D    AI     LK       
Sbjct: 342 QLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGE 401

Query: 184 KSLKE 188
           KS+KE
Sbjct: 402 KSMKE 406

Length = 518

>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase

 Score = 95.8 bits (239), Expect = 3e-25
 Identities = 38/99 (38%), Positives = 58/99 (58%), Gaps = 2/99 (2%)

Query: 10  PIPLRTCLAIGGVPMNQSLDVIKKG-CHMMVATPGRLMDMLDKKMVSL-DVCRYLCLDEA 67
            + LR  L  GG  + +    +KKG   ++V TPGRL+D+L +  + L    + L LDEA
Sbjct: 71  ILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLKNLKLLVLDEA 130

Query: 68  DRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNF 106
            R++DMGF +D+  I S     RQ LL SAT+P+ +++ 
Sbjct: 131 HRLLDMGFGDDLEEILSRLPPDRQILLLSATLPRNLEDL 169

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. Length = 169

>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily

 Score = 96.4 bits (240), Expect = 4e-25
 Identities = 37/114 (32%), Positives = 59/114 (51%), Gaps = 1/114 (0%)

Query: 10  PIPLRTCLAIGGVPMNQSLDVIKKGC-HMMVATPGRLMDMLDKKMVSLDVCRYLCLDEAD 68
            + L+     GG    + L  ++ G   ++V TPGRL+D+L+   +SL     + LDEA 
Sbjct: 80  SLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAH 139

Query: 69  RMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRA 122
           R++D GF + +  +        Q LL SAT P++I+N     L  P+ I+VG  
Sbjct: 140 RLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIENLLELFLNDPVFIDVGFT 193

Length = 201

>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional

 Score = 98.1 bits (244), Expect = 6e-24
 Identities = 53/144 (36%), Positives = 82/144 (56%), Gaps = 3/144 (2%)

Query: 13  LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDK-KMVSLDVCRYLCLDEADRMV 71
           LR  L  GGV  ++  +++++G  +++ATPGRL+D + + K+VSL  C    LDEADRM 
Sbjct: 113 LRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMF 172

Query: 72  DMGFEEDVRTIFSFF--RGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNV 129
           D+GF +D+R +      RG RQTLLFSAT+  ++   A   + +P  + V      +  V
Sbjct: 173 DLGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARV 232

Query: 130 VQEVEYVKQEAKIVYLLECLQKTE 153
            Q + +   E K   LL  L ++E
Sbjct: 233 RQRIYFPADEEKQTLLLGLLSRSE 256

Length = 572

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 93.5 bits (233), Expect = 1e-22
 Identities = 42/102 (41%), Positives = 62/102 (60%), Gaps = 3/102 (2%)

Query: 20  GGVP-MNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEED 78
           GGV  MN + +V  +   ++VATPGRL+  + ++         L LDEADRM+DMGF +D
Sbjct: 109 GGVAYMNHA-EVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQD 167

Query: 79  VRTIFSFFRGQRQTLLFSATMP-KKIQNFARSALVKPITINV 119
           + TI +  R ++QTLLFSAT+    +Q+FA   L  P+ +  
Sbjct: 168 IETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEA 209

Length = 434

>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily

 Score = 76.6 bits (189), Expect = 4e-18
 Identities = 30/95 (31%), Positives = 44/95 (46%)

Query: 5   FISALPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCL 64
                   ++    IGG  + Q   ++     ++V TPGRL+D L++  +SL     L L
Sbjct: 50  LKELFGEGIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLIL 109

Query: 65  DEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATM 99
           DEA R+++ GF      I       RQ LL SAT 
Sbjct: 110 DEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP 144

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Length = 144

>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional

 Score = 80.7 bits (199), Expect = 5e-18
 Identities = 40/95 (42%), Positives = 55/95 (57%)

Query: 20  GGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDV 79
           GG   +  L  +++G  ++V TPGRL+D L +  + L     L LDEAD M+ MGF EDV
Sbjct: 111 GGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDV 170

Query: 80  RTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKP 114
            TI +      QT LFSATMP+ I+   R  + +P
Sbjct: 171 ETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEP 205

Length = 629

>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional

 Score = 79.6 bits (197), Expect = 9e-18
 Identities = 50/166 (30%), Positives = 85/166 (51%), Gaps = 7/166 (4%)

Query: 13  LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
           L+  LA GG   ++ L V++ G  +++ T GRL+D   +  ++L   + + LDEADRM D
Sbjct: 112 LKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFD 171

Query: 73  MGFEEDVRTIFSFFR----GQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMN 128
           +GF +D+R  + F R     QR  +LFSAT+  +++  A   +  P  + V         
Sbjct: 172 LGFIKDIR--WLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHR 229

Query: 129 VVQEVEYVKQEAKIVYLLECLQKTEPP-VLIFAEKKQDVDAIHEYL 173
           + +E+ Y   E K+  L   +++  P   +IFA  K   + I  +L
Sbjct: 230 IKEELFYPSNEEKMRLLQTLIEEEWPDRAIIFANTKHRCEEIWGHL 275

Length = 423

>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional

 Score = 79.5 bits (196), Expect = 1e-17
 Identities = 37/101 (36%), Positives = 55/101 (54%)

Query: 19  IGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEED 78
           +GG  +   ++ +K G HM+V TPGR+ DM+DK+ + +D  +   LDEAD M+  GF+  
Sbjct: 131 VGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQ 190

Query: 79  VRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINV 119
           +  +F       Q  LFSATMP +I       +  P  I V
Sbjct: 191 IYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILV 231

Length = 401

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	197
KOG0328|consensus	400		100.0
KOG0330|consensus	476		100.0
KOG0331|consensus	519		100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
KOG0333|consensus	673		100.0
KOG0326|consensus	459		100.0
KOG0339|consensus	731		100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
KOG0345|consensus	567		100.0
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
PTZ00110	545	helicase; Provisional	100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.98
KOG0338|consensus	691		99.98
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.97
KOG0341|consensus	610		99.97
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.97
KOG0343|consensus	758		99.97
KOG0327|consensus	397		99.97
KOG0342|consensus	543		99.97
KOG0337|consensus	529		99.97
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.97
KOG4284|consensus	980		99.97
KOG0335|consensus	482		99.96
KOG0347|consensus	731		99.96
KOG0346|consensus	569		99.96
PTZ00424	401	helicase 45; Provisional	99.96
KOG0336|consensus	629		99.96
KOG0340|consensus	442		99.96
KOG0334|consensus	997		99.94
KOG0329|consensus	387		99.94
KOG0332|consensus	477		99.94
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.93
KOG0348|consensus	708		99.92
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.91
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.91
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.9
PRK09401	1176	reverse gyrase; Reviewed	99.9
PRK13767	876	ATP-dependent helicase; Provisional	99.89
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.88
PRK00254	720	ski2-like helicase; Provisional	99.87
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.87
PRK14701	1638	reverse gyrase; Provisional	99.87
PRK02362	737	ski2-like helicase; Provisional	99.86
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.86
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.86
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.85
PRK10689	1147	transcription-repair coupling factor; Provisional	99.85
COG1202	830	Superfamily II helicase, archaea-specific [General	99.85
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.84
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.83
KOG0349|consensus	725		99.83
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.83
KOG0350|consensus	620		99.82
PRK01172	674	ski2-like helicase; Provisional	99.82
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.82
KOG0344|consensus	593		99.81
PHA02653	675	RNA helicase NPH-II; Provisional	99.79
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.78
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.77
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.77
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.77
COG1204	766	Superfamily II helicase [General function predicti	99.77
COG1205	851	Distinct helicase family with a unique C-terminal	99.75
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.73
KOG0351|consensus	941		99.73
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.71
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.68
PHA02558	501	uvsW UvsW helicase; Provisional	99.67
KOG0952|consensus	1230		99.63
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.59
PRK13766	773	Hef nuclease; Provisional	99.55
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.55
KOG0947|consensus	1248		99.54
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.54
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.53
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.52
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.51
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.5
KOG0352|consensus	641		99.49
PRK09694	878	helicase Cas3; Provisional	99.47
KOG0951|consensus	1674		99.46
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.46
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.46
KOG0948|consensus	1041		99.4
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.29
KOG0353|consensus	695		99.29
PRK05580	679	primosome assembly protein PriA; Validated	99.28
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.28
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.25
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.21
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.18
KOG0950|consensus	1008		99.16
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.15
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	99.14
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.11
PRK04914	956	ATP-dependent helicase HepA; Validated	98.99
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	98.99
KOG0354|consensus	746		98.97
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	98.96
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.96
KOG0922|consensus	674		98.93
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	98.88
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.83
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	98.62
KOG0920|consensus	924		98.61
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	98.52
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	98.46
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	98.38
PRK05298	652	excinuclease ABC subunit B; Provisional	98.37
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	98.31
KOG0923|consensus	902		98.28
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.2
KOG0385|consensus	971		98.19
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	98.18
COG4096	875	HsdR Type I site-specific restriction-modification	98.05
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	98.03
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	97.99
KOG0925|consensus	699		97.97
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	97.93
KOG0924|consensus	1042		97.9
KOG4150|consensus	1034		97.87
KOG2340|consensus	698		97.87
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	97.75
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	97.54
KOG0951|consensus	1674		97.51
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	97.5
KOG0926|consensus	1172		97.49
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	97.47
KOG0949|consensus	1330		97.46
KOG1123|consensus	776		97.31
COG1198	730	PriA Primosomal protein N' (replication factor Y)	97.31
KOG0952|consensus	1230		97.13
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	97.07
KOG0384|consensus	1373		96.99
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	96.94
PRK12326	764	preprotein translocase subunit SecA; Reviewed	96.62
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	96.57
PRK14873	665	primosome assembly protein PriA; Provisional	96.46
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	96.44
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	96.43
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	96.22
KOG1000|consensus	689		96.17
CHL00122	870	secA preprotein translocase subunit SecA; Validate	95.81
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	95.5
cd01524	90	RHOD_Pyr_redox Member of the Rhodanese Homology Do	95.11
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	95.04
KOG0387|consensus	923		95.0
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	94.94
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	94.41
smart00490	82	HELICc helicase superfamily c-terminal domain.	94.3
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	94.25
cd01533	109	4RHOD_Repeat_2 Member of the Rhodanese Homology Do	94.05
cd01534	95	4RHOD_Repeat_3 Member of the Rhodanese Homology Do	93.92
KOG0389|consensus	941		93.42
PRK12326	764	preprotein translocase subunit SecA; Reviewed	93.32
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	93.24
COG0610	962	Type I site-specific restriction-modification syst	93.03
cd01523	100	RHOD_Lact_B Member of the Rhodanese Homology Domai	92.94
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	92.83
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	92.68
KOG3089|consensus	271		92.58
cd01526	122	RHOD_ThiF Member of the Rhodanese Homology Domain	92.57
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	92.51
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	92.14
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	91.86
KOG0391|consensus	1958		91.8
cd00158	89	RHOD Rhodanese Homology Domain (RHOD); an alpha be	91.69
smart00450	100	RHOD Rhodanese Homology Domain. An alpha beta fold	91.67
CHL00122	870	secA preprotein translocase subunit SecA; Validate	91.37
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	91.34
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	91.34
cd01529	96	4RHOD_Repeats Member of the Rhodanese Homology Dom	91.14
PRK05642	234	DNA replication initiation factor; Validated	90.97
cd01532	92	4RHOD_Repeat_1 Member of the Rhodanese Homology Do	90.56
KOG0391|consensus	1958		90.45
KOG0921|consensus	1282		90.21
cd01528	101	RHOD_2 Member of the Rhodanese Homology Domain sup	89.94
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	89.82
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	89.67
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	89.5
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	89.48
PF02463	220	SMC_N: RecF/RecN/SMC N terminal domain; InterPro:	89.46
cd01518	101	RHOD_YceA Member of the Rhodanese Homology Domain	89.13
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	89.11
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	89.03
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	88.98
cd01520	128	RHOD_YbbB Member of the Rhodanese Homology Domain	88.91
cd01527	99	RHOD_YgaP Member of the Rhodanese Homology Domain	88.87
PF13173	128	AAA_14: AAA domain	88.86
TIGR02981	101	phageshock_pspE phage shock operon rhodanese PspE.	88.8
cd01521	110	RHOD_PspE2 Member of the Rhodanese Homology Domain	88.59
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	88.43
COG1198	730	PriA Primosomal protein N' (replication factor Y)	88.12
PRK12422	445	chromosomal replication initiation protein; Provis	88.02
PRK06893	229	DNA replication initiation factor; Validated	87.92
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	87.9
PRK14087	450	dnaA chromosomal replication initiation protein; P	87.88
cd01444	96	GlpE_ST GlpE sulfurtransferase (ST) and homologs a	87.74
KOG0392|consensus	1549		87.71
cd01525	105	RHOD_Kc Member of the Rhodanese Homology Domain su	87.41
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	87.19
PRK14873	665	primosome assembly protein PriA; Provisional	87.06
KOG0964|consensus	1200		86.83
PRK10287	104	thiosulfate:cyanide sulfurtransferase; Provisional	86.51
cd01447	103	Polysulfide_ST Polysulfide-sulfurtransferase - Rho	86.36
PRK08727	233	hypothetical protein; Validated	86.16
KOG0953|consensus	700		85.91
KOG0347|consensus	731		85.88
cd01519	106	RHOD_HSP67B2 Member of the Rhodanese Homology Doma	85.87
PF11019	252	DUF2608: Protein of unknown function (DUF2608); In	85.38
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	85.36
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	85.15
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	85.01
KOG0390|consensus	776		85.0
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	84.97
PF05872	502	DUF853: Bacterial protein of unknown function (DUF	84.47
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	84.45
cd01449	118	TST_Repeat_2 Thiosulfate sulfurtransferase (TST),	83.99
cd01448	122	TST_Repeat_1 Thiosulfate sulfurtransferase (TST),	83.98
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	83.89
PRK00149	450	dnaA chromosomal replication initiation protein; R	83.79
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	83.52
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	83.43
PRK08762	376	molybdopterin biosynthesis protein MoeB; Validated	83.43
cd01522	117	RHOD_1 Member of the Rhodanese Homology Domain sup	83.4
PRK05580	679	primosome assembly protein PriA; Validated	83.29
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	83.25
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	83.17
PRK14086	617	dnaA chromosomal replication initiation protein; P	82.82
KOG4439|consensus	901		82.79
PRK06835	329	DNA replication protein DnaC; Validated	82.3
TIGR00595	505	priA primosomal protein N'. All proteins in this f	82.17
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	82.01
cd01535	145	4RHOD_Repeat_4 Member of the Rhodanese Homology Do	81.97
PRK08084	235	DNA replication initiation factor; Provisional	81.87
PRK04296	190	thymidine kinase; Provisional	81.55
PRK07414	178	cob(I)yrinic acid a,c-diamide adenosyltransferase;	81.43
PRK00162	108	glpE thiosulfate sulfurtransferase; Validated	81.31
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	81.17
PRK06526	254	transposase; Provisional	81.03
COG0593	408	DnaA ATPase involved in DNA replication initiation	80.98
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	80.97
PRK10689	1147	transcription-repair coupling factor; Provisional	80.55

>KOG0328|consensus

Probab=100.00  E-value=1.1e-37  Score=233.64  Aligned_cols=188  Identities=24%  Similarity=0.407  Sum_probs=179.2

Q ss_pred             CCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCC
Q psy7789          10 PIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        10 ~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~   89 (197)
                      +.|+.|..+.||.+.-+..+.+.-|.|++.+|||++++++++..+..+.++++|+||||.+++.+|.+++-.|.+++|++
T Consensus       121 ~mnvq~hacigg~n~gedikkld~G~hvVsGtPGrv~dmikr~~L~tr~vkmlVLDEaDemL~kgfk~Qiydiyr~lp~~  200 (400)
T KOG0328|consen  121 YMNVQCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVLDMIKRRSLRTRAVKMLVLDEADEMLNKGFKEQIYDIYRYLPPG  200 (400)
T ss_pred             cccceEEEEecCCccchhhhhhcccceEeeCCCchHHHHHHhccccccceeEEEeccHHHHHHhhHHHHHHHHHHhCCCC
Confidence            36899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCc-hhhHHHHHHHhhcCC-CCEEEEecccccHH
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQ-EAKIVYLLECLQKTE-PPVLIFAEKKQDVD  167 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~  167 (197)
                      .|++++|||+|.++.++.+.|+.+|+.+-+.......++++|+|+.+.. ++|++.|+++..... .+++|||||++.++
T Consensus       201 ~Qvv~~SATlp~eilemt~kfmtdpvrilvkrdeltlEgIKqf~v~ve~EewKfdtLcdLYd~LtItQavIFcnTk~kVd  280 (400)
T KOG0328|consen  201 AQVVLVSATLPHEILEMTEKFMTDPVRILVKRDELTLEGIKQFFVAVEKEEWKFDTLCDLYDTLTITQAVIFCNTKRKVD  280 (400)
T ss_pred             ceEEEEeccCcHHHHHHHHHhcCCceeEEEecCCCchhhhhhheeeechhhhhHhHHHHHhhhhehheEEEEecccchhh
Confidence            9999999999999999999999999999999999999999999999865 559999999998764 58999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      +|.+.|++.++.+...||+|++++|+++++
T Consensus       281 wLtekm~~~nftVssmHGDm~qkERd~im~  310 (400)
T KOG0328|consen  281 WLTEKMREANFTVSSMHGDMEQKERDKIMN  310 (400)
T ss_pred             HHHHHHHhhCceeeeccCCcchhHHHHHHH
Confidence            999999999999999999999999999875

>KOG0330|consensus

Probab=100.00  E-value=6.1e-38  Score=243.51  Aligned_cols=187  Identities=32%  Similarity=0.457  Sum_probs=179.1

Q ss_pred             CCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHh-cCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccC
Q psy7789          10 PIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLD-KKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRG   88 (197)
Q Consensus        10 ~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~-~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~   88 (197)
                      +.|++++.+.||.++..|...+.+.|||+|||||+|.+.+. .+.++++.++++|+||||.+++..|.+.+..|++.+|.
T Consensus       155 ~iglr~~~lvGG~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADrlLd~dF~~~ld~ILk~ip~  234 (476)
T KOG0330|consen  155 GIGLRVAVLVGGMDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADRLLDMDFEEELDYILKVIPR  234 (476)
T ss_pred             ccCeEEEEEecCchHHHHHHHhhcCCCEEEeCcHHHHHHHHhccCccHHHhHHHhhchHHhhhhhhhHHHHHHHHHhcCc
Confidence            46999999999999999999999999999999999999998 67899999999999999999999999999999999999


Q ss_pred             CceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCC-CCEEEEecccccHH
Q psy7789          89 QRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTE-PPVLIFAEKKQDVD  167 (197)
Q Consensus        89 ~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~  167 (197)
                      .+|+++||||++..+.......+.+|..+.+...+...+.++|.|.+++..+|..+|++++++.. ..+||||+|..+++
T Consensus       235 erqt~LfsATMt~kv~kL~rasl~~p~~v~~s~ky~tv~~lkQ~ylfv~~k~K~~yLV~ll~e~~g~s~iVF~~t~~tt~  314 (476)
T KOG0330|consen  235 ERQTFLFSATMTKKVRKLQRASLDNPVKVAVSSKYQTVDHLKQTYLFVPGKDKDTYLVYLLNELAGNSVIVFCNTCNTTR  314 (476)
T ss_pred             cceEEEEEeecchhhHHHHhhccCCCeEEeccchhcchHHhhhheEeccccccchhHHHHHHhhcCCcEEEEEeccchHH
Confidence            99999999999999999999999999999999999999999999999999999999999999874 58999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +++-.|+..|+.+..+||.|+++.|...+
T Consensus       315 ~la~~L~~lg~~a~~LhGqmsq~~Rlg~l  343 (476)
T KOG0330|consen  315 FLALLLRNLGFQAIPLHGQMSQSKRLGAL  343 (476)
T ss_pred             HHHHHHHhcCcceecccchhhHHHHHHHH
Confidence            99999999999999999999999998664

>KOG0331|consensus

Probab=100.00  E-value=5e-37  Score=250.11  Aligned_cols=186  Identities=39%  Similarity=0.595  Sum_probs=172.8

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhc-cCCc
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF-RGQR   90 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~-~~~~   90 (197)
                      ++++.+++||.+...|.+.++.+.||+|||||+|.++++.+.++++++.|+|+||||.|++.+|.++++.|+..+ ++..
T Consensus       193 ~~~~~cvyGG~~~~~Q~~~l~~gvdiviaTPGRl~d~le~g~~~l~~v~ylVLDEADrMldmGFe~qI~~Il~~i~~~~r  272 (519)
T KOG0331|consen  193 RLRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEADRMLDMGFEPQIRKILSQIPRPDR  272 (519)
T ss_pred             CccEEEEeCCCCccHHHHHHhcCCcEEEeCChHHHHHHHcCCccccceeEEEeccHHhhhccccHHHHHHHHHhcCCCcc
Confidence            588999999999999999999999999999999999999999999999999999999999999999999999999 5667


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCC--CccCcceeEEEEEcCchhhHHHHHHHhhcC----CCCEEEEecccc
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRA--GAASMNVVQEVEYVKQEAKIVYLLECLQKT----EPPVLIFAEKKQ  164 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~--~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~----~~~~lIF~~s~~  164 (197)
                      |++++|||||.+++.++..|+.+|..+.+...  .....++.|....|.+..|...|..+|+..    .+|+||||+|++
T Consensus       273 Qtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~~~~K~~~l~~lL~~~~~~~~~KvIIFc~tkr  352 (519)
T KOG0331|consen  273 QTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCDETAKLRKLGKLLEDISSDSEGKVIIFCETKR  352 (519)
T ss_pred             cEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhcCHHHHHHHHHHHHHHHhccCCCcEEEEecchh
Confidence            99999999999999999999999999988744  366778899888889888988888888754    358999999999


Q ss_pred             cHHHHHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         165 DVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       165 ~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      .|++|+..|+..++++.++||+.+|+||+.+++
T Consensus       353 ~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~  385 (519)
T KOG0331|consen  353 TCDELARNLRRKGWPAVAIHGDKSQSERDWVLK  385 (519)
T ss_pred             hHHHHHHHHHhcCcceeeecccccHHHHHHHHH
Confidence            999999999999999999999999999998864

>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=3.3e-36  Score=251.72  Aligned_cols=185  Identities=34%  Similarity=0.534  Sum_probs=175.3

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCce
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQ   91 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q   91 (197)
                      +++++.++||.++..|...++.++||+|||||||++++.++.+++++++++|+||||.|++.||.+.+..|+..+|.+.|
T Consensus       128 ~~~~~~i~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~~~l~l~~v~~lVlDEADrmLd~Gf~~~i~~I~~~~p~~~q  207 (513)
T COG0513         128 GLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDMGFIDDIEKILKALPPDRQ  207 (513)
T ss_pred             CccEEEEECCCCHHHHHHHHhcCCCEEEECccHHHHHHHcCCcchhhcCEEEeccHhhhhcCCCHHHHHHHHHhCCcccE
Confidence            78999999999999999999989999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeecCChhHHHHHHHhcCCCeEEEeCCCCc--cCcceeEEEEEcCchh-hHHHHHHHhhcCCC-CEEEEecccccHH
Q psy7789          92 TLLFSATMPKKIQNFARSALVKPITINVGRAGA--ASMNVVQEVEYVKQEA-KIVYLLECLQKTEP-PVLIFAEKKQDVD  167 (197)
Q Consensus        92 ~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~--~~~~i~~~~~~~~~~~-k~~~l~~~l~~~~~-~~lIF~~s~~~~~  167 (197)
                      +++||||++.++..+.+.++++|..+.+.....  ....+.|+++.+...+ |...|..+++.... ++||||+|++.|+
T Consensus       208 tllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~~k~~~L~~ll~~~~~~~~IVF~~tk~~~~  287 (513)
T COG0513         208 TLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVE  287 (513)
T ss_pred             EEEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCceEEEEEeCCHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHH
Confidence            999999999999999999999999888875554  7899999999998866 99999999997754 6999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .++..|...|+++..+||+|+|++|++++
T Consensus       288 ~l~~~l~~~g~~~~~lhG~l~q~~R~~~l  316 (513)
T COG0513         288 ELAESLRKRGFKVAALHGDLPQEERDRAL  316 (513)
T ss_pred             HHHHHHHHCCCeEEEecCCCCHHHHHHHH
Confidence            99999999999999999999999999875

>KOG0333|consensus

Probab=100.00  E-value=1.2e-33  Score=226.60  Aligned_cols=188  Identities=38%  Similarity=0.672  Sum_probs=178.5

Q ss_pred             CCCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccC
Q psy7789           9 LPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRG   88 (197)
Q Consensus         9 ~~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~   88 (197)
                      .++|+++..++||.+.++|.-.++.||+|+||||++|.+.+.+..+-++++.+||+||||.+++.||.+++..++.++|.
T Consensus       347 ~~lg~r~vsvigg~s~EEq~fqls~gceiviatPgrLid~Lenr~lvl~qctyvvldeadrmiDmgfE~dv~~iL~~mPs  426 (673)
T KOG0333|consen  347 KPLGIRTVSVIGGLSFEEQGFQLSMGCEIVIATPGRLIDSLENRYLVLNQCTYVVLDEADRMIDMGFEPDVQKILEQMPS  426 (673)
T ss_pred             ccccceEEEEecccchhhhhhhhhccceeeecCchHHHHHHHHHHHHhccCceEeccchhhhhcccccHHHHHHHHhCCc
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999963


Q ss_pred             C-------------------------ceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHH
Q psy7789          89 Q-------------------------RQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIV  143 (197)
Q Consensus        89 ~-------------------------~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~  143 (197)
                      .                         +|+++||||+++.+..+++.|+++|.++.++......+.+.|.++.+.+.+|..
T Consensus       427 sn~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p~verlar~ylr~pv~vtig~~gk~~~rveQ~v~m~~ed~k~k  506 (673)
T KOG0333|consen  427 SNAKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLARSYLRRPVVVTIGSAGKPTPRVEQKVEMVSEDEKRK  506 (673)
T ss_pred             cccCCCccchhhHHHHHhhcccccceeEEEEEecCCChHHHHHHHHHhhCCeEEEeccCCCCccchheEEEEecchHHHH
Confidence            1                         699999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhcC-CCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         144 YLLECLQKT-EPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       144 ~l~~~l~~~-~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .|.+++... .+++|||+|+++.|+.+|+.|.+.|++|..+||+-++++|+.++
T Consensus       507 kL~eil~~~~~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL  560 (673)
T KOG0333|consen  507 KLIEILESNFDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGKSQEQRENAL  560 (673)
T ss_pred             HHHHHHHhCCCCCEEEEEechhhHHHHHHHHhhccceEEEeeCCccHHHHHHHH
Confidence            999999987 67999999999999999999999999999999999999999765

>KOG0326|consensus

Probab=100.00  E-value=5.2e-34  Score=217.13  Aligned_cols=185  Identities=24%  Similarity=0.463  Sum_probs=174.2

Q ss_pred             CCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCC
Q psy7789          10 PIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        10 ~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~   89 (197)
                      +.|+++..-+||.+.++....+.++.|++|+||||+++++.++.-.+++...+|+||||.+++..|.+.+..++..+|++
T Consensus       179 h~~i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~KgVa~ls~c~~lV~DEADKlLs~~F~~~~e~li~~lP~~  258 (459)
T KOG0326|consen  179 HLGIKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKKGVADLSDCVILVMDEADKLLSVDFQPIVEKLISFLPKE  258 (459)
T ss_pred             ccCeEEEEecCCcccccceeeecCceEEEEcCChhHHHHHhcccccchhceEEEechhhhhhchhhhhHHHHHHHhCCcc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCC-CCEEEEecccccHHH
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTE-PPVLIFAEKKQDVDA  168 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~~  168 (197)
                      +|++++|||+|-.+..+..+++.+|-.|.+-+ +..+.+++|+|-++.+.+|+--|.-+....+ .+.||||||..++|.
T Consensus       259 rQillySATFP~tVk~Fm~~~l~kPy~INLM~-eLtl~GvtQyYafV~e~qKvhCLntLfskLqINQsIIFCNS~~rVEL  337 (459)
T KOG0326|consen  259 RQILLYSATFPLTVKGFMDRHLKKPYEINLME-ELTLKGVTQYYAFVEERQKVHCLNTLFSKLQINQSIIFCNSTNRVEL  337 (459)
T ss_pred             ceeeEEecccchhHHHHHHHhccCcceeehhh-hhhhcchhhheeeechhhhhhhHHHHHHHhcccceEEEeccchHhHH
Confidence            99999999999999999999999999998874 4456789999999999999998888887664 589999999999999


Q ss_pred             HHHHHHhCCCCeEeecCCCChhhhhhh
Q psy7789         169 IHEYLLLKGKPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       169 l~~~L~~~~~~~~~~h~~~~~~~R~~i  195 (197)
                      +|....+.||+|+++|+.|.++.|.+|
T Consensus       338 LAkKITelGyscyyiHakM~Q~hRNrV  364 (459)
T KOG0326|consen  338 LAKKITELGYSCYYIHAKMAQEHRNRV  364 (459)
T ss_pred             HHHHHHhccchhhHHHHHHHHhhhhhh
Confidence            999999999999999999999999886

>KOG0339|consensus

Probab=100.00  E-value=6.6e-33  Score=221.86  Aligned_cols=186  Identities=40%  Similarity=0.575  Sum_probs=175.9

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .||+++.++||.+..+|...|+.+|.|||||||||.+++.-+..++.++.|||+||||+|++.||..+++.|.+.+++++
T Consensus       323 ygl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~rvS~LV~DEadrmfdmGfe~qVrSI~~hirpdr  402 (731)
T KOG0339|consen  323 YGLRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDMVKMKATNLSRVSYLVLDEADRMFDMGFEPQVRSIKQHIRPDR  402 (731)
T ss_pred             ccceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHHHHhhcccceeeeEEEEechhhhhccccHHHHHHHHhhcCCcc
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcC-chhhHHHHHHHhhcCC--CCEEEEecccccHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVK-QEAKIVYLLECLQKTE--PPVLIFAEKKQDVD  167 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~-~~~k~~~l~~~l~~~~--~~~lIF~~s~~~~~  167 (197)
                      |+++||||++..+...++.++.+|+.+...+.......|+|.+..|+ ++.|+.+|...|-...  +++|||+.....++
T Consensus       403 QtllFsaTf~~kIe~lard~L~dpVrvVqg~vgean~dITQ~V~V~~s~~~Kl~wl~~~L~~f~S~gkvlifVTKk~~~e  482 (731)
T KOG0339|consen  403 QTLLFSATFKKKIEKLARDILSDPVRVVQGEVGEANEDITQTVSVCPSEEKKLNWLLRHLVEFSSEGKVLIFVTKKADAE  482 (731)
T ss_pred             eEEEeeccchHHHHHHHHHHhcCCeeEEEeehhccccchhheeeeccCcHHHHHHHHHHhhhhccCCcEEEEEeccCCHH
Confidence            99999999999999999999999999999888888888999877775 5678999999888764  59999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +++..|+-.|+++..+||+|.|.+|.+++
T Consensus       483 ~i~a~Lklk~~~v~llhgdkdqa~rn~~l  511 (731)
T KOG0339|consen  483 EIAANLKLKGFNVSLLHGDKDQAERNEVL  511 (731)
T ss_pred             HHHHHhccccceeeeecCchhhHHHHHHH
Confidence            99999999999999999999999999875

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=4.9e-32  Score=225.13  Aligned_cols=185  Identities=29%  Similarity=0.486  Sum_probs=171.2

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCce
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQ   91 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q   91 (197)
                      ++++..++||.+...+.+.+..+++|+|+||+++.+++.++.+.++++++||+||||++++.+|...+..+++.+++..|
T Consensus       101 ~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~~~~~l~~l~~lViDEad~~l~~g~~~~l~~i~~~~~~~~q  180 (460)
T PRK11776        101 NIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAPARRQ  180 (460)
T ss_pred             CcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHcCCccHHHCCEEEEECHHHHhCcCcHHHHHHHHHhCCcccE
Confidence            79999999999999999999999999999999999999988889999999999999999999999999999999999999


Q ss_pred             EEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCC-CCEEEEecccccHHHHH
Q psy7789          92 TLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTE-PPVLIFAEKKQDVDAIH  170 (197)
Q Consensus        92 ~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~~l~  170 (197)
                      ++++|||+++.+..+...++++|..+.+.... ....+.+.++.+...+|...+..++.... .++||||+|++.|+.++
T Consensus       181 ~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~~-~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lVF~~t~~~~~~l~  259 (460)
T PRK11776        181 TLLFSATYPEGIAAISQRFQRDPVEVKVESTH-DLPAIEQRFYEVSPDERLPALQRLLLHHQPESCVVFCNTKKECQEVA  259 (460)
T ss_pred             EEEEEecCcHHHHHHHHHhcCCCEEEEECcCC-CCCCeeEEEEEeCcHHHHHHHHHHHHhcCCCceEEEECCHHHHHHHH
Confidence            99999999999999999999999988886554 34558888888888889999999998654 57999999999999999


Q ss_pred             HHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         171 EYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       171 ~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      +.|.+.|+++..+||+|++++|+++++
T Consensus       260 ~~L~~~~~~v~~~hg~~~~~eR~~~l~  286 (460)
T PRK11776        260 DALNAQGFSALALHGDLEQRDRDQVLV  286 (460)
T ss_pred             HHHHhCCCcEEEEeCCCCHHHHHHHHH
Confidence            999999999999999999999998863

>KOG0345|consensus

Probab=100.00  E-value=1.7e-32  Score=217.54  Aligned_cols=194  Identities=29%  Similarity=0.516  Sum_probs=175.9

Q ss_pred             CccccccCCCCeeEEEEEcCCChHHhHHHHh-cCCcEEEeCchHHHHHHhcC--CccCCCccEEEeehhhhhhcCCCHHH
Q psy7789           2 GIPFISALPIPLRTCLAIGGVPMNQSLDVIK-KGCHMMVATPGRLMDMLDKK--MVSLDVCRYLCLDEADRMVDMGFEED   78 (197)
Q Consensus         2 ~~~~~~~~~~~i~~~~~~gg~~~~~~~~~l~-~~~~Ili~TP~~l~~~l~~~--~~~l~~l~~vViDEad~l~~~~~~~~   78 (197)
                      +++|.+.+. ++++.+++||.+.++..+.+. ++|.|+|||||||.+++.+.  .+++++++++|+||||++++.||..+
T Consensus        99 ~~~F~~~l~-~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVLDEADrLldmgFe~~  177 (567)
T KOG0345|consen   99 AQPFLEHLP-NLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVLDEADRLLDMGFEAS  177 (567)
T ss_pred             HHHHHHhhh-ccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccccceEEecchHhHhcccHHHH
Confidence            356777764 799999999999999998884 58999999999999999874  45567999999999999999999999


Q ss_pred             HHHHHhhccCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCc--cCcceeEEEEEcCchhhHHHHHHHhhcCC-CC
Q psy7789          79 VRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGA--ASMNVVQEVEYVKQEAKIVYLLECLQKTE-PP  155 (197)
Q Consensus        79 i~~i~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~--~~~~i~~~~~~~~~~~k~~~l~~~l~~~~-~~  155 (197)
                      +..|+..+|+.+++.+||||.+.++.+..+..++||+.+.+.....  .+..+..+|..|...+|...++++|.... ++
T Consensus       178 ~n~ILs~LPKQRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~~a~eK~~~lv~~L~~~~~kK  257 (567)
T KOG0345|consen  178 VNTILSFLPKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYLVCEADEKLSQLVHLLNNNKDKK  257 (567)
T ss_pred             HHHHHHhcccccccccccchhhHHHHHHHHhhccCceeeeecccccccCchhhcceeeEecHHHHHHHHHHHHhcccccc
Confidence            9999999999999999999999999999999999999999987665  77778889999999999999999999864 68


Q ss_pred             EEEEecccccHHHHHHHHHhC--CCCeEeecCCCChhhhhhhh
Q psy7789         156 VLIFAEKKQDVDAIHEYLLLK--GKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       156 ~lIF~~s~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +|||++|+..++..+..+...  ..++..+||.|++.+|.++.
T Consensus       258 ~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHGK~~q~~R~k~~  300 (567)
T KOG0345|consen  258 CIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKMSQKARAKVL  300 (567)
T ss_pred             EEEEecCcchHHHHHHHHHHHhCCCcEEEecchhcchhHHHHH
Confidence            999999999999999999765  67899999999999998764

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=1.7e-31  Score=227.43  Aligned_cols=186  Identities=28%  Similarity=0.362  Sum_probs=174.0

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .++++..++||.+.+.+.+.+..+++|+|+||+++.+++.+..++++++++||+||||.+++++|.+.+..++..+|...
T Consensus       102 ~~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~~l~l~~l~~lVlDEAd~ml~~gf~~di~~Il~~lp~~~  181 (629)
T PRK11634        102 RGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGH  181 (629)
T ss_pred             CCceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcchhhceEEEeccHHHHhhcccHHHHHHHHHhCCCCC
Confidence            37999999999999999999988999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCC-CCEEEEecccccHHHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTE-PPVLIFAEKKQDVDAI  169 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~~l  169 (197)
                      |+++||||+++.+..+...++.+|..+.+.......+.+.+.++.+....|...|..++.... .++||||+|+..|+.+
T Consensus       182 q~llfSAT~p~~i~~i~~~~l~~~~~i~i~~~~~~~~~i~q~~~~v~~~~k~~~L~~~L~~~~~~~~IVF~~tk~~a~~l  261 (629)
T PRK11634        182 QTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMRKNEALVRFLEAEDFDAAIIFVRTKNATLEV  261 (629)
T ss_pred             eEEEEEccCChhHHHHHHHHcCCCeEEEccCccccCCceEEEEEEechhhHHHHHHHHHHhcCCCCEEEEeccHHHHHHH
Confidence            999999999999999999999999998888777777788999998888899999999998654 5899999999999999


Q ss_pred             HHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         170 HEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       170 ~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      ++.|.+.|+.+..+||+|++++|++++
T Consensus       262 ~~~L~~~g~~~~~lhgd~~q~~R~~il  288 (629)
T PRK11634        262 AEALERNGYNSAALNGDMNQALREQTL  288 (629)
T ss_pred             HHHHHhCCCCEEEeeCCCCHHHHHHHH
Confidence            999999999999999999999999876

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=1.8e-31  Score=224.92  Aligned_cols=186  Identities=38%  Similarity=0.594  Sum_probs=167.4

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .++++..++||.+...+...+..+++|+|+||++|.+++.....+++++++||+||||++++++|..++..|+..+++++
T Consensus       230 ~~i~~~~~~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~~~~~l~~v~~lViDEAd~mld~gf~~~i~~il~~~~~~~  309 (545)
T PTZ00110        230 SKIRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQIRPDR  309 (545)
T ss_pred             cCccEEEEeCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHcCCCChhhCcEEEeehHHhhhhcchHHHHHHHHHhCCCCC
Confidence            36899999999999989888999999999999999999998888999999999999999999999999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcC-CCeEEEeCCCC-ccCcceeEEEEEcCchhhHHHHHHHhhcC---CCCEEEEeccccc
Q psy7789          91 QTLLFSATMPKKIQNFARSALV-KPITINVGRAG-AASMNVVQEVEYVKQEAKIVYLLECLQKT---EPPVLIFAEKKQD  165 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~-~~~~i~~~~~~-~~~~~i~~~~~~~~~~~k~~~l~~~l~~~---~~~~lIF~~s~~~  165 (197)
                      |++++|||+++++..+.+.++. +++.+.+.... .....+.+.+..+.+.+|...|.+++...   ..++||||+|++.
T Consensus       310 q~l~~SAT~p~~v~~l~~~l~~~~~v~i~vg~~~l~~~~~i~q~~~~~~~~~k~~~L~~ll~~~~~~~~k~LIF~~t~~~  389 (545)
T PTZ00110        310 QTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKG  389 (545)
T ss_pred             eEEEEEeCCCHHHHHHHHHHhccCCEEEEECCCccccCCCeeEEEEEEechhHHHHHHHHHHHhcccCCeEEEEecChHH
Confidence            9999999999999999988886 57777776443 34467888888888888888888888753   4689999999999


Q ss_pred             HHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         166 VDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       166 ~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      |+.++..|+..|+++..+||+|++++|++++
T Consensus       390 a~~l~~~L~~~g~~~~~ihg~~~~~eR~~il  420 (545)
T PTZ00110        390 ADFLTKELRLDGWPALCIHGDKKQEERTWVL  420 (545)
T ss_pred             HHHHHHHHHHcCCcEEEEECCCcHHHHHHHH
Confidence            9999999999999999999999999999876

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2.8e-31  Score=218.54  Aligned_cols=186  Identities=27%  Similarity=0.431  Sum_probs=170.2

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccC--
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRG--   88 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~--   88 (197)
                      .|+++..++||.+...+.+.+.+++||+|+||++|.+++.++.+++++++++|+||||++++++|...+..+++.++.  
T Consensus       110 ~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~~~~~l~~v~~lViDEad~l~~~~f~~~i~~i~~~~~~~~  189 (423)
T PRK04837        110 TGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLGFIKDIRWLFRRMPPAN  189 (423)
T ss_pred             CCceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccccEEEEecHHHHhhcccHHHHHHHHHhCCCcc
Confidence            479999999999999898889889999999999999999988899999999999999999999999999999999975  


Q ss_pred             CceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcC-CCCEEEEecccccHH
Q psy7789          89 QRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKT-EPPVLIFAEKKQDVD  167 (197)
Q Consensus        89 ~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~-~~~~lIF~~s~~~~~  167 (197)
                      ..|.+++|||++..+......++.+|..+.+.........+.+.+.+...++|...+.+++... ..++||||+++..|+
T Consensus       190 ~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lVF~~t~~~~~  269 (423)
T PRK04837        190 QRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYPSNEEKMRLLQTLIEEEWPDRAIIFANTKHRCE  269 (423)
T ss_pred             ceeEEEEeccCCHHHHHHHHHHCCCCEEEEEcCCCcCCCceeEEEEeCCHHHHHHHHHHHHHhcCCCeEEEEECCHHHHH
Confidence            5678999999999999999999999999888777766777888888888888999999998765 468999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .+++.|+..|+++..+||+|++++|.+++
T Consensus       270 ~l~~~L~~~g~~v~~lhg~~~~~~R~~~l  298 (423)
T PRK04837        270 EIWGHLAADGHRVGLLTGDVAQKKRLRIL  298 (423)
T ss_pred             HHHHHHHhCCCcEEEecCCCChhHHHHHH
Confidence            99999999999999999999999999876

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=4.5e-31  Score=218.96  Aligned_cols=187  Identities=34%  Similarity=0.535  Sum_probs=171.5

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .++++..++||.+.+.+...+.+++||+|+||++|++++.+..++++++++||+||||++++++|...+..++..++...
T Consensus       102 ~~~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~~~~~l~~v~~lViDEah~ll~~~~~~~i~~il~~l~~~~  181 (456)
T PRK10590        102 LNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVLAKLPAKR  181 (456)
T ss_pred             CCCEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHcCCcccccceEEEeecHHHHhccccHHHHHHHHHhCCccC
Confidence            46899999999999988888888999999999999999998888999999999999999999999999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCC-CCEEEEecccccHHHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTE-PPVLIFAEKKQDVDAI  169 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~~l  169 (197)
                      |++++|||+++++..+...++.+|..+.+.........+.+.+..+....|...+..++.... .++||||+|+..|+.+
T Consensus       182 q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~l~~~~~~~~~lVF~~t~~~~~~l  261 (456)
T PRK10590        182 QNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDKKRKRELLSQMIGKGNWQQVLVFTRTKHGANHL  261 (456)
T ss_pred             eEEEEeCCCcHHHHHHHHHHcCCCeEEEEecccccccceeEEEEEcCHHHHHHHHHHHHHcCCCCcEEEEcCcHHHHHHH
Confidence            999999999999999999999999988887766667788888888888888888888887654 5899999999999999


Q ss_pred             HHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         170 HEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       170 ~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      ++.|.+.|+++..+||+|++++|.++++
T Consensus       262 ~~~L~~~g~~~~~lhg~~~~~~R~~~l~  289 (456)
T PRK10590        262 AEQLNKDGIRSAAIHGNKSQGARTRALA  289 (456)
T ss_pred             HHHHHHCCCCEEEEECCCCHHHHHHHHH
Confidence            9999999999999999999999998763

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.98  E-value=7.6e-31  Score=222.04  Aligned_cols=187  Identities=30%  Similarity=0.498  Sum_probs=169.2

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcC-CccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccC-
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKK-MVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRG-   88 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~-~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~-   88 (197)
                      .++++..++||.+...+.+.+.+++||+|+||++|++++.+. .+.++.+++||+||||.+++++|...+..+++.++. 
T Consensus       111 ~~i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l~~v~~lViDEAh~lld~gf~~~i~~il~~lp~~  190 (572)
T PRK04537        111 LGLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMPER  190 (572)
T ss_pred             CCceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhccccchhheeeeEecCHHHHhhcchHHHHHHHHHhcccc
Confidence            479999999999999998888888999999999999998764 577899999999999999999999999999999987 


Q ss_pred             -CceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcC-CCCEEEEecccccH
Q psy7789          89 -QRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKT-EPPVLIFAEKKQDV  166 (197)
Q Consensus        89 -~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~-~~~~lIF~~s~~~~  166 (197)
                       ..|+++||||++..+......++.+|..+.+.........+.+.++.+...+|...+..++... ..++||||||+..|
T Consensus       191 ~~~q~ll~SATl~~~v~~l~~~~l~~p~~i~v~~~~~~~~~i~q~~~~~~~~~k~~~L~~ll~~~~~~k~LVF~nt~~~a  270 (572)
T PRK04537        191 GTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFPADEEKQTLLLGLLSRSEGARTMVFVNTKAFV  270 (572)
T ss_pred             cCceEEEEeCCccHHHHHHHHHHhcCCcEEEeccccccccceeEEEEecCHHHHHHHHHHHHhcccCCcEEEEeCCHHHH
Confidence             7899999999999999999999999887777666666677888888888888999999998865 45899999999999


Q ss_pred             HHHHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         167 DAIHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       167 ~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      +.+++.|.+.|+++..+||+|++.+|+++++
T Consensus       271 e~l~~~L~~~g~~v~~lhg~l~~~eR~~il~  301 (572)
T PRK04537        271 ERVARTLERHGYRVGVLSGDVPQKKRESLLN  301 (572)
T ss_pred             HHHHHHHHHcCCCEEEEeCCCCHHHHHHHHH
Confidence            9999999999999999999999999998863

>KOG0338|consensus

Probab=99.98  E-value=5.1e-32  Score=216.85  Aligned_cols=186  Identities=27%  Similarity=0.422  Sum_probs=171.3

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhc-CCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCC
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDK-KMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~-~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~   89 (197)
                      ..|.+++++||.+...|...|..+|||+|+|||++.+.+.+ ..++++++..+|+||||+|++.+|.+++..|++.+|++
T Consensus       279 t~I~~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDEADRMLeegFademnEii~lcpk~  358 (691)
T KOG0338|consen  279 TDITVGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEADRMLEEGFADEMNEIIRLCPKN  358 (691)
T ss_pred             ccceeeeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccceeEEEechHHHHHHHHHHHHHHHHHHhcccc
Confidence            36999999999999999999999999999999999999986 47899999999999999999999999999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcC---chhhHHHHHHHhhc-CCCCEEEEeccccc
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVK---QEAKIVYLLECLQK-TEPPVLIFAEKKQD  165 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~---~~~k~~~l~~~l~~-~~~~~lIF~~s~~~  165 (197)
                      +|+++||||++.++.+.+...++.|+.+.+.+.......+.|.|+.+.   +..+-..+..++.. .+.+++||+.|++.
T Consensus       359 RQTmLFSATMteeVkdL~slSL~kPvrifvd~~~~~a~~LtQEFiRIR~~re~dRea~l~~l~~rtf~~~~ivFv~tKk~  438 (691)
T KOG0338|consen  359 RQTMLFSATMTEEVKDLASLSLNKPVRIFVDPNKDTAPKLTQEFIRIRPKREGDREAMLASLITRTFQDRTIVFVRTKKQ  438 (691)
T ss_pred             ccceeehhhhHHHHHHHHHhhcCCCeEEEeCCccccchhhhHHHheeccccccccHHHHHHHHHHhcccceEEEEehHHH
Confidence            999999999999999999999999999999998888899999888774   45577777777764 46789999999999


Q ss_pred             HHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         166 VDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       166 ~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      |..+.-+|=-.|.++.-+||.|+|++|-+.+
T Consensus       439 AHRl~IllGLlgl~agElHGsLtQ~QRlesL  469 (691)
T KOG0338|consen  439 AHRLRILLGLLGLKAGELHGSLTQEQRLESL  469 (691)
T ss_pred             HHHHHHHHHHhhchhhhhcccccHHHHHHHH
Confidence            9999999989999999999999999997654

>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional

Probab=99.97  E-value=2.7e-30  Score=216.97  Aligned_cols=186  Identities=31%  Similarity=0.530  Sum_probs=168.0

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .++++..++||.+...+...+..+++|+|+||++|.+++.+....++++++||+||||++++++|+..+..++..++ ++
T Consensus       223 ~~~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~~~l~~v~~lViDEad~ml~~gf~~~i~~i~~~l~-~~  301 (518)
T PLN00206        223 LPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERGFRDQVMQIFQALS-QP  301 (518)
T ss_pred             CCceEEEEECCcchHHHHHHhcCCCCEEEECHHHHHHHHHcCCccchheeEEEeecHHHHhhcchHHHHHHHHHhCC-CC
Confidence            46899999999999989888888999999999999999998888999999999999999999999999999998884 78


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcC---CCCEEEEecccccHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKT---EPPVLIFAEKKQDVD  167 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~---~~~~lIF~~s~~~~~  167 (197)
                      |++++|||+++++..+...++.++..+.+.........+.+.+..+....|...+.+++...   .+++||||+|+..|+
T Consensus       302 q~l~~SATl~~~v~~l~~~~~~~~~~i~~~~~~~~~~~v~q~~~~~~~~~k~~~l~~~l~~~~~~~~~~iVFv~s~~~a~  381 (518)
T PLN00206        302 QVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGAD  381 (518)
T ss_pred             cEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCCCCCCcceeEEEEeccchhHHHHHHHHHHhhcccCCCEEEEcCCchhHH
Confidence            99999999999999999999999999988777666677888888888888888888888753   368999999999999


Q ss_pred             HHHHHHHh-CCCCeEeecCCCChhhhhhhhC
Q psy7789         168 AIHEYLLL-KGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       168 ~l~~~L~~-~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      .+++.|.. .|+++..+||+|++++|+++++
T Consensus       382 ~l~~~L~~~~g~~~~~~Hg~~~~~eR~~il~  412 (518)
T PLN00206        382 LLANAITVVTGLKALSIHGEKSMKERREVMK  412 (518)
T ss_pred             HHHHHHhhccCcceEEeeCCCCHHHHHHHHH
Confidence            99999985 5999999999999999998863

>KOG0341|consensus

Probab=99.97  E-value=2.5e-32  Score=212.73  Aligned_cols=185  Identities=73%  Similarity=1.149  Sum_probs=178.2

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      ..+|++++.||.+..+|.+.++.|.||+|+|||+|.+++.++..+++-++|+++||||++++.||.+.++.|+..+...+
T Consensus       279 P~lRs~LciGG~~v~eql~~v~~GvHivVATPGRL~DmL~KK~~sLd~CRyL~lDEADRmiDmGFEddir~iF~~FK~QR  358 (610)
T KOG0341|consen  279 PELRSLLCIGGVPVREQLDVVRRGVHIVVATPGRLMDMLAKKIMSLDACRYLTLDEADRMIDMGFEDDIRTIFSFFKGQR  358 (610)
T ss_pred             hhhhhhhhhcCccHHHHHHHHhcCeeEEEcCcchHHHHHHHhhccHHHHHHhhhhhHHHHhhccchhhHHHHHHHHhhhh
Confidence            35999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecccccHHHHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIH  170 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~  170 (197)
                      |+++||||+|..++.+++..+-.|+.+.+......+-++.|.+.++..+.|.-+|++-|+...+|+||||..+.++..+.
T Consensus       359 QTLLFSATMP~KIQ~FAkSALVKPvtvNVGRAGAAsldViQevEyVkqEaKiVylLeCLQKT~PpVLIFaEkK~DVD~Ih  438 (610)
T KOG0341|consen  359 QTLLFSATMPKKIQNFAKSALVKPVTVNVGRAGAASLDVIQEVEYVKQEAKIVYLLECLQKTSPPVLIFAEKKADVDDIH  438 (610)
T ss_pred             heeeeeccccHHHHHHHHhhcccceEEecccccccchhHHHHHHHHHhhhhhhhHHHHhccCCCceEEEeccccChHHHH
Confidence            99999999999999999999999999999988888888999889999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCeEeecCCCChhhhhhh
Q psy7789         171 EYLLLKGKPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       171 ~~L~~~~~~~~~~h~~~~~~~R~~i  195 (197)
                      ++|.-.|+.+..+|||-.+++|..-
T Consensus       439 EYLLlKGVEavaIHGGKDQedR~~a  463 (610)
T KOG0341|consen  439 EYLLLKGVEAVAIHGGKDQEDRHYA  463 (610)
T ss_pred             HHHHHccceeEEeecCcchhHHHHH
Confidence            9999999999999999999999753

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.97  E-value=7.4e-30  Score=210.76  Aligned_cols=186  Identities=27%  Similarity=0.391  Sum_probs=168.3

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .++++..++||.+...+.+.+.++++|+|+||++|++++.+..++++++++||+||||++++++|...+..+...++...
T Consensus       100 ~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~~~~~~~~v~~lViDEah~~l~~~~~~~~~~i~~~~~~~~  179 (434)
T PRK11192        100 THLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIETIAAETRWRK  179 (434)
T ss_pred             CCcEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCcCcccCCEEEEECHHHHhCCCcHHHHHHHHHhCcccc
Confidence            47899999999999999888888999999999999999999999999999999999999999999999999999998899


Q ss_pred             eEEEEeecCCh-hHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCc-hhhHHHHHHHhhcC-CCCEEEEecccccHH
Q psy7789          91 QTLLFSATMPK-KIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQ-EAKIVYLLECLQKT-EPPVLIFAEKKQDVD  167 (197)
Q Consensus        91 q~i~~SAT~~~-~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~~l~~~-~~~~lIF~~s~~~~~  167 (197)
                      |+++||||++. .+..+...++.+|..+...........+.+.++.+.. +.|...+..+++.. ..++||||+|++.|+
T Consensus       180 q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~lVF~~s~~~~~  259 (434)
T PRK11192        180 QTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLCHLLKQPEVTRSIVFVRTRERVH  259 (434)
T ss_pred             EEEEEEeecCHHHHHHHHHHHccCCEEEEecCCcccccCceEEEEEeCCHHHHHHHHHHHHhcCCCCeEEEEeCChHHHH
Confidence            99999999985 4788888899999998887777767778887777754 67888888888864 468999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .+++.|++.|+++..+||+|++.+|.+++
T Consensus       260 ~l~~~L~~~~~~~~~l~g~~~~~~R~~~l  288 (434)
T PRK11192        260 ELAGWLRKAGINCCYLEGEMVQAKRNEAI  288 (434)
T ss_pred             HHHHHHHhCCCCEEEecCCCCHHHHHHHH
Confidence            99999999999999999999999999875

>KOG0343|consensus

Probab=99.97  E-value=1.4e-30  Score=210.31  Aligned_cols=184  Identities=30%  Similarity=0.453  Sum_probs=169.9

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhc-CCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDK-KMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~-~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      +..+.++.||.+...+.+.+++ ..|+|||||||+..+.. ..++..++.++|+||||++++.||...+..|+.++|+.+
T Consensus       169 ~fSaGLiiGG~~~k~E~eRi~~-mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDEADR~LDMGFk~tL~~Ii~~lP~~R  247 (758)
T KOG0343|consen  169 DFSAGLIIGGKDVKFELERISQ-MNILVCTPGRLLQHMDENPNFSTSNLQMLVLDEADRMLDMGFKKTLNAIIENLPKKR  247 (758)
T ss_pred             ccccceeecCchhHHHHHhhhc-CCeEEechHHHHHHhhhcCCCCCCcceEEEeccHHHHHHHhHHHHHHHHHHhCChhh
Confidence            6888999999998888888876 89999999999998864 578899999999999999999999999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeC--CCCccCcceeEEEEEcCchhhHHHHHHHhhcCC-CCEEEEecccccHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVG--RAGAASMNVVQEVEYVKQEAKIVYLLECLQKTE-PPVLIFAEKKQDVD  167 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~--~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~  167 (197)
                      |+++||||-+..+...++..+++|..|.+.  .....|.++.|+|+.++.++|+..|+.+++.+. .++|||++|++.+.
T Consensus       248 QTLLFSATqt~svkdLaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v~l~~Ki~~L~sFI~shlk~K~iVF~SscKqvk  327 (758)
T KOG0343|consen  248 QTLLFSATQTKSVKDLARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPLEDKIDMLWSFIKSHLKKKSIVFLSSCKQVK  327 (758)
T ss_pred             eeeeeecccchhHHHHHHhhcCCCcEEEEeccccccChhhhhheEEEEehhhHHHHHHHHHHhccccceEEEEehhhHHH
Confidence            999999999999999999999999877765  446788999999999999999999999999885 48999999999999


Q ss_pred             HHHHHHHhC--CCCeEeecCCCChhhhhhhh
Q psy7789         168 AIHEYLLLK--GKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       168 ~l~~~L~~~--~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .+++.+...  |+++.++||.|+|..|.++-
T Consensus       328 f~~e~F~rlrpg~~l~~L~G~~~Q~~R~ev~  358 (758)
T KOG0343|consen  328 FLYEAFCRLRPGIPLLALHGTMSQKKRIEVY  358 (758)
T ss_pred             HHHHHHHhcCCCCceeeeccchhHHHHHHHH
Confidence            999999877  89999999999999998763

>KOG0327|consensus

Probab=99.97  E-value=3e-30  Score=200.50  Aligned_cols=185  Identities=26%  Similarity=0.421  Sum_probs=173.6

Q ss_pred             CCeeEEEEEcCCChHHhHHHH-hcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCC
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVI-KKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l-~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~   89 (197)
                      .+.++..++||.+...+-..+ ..+++|+++||+++.+++....+..+.++++|+||||.++..+|.+++..|.+.+|++
T Consensus       121 ~~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~~l~~~~iKmfvlDEaDEmLs~gfkdqI~~if~~lp~~  200 (397)
T KOG0327|consen  121 MDVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRGSLSTDGIKMFVLDEADEMLSRGFKDQIYDIFQELPSD  200 (397)
T ss_pred             cceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhccccccccceeEEeecchHhhhccchHHHHHHHHHHcCcc
Confidence            468999999999988666555 4579999999999999999888889999999999999999999999999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecccccHHHH
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAI  169 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l  169 (197)
                      .|++++|||+++++....+.++++|+.+.+.........++|++..+..++|+..|.++.+ .-.+++|||||++.+.++
T Consensus       201 vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk~~ltl~gikq~~i~v~k~~k~~~l~dl~~-~~~q~~if~nt~r~v~~l  279 (397)
T KOG0327|consen  201 VQVVLLSATMPSDVLEVTKKFMREPVRILVKKDELTLEGIKQFYINVEKEEKLDTLCDLYR-RVTQAVIFCNTRRKVDNL  279 (397)
T ss_pred             hhheeecccCcHHHHHHHHHhccCceEEEecchhhhhhheeeeeeeccccccccHHHHHHH-hhhcceEEecchhhHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999 556899999999999999


Q ss_pred             HHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         170 HEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       170 ~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      ..+|..+|..+.++||+|.+.+|+.++
T Consensus       280 ~~~L~~~~~~~s~~~~d~~q~~R~~~~  306 (397)
T KOG0327|consen  280 TDKLRAHGFTVSAIHGDMEQNERDTLM  306 (397)
T ss_pred             HHHHhhCCceEEEeecccchhhhhHHH
Confidence            999999999999999999999998765

>KOG0342|consensus

Probab=99.97  E-value=4.9e-30  Score=204.53  Aligned_cols=185  Identities=32%  Similarity=0.518  Sum_probs=168.1

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcC-CccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCC
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKK-MVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~-~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~   89 (197)
                      .++.+.+..||.+.....+.+..++.|+|+|||+|++.+++. .+-.++++++|+||||++++.||++.+..|++.+|..
T Consensus       182 ~~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~lvlDEADrlLd~GF~~di~~Ii~~lpk~  261 (543)
T KOG0342|consen  182 ESITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCLVLDEADRLLDIGFEEDVEQIIKILPKQ  261 (543)
T ss_pred             CCcceEEEeCCccchHHHHHhhccccEEEeCCchHHhHhhcCCcchhhccceeEeecchhhhhcccHHHHHHHHHhcccc
Confidence            378999999999999888889889999999999999999874 4567889999999999999999999999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcC-CCeEEEeCCCC--ccCcceeEEEEEcCchhhHHHHHHHhhcCC--CCEEEEecccc
Q psy7789          90 RQTLLFSATMPKKIQNFARSALV-KPITINVGRAG--AASMNVVQEVEYVKQEAKIVYLLECLQKTE--PPVLIFAEKKQ  164 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~-~~~~i~~~~~~--~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~--~~~lIF~~s~~  164 (197)
                      +|..+||||.++++.+.++..++ +|..+.+.+..  ...+.+.|-++.++...++-.+..+|+++.  .+++|||+|..
T Consensus       262 rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~~~~f~ll~~~LKk~~~~~KiiVF~sT~~  341 (543)
T KOG0342|consen  262 RQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAPSDSRFSLLYTFLKKNIKRYKIIVFFSTCM  341 (543)
T ss_pred             ceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEEeccccchHHHHHHHHHHhcCCceEEEEechhh
Confidence            99999999999999999999887 48888876544  566889998888888888999999998774  58999999999


Q ss_pred             cHHHHHHHHHhCCCCeEeecCCCChhhhhhh
Q psy7789         165 DVDAIHEYLLLKGKPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       165 ~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i  195 (197)
                      .+..++++|+....+|..+||+++|..|..+
T Consensus       342 ~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~  372 (543)
T KOG0342|consen  342 SVKFHAELLNYIDLPVLEIHGKQKQNKRTST  372 (543)
T ss_pred             HHHHHHHHHhhcCCchhhhhcCCcccccchH
Confidence            9999999999999999999999999999765

>KOG0337|consensus

Probab=99.97  E-value=2.6e-30  Score=202.93  Aligned_cols=183  Identities=28%  Similarity=0.449  Sum_probs=175.2

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .++++.+++||.++++|...+..+||||+|||+++.++.-.-.+.++.+.|||+||+|.+++.||.+++..++.++|.++
T Consensus       117 t~lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~vem~l~l~sveyVVfdEadrlfemgfqeql~e~l~rl~~~~  196 (529)
T KOG0337|consen  117 TKLRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEADRLFEMGFQEQLHEILSRLPESR  196 (529)
T ss_pred             cchhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehheeccccceeeeeehhhhHHHhhhhHHHHHHHHHhCCCcc
Confidence            47999999999999999999999999999999999999887788999999999999999999999999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCCC--CEEEEecccccHHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEP--PVLIFAEKKQDVDA  168 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~--~~lIF~~s~~~~~~  168 (197)
                      |+++||||+|....++++.-+.+|..+.+.-+....+.+...+..+..++|..+|+.++....+  +++|||.|...++.
T Consensus       197 QTllfSatlp~~lv~fakaGl~~p~lVRldvetkise~lk~~f~~~~~a~K~aaLl~il~~~~~~~~t~vf~~tk~hve~  276 (529)
T KOG0337|consen  197 QTLLFSATLPRDLVDFAKAGLVPPVLVRLDVETKISELLKVRFFRVRKAEKEAALLSILGGRIKDKQTIVFVATKHHVEY  276 (529)
T ss_pred             eEEEEeccCchhhHHHHHccCCCCceEEeehhhhcchhhhhheeeeccHHHHHHHHHHHhccccccceeEEecccchHHH
Confidence            9999999999999999999999999999988888999999999999999999999999998754  89999999999999


Q ss_pred             HHHHHHhCCCCeEeecCCCChhhhh
Q psy7789         169 IHEYLLLKGKPFFTLKSLKEDQNNQ  193 (197)
Q Consensus       169 l~~~L~~~~~~~~~~h~~~~~~~R~  193 (197)
                      +...|+..|+.+..++|.|.+..|.
T Consensus       277 ~~~ll~~~g~~~s~iysslD~~aRk  301 (529)
T KOG0337|consen  277 VRGLLRDFGGEGSDIYSSLDQEARK  301 (529)
T ss_pred             HHHHHHhcCCCccccccccChHhhh
Confidence            9999999999999999999999987

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.97  E-value=1e-28  Score=206.00  Aligned_cols=187  Identities=32%  Similarity=0.465  Sum_probs=168.0

Q ss_pred             CCeeEEEEEcCCChHHhHHHHh-cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccC-
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIK-KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRG-   88 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~-~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~-   88 (197)
                      .|+++..++||.+...+.+.+. ++++|+|+||++|+.++.+....++++++|||||||.+++++|...+..+++.++. 
T Consensus       189 ~~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~~lViDEah~l~~~~~~~~l~~i~~~~~~~  268 (475)
T PRK01297        189 TGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFIPQVRQIIRQTPRK  268 (475)
T ss_pred             CCCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcCCcccccCceEEechHHHHHhcccHHHHHHHHHhCCCC
Confidence            4789999999999888887774 56999999999999999888888999999999999999999999999999999865 


Q ss_pred             -CceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCC-CCEEEEecccccH
Q psy7789          89 -QRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTE-PPVLIFAEKKQDV  166 (197)
Q Consensus        89 -~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~-~~~lIF~~s~~~~  166 (197)
                       +.|++++|||++.++......++.++..+.+.........+.+.++.+...+|...+.+++.... .++||||++++.|
T Consensus       269 ~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~ll~~~~~~~~IVF~~s~~~~  348 (475)
T PRK01297        269 EERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAGSDKYKLLYNLVTQNPWERVMVFANRKDEV  348 (475)
T ss_pred             CCceEEEEEeecCHHHHHHHHHhccCCEEEEeccCcCCCCcccEEEEEecchhHHHHHHHHHHhcCCCeEEEEeCCHHHH
Confidence             57999999999999999999999999988887777666778888888888888888888887654 5899999999999


Q ss_pred             HHHHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         167 DAIHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       167 ~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      +.+++.|.+.|+++..+||+|++++|.++++
T Consensus       349 ~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~  379 (475)
T PRK01297        349 RRIEERLVKDGINAAQLSGDVPQHKRIKTLE  379 (475)
T ss_pred             HHHHHHHHHcCCCEEEEECCCCHHHHHHHHH
Confidence            9999999999999999999999999988763

>KOG4284|consensus

Probab=99.97  E-value=7.2e-30  Score=209.42  Aligned_cols=185  Identities=21%  Similarity=0.332  Sum_probs=170.8

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhc-CCCHHHHHHHHhhccCC
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD-MGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~-~~~~~~i~~i~~~~~~~   89 (197)
                      .|.+|..++||.+.......++. ++|+||||||+..++..+.++.++++++|+||||.|++ ..|++++..|+..+|..
T Consensus       121 ~g~~csvfIGGT~~~~d~~rlk~-~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEADkL~~t~sfq~~In~ii~slP~~  199 (980)
T KOG4284|consen  121 TGARCSVFIGGTAHKLDLIRLKQ-TRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEADKLMDTESFQDDINIIINSLPQI  199 (980)
T ss_pred             cCcceEEEecCchhhhhhhhhhh-ceEEecCchHHHHHHHhcCCCccceeEEEeccHHhhhchhhHHHHHHHHHHhcchh
Confidence            68999999999998888777776 89999999999999999999999999999999999998 56999999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCc--------hhhHHHHHHHhhcCCC-CEEEEe
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQ--------EAKIVYLLECLQKTEP-PVLIFA  160 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~--------~~k~~~l~~~l~~~~~-~~lIF~  160 (197)
                      +|+++||||.|..+.+....+|++|..+........+-+++|+++.++.        +.|++.|-++.++.+- ++||||
T Consensus       200 rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~d~~L~GikQyv~~~~s~nnsveemrlklq~L~~vf~~ipy~QAlVF~  279 (980)
T KOG4284|consen  200 RQVAAFSATYPRNLDNLLSKFMRDPALVRFNADDVQLFGIKQYVVAKCSPNNSVEEMRLKLQKLTHVFKSIPYVQALVFC  279 (980)
T ss_pred             heeeEEeccCchhHHHHHHHHhcccceeecccCCceeechhheeeeccCCcchHHHHHHHHHHHHHHHhhCchHHHHhhh
Confidence            9999999999999999999999999999999888888899999887754        3478888888888763 899999


Q ss_pred             cccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         161 EKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       161 ~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +...+|+-++..|+..|++|.+++|.|++.+|.-+.
T Consensus       280 ~~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~  315 (980)
T KOG4284|consen  280 DQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAV  315 (980)
T ss_pred             hhhhhhhHHHHHhhccCCCeEEeccccchhHHHHHH
Confidence            999999999999999999999999999999997653

>KOG0335|consensus

Probab=99.96  E-value=5.6e-29  Score=200.35  Aligned_cols=186  Identities=38%  Similarity=0.648  Sum_probs=172.5

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhc-CCCHHHHHHHHhhccC-
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD-MGFEEDVRTIFSFFRG-   88 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~-~~~~~~i~~i~~~~~~-   88 (197)
                      .+++++..+||.+...|.+.+..++||+|||||+|.+++..+.+.+.+++++|+||||.|++ .+|.++++.|+..... 
T Consensus       179 s~~~~~~~ygg~~~~~q~~~~~~gcdIlvaTpGrL~d~~e~g~i~l~~~k~~vLDEADrMlD~mgF~p~Ir~iv~~~~~~  258 (482)
T KOG0335|consen  179 SGMKSVVVYGGTDLGAQLRFIKRGCDILVATPGRLKDLIERGKISLDNCKFLVLDEADRMLDEMGFEPQIRKIVEQLGMP  258 (482)
T ss_pred             ccceeeeeeCCcchhhhhhhhccCccEEEecCchhhhhhhcceeehhhCcEEEecchHHhhhhccccccHHHHhcccCCC
Confidence            47999999999999999999999999999999999999999999999999999999999999 8999999999988743 


Q ss_pred             ---CceEEEEeecCChhHHHHHHHhcCC-CeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcC-----CC-----
Q psy7789          89 ---QRQTLLFSATMPKKIQNFARSALVK-PITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKT-----EP-----  154 (197)
Q Consensus        89 ---~~q~i~~SAT~~~~~~~~~~~~~~~-~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~-----~~-----  154 (197)
                         +.|.++||||++.++...+..++.+ .+.+.+......++++.|.+..+.+.+|...|+++|...     .+     
T Consensus       259 ~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~rvg~~~~ni~q~i~~V~~~~kr~~Lldll~~~~~~~~~~~~~~e  338 (482)
T KOG0335|consen  259 PKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVGRVGSTSENITQKILFVNEMEKRSKLLDLLNKDDGPPSDGEPKWE  338 (482)
T ss_pred             CccceeEEEEeccCChhhhhhHHHHhhccceEEEEeeeccccccceeEeeeecchhhHHHHHHHhhcccCCcccCCcccc
Confidence               7899999999999999988888886 788888888888999999999999999999999999733     12     


Q ss_pred             CEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         155 PVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       155 ~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +++|||.|++.|..++.+|...++++..+||+-.+.+|++-+
T Consensus       339 ~tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~al  380 (482)
T KOG0335|consen  339 KTLVFVETKRGADELAAFLSSNGYPAKSIHGDRTQIEREQAL  380 (482)
T ss_pred             eEEEEeeccchhhHHHHHHhcCCCCceeecchhhhhHHHHHH
Confidence            699999999999999999999999999999999999998764

>KOG0347|consensus

Probab=99.96  E-value=4.7e-30  Score=207.16  Aligned_cols=186  Identities=25%  Similarity=0.362  Sum_probs=162.9

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCc---cCCCccEEEeehhhhhhcCCCHHHHHHHHhhcc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMV---SLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFR   87 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~---~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~   87 (197)
                      .+|+++.++||.+...|.+.|+..|||+|||||||+.++.....   ++++++++|+||+|+|++.|+.+.+..+++.+.
T Consensus       290 t~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n~~l~~~k~vkcLVlDEaDRmvekghF~Els~lL~~L~  369 (731)
T KOG0347|consen  290 TQIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNTHLGNFKKVKCLVLDEADRMVEKGHFEELSKLLKHLN  369 (731)
T ss_pred             cCeEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhhhhhhhhhhceEEEEccHHHHhhhccHHHHHHHHHHhh
Confidence            58999999999999999999999999999999999999986544   578999999999999999999999999988885


Q ss_pred             -----CCceEEEEeecCCh-----------------h----HHHHHHH--hcCCCeEEEeCCCCccCcceeEEEEEcCch
Q psy7789          88 -----GQRQTLLFSATMPK-----------------K----IQNFARS--ALVKPITINVGRAGAASMNVVQEVEYVKQE  139 (197)
Q Consensus        88 -----~~~q~i~~SAT~~~-----------------~----~~~~~~~--~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~  139 (197)
                           ..+|+++||||++-                 +    ++.+...  +..+|..|++.+...+...+....+.|+..
T Consensus       370 e~~~~~qrQTlVFSATlt~~~~~~~~~~~k~~~k~~~~~~kiq~Lmk~ig~~~kpkiiD~t~q~~ta~~l~Es~I~C~~~  449 (731)
T KOG0347|consen  370 EEQKNRQRQTLVFSATLTLVLQQPLSSSRKKKDKEDELNAKIQHLMKKIGFRGKPKIIDLTPQSATASTLTESLIECPPL  449 (731)
T ss_pred             hhhcccccceEEEEEEeehhhcChhHHhhhccchhhhhhHHHHHHHHHhCccCCCeeEecCcchhHHHHHHHHhhcCCcc
Confidence                 35699999999861                 1    1122221  335778999988888888888888899999


Q ss_pred             hhHHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         140 AKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       140 ~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +|-.+|.++|..+++++|||||++..+..|+-+|+..++..+.+|+.|.|.+|-+-+
T Consensus       450 eKD~ylyYfl~ryPGrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA~M~QKqRLknL  506 (731)
T KOG0347|consen  450 EKDLYLYYFLTRYPGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHASMIQKQRLKNL  506 (731)
T ss_pred             ccceeEEEEEeecCCceEEEechHHHHHHHHHHHhhcCCCCchhhHHHHHHHHHHhH
Confidence            999999999999999999999999999999999999999999999999999997654

>KOG0346|consensus

Probab=99.96  E-value=2.6e-29  Score=198.29  Aligned_cols=193  Identities=21%  Similarity=0.262  Sum_probs=172.3

Q ss_pred             ccccCCCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCC-ccCCCccEEEeehhhhhhcCCCHHHHHHHH
Q psy7789           5 FISALPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKM-VSLDVCRYLCLDEADRMVDMGFEEDVRTIF   83 (197)
Q Consensus         5 ~~~~~~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~-~~l~~l~~vViDEad~l~~~~~~~~i~~i~   83 (197)
                      +.+.++..+|++-+....+-......+.+.|||+|+||++++.++..+. ..++.++++|+||||.++..||.+.+..+.
T Consensus       116 L~~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~~~~~~~l~~LVvDEADLllsfGYeedlk~l~  195 (569)
T KOG0346|consen  116 LVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGVLEYLDSLSFLVVDEADLLLSFGYEEDLKKLR  195 (569)
T ss_pred             HHHHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhccchhhhheeeEEechhhhhhhcccHHHHHHHH
Confidence            3455666788887887766666667777889999999999999998776 678999999999999999999999999999


Q ss_pred             hhccCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCC-ccCcceeEEEEEcCchhhHHHHHHHhhcC--CCCEEEEe
Q psy7789          84 SFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAG-AASMNVVQEVEYVKQEAKIVYLLECLQKT--EPPVLIFA  160 (197)
Q Consensus        84 ~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~-~~~~~i~~~~~~~~~~~k~~~l~~~l~~~--~~~~lIF~  160 (197)
                      ..+|+..|.+++|||+++++......++.+|+.+.+.+.. ..++.+.|+++.|++++|+..+..+++-.  .++.|||+
T Consensus       196 ~~LPr~~Q~~LmSATl~dDv~~LKkL~l~nPviLkl~e~el~~~dqL~Qy~v~cse~DKflllyallKL~LI~gKsliFV  275 (569)
T KOG0346|consen  196 SHLPRIYQCFLMSATLSDDVQALKKLFLHNPVILKLTEGELPNPDQLTQYQVKCSEEDKFLLLYALLKLRLIRGKSLIFV  275 (569)
T ss_pred             HhCCchhhheeehhhhhhHHHHHHHHhccCCeEEEeccccCCCcccceEEEEEeccchhHHHHHHHHHHHHhcCceEEEE
Confidence            9999999999999999999999999999999999887665 45578999999999999999999888754  68999999


Q ss_pred             cccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         161 EKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       161 ~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      ||+.+|-.+.-+|..-|++...++|.|+.+-|..|++
T Consensus       276 NtIdr~YrLkLfLeqFGiksciLNseLP~NSR~Hii~  312 (569)
T KOG0346|consen  276 NTIDRCYRLKLFLEQFGIKSCILNSELPANSRCHIIE  312 (569)
T ss_pred             echhhhHHHHHHHHHhCcHhhhhcccccccchhhHHH
Confidence            9999999999999999999999999999999987753

>PTZ00424 helicase 45; Provisional

Probab=99.96  E-value=1.7e-27  Score=194.81  Aligned_cols=187  Identities=25%  Similarity=0.403  Sum_probs=164.9

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .++++..++||....++...+..+++|+|+||+++.+++.+....+++++++|+||||+++++++...+..+++.++++.
T Consensus       123 ~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~l~~i~lvViDEah~~~~~~~~~~~~~i~~~~~~~~  202 (401)
T PTZ00424        123 LKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQIYDVFKKLPPDV  202 (401)
T ss_pred             cCceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCCcccccccEEEEecHHHHHhcchHHHHHHHHhhCCCCc
Confidence            36788889999988888888888899999999999999988888899999999999999999999999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCc-hhhHHHHHHHhhcC-CCCEEEEecccccHHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQ-EAKIVYLLECLQKT-EPPVLIFAEKKQDVDA  168 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~~l~~~-~~~~lIF~~s~~~~~~  168 (197)
                      |++++|||++++.......++++|..+.+.........+.+.+..+.. +.+...+.++++.. ..++||||+|++.|+.
T Consensus       203 ~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ivF~~t~~~~~~  282 (401)
T PTZ00424        203 QVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLCDLYETLTITQAIIYCNTRRKVDY  282 (401)
T ss_pred             EEEEEEecCCHHHHHHHHHHcCCCEEEEeCCCCcccCCceEEEEecChHHHHHHHHHHHHHhcCCCeEEEEecCcHHHHH
Confidence            999999999999999999999999888777666666777777776654 45777777777754 3589999999999999


Q ss_pred             HHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         169 IHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       169 l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      +++.|++.++.+..+||+|++++|+++++
T Consensus       283 l~~~l~~~~~~~~~~h~~~~~~~R~~i~~  311 (401)
T PTZ00424        283 LTKKMHERDFTVSCMHGDMDQKDRDLIMR  311 (401)
T ss_pred             HHHHHHHCCCcEEEEeCCCCHHHHHHHHH
Confidence            99999999999999999999999998763

>KOG0336|consensus

Probab=99.96  E-value=2.5e-28  Score=191.62  Aligned_cols=186  Identities=31%  Similarity=0.475  Sum_probs=169.5

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .|++...++||.+..+|.+.++.+.+|+|+||++|.++...+.++++.+.|+|+||||.+++.+|.+++++|+--+.+++
T Consensus       320 ng~ksvc~ygggnR~eqie~lkrgveiiiatPgrlndL~~~n~i~l~siTYlVlDEADrMLDMgFEpqIrkilldiRPDR  399 (629)
T KOG0336|consen  320 NGLKSVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINLASITYLVLDEADRMLDMGFEPQIRKILLDIRPDR  399 (629)
T ss_pred             cCcceEEEecCCCchhHHHHHhcCceEEeeCCchHhhhhhcCeeeeeeeEEEEecchhhhhcccccHHHHHHhhhcCCcc
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccC-cceeEEEEEcCchhhHHHHHHHhhcCC--CCEEEEecccccHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAAS-MNVVQEVEYVKQEAKIVYLLECLQKTE--PPVLIFAEKKQDVD  167 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~-~~i~~~~~~~~~~~k~~~l~~~l~~~~--~~~lIF~~s~~~~~  167 (197)
                      |+++.|||||+.++..+..|+++|+.+-+....... ..++|.++...+.+|+..+..++....  -++||||..+..|.
T Consensus       400 qtvmTSATWP~~VrrLa~sY~Kep~~v~vGsLdL~a~~sVkQ~i~v~~d~~k~~~~~~f~~~ms~ndKvIiFv~~K~~AD  479 (629)
T KOG0336|consen  400 QTVMTSATWPEGVRRLAQSYLKEPMIVYVGSLDLVAVKSVKQNIIVTTDSEKLEIVQFFVANMSSNDKVIIFVSRKVMAD  479 (629)
T ss_pred             eeeeecccCchHHHHHHHHhhhCceEEEecccceeeeeeeeeeEEecccHHHHHHHHHHHHhcCCCceEEEEEechhhhh
Confidence            999999999999999999999999998887666433 456777755567788888777877664  48999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .|..-|.-.|+.+..+||+-.|.+|+.-+
T Consensus       480 ~LSSd~~l~gi~~q~lHG~r~Q~DrE~al  508 (629)
T KOG0336|consen  480 HLSSDFCLKGISSQSLHGNREQSDREMAL  508 (629)
T ss_pred             hccchhhhcccchhhccCChhhhhHHHHH
Confidence            99999999999999999999999998754

>KOG0340|consensus

Probab=99.96  E-value=3.1e-28  Score=187.70  Aligned_cols=186  Identities=25%  Similarity=0.345  Sum_probs=165.3

Q ss_pred             CCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcC----CccCCCccEEEeehhhhhhcCCCHHHHHHHHhh
Q psy7789          10 PIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKK----MVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSF   85 (197)
Q Consensus        10 ~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~----~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~   85 (197)
                      .+++|+++++||.+.-.|...|...||++|+|||++-+++...    .+.+++++++|+||||.+++..|-+.+..+++-
T Consensus       101 ~l~lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflVlDEADrvL~~~f~d~L~~i~e~  180 (442)
T KOG0340|consen  101 LLNLKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLVLDEADRVLAGCFPDILEGIEEC  180 (442)
T ss_pred             cccceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeEEecchhhhhccchhhHHhhhhcc
Confidence            3589999999999999999999999999999999999998754    456899999999999999999999999999999


Q ss_pred             ccCCceEEEEeecCChhHHHHHHHhcCC--CeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcC----CCCEEEE
Q psy7789          86 FRGQRQTLLFSATMPKKIQNFARSALVK--PITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKT----EPPVLIF  159 (197)
Q Consensus        86 ~~~~~q~i~~SAT~~~~~~~~~~~~~~~--~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~----~~~~lIF  159 (197)
                      +|..+|..+||||+++.+.+...--...  +......+..+..+.+.|.|+.++...|..++.++|+..    .+.++||
T Consensus       181 lP~~RQtLlfSATitd~i~ql~~~~i~k~~a~~~e~~~~vstvetL~q~yI~~~~~vkdaYLv~~Lr~~~~~~~~simIF  260 (442)
T KOG0340|consen  181 LPKPRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYILVSIDVKDAYLVHLLRDFENKENGSIMIF  260 (442)
T ss_pred             CCCccceEEEEeehhhHHHHhhcCCcccccceEEeccCCCCchhhhhhheeecchhhhHHHHHHHHhhhhhccCceEEEE
Confidence            9999999999999998877765444444  445566667788889999999999999999999999854    3469999


Q ss_pred             ecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhh
Q psy7789         160 AEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       160 ~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i  195 (197)
                      +|+..+|+.|+..|+..++++..+||.|+|.+|-.-
T Consensus       261 vnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~a  296 (442)
T KOG0340|consen  261 VNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAA  296 (442)
T ss_pred             eehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHH
Confidence            999999999999999999999999999999999653

>KOG0334|consensus

Probab=99.94  E-value=6.9e-27  Score=200.41  Aligned_cols=186  Identities=34%  Similarity=0.552  Sum_probs=172.5

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcC---CccCCCccEEEeehhhhhhcCCCHHHHHHHHhhcc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKK---MVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFR   87 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~---~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~   87 (197)
                      .|++++..+||..+..|...++.++.|+|||||+..+++..+   ..+++++.++|+||||++++.+|.+++-.|++.++
T Consensus       465 l~ir~v~vygg~~~~~qiaelkRg~eIvV~tpGRmiD~l~~n~grvtnlrR~t~lv~deaDrmfdmgfePq~~~Ii~nlr  544 (997)
T KOG0334|consen  465 LGIRVVCVYGGSGISQQIAELKRGAEIVVCTPGRMIDILCANSGRVTNLRRVTYLVLDEADRMFDMGFEPQITRILQNLR  544 (997)
T ss_pred             cCceEEEecCCccHHHHHHHHhcCCceEEeccchhhhhHhhcCCccccccccceeeechhhhhheeccCcccchHHhhcc
Confidence            689999999999999999999999999999999999998643   45677777999999999999999999999999999


Q ss_pred             CCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcC-chhhHHHHHHHhhcC--CCCEEEEecccc
Q psy7789          88 GQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVK-QEAKIVYLLECLQKT--EPPVLIFAEKKQ  164 (197)
Q Consensus        88 ~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~-~~~k~~~l~~~l~~~--~~~~lIF~~s~~  164 (197)
                      +.+|+++||||++..+..+++..+..|+.+.+.........+.+.+..++ +++|+..|.++|...  ..++||||.+..
T Consensus       545 pdrQtvlfSatfpr~m~~la~~vl~~Pveiiv~~~svV~k~V~q~v~V~~~e~eKf~kL~eLl~e~~e~~~tiiFv~~qe  624 (997)
T KOG0334|consen  545 PDRQTVLFSATFPRSMEALARKVLKKPVEIIVGGRSVVCKEVTQVVRVCAIENEKFLKLLELLGERYEDGKTIIFVDKQE  624 (997)
T ss_pred             hhhhhhhhhhhhhHHHHHHHHHhhcCCeeEEEccceeEeccceEEEEEecCchHHHHHHHHHHHHHhhcCCEEEEEcCch
Confidence            99999999999999999999999999999888877788888999999998 899999999999764  579999999999


Q ss_pred             cHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         165 DVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       165 ~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .|..+...|.+.|+.|..+||+-++.+|..++
T Consensus       625 ~~d~l~~~L~~ag~~~~slHGgv~q~dR~sti  656 (997)
T KOG0334|consen  625 KADALLRDLQKAGYNCDSLHGGVDQHDRSSTI  656 (997)
T ss_pred             HHHHHHHHHHhcCcchhhhcCCCchHHHHhHH
Confidence            99999999999999999999999999998765

>KOG0329|consensus

Probab=99.94  E-value=3.2e-27  Score=175.38  Aligned_cols=186  Identities=23%  Similarity=0.403  Sum_probs=156.2

Q ss_pred             cccccCCCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcC-CCHHHHHHH
Q psy7789           4 PFISALPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDM-GFEEDVRTI   82 (197)
Q Consensus         4 ~~~~~~~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~-~~~~~i~~i   82 (197)
                      +|++.++ +++++.++||.++....+.+++-|||+|+|||+++.+.+++.+++++++.+|+||||.++++ ..+..++.|
T Consensus       132 rfskymP-~vkvaVFfGG~~Ikkdee~lk~~PhivVgTPGrilALvr~k~l~lk~vkhFvlDEcdkmle~lDMrRDvQEi  210 (387)
T KOG0329|consen  132 RFSKYMP-SVKVSVFFGGLFIKKDEELLKNCPHIVVGTPGRILALVRNRSLNLKNVKHFVLDECDKMLEQLDMRRDVQEI  210 (387)
T ss_pred             HHHhhCC-CceEEEEEcceeccccHHHHhCCCeEEEcCcHHHHHHHHhccCchhhcceeehhhHHHHHHHHHHHHHHHHH
Confidence            3566666 79999999999999999999999999999999999999999999999999999999999875 588899999


Q ss_pred             HhhccCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCC-ccCcceeEEEEEcCchhhHHHHHHHhhcCC-CCEEEEe
Q psy7789          83 FSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAG-AASMNVVQEVEYVKQEAKIVYLLECLQKTE-PPVLIFA  160 (197)
Q Consensus        83 ~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~-~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~-~~~lIF~  160 (197)
                      .+..|...|+.+||||++++++..++.++++|..+.+.++. ...-++.|+|+...+.+|...+.++|.... .+++||+
T Consensus       211 fr~tp~~KQvmmfsatlskeiRpvC~kFmQdPmEi~vDdE~KLtLHGLqQ~YvkLke~eKNrkl~dLLd~LeFNQVvIFv  290 (387)
T KOG0329|consen  211 FRMTPHEKQVMMFSATLSKEIRPVCHKFMQDPMEIFVDDEAKLTLHGLQQYYVKLKENEKNRKLNDLLDVLEFNQVVIFV  290 (387)
T ss_pred             hhcCcccceeeeeeeecchhhHHHHHhhhcCchhhhccchhhhhhhhHHHHHHhhhhhhhhhhhhhhhhhhhhcceeEee
Confidence            99999999999999999999999999999999999998766 455678888888888888888888777543 5899999


Q ss_pred             cccccHHH----HHHHHHhCCCCe----EeecCCCChh
Q psy7789         161 EKKQDVDA----IHEYLLLKGKPF----FTLKSLKEDQ  190 (197)
Q Consensus       161 ~s~~~~~~----l~~~L~~~~~~~----~~~h~~~~~~  190 (197)
                      .|..+...    ++..|-.+|..+    ..++-+|+.+
T Consensus       291 Ksv~Rl~f~kr~vat~lfgrgmdiervNi~~NYdmp~~  328 (387)
T KOG0329|consen  291 KSVQRLSFQKRLVATDLFGRGMDIERVNIVFNYDMPED  328 (387)
T ss_pred             ehhhhhhhhhhhHHhhhhccccCcccceeeeccCCCCC
Confidence            98877442    444444555432    2455666654

>KOG0332|consensus

Probab=99.94  E-value=1.6e-26  Score=179.41  Aligned_cols=182  Identities=24%  Similarity=0.302  Sum_probs=160.6

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhc-CCccCCCccEEEeehhhhhhc-CCCHHHHHHHHhhccCC
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDK-KMVSLDVCRYLCLDEADRMVD-MGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~-~~~~l~~l~~vViDEad~l~~-~~~~~~i~~i~~~~~~~   89 (197)
                      ++++....-|....+-. .+  ..+|+|+||+.+.+++.. +.+++..++.+|+||||.+++ .||+++-..|...+|++
T Consensus       188 ~ita~yair~sk~~rG~-~i--~eqIviGTPGtv~Dlm~klk~id~~kikvfVlDEAD~Mi~tqG~~D~S~rI~~~lP~~  264 (477)
T KOG0332|consen  188 ELTASYAIRGSKAKRGN-KL--TEQIVIGTPGTVLDLMLKLKCIDLEKIKVFVLDEADVMIDTQGFQDQSIRIMRSLPRN  264 (477)
T ss_pred             eeeEEEEecCcccccCC-cc--hhheeeCCCccHHHHHHHHHhhChhhceEEEecchhhhhhcccccccchhhhhhcCCc
Confidence            67777777776222111 11  257999999999999987 888999999999999999986 57999999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcC-chhhHHHHHHHhhcC-CCCEEEEecccccHH
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVK-QEAKIVYLLECLQKT-EPPVLIFAEKKQDVD  167 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~-~~~k~~~l~~~l~~~-~~~~lIF~~s~~~~~  167 (197)
                      .|+++||||+...+..++....+++..+.+..+....++++|++..|. +.+|.+.|.++.... -+++||||.|+++|+
T Consensus       265 ~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk~eel~L~~IkQlyv~C~~~~~K~~~l~~lyg~~tigqsiIFc~tk~ta~  344 (477)
T KOG0332|consen  265 QQLLLFSATFVEKVAAFALKIVPNANVIILKREELALDNIKQLYVLCACRDDKYQALVNLYGLLTIGQSIIFCHTKATAM  344 (477)
T ss_pred             ceEEeeechhHHHHHHHHHHhcCCCceeeeehhhccccchhhheeeccchhhHHHHHHHHHhhhhhhheEEEEeehhhHH
Confidence            999999999999999999999999999999999999999999999995 567999999977654 379999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +++..|+..|+.+..+||+|..++|..|.
T Consensus       345 ~l~~~m~~~Gh~V~~l~G~l~~~~R~~ii  373 (477)
T KOG0332|consen  345 WLYEEMRAEGHQVSLLHGDLTVEQRAAII  373 (477)
T ss_pred             HHHHHHHhcCceeEEeeccchhHHHHHHH
Confidence            99999999999999999999999999875

>TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype

Probab=99.93  E-value=7.7e-25  Score=188.62  Aligned_cols=174  Identities=15%  Similarity=0.138  Sum_probs=139.7

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCc----------------cCCCccEEEeehhhhhhcCC
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMV----------------SLDVCRYLCLDEADRMVDMG   74 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~----------------~l~~l~~vViDEad~l~~~~   74 (197)
                      .++++..++||.+...|.+.+..+|+|||||+    +++.++.+                .+++++++|+||||  ++.+
T Consensus       112 ~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~----D~i~sr~L~~gYg~~~~~~pi~ag~L~~v~~LVLDEAD--Ld~g  185 (844)
T TIGR02621       112 RPLAISTLRGQFADNDEWMLDPHRPAVIVGTV----DMIGSRLLFSGYGCGFKSRPLHAGFLGQDALIVHDEAH--LEPA  185 (844)
T ss_pred             CCeEEEEEECCCChHHHHHhcCCCCcEEEECH----HHHcCCccccccccccccccchhhhhccceEEEEehhh--hccc
Confidence            36999999999999999999999999999996    55544443                27899999999999  5778


Q ss_pred             CHHHHHHHHhhc--cCC---ceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHH-
Q psy7789          75 FEEDVRTIFSFF--RGQ---RQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLEC-  148 (197)
Q Consensus        75 ~~~~i~~i~~~~--~~~---~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~-  148 (197)
                      |.+.+..|++.+  ++.   .|+++||||++.++......++.++..+.+.........+.+ ++.+..+.|...+... 
T Consensus       186 F~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~~l~~~~~~~p~~i~V~~~~l~a~ki~q-~v~v~~e~Kl~~lv~~L  264 (844)
T TIGR02621       186 FQELLKQIMNEQQRPPDFLPLRVVELTATSRTDGPDRTTLLSAEDYKHPVLKKRLAAKKIVK-LVPPSDEKFLSTMVKEL  264 (844)
T ss_pred             cHHHHHHHHHhcccCcccccceEEEEecCCCccHHHHHHHHccCCceeecccccccccceEE-EEecChHHHHHHHHHHH
Confidence            999999999965  432   699999999999888888888878776666555555555665 3455555555444333 


Q ss_pred             ---hhcCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhh
Q psy7789         149 ---LQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQ  193 (197)
Q Consensus       149 ---l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~  193 (197)
                         +...++++||||||+++|+.+++.|++.++  ..+||+|++.+|+
T Consensus       265 ~~ll~e~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~q~dR~  310 (844)
T TIGR02621       265 NLLMKDSGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLRGAERD  310 (844)
T ss_pred             HHHHhhCCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCCHHHHh
Confidence               344457899999999999999999999887  8999999999999

This model describes a CRISPR-associated putative DEAH-box helicase, or Cas3, of a subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. This protein includes both DEAH and HD motifs.

>KOG0348|consensus

Probab=99.92  E-value=6.5e-25  Score=177.10  Aligned_cols=192  Identities=24%  Similarity=0.416  Sum_probs=160.3

Q ss_pred             cccccCCCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhc-CCccCCCccEEEeehhhhhhcCCCHHHHHHH
Q psy7789           4 PFISALPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDK-KMVSLDVCRYLCLDEADRMVDMGFEEDVRTI   82 (197)
Q Consensus         4 ~~~~~~~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~-~~~~l~~l~~vViDEad~l~~~~~~~~i~~i   82 (197)
                      ++.+.++ +|-.+.+.||.....+...|.+|+.|+|+|||||.+.+.+ ..+.+++++++|+||+|++++-||...+..|
T Consensus       233 KLl~~~h-WIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~LRwlVlDEaDrlleLGfekdit~I  311 (708)
T KOG0348|consen  233 KLLKPFH-WIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRLRWLVLDEADRLLELGFEKDITQI  311 (708)
T ss_pred             HHhcCce-EEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhccchheeeeeeEEEecchhHHHhccchhhHHHH
Confidence            3444444 5888999999999989999999999999999999999875 5788999999999999999999999999999


Q ss_pred             Hhhcc-------------CCceEEEEeecCChhHHHHHHHhcCCCeEEEeCC-------------------------CCc
Q psy7789          83 FSFFR-------------GQRQTLLFSATMPKKIQNFARSALVKPITINVGR-------------------------AGA  124 (197)
Q Consensus        83 ~~~~~-------------~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~-------------------------~~~  124 (197)
                      ++.+.             +..|.+++|||++..+.......+.+|..|..+.                         ...
T Consensus       312 l~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~~~~~p~~~a~~ev~~~~~~~~l~~~~  391 (708)
T KOG0348|consen  312 LKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKSHSQLNPKDKAVQEVDDGPAGDKLDSFA  391 (708)
T ss_pred             HHHHhhccchhcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeeeccchhhhcCcchhhhhhcCCccccccccccc
Confidence            88872             2358899999999999999999999999888321                         123


Q ss_pred             cCcceeEEEEEcCchhhHHHHHHHhhcC-----CCCEEEEecccccHHHHHHHHHhC----------------------C
Q psy7789         125 ASMNVVQEVEYVKQEAKIVYLLECLQKT-----EPPVLIFAEKKQDVDAIHEYLLLK----------------------G  177 (197)
Q Consensus       125 ~~~~i~~~~~~~~~~~k~~~l~~~l~~~-----~~~~lIF~~s~~~~~~l~~~L~~~----------------------~  177 (197)
                      .++.+.|.+..++..-++-.|..+|...     ..++|||+++.+.++.=++.|...                      +
T Consensus       392 iPeqL~qry~vVPpKLRLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~~~~s~g~~~l~~~  471 (708)
T KOG0348|consen  392 IPEQLLQRYTVVPPKLRLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSGAPDSEGLPPLFMD  471 (708)
T ss_pred             CcHHhhhceEecCCchhHHHHHHHHHHHhhhhhhceeEEEEechhHHHHHHHHHHhhhhcccccccCCcccCCChhhhhc
Confidence            4556777888888888888888877643     347999999999999999988531                      3


Q ss_pred             CCeEeecCCCChhhhhhhh
Q psy7789         178 KPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       178 ~~~~~~h~~~~~~~R~~i~  196 (197)
                      .+++-+||+|+|++|..+.
T Consensus       472 ~k~~rLHGsm~QeeRts~f  490 (708)
T KOG0348|consen  472 LKFYRLHGSMEQEERTSVF  490 (708)
T ss_pred             ceEEEecCchhHHHHHHHH
Confidence            4689999999999998764

>TIGR03817 DECH_helic helicase/secretion neighborhood putative DEAH-box helicase

Probab=99.91  E-value=2.5e-23  Score=180.64  Aligned_cols=182  Identities=14%  Similarity=0.131  Sum_probs=130.9

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHh-cC---CccCCCccEEEeehhhhhhcCCCHHHHHHHHhhc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLD-KK---MVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF   86 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~-~~---~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~   86 (197)
                      .++++..+.|+.+.. +.+.+.++++|+|+||++|...+. ..   ...++++++||+||||.+.+ .|+.++..+++++
T Consensus       107 ~~i~v~~~~Gdt~~~-~r~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDEah~~~g-~fg~~~~~il~rL  184 (742)
T TIGR03817       107 RGVRPATYDGDTPTE-ERRWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDECHSYRG-VFGSHVALVLRRL  184 (742)
T ss_pred             CCeEEEEEeCCCCHH-HHHHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeChhhccC-ccHHHHHHHHHHH
Confidence            478998888877744 556677789999999999986432 11   12378999999999999976 3777766665544


Q ss_pred             -------cCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcC----------------chhhHH
Q psy7789          87 -------RGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVK----------------QEAKIV  143 (197)
Q Consensus        87 -------~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~----------------~~~k~~  143 (197)
                             +.++|++++|||++++.. .+..++..+..+ +.............++...                ..++..
T Consensus       185 ~ri~~~~g~~~q~i~~SATi~n~~~-~~~~l~g~~~~~-i~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~  262 (742)
T TIGR03817       185 RRLCARYGASPVFVLASATTADPAA-AASRLIGAPVVA-VTEDGSPRGARTVALWEPPLTELTGENGAPVRRSASAEAAD  262 (742)
T ss_pred             HHHHHhcCCCCEEEEEecCCCCHHH-HHHHHcCCCeEE-ECCCCCCcCceEEEEecCCccccccccccccccchHHHHHH
Confidence                   467899999999997754 577777777554 3322222222333222221                123555


Q ss_pred             HHHHHhhcCCCCEEEEecccccHHHHHHHHHhC--------CCCeEeecCCCChhhhhhhhC
Q psy7789         144 YLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLK--------GKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       144 ~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~--------~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      .+.++++. +.++||||||++.|+.++..|++.        +.++..+||+|++++|+++++
T Consensus       263 ~l~~l~~~-~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~  323 (742)
T TIGR03817       263 LLADLVAE-GARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELER  323 (742)
T ss_pred             HHHHHHHC-CCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHH
Confidence            66666654 579999999999999999998764        568899999999999999874

A conserved gene neighborhood widely spread in the Actinobacteria contains this uncharacterized DEAH-box family helicase encoded convergently towards an operon of genes for protein homologous to type II secretion and pilus formation proteins. The context suggests that this helicase may play a role in conjugal transfer of DNA.

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.91  E-value=4.1e-23  Score=186.76  Aligned_cols=183  Identities=14%  Similarity=0.131  Sum_probs=129.0

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcC-CccCCCccEEEeehhhhhhcCCCHH----HHHHHHhh
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKK-MVSLDVCRYLCLDEADRMVDMGFEE----DVRTIFSF   85 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~-~~~l~~l~~vViDEad~l~~~~~~~----~i~~i~~~   85 (197)
                      .++++..++||.+..++.+.++++|||||+|||+|..++.++ ...++++++|||||+|.+.+..++.    .+..+...
T Consensus        76 ~~i~V~vrtGDt~~~eR~rll~~ppdILVTTPEsL~~LLtsk~r~~L~~Vr~VIVDE~H~L~g~kRG~~Lel~LeRL~~l  155 (1490)
T PRK09751         76 VNLRVGIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARETLRGVETVIIDEVHAVAGSKRGAHLALSLERLDAL  155 (1490)
T ss_pred             CceEEEEEECCCCHHHHHHHhcCCCCEEEecHHHHHHHHhhhhhhhhccCCEEEEecHHHhcccccccHHHHHHHHHHHh
Confidence            489999999999999888888888999999999999988643 3468999999999999999764444    45555555


Q ss_pred             ccCCceEEEEeecCChhHHHHHHHhcC-CCeEEEeCCCCccCcceeEEEEEcCchhh-----------------------
Q psy7789          86 FRGQRQTLLFSATMPKKIQNFARSALV-KPITINVGRAGAASMNVVQEVEYVKQEAK-----------------------  141 (197)
Q Consensus        86 ~~~~~q~i~~SAT~~~~~~~~~~~~~~-~~~~i~~~~~~~~~~~i~~~~~~~~~~~k-----------------------  141 (197)
                      ++.+.|+|++|||+++ ..++.+.+.. ++..+...+.. ....+. .++.+....+                       
T Consensus       156 ~~~~~QrIgLSATI~n-~eevA~~L~g~~pv~Iv~~~~~-r~~~l~-v~vp~~d~~~~~~~~~~~~~~~~~~r~~~i~~~  232 (1490)
T PRK09751        156 LHTSAQRIGLSATVRS-ASDVAAFLGGDRPVTVVNPPAM-RHPQIR-IVVPVANMDDVSSVASGTGEDSHAGREGSIWPY  232 (1490)
T ss_pred             CCCCCeEEEEEeeCCC-HHHHHHHhcCCCCEEEECCCCC-cccceE-EEEecCchhhccccccccccccchhhhhhhhHH
Confidence            6678899999999986 4566544433 35544332222 112222 2222211100                       


Q ss_pred             -HHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCC---------------------------------CCeEeecCCC
Q psy7789         142 -IVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKG---------------------------------KPFFTLKSLK  187 (197)
Q Consensus       142 -~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~---------------------------------~~~~~~h~~~  187 (197)
                       ...+++.+. .+.++||||||++.|+.++..|++..                                 +.+..+||+|
T Consensus       233 v~~~il~~i~-~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsL  311 (1490)
T PRK09751        233 IETGILDEVL-RHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSV  311 (1490)
T ss_pred             HHHHHHHHHh-cCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccC
Confidence             012222222 24689999999999999999997642                                 1267899999


Q ss_pred             ChhhhhhhhC
Q psy7789         188 EDQNNQTLEN  197 (197)
Q Consensus       188 ~~~~R~~i~~  197 (197)
                      ++++|..|++
T Consensus       312 SkeeR~~IE~  321 (1490)
T PRK09751        312 SKEQRAITEQ  321 (1490)
T ss_pred             CHHHHHHHHH
Confidence            9999999874

>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional

Probab=99.90  E-value=1.3e-22  Score=177.94  Aligned_cols=184  Identities=14%  Similarity=0.182  Sum_probs=133.1

Q ss_pred             CCCCeeEEEEEcCCChHHhHHHHh------cCCcEEEeCchHHHH--HHhc---CCccCCCccEEEeehhhhhhcCC--C
Q psy7789           9 LPIPLRTCLAIGGVPMNQSLDVIK------KGCHMMVATPGRLMD--MLDK---KMVSLDVCRYLCLDEADRMVDMG--F   75 (197)
Q Consensus         9 ~~~~i~~~~~~gg~~~~~~~~~l~------~~~~Ili~TP~~l~~--~l~~---~~~~l~~l~~vViDEad~l~~~~--~   75 (197)
                      ...|++++.+.||.+..++.+.+.      +.++||++|||+|..  .+.+   .......+.+|||||||++++||  |
T Consensus       521 ~~~GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~LslIVIDEAHcVSqWGhDF  600 (1195)
T PLN03137        521 LQANIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARFVIDEAHCVSQWGHDF  600 (1195)
T ss_pred             HhCCCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhccccceeccCcchhhhhcccch
Confidence            446899999999998877766553      468999999999863  1221   11123568999999999999997  8


Q ss_pred             HHHHHHH--HhhccCCceEEEEeecCChhHHHHHHHhcC--CCeEEEeCCCCccCcceeEEEEEcCchh-hHHHHHHHhh
Q psy7789          76 EEDVRTI--FSFFRGQRQTLLFSATMPKKIQNFARSALV--KPITINVGRAGAASMNVVQEVEYVKQEA-KIVYLLECLQ  150 (197)
Q Consensus        76 ~~~i~~i--~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~--~~~~i~~~~~~~~~~~i~~~~~~~~~~~-k~~~l~~~l~  150 (197)
                      ++.+..+  +....+..|++++|||+++.+.+.+...+.  ++..+...   ..++++...+  +.... ....+.++++
T Consensus       601 RpdYr~L~~Lr~~fp~vPilALTATAT~~V~eDI~~~L~l~~~~vfr~S---f~RpNL~y~V--v~k~kk~le~L~~~I~  675 (1195)
T PLN03137        601 RPDYQGLGILKQKFPNIPVLALTATATASVKEDVVQALGLVNCVVFRQS---FNRPNLWYSV--VPKTKKCLEDIDKFIK  675 (1195)
T ss_pred             HHHHHHHHHHHHhCCCCCeEEEEecCCHHHHHHHHHHcCCCCcEEeecc---cCccceEEEE--eccchhHHHHHHHHHH
Confidence            8877653  333345788999999999998886655554  33332221   2233443322  22222 3456677776


Q ss_pred             cC--CCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         151 KT--EPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       151 ~~--~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      ..  ..++||||+|++.|+.+++.|++.|+++..+||+|++++|+.+++
T Consensus       676 ~~~~~esgIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe  724 (1195)
T PLN03137        676 ENHFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQK  724 (1195)
T ss_pred             hcccCCCceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHH
Confidence            43  457999999999999999999999999999999999999998863

>PRK09401 reverse gyrase; Reviewed

Probab=99.90  E-value=4.1e-22  Score=178.98  Aligned_cols=171  Identities=18%  Similarity=0.184  Sum_probs=135.2

Q ss_pred             CCeeEEEEEcCCCh-----HHhHHHHh-cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhc-----------C
Q psy7789          11 IPLRTCLAIGGVPM-----NQSLDVIK-KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD-----------M   73 (197)
Q Consensus        11 ~~i~~~~~~gg~~~-----~~~~~~l~-~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~-----------~   73 (197)
                      .++++..++||.+.     +++.+.+. +++||+|+||++|.+.+.  .+...+++++|+||||++++           .
T Consensus       150 ~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~--~l~~~~~~~lVvDEaD~~L~~~k~id~~l~~l  227 (1176)
T PRK09401        150 VGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFD--ELPKKKFDFVFVDDVDAVLKSSKNIDKLLYLL  227 (1176)
T ss_pred             cCceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHH--hccccccCEEEEEChHHhhhcccchhhHHHhC
Confidence            36788888887652     33344555 459999999999999876  45567799999999999986           4


Q ss_pred             CCH-HHHHHHHhhccC------------------------CceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcc
Q psy7789          74 GFE-EDVRTIFSFFRG------------------------QRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMN  128 (197)
Q Consensus        74 ~~~-~~i~~i~~~~~~------------------------~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~  128 (197)
                      ||. +.+..++..++.                        ..|++++|||+++....  ..+++++..+.+........+
T Consensus       228 GF~~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~~~~--~~l~~~ll~~~v~~~~~~~rn  305 (1176)
T PRK09401        228 GFSEEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNR--VKLFRELLGFEVGSPVFYLRN  305 (1176)
T ss_pred             CCCHHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCccchH--HHHhhccceEEecCcccccCC
Confidence            564 678888777764                        68999999999875222  134566666777766666778


Q ss_pred             eeEEEEEcCchhhHHHHHHHhhcCCCCEEEEeccccc---HHHHHHHHHhCCCCeEeecCCC
Q psy7789         129 VVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQD---VDAIHEYLLLKGKPFFTLKSLK  187 (197)
Q Consensus       129 i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~---~~~l~~~L~~~~~~~~~~h~~~  187 (197)
                      +.+.++.+.  +|...+.++++..+.++||||+|++.   |+++++.|++.|+++..+||+|
T Consensus       306 I~~~yi~~~--~k~~~L~~ll~~l~~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l  365 (1176)
T PRK09401        306 IVDSYIVDE--DSVEKLVELVKRLGDGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF  365 (1176)
T ss_pred             ceEEEEEcc--cHHHHHHHHHHhcCCCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH
Confidence            888877665  67778888888777799999999988   9999999999999999999999

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.89  E-value=8.8e-22  Score=173.95  Aligned_cols=183  Identities=16%  Similarity=0.194  Sum_probs=126.1

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCc--cCCCccEEEeehhhhhhcCCCHHHHHHHHhh----
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMV--SLDVCRYLCLDEADRMVDMGFEEDVRTIFSF----   85 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~--~l~~l~~vViDEad~l~~~~~~~~i~~i~~~----   85 (197)
                      ++++...+|+.+...+.+.+.++|+|+|+||++|..++....+  .++++++||+||+|.+.+..++.++...+.+    
T Consensus       124 ~i~v~v~~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll~~~~~~~~l~~l~~VVIDE~H~l~~~~RG~~l~~~L~rL~~l  203 (876)
T PRK13767        124 EIRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILLNSPKFREKLRTVKWVIVDEIHSLAENKRGVHLSLSLERLEEL  203 (876)
T ss_pred             CeeEEEEcCCCCHHHHHHHHhCCCCEEEecHHHHHHHhcChhHHHHHhcCCEEEEechhhhccCccHHHHHHHHHHHHHh
Confidence            7899999999998888888888899999999999988865543  5799999999999999987666665544433    


Q ss_pred             ccCCceEEEEeecCChhHHHHHHHhcC-------CCeEEEeCCCCccCcceeEE-----EEEcCch----hhHHHHHHHh
Q psy7789          86 FRGQRQTLLFSATMPKKIQNFARSALV-------KPITINVGRAGAASMNVVQE-----VEYVKQE----AKIVYLLECL  149 (197)
Q Consensus        86 ~~~~~q~i~~SAT~~~~~~~~~~~~~~-------~~~~i~~~~~~~~~~~i~~~-----~~~~~~~----~k~~~l~~~l  149 (197)
                      .+...|++++|||+++ ..........       .+..+ +.........+...     .......    .....+.+++
T Consensus       204 ~~~~~q~IglSATl~~-~~~va~~L~~~~~~~~~r~~~i-v~~~~~k~~~i~v~~p~~~l~~~~~~~~~~~l~~~L~~~i  281 (876)
T PRK13767        204 AGGEFVRIGLSATIEP-LEEVAKFLVGYEDDGEPRDCEI-VDARFVKPFDIKVISPVDDLIHTPAEEISEALYETLHELI  281 (876)
T ss_pred             cCCCCeEEEEecccCC-HHHHHHHhcCccccCCCCceEE-EccCCCccceEEEeccCccccccccchhHHHHHHHHHHHH
Confidence            3467899999999975 2333333221       11122 11111111001100     0111111    1233444444


Q ss_pred             hcCCCCEEEEecccccHHHHHHHHHhC------CCCeEeecCCCChhhhhhhhC
Q psy7789         150 QKTEPPVLIFAEKKQDVDAIHEYLLLK------GKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       150 ~~~~~~~lIF~~s~~~~~~l~~~L~~~------~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      +. ++++||||||++.|+.++..|++.      +..+..+||+|++++|..+++
T Consensus       282 ~~-~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~  334 (876)
T PRK13767        282 KE-HRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEE  334 (876)
T ss_pred             hc-CCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHH
Confidence            43 468999999999999999999873      467999999999999999874

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.88  E-value=2.8e-21  Score=161.06  Aligned_cols=182  Identities=14%  Similarity=0.136  Sum_probs=128.5

Q ss_pred             CCeeEEEEEcCCChHHhHHH---H-hcCCcEEEeCchHHHHHH-hcCCc-cCCCccEEEeehhhhhhcCC--CHHHHHHH
Q psy7789          11 IPLRTCLAIGGVPMNQSLDV---I-KKGCHMMVATPGRLMDML-DKKMV-SLDVCRYLCLDEADRMVDMG--FEEDVRTI   82 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~---l-~~~~~Ili~TP~~l~~~l-~~~~~-~l~~l~~vViDEad~l~~~~--~~~~i~~i   82 (197)
                      .|+++..+.|+.+..++...   + .+.++|+++||+++.... ....+ ...+++++||||||++.+|+  |++.+..+
T Consensus        74 ~gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~~iViDEaH~i~~~g~~fr~~~~~l  153 (470)
T TIGR00614        74 SGIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKAL  153 (470)
T ss_pred             cCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCcCEEEEeCCcccCccccccHHHHHHH
Confidence            47888888888776544332   2 345899999999986432 11122 56899999999999999886  67766554


Q ss_pred             ---HhhccCCceEEEEeecCChhHHHHHHHhc--CCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhh-cC-CCC
Q psy7789          83 ---FSFFRGQRQTLLFSATMPKKIQNFARSAL--VKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQ-KT-EPP  155 (197)
Q Consensus        83 ---~~~~~~~~q~i~~SAT~~~~~~~~~~~~~--~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~-~~-~~~  155 (197)
                         ...+ ++.|++++|||+++.+.......+  .+|..+....   .++++...+.. ........+.+++. .. +++
T Consensus       154 ~~l~~~~-~~~~~l~lTAT~~~~~~~di~~~l~l~~~~~~~~s~---~r~nl~~~v~~-~~~~~~~~l~~~l~~~~~~~~  228 (470)
T TIGR00614       154 GSLKQKF-PNVPIMALTATASPSVREDILRQLNLKNPQIFCTSF---DRPNLYYEVRR-KTPKILEDLLRFIRKEFKGKS  228 (470)
T ss_pred             HHHHHHc-CCCceEEEecCCCHHHHHHHHHHcCCCCCcEEeCCC---CCCCcEEEEEe-CCccHHHHHHHHHHHhcCCCc
Confidence               3344 578899999999988776555544  3554443321   12333322221 22245666777776 33 346


Q ss_pred             EEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         156 VLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       156 ~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      +||||+|++.|+.+++.|++.|+++..+||+|++++|+++++
T Consensus       229 ~IIF~~s~~~~e~la~~L~~~g~~~~~~H~~l~~~eR~~i~~  270 (470)
T TIGR00614       229 GIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHH  270 (470)
T ss_pred             eEEEECcHHHHHHHHHHHHhcCCCeeEeeCCCCHHHHHHHHH
Confidence            799999999999999999999999999999999999998863

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK00254 ski2-like helicase; Provisional

Probab=99.87  E-value=1.8e-21  Score=169.61  Aligned_cols=179  Identities=13%  Similarity=0.129  Sum_probs=126.2

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .|+++..++|+.+...+   +.+.++|+|+||+++..++.+....+++++++|+||+|.+.+.+++..+..++..++...
T Consensus        94 ~g~~v~~~~Gd~~~~~~---~~~~~~IiV~Tpe~~~~ll~~~~~~l~~l~lvViDE~H~l~~~~rg~~le~il~~l~~~~  170 (720)
T PRK00254         94 LGLRVAMTTGDYDSTDE---WLGKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIHLIGSYDRGATLEMILTHMLGRA  170 (720)
T ss_pred             cCCEEEEEeCCCCCchh---hhccCCEEEEcHHHHHHHHhCCchhhhcCCEEEEcCcCccCCccchHHHHHHHHhcCcCC
Confidence            58999999999765432   234599999999999999987777789999999999999998889999999999999899


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccC---cceeEEEEEcCch--h-----hHHHHHHHhhcCCCCEEEEe
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAAS---MNVVQEVEYVKQE--A-----KIVYLLECLQKTEPPVLIFA  160 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~---~~i~~~~~~~~~~--~-----k~~~l~~~l~~~~~~~lIF~  160 (197)
                      |++++|||++. ..++.. |+......  ......+   ....+.+......  .     ....+.+.++ .++++||||
T Consensus       171 qiI~lSATl~n-~~~la~-wl~~~~~~--~~~rpv~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~-~~~~vLVF~  245 (720)
T PRK00254        171 QILGLSATVGN-AEELAE-WLNAELVV--SDWRPVKLRKGVFYQGFLFWEDGKIERFPNSWESLVYDAVK-KGKGALVFV  245 (720)
T ss_pred             cEEEEEccCCC-HHHHHH-HhCCcccc--CCCCCCcceeeEecCCeeeccCcchhcchHHHHHHHHHHHH-hCCCEEEEE
Confidence            99999999975 455554 44332211  1111111   0011111111111  1     1123334444 357999999


Q ss_pred             cccccHHHHHHHHHhC---------------------------------CCCeEeecCCCChhhhhhhhC
Q psy7789         161 EKKQDVDAIHEYLLLK---------------------------------GKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       161 ~s~~~~~~l~~~L~~~---------------------------------~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      ||++.|+.++..|.+.                                 ...+.++||+|++++|+.|++
T Consensus       246 ~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~~~eR~~ve~  315 (720)
T PRK00254        246 NTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLGRTERVLIED  315 (720)
T ss_pred             cChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCCHHHHHHHHH
Confidence            9999999888776421                                 235899999999999999873

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.87  E-value=4.2e-21  Score=164.10  Aligned_cols=180  Identities=17%  Similarity=0.194  Sum_probs=134.5

Q ss_pred             CCeeEEEEEcCCChHHhHHHH----hcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCC--CHHHHHHH--
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVI----KKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMG--FEEDVRTI--   82 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l----~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~--~~~~i~~i--   82 (197)
                      .|+.+..+.|+.+..++...+    .+.++|+++||+++........+...++++|||||||++.+|+  |++.+..+  
T Consensus        76 ~gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~~l~~~~l~~iViDEaH~i~~~g~~frp~y~~l~~  155 (591)
T TIGR01389        76 AGVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLNMLQRIPIALVAVDEAHCVSQWGHDFRPEYQRLGS  155 (591)
T ss_pred             cCCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHHHHhcCCCCEEEEeCCcccccccCccHHHHHHHHH
Confidence            478888899988766554332    3468999999999976544445567899999999999999876  77766655  


Q ss_pred             -HhhccCCceEEEEeecCChhHHHHHHHhcC--CCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcC-CCCEEE
Q psy7789          83 -FSFFRGQRQTLLFSATMPKKIQNFARSALV--KPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKT-EPPVLI  158 (197)
Q Consensus        83 -~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~--~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~-~~~~lI  158 (197)
                       ...++ ..+++++|||.++.+......++.  ++..+..   ...++++...  ......+...+.+++... +.++||
T Consensus       156 l~~~~~-~~~vi~lTAT~~~~~~~~i~~~l~~~~~~~~~~---~~~r~nl~~~--v~~~~~~~~~l~~~l~~~~~~~~II  229 (591)
T TIGR01389       156 LAERFP-QVPRIALTATADAETRQDIRELLRLADANEFIT---SFDRPNLRFS--VVKKNNKQKFLLDYLKKHRGQSGII  229 (591)
T ss_pred             HHHhCC-CCCEEEEEeCCCHHHHHHHHHHcCCCCCCeEec---CCCCCCcEEE--EEeCCCHHHHHHHHHHhcCCCCEEE
Confidence             34444 445999999999998876666654  3333321   1222333322  234456777888888765 468999


Q ss_pred             EecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         159 FAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       159 F~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      ||+|++.|+.+++.|...|+++..+||+|++++|++++
T Consensus       230 f~~sr~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~  267 (591)
T TIGR01389       230 YASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQ  267 (591)
T ss_pred             EECcHHHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHH
Confidence            99999999999999999999999999999999999875

The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.

>PRK14701 reverse gyrase; Provisional

Probab=99.87  E-value=8.1e-21  Score=174.24  Aligned_cols=176  Identities=18%  Similarity=0.178  Sum_probs=135.5

Q ss_pred             cccCCCCeeEEEEEcCCChHHhHH---HHhc-CCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcC--------
Q psy7789           6 ISALPIPLRTCLAIGGVPMNQSLD---VIKK-GCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDM--------   73 (197)
Q Consensus         6 ~~~~~~~i~~~~~~gg~~~~~~~~---~l~~-~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~--------   73 (197)
                      .+..+.+++++.++||.+..++.+   .+.. .+||+|+||++|...+... . ..+++++|+||||++++|        
T Consensus       146 ~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l-~-~~~i~~iVVDEAD~ml~~~knid~~L  223 (1638)
T PRK14701        146 CEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEM-K-HLKFDFIFVDDVDAFLKASKNIDRSL  223 (1638)
T ss_pred             HhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHH-h-hCCCCEEEEECceeccccccccchhh
Confidence            344556889999999998776653   3444 4999999999998876542 2 278999999999999873        


Q ss_pred             ---CCHHHHHH----HHh----------------------hccCCce-EEEEeecCChhHHHHHHHhcCCCeEEEeCCCC
Q psy7789          74 ---GFEEDVRT----IFS----------------------FFRGQRQ-TLLFSATMPKKIQNFARSALVKPITINVGRAG  123 (197)
Q Consensus        74 ---~~~~~i~~----i~~----------------------~~~~~~q-~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~  123 (197)
                         ||.+++..    +++                      .+++.+| ++++|||.++.  .....+++++..+.+....
T Consensus       224 ~llGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~~r--~~~~~l~~~~l~f~v~~~~  301 (1638)
T PRK14701        224 QLLGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGKAK--GDRVKLYRELLGFEVGSGR  301 (1638)
T ss_pred             hcCCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCCch--hHHHHHhhcCeEEEecCCC
Confidence               67777754    432                      2355566 67799999864  2222456788888888777


Q ss_pred             ccCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecccccH---HHHHHHHHhCCCCeEeecCC
Q psy7789         124 AASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDV---DAIHEYLLLKGKPFFTLKSL  186 (197)
Q Consensus       124 ~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~---~~l~~~L~~~~~~~~~~h~~  186 (197)
                      ....++.+.++.+..+.| ..+.++++..+.++||||+|++.+   +++++.|.+.|+++..+||+
T Consensus       302 ~~lr~i~~~yi~~~~~~k-~~L~~ll~~~g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~  366 (1638)
T PRK14701        302 SALRNIVDVYLNPEKIIK-EHVRELLKKLGKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAK  366 (1638)
T ss_pred             CCCCCcEEEEEECCHHHH-HHHHHHHHhCCCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecch
Confidence            777888888887766655 578888887777899999998864   89999999999999999996

>PRK02362 ski2-like helicase; Provisional

Probab=99.86  E-value=6.4e-21  Score=166.49  Aligned_cols=182  Identities=15%  Similarity=0.171  Sum_probs=123.0

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhc---c
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF---R   87 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~---~   87 (197)
                      .|+++..++|+.+...+   ..+.+||+|+|||++..++++....+++++++|+||+|.+.+.+++..++.++.++   +
T Consensus        93 ~g~~v~~~tGd~~~~~~---~l~~~~IiV~Tpek~~~llr~~~~~l~~v~lvViDE~H~l~d~~rg~~le~il~rl~~~~  169 (737)
T PRK02362         93 LGVRVGISTGDYDSRDE---WLGDNDIIVATSEKVDSLLRNGAPWLDDITCVVVDEVHLIDSANRGPTLEVTLAKLRRLN  169 (737)
T ss_pred             CCCEEEEEeCCcCcccc---ccCCCCEEEECHHHHHHHHhcChhhhhhcCEEEEECccccCCCcchHHHHHHHHHHHhcC
Confidence            48999999998765432   22458999999999999998776678999999999999999888888888776555   4


Q ss_pred             CCceEEEEeecCChhHHHHHHHhcCC-------CeEEE--eCCCCccCcceeEEEEEcCc-hhhHHHHHHHhhcCCCCEE
Q psy7789          88 GQRQTLLFSATMPKKIQNFARSALVK-------PITIN--VGRAGAASMNVVQEVEYVKQ-EAKIVYLLECLQKTEPPVL  157 (197)
Q Consensus        88 ~~~q~i~~SAT~~~~~~~~~~~~~~~-------~~~i~--~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~~l~~~~~~~l  157 (197)
                      ++.|++++|||++. ..++..++...       |+.+.  +.........-.+....... ......+.+.++ .++++|
T Consensus       170 ~~~qii~lSATl~n-~~~la~wl~~~~~~~~~rpv~l~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~L  247 (737)
T PRK02362        170 PDLQVVALSATIGN-ADELADWLDAELVDSEWRPIDLREGVFYGGAIHFDDSQREVEVPSKDDTLNLVLDTLE-EGGQCL  247 (737)
T ss_pred             CCCcEEEEcccCCC-HHHHHHHhCCCcccCCCCCCCCeeeEecCCeeccccccccCCCccchHHHHHHHHHHH-cCCCeE
Confidence            67899999999974 34444333211       11110  00000000000011111111 223344444444 456999


Q ss_pred             EEecccccHHHHHHHHHhCC------------------------------------CCeEeecCCCChhhhhhhhC
Q psy7789         158 IFAEKKQDVDAIHEYLLLKG------------------------------------KPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       158 IF~~s~~~~~~l~~~L~~~~------------------------------------~~~~~~h~~~~~~~R~~i~~  197 (197)
                      |||+|++.|+.++..|.+..                                    ..++++||+|++++|+.|++
T Consensus       248 VF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hHagl~~~eR~~ve~  323 (737)
T PRK02362        248 VFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHAGLSREHRELVED  323 (737)
T ss_pred             EEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCEEeecCCCCHHHHHHHHH
Confidence            99999999999999886431                                    35889999999999999874

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.86  E-value=2.2e-20  Score=159.83  Aligned_cols=181  Identities=14%  Similarity=0.130  Sum_probs=128.2

Q ss_pred             CCeeEEEEEcCCChHHhHHH---Hh-cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCC--CHHHHHHH--
Q psy7789          11 IPLRTCLAIGGVPMNQSLDV---IK-KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMG--FEEDVRTI--   82 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~---l~-~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~--~~~~i~~i--   82 (197)
                      .|+.+..+.++.+...+...   +. +.++++++||+++........+...+++++||||||++.+|+  |++.+..+  
T Consensus        88 ~gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~~~l~~~~l~~iVIDEaH~i~~~G~~fr~~y~~L~~  167 (607)
T PRK11057         88 NGVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLEHLAHWNPALLAVDEAHCISQWGHDFRPEYAALGQ  167 (607)
T ss_pred             cCCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHHHHHhhCCCCEEEEeCccccccccCcccHHHHHHHH
Confidence            47888888888776554433   32 358999999999984322233445689999999999999886  66655443  


Q ss_pred             -HhhccCCceEEEEeecCChhHHHHHHHhc--CCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcC-CCCEEE
Q psy7789          83 -FSFFRGQRQTLLFSATMPKKIQNFARSAL--VKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKT-EPPVLI  158 (197)
Q Consensus        83 -~~~~~~~~q~i~~SAT~~~~~~~~~~~~~--~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~-~~~~lI  158 (197)
                       .+.+ ++.|++++|||.++.+.......+  .+|...... .  .++++..  ..+....+...+..++... +.++||
T Consensus       168 l~~~~-p~~~~v~lTAT~~~~~~~di~~~l~l~~~~~~~~~-~--~r~nl~~--~v~~~~~~~~~l~~~l~~~~~~~~II  241 (607)
T PRK11057        168 LRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPLIQISS-F--DRPNIRY--TLVEKFKPLDQLMRYVQEQRGKSGII  241 (607)
T ss_pred             HHHhC-CCCcEEEEecCCChhHHHHHHHHhCCCCeEEEECC-C--CCCccee--eeeeccchHHHHHHHHHhcCCCCEEE
Confidence             3444 478899999999988766444433  455433222 1  1233322  2233344566677777654 468999


Q ss_pred             EecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         159 FAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       159 F~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      ||+|++.|+.+++.|++.|+++..+||+|++++|+++++
T Consensus       242 Fc~tr~~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~  280 (607)
T PRK11057        242 YCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQE  280 (607)
T ss_pred             EECcHHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHH
Confidence            999999999999999999999999999999999998863

>COG1201 Lhr Lhr-like helicases [General function prediction only]

Probab=99.86  E-value=7e-21  Score=163.60  Aligned_cols=181  Identities=17%  Similarity=0.166  Sum_probs=133.5

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCc--cCCCccEEEeehhhhhhcCCCHHHHH----HHHh
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMV--SLDVCRYLCLDEADRMVDMGFEEDVR----TIFS   84 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~--~l~~l~~vViDEad~l~~~~~~~~i~----~i~~   84 (197)
                      .|+.+..-+|+.+..+..++..++|||+|+|||+|.-++..+.+  .|+++++||+||.|.+.+...+.++.    .+..
T Consensus       100 ~G~~v~vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEiHel~~sKRG~~Lsl~LeRL~~  179 (814)
T COG1201         100 LGIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEIHALAESKRGVQLALSLERLRE  179 (814)
T ss_pred             cCCccceecCCCChHHhhhccCCCCcEEEeChhHHHHHhcCHHHHHHhcCCcEEEeehhhhhhccccchhhhhhHHHHHh
Confidence            37778899999998888888899999999999999999976543  48999999999999998765555544    4333


Q ss_pred             hccCCceEEEEeecCChhHHHHHHHhcCC--CeEEEeCCCCccCcceeEEEEEc---------CchhhHHHHHHHhhcCC
Q psy7789          85 FFRGQRQTLLFSATMPKKIQNFARSALVK--PITINVGRAGAASMNVVQEVEYV---------KQEAKIVYLLECLQKTE  153 (197)
Q Consensus        85 ~~~~~~q~i~~SAT~~~~~~~~~~~~~~~--~~~i~~~~~~~~~~~i~~~~~~~---------~~~~k~~~l~~~l~~~~  153 (197)
                      ..+ +.|.|++|||.. +....++.+...  +..|.-.......   .......         ........+.++++++.
T Consensus       180 l~~-~~qRIGLSATV~-~~~~varfL~g~~~~~~Iv~~~~~k~~---~i~v~~p~~~~~~~~~~~~~~~~~i~~~v~~~~  254 (814)
T COG1201         180 LAG-DFQRIGLSATVG-PPEEVAKFLVGFGDPCEIVDVSAAKKL---EIKVISPVEDLIYDEELWAALYERIAELVKKHR  254 (814)
T ss_pred             hCc-ccEEEeehhccC-CHHHHHHHhcCCCCceEEEEcccCCcc---eEEEEecCCccccccchhHHHHHHHHHHHhhcC
Confidence            334 889999999997 445555555544  3333222222111   1111111         11234556666666665


Q ss_pred             CCEEEEecccccHHHHHHHHHhCC-CCeEeecCCCChhhhhhhhC
Q psy7789         154 PPVLIFAEKKQDVDAIHEYLLLKG-KPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       154 ~~~lIF~~s~~~~~~l~~~L~~~~-~~~~~~h~~~~~~~R~~i~~  197 (197)
                       .+|||+||+..+|.++..|++.+ ..+..+||.+|.++|..+++
T Consensus       255 -ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~  298 (814)
T COG1201         255 -TTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEE  298 (814)
T ss_pred             -cEEEEEeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHH
Confidence             89999999999999999999987 89999999999999998874

>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]

Probab=99.85  E-value=2.6e-21  Score=160.99  Aligned_cols=184  Identities=15%  Similarity=0.204  Sum_probs=136.3

Q ss_pred             CCCeeEEEEEcCCChHHhHHHH---h-cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCC--CHHHHHHHH
Q psy7789          10 PIPLRTCLAIGGVPMNQSLDVI---K-KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMG--FEEDVRTIF   83 (197)
Q Consensus        10 ~~~i~~~~~~gg~~~~~~~~~l---~-~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~--~~~~i~~i~   83 (197)
                      ..|++++.+.+..+.++....+   . +..+++.-+||+|...-....+.-..+.++|||||||+.+||  |++.+..+-
T Consensus        79 ~~Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~L~~~~i~l~vIDEAHCiSqWGhdFRP~Y~~lg  158 (590)
T COG0514          79 AAGIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPDYRRLG  158 (590)
T ss_pred             HcCceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHHHHHHhCCCceEEechHHHHhhcCCccCHhHHHHH
Confidence            3589999999987766655433   3 348999999999997654444556788899999999999997  998877664


Q ss_pred             ---hhccCCceEEEEeecCChhHHHHHHHhcC--CCeEEEeCCCCccCcceeEEEEEcC-chhhHHHHHHHhhcCCCCEE
Q psy7789          84 ---SFFRGQRQTLLFSATMPKKIQNFARSALV--KPITINVGRAGAASMNVVQEVEYVK-QEAKIVYLLECLQKTEPPVL  157 (197)
Q Consensus        84 ---~~~~~~~q~i~~SAT~~~~~~~~~~~~~~--~~~~i~~~~~~~~~~~i~~~~~~~~-~~~k~~~l~~~l~~~~~~~l  157 (197)
                         ..+| ++.++++|||.++.+...+...+.  .+..+...   -.++++........ ...+..++.+......+++|
T Consensus       159 ~l~~~~~-~~p~~AlTATA~~~v~~DI~~~L~l~~~~~~~~s---fdRpNi~~~v~~~~~~~~q~~fi~~~~~~~~~~GI  234 (590)
T COG0514         159 RLRAGLP-NPPVLALTATATPRVRDDIREQLGLQDANIFRGS---FDRPNLALKVVEKGEPSDQLAFLATVLPQLSKSGI  234 (590)
T ss_pred             HHHhhCC-CCCEEEEeCCCChHHHHHHHHHhcCCCcceEEec---CCCchhhhhhhhcccHHHHHHHHHhhccccCCCeE
Confidence               4444 789999999999998886666554  44333332   22344544433332 23444444443344456799


Q ss_pred             EEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         158 IFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       158 IF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      |||.|++.|+.++++|...|+++..+||||+.++|+.+++
T Consensus       235 IYc~sRk~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~  274 (590)
T COG0514         235 IYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQ  274 (590)
T ss_pred             EEEeeHHhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999998863

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.85  E-value=9.9e-20  Score=163.46  Aligned_cols=173  Identities=16%  Similarity=0.124  Sum_probs=129.8

Q ss_pred             CCeeEEEEEcCCChHHhHHHHh----cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIK----KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF   86 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~----~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~   86 (197)
                      .++++..++|+.+..++...+.    +++||+||||+.+    . ..+.+++++++||||+|++   ++.  ....++.+
T Consensus       676 ~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL----~-~~v~~~~L~lLVIDEahrf---G~~--~~e~lk~l  745 (1147)
T PRK10689        676 WPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLL----Q-SDVKWKDLGLLIVDEEHRF---GVR--HKERIKAM  745 (1147)
T ss_pred             CCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHH----h-CCCCHhhCCEEEEechhhc---chh--HHHHHHhc
Confidence            4789999999988777765543    4699999999633    2 4456789999999999997   222  24556778


Q ss_pred             cCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCch-hhHHHHHHHhhcCCCCEEEEeccccc
Q psy7789          87 RGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQE-AKIVYLLECLQKTEPPVLIFAEKKQD  165 (197)
Q Consensus        87 ~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~-~k~~~l~~~l~~~~~~~lIF~~s~~~  165 (197)
                      +.+.|+++||||..+.+..+....++++..+...+...  ..+.+.+...... .+...+.++.  .+++++||||+++.
T Consensus       746 ~~~~qvLl~SATpiprtl~l~~~gl~d~~~I~~~p~~r--~~v~~~~~~~~~~~~k~~il~el~--r~gqv~vf~n~i~~  821 (1147)
T PRK10689        746 RADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARR--LAVKTFVREYDSLVVREAILREIL--RGGQVYYLYNDVEN  821 (1147)
T ss_pred             CCCCcEEEEcCCCCHHHHHHHHhhCCCcEEEecCCCCC--CCceEEEEecCcHHHHHHHHHHHh--cCCeEEEEECCHHH
Confidence            88999999999998888888888888988887654332  2344444433322 2333333333  24689999999999


Q ss_pred             HHHHHHHHHhC--CCCeEeecCCCChhhhhhhhC
Q psy7789         166 VDAIHEYLLLK--GKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       166 ~~~l~~~L~~~--~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      ++.+++.|++.  +.++..+||+|++++|+++++
T Consensus       822 ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~  855 (1147)
T PRK10689        822 IQKAAERLAELVPEARIAIGHGQMRERELERVMN  855 (1147)
T ss_pred             HHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHH
Confidence            99999999987  789999999999999998863

>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]

Probab=99.85  E-value=1.4e-20  Score=153.70  Aligned_cols=181  Identities=12%  Similarity=0.171  Sum_probs=138.1

Q ss_pred             CCCCeeEEEEEcCCChHHhHHHH----hcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHH--
Q psy7789           9 LPIPLRTCLAIGGVPMNQSLDVI----KKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTI--   82 (197)
Q Consensus         9 ~~~~i~~~~~~gg~~~~~~~~~l----~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i--   82 (197)
                      .++|+++++-+|-.-+....+..    ...+||||+|=+-+-.+++.+ -.+.++..|||||+|.+-+...++.+..+  
T Consensus       286 s~LglkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg-~~lgdiGtVVIDEiHtL~deERG~RLdGLI~  364 (830)
T COG1202         286 SKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTG-KDLGDIGTVVIDEIHTLEDEERGPRLDGLIG  364 (830)
T ss_pred             hcccceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcC-CcccccceEEeeeeeeccchhcccchhhHHH
Confidence            34688888888876555443222    234899999999999999877 56899999999999999875555544444  


Q ss_pred             -HhhccCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcC-chhhHHHHHHHhhc---------
Q psy7789          83 -FSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVK-QEAKIVYLLECLQK---------  151 (197)
Q Consensus        83 -~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~-~~~k~~~l~~~l~~---------  151 (197)
                       ++++-+.+|++.+|||+..+ .+.++.+.-..+..+-     .|..+..+.+++. +.+|.+.+..+.+.         
T Consensus       365 RLr~l~~~AQ~i~LSATVgNp-~elA~~l~a~lV~y~~-----RPVplErHlvf~~~e~eK~~ii~~L~k~E~~~~sskg  438 (830)
T COG1202         365 RLRYLFPGAQFIYLSATVGNP-EELAKKLGAKLVLYDE-----RPVPLERHLVFARNESEKWDIIARLVKREFSTESSKG  438 (830)
T ss_pred             HHHHhCCCCeEEEEEeecCCh-HHHHHHhCCeeEeecC-----CCCChhHeeeeecCchHHHHHHHHHHHHHHhhhhccC
Confidence             44455689999999999644 6666666555544422     2233555556664 78888888777753         


Q ss_pred             CCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         152 TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       152 ~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +.+|+|||++|++.|..+|..|..+|+++.++|+||+..+|+.++
T Consensus       439 ~rGQtIVFT~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE  483 (830)
T COG1202         439 YRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVE  483 (830)
T ss_pred             cCCceEEEecchhhHHHHHHHhhcCCcccccccCCCcHHHHHHHH
Confidence            246999999999999999999999999999999999999999886

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.84  E-value=1.6e-19  Score=157.50  Aligned_cols=172  Identities=16%  Similarity=0.145  Sum_probs=127.9

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhh-hhcCCCHHH-HHHHHhhccCC
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADR-MVDMGFEED-VRTIFSFFRGQ   89 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~-l~~~~~~~~-i~~i~~~~~~~   89 (197)
                      |..|...+++.+      ..+..++|+|+|||+|+..+.+. ..++++++|||||+|. .++.++... +..+.+.++++
T Consensus        74 g~~VGy~vr~~~------~~s~~t~I~v~T~G~Llr~l~~d-~~L~~v~~VIiDEaHER~L~~Dl~L~ll~~i~~~lr~d  146 (819)
T TIGR01970        74 GQTVGYRVRGEN------KVSRRTRLEVVTEGILTRMIQDD-PELDGVGALIFDEFHERSLDADLGLALALDVQSSLRED  146 (819)
T ss_pred             CcEEEEEEcccc------ccCCCCcEEEECCcHHHHHHhhC-cccccCCEEEEeccchhhhccchHHHHHHHHHHhcCCC
Confidence            455655555533      12345899999999999998764 5789999999999994 677655443 45566667889


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhH-----HHHHHHhhcCCCCEEEEecccc
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKI-----VYLLECLQKTEPPVLIFAEKKQ  164 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~-----~~l~~~l~~~~~~~lIF~~s~~  164 (197)
                      .|+++||||++.+.   ...++.++..+.+....   ..+.++|..+...++.     ..+..+++...+++|||+++..
T Consensus       147 lqlIlmSATl~~~~---l~~~l~~~~vI~~~gr~---~pVe~~y~~~~~~~~~~~~v~~~l~~~l~~~~g~iLVFlpg~~  220 (819)
T TIGR01970       147 LKILAMSATLDGER---LSSLLPDAPVVESEGRS---FPVEIRYLPLRGDQRLEDAVSRAVEHALASETGSILVFLPGQA  220 (819)
T ss_pred             ceEEEEeCCCCHHH---HHHHcCCCcEEEecCcc---eeeeeEEeecchhhhHHHHHHHHHHHHHHhcCCcEEEEECCHH
Confidence            99999999998654   35677766666654322   2356666655444432     3455666666689999999999


Q ss_pred             cHHHHHHHHHh---CCCCeEeecCCCChhhhhhhh
Q psy7789         165 DVDAIHEYLLL---KGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       165 ~~~~l~~~L~~---~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +++.+++.|++   .++.+..+||+|++++|+++.
T Consensus       221 eI~~l~~~L~~~~~~~~~v~pLHg~L~~~eq~~~~  255 (819)
T TIGR01970       221 EIRRVQEQLAERLDSDVLICPLYGELSLAAQDRAI  255 (819)
T ss_pred             HHHHHHHHHHhhcCCCcEEEEecCCCCHHHHHHHH
Confidence            99999999987   478999999999999998875

This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.

>TIGR01054 rgy reverse gyrase

Probab=99.83  E-value=2.3e-19  Score=161.55  Aligned_cols=166  Identities=17%  Similarity=0.283  Sum_probs=124.0

Q ss_pred             EEEEcCCChHHhH---HHHhc-CCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhc-----------CCCHHH-H
Q psy7789          16 CLAIGGVPMNQSL---DVIKK-GCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD-----------MGFEED-V   79 (197)
Q Consensus        16 ~~~~gg~~~~~~~---~~l~~-~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~-----------~~~~~~-i   79 (197)
                      ..++||.+..++.   +.+.+ +++|+|+||++|...+..  +.. +++++|+||||.+++           .||.++ +
T Consensus       156 ~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~--l~~-~~~~iVvDEaD~~L~~~k~vd~il~llGF~~e~i  232 (1171)
T TIGR01054       156 GAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDE--LGP-KFDFIFVDDVDALLKASKNVDKLLKLLGFSEELI  232 (1171)
T ss_pred             eeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHH--hcC-CCCEEEEeChHhhhhccccHHHHHHHcCCCHHHH
Confidence            3577888876554   33443 599999999999988764  122 899999999999997           456653 4


Q ss_pred             HHHH----------------------hhccCCce--EEEEeec-CChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEE
Q psy7789          80 RTIF----------------------SFFRGQRQ--TLLFSAT-MPKKIQNFARSALVKPITINVGRAGAASMNVVQEVE  134 (197)
Q Consensus        80 ~~i~----------------------~~~~~~~q--~i~~SAT-~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~  134 (197)
                      ..++                      +.+++..|  ++++||| .+..+.   ..+++++..+.+........++.+.+.
T Consensus       233 ~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~li~~SAT~~p~~~~---~~l~r~ll~~~v~~~~~~~r~I~~~~~  309 (1171)
T TIGR01054       233 EKAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRGCLIVSSATGRPRGKR---AKLFRELLGFEVGGGSDTLRNVVDVYV  309 (1171)
T ss_pred             HHHHHHhhhccccchHHHHHHHHHHHHhhhhccCcEEEEEeCCCCccccH---HHHcccccceEecCccccccceEEEEE
Confidence            4432                      33455555  6779999 454433   245677777777776667778888876


Q ss_pred             EcCchhhHHHHHHHhhcCCCCEEEEeccc---ccHHHHHHHHHhCCCCeEeecCCCCh
Q psy7789         135 YVKQEAKIVYLLECLQKTEPPVLIFAEKK---QDVDAIHEYLLLKGKPFFTLKSLKED  189 (197)
Q Consensus       135 ~~~~~~k~~~l~~~l~~~~~~~lIF~~s~---~~~~~l~~~L~~~~~~~~~~h~~~~~  189 (197)
                      .+..  +...+.++++..+.++||||+|+   +.|+++++.|++.|+++..+||+|++
T Consensus       310 ~~~~--~~~~L~~ll~~l~~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~~  365 (1171)
T TIGR01054       310 EDED--LKETLLEIVKKLGTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKPK  365 (1171)
T ss_pred             eccc--HHHHHHHHHHHcCCCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCCH
Confidence            5543  34567788877777899999999   99999999999999999999999974

Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.

>KOG0349|consensus

Probab=99.83  E-value=2e-20  Score=148.49  Aligned_cols=186  Identities=24%  Similarity=0.401  Sum_probs=152.3

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccC--
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRG--   88 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~--   88 (197)
                      ..+|..++.||...+.|...+.++.||+|+||+|+..++..+.+.+.+++++|+||+|.++..++-+.+..+...+|+  
T Consensus       316 p~~r~lLmiggv~~r~Q~~ql~~g~~ivvGtpgRl~~~is~g~~~lt~crFlvlDead~lL~qgy~d~I~r~h~qip~~t  395 (725)
T KOG0349|consen  316 PEVRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPISKGLVTLTHCRFLVLDEADLLLGQGYDDKIYRFHGQIPHMT  395 (725)
T ss_pred             hhhhhhhhhhhHHhHHHHHHhhcCceeeecCchhhhhhhhccceeeeeeEEEEecchhhhhhcccHHHHHHHhccchhhh
Confidence            357888999999999999999999999999999999999999999999999999999999999999999988888874  


Q ss_pred             ----CceEEEEeecCCh-hHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCch------------------------
Q psy7789          89 ----QRQTLLFSATMPK-KIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQE------------------------  139 (197)
Q Consensus        89 ----~~q~i~~SAT~~~-~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~------------------------  139 (197)
                          ..|.+++|||+.. ++..+.++.|-=|.++++..+...++.+.+....+...                        
T Consensus       396 sdg~rlq~~vCsatlh~feVkk~~ervmhfptwVdLkgeD~vpetvHhvv~lv~p~~d~sw~~lr~~i~td~vh~kdn~~  475 (725)
T KOG0349|consen  396 SDGFRLQSPVCSATLHIFEVKKVGERVMHFPTWVDLKGEDLVPETVHHVVKLVCPSVDGSWCDLRQFIETDKVHTKDNLL  475 (725)
T ss_pred             cCCcccccceeeeEEeEEEeeehhhhhccCceeEecccccccchhhccceeecCCccCccHHHHhhhhccCCcccccccc
Confidence                4599999999863 46667778888899999998888888777765543210                        


Q ss_pred             ------hhH---------HHHHHHhhcC-CCCEEEEecccccHHHHHHHHHhCC---CCeEeecCCCChhhhhhhh
Q psy7789         140 ------AKI---------VYLLECLQKT-EPPVLIFAEKKQDVDAIHEYLLLKG---KPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       140 ------~k~---------~~l~~~l~~~-~~~~lIF~~s~~~~~~l~~~L~~~~---~~~~~~h~~~~~~~R~~i~  196 (197)
                            +-.         .+-+..++++ ..++||||.|+.+|..|-..++++|   |+|.++||+..++||++-+
T Consensus       476 pg~~Spe~~s~a~kilkgEy~v~ai~~h~mdkaiifcrtk~dcDnLer~~~qkgg~~~scvclhgDrkP~Erk~nl  551 (725)
T KOG0349|consen  476 PGQVSPENPSSATKILKGEYGVVAIRRHAMDKAIIFCRTKQDCDNLERMMNQKGGKHYSCVCLHGDRKPDERKANL  551 (725)
T ss_pred             cccCCCCChhhhhHHhcCchhhhhhhhhccCceEEEEeccccchHHHHHHHHcCCccceeEEEecCCChhHHHHHH
Confidence                  001         1111222222 2489999999999999999999884   7999999999888887654

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.83  E-value=3.6e-19  Score=155.53  Aligned_cols=173  Identities=14%  Similarity=0.109  Sum_probs=129.1

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhh-hhcCCC-HHHHHHHHhhccC
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADR-MVDMGF-EEDVRTIFSFFRG   88 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~-l~~~~~-~~~i~~i~~~~~~   88 (197)
                      .|..+...++|.+...      ...+|+|+|||+|.+++... ..++++++||+||+|. .++.++ ...+..+++.+++
T Consensus        76 ~g~~VGy~vr~~~~~~------~~t~I~v~T~G~Llr~l~~d-~~L~~v~~IIlDEaHER~l~~Dl~L~ll~~i~~~lr~  148 (812)
T PRK11664         76 PGETVGYRMRAESKVG------PNTRLEVVTEGILTRMIQRD-PELSGVGLVILDEFHERSLQADLALALLLDVQQGLRD  148 (812)
T ss_pred             cCceEEEEecCccccC------CCCcEEEEChhHHHHHHhhC-CCcCcCcEEEEcCCCccccccchHHHHHHHHHHhCCc
Confidence            3667777777654322      24689999999999998754 4789999999999997 344333 2334566677888


Q ss_pred             CceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHH-----HHHHHhhcCCCCEEEEeccc
Q psy7789          89 QRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIV-----YLLECLQKTEPPVLIFAEKK  163 (197)
Q Consensus        89 ~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~-----~l~~~l~~~~~~~lIF~~s~  163 (197)
                      +.|+++||||++.+.   ...++.++..+.+....   ..+.++|..+...++..     .+..+++...+++|||+++.
T Consensus       149 ~lqlilmSATl~~~~---l~~~~~~~~~I~~~gr~---~pV~~~y~~~~~~~~~~~~v~~~l~~~l~~~~g~iLVFlpg~  222 (812)
T PRK11664        149 DLKLLIMSATLDNDR---LQQLLPDAPVIVSEGRS---FPVERRYQPLPAHQRFDEAVARATAELLRQESGSLLLFLPGV  222 (812)
T ss_pred             cceEEEEecCCCHHH---HHHhcCCCCEEEecCcc---ccceEEeccCchhhhHHHHHHHHHHHHHHhCCCCEEEEcCCH
Confidence            999999999998652   35677766666554322   23666666666555543     45566666668999999999


Q ss_pred             ccHHHHHHHHHh---CCCCeEeecCCCChhhhhhhh
Q psy7789         164 QDVDAIHEYLLL---KGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       164 ~~~~~l~~~L~~---~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .+++.+++.|++   .++.+..+||+|++++|+++.
T Consensus       223 ~ei~~l~~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~  258 (812)
T PRK11664        223 GEIQRVQEQLASRVASDVLLCPLYGALSLAEQQKAI  258 (812)
T ss_pred             HHHHHHHHHHHHhccCCceEEEeeCCCCHHHHHHHh
Confidence            999999999987   578899999999999988765

>KOG0350|consensus

Probab=99.82  E-value=4.4e-20  Score=148.33  Aligned_cols=187  Identities=20%  Similarity=0.288  Sum_probs=150.4

Q ss_pred             CCCeeEEEEEcCCChHHhHHHHhc-CC----cEEEeCchHHHHHHh-cCCccCCCccEEEeehhhhhhcCCCHHHHHHHH
Q psy7789          10 PIPLRTCLAIGGVPMNQSLDVIKK-GC----HMMVATPGRLMDMLD-KKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIF   83 (197)
Q Consensus        10 ~~~i~~~~~~gg~~~~~~~~~l~~-~~----~Ili~TP~~l~~~l~-~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~   83 (197)
                      +.|+.|+.+.|-.+.+.+.+.|.+ .+    ||+|+|||||.+.++ .+.++|++++|+||||||+|++..|.+.+-.+.
T Consensus       241 ~tgL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~LrfLVIDEADRll~qsfQ~Wl~~v~  320 (620)
T KOG0350|consen  241 GTGLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNNTKSFDLKHLRFLVIDEADRLLDQSFQEWLDTVM  320 (620)
T ss_pred             CCceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhccCCCCcchhhceEEEechHHHHHHHHHHHHHHHHH
Confidence            468999999999999999988864 45    999999999999998 578999999999999999999876666555443


Q ss_pred             hhcc----------------------------------CCceEEEEeecCChhHHHHHHHhcCCCeEEEeC----CCCcc
Q psy7789          84 SFFR----------------------------------GQRQTLLFSATMPKKIQNFARSALVKPITINVG----RAGAA  125 (197)
Q Consensus        84 ~~~~----------------------------------~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~----~~~~~  125 (197)
                      ..+.                                  +..+.+++|||++.........-+..|....+.    ...+.
T Consensus       321 ~~~~~~k~~~~~~nii~~~~~~~pt~~~e~~t~~~~~~~~l~kL~~satLsqdP~Kl~~l~l~~Prl~~v~~~~~~rysl  400 (620)
T KOG0350|consen  321 SLCKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKLYPPLWKLVFSATLSQDPSKLKDLTLHIPRLFHVSKPLIGRYSL  400 (620)
T ss_pred             HHhCCchhhcChhhhhhhcccCCchhhHHHHhhcCCcCchhHhhhcchhhhcChHHHhhhhcCCCceEEeecccceeeec
Confidence            3331                                  112467899999877777777777777665554    34567


Q ss_pred             CcceeEEEEEcCchhhHHHHHHHhhcCC-CCEEEEecccccHHHHHHHHH----hCCCCeEeecCCCChhhhhhhh
Q psy7789         126 SMNVVQEVEYVKQEAKIVYLLECLQKTE-PPVLIFAEKKQDVDAIHEYLL----LKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       126 ~~~i~~~~~~~~~~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~~l~~~L~----~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +..+.++.+.+....|...+..++.... .++|+|+++...+..++..|+    +.+.++..+.|.++.+.|.+.+
T Consensus       401 p~~l~~~~vv~~~~~kpl~~~~lI~~~k~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l  476 (620)
T KOG0350|consen  401 PSSLSHRLVVTEPKFKPLAVYALITSNKLNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTGQLNGKRRYKML  476 (620)
T ss_pred             ChhhhhceeecccccchHhHHHHHHHhhcceEEEEecchHHHHHHHHHHHHHhccccchhhhhhhhhhHHHHHHHH
Confidence            7778888777777788888998888765 589999999999999999887    3467788899999999998754

>PRK01172 ski2-like helicase; Provisional

Probab=99.82  E-value=1.9e-19  Score=156.03  Aligned_cols=179  Identities=14%  Similarity=0.177  Sum_probs=120.3

Q ss_pred             CCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhh---c
Q psy7789          10 PIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSF---F   86 (197)
Q Consensus        10 ~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~---~   86 (197)
                      ..|+++...+|+.+....  .+ +.+||+|+|||++..++.+....+.+++++|+||+|.+.+.+++..+..++..   +
T Consensus        90 ~~g~~v~~~~G~~~~~~~--~~-~~~dIiv~Tpek~~~l~~~~~~~l~~v~lvViDEaH~l~d~~rg~~le~ll~~~~~~  166 (674)
T PRK01172         90 SLGMRVKISIGDYDDPPD--FI-KRYDVVILTSEKADSLIHHDPYIINDVGLIVADEIHIIGDEDRGPTLETVLSSARYV  166 (674)
T ss_pred             hcCCeEEEEeCCCCCChh--hh-ccCCEEEECHHHHHHHHhCChhHHhhcCEEEEecchhccCCCccHHHHHHHHHHHhc
Confidence            458899999998654322  22 35899999999999998877767899999999999999887788777776544   4


Q ss_pred             cCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEE-----EcCchh-hHHHHHHHhh---cCCCCEE
Q psy7789          87 RGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVE-----YVKQEA-KIVYLLECLQ---KTEPPVL  157 (197)
Q Consensus        87 ~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~-----~~~~~~-k~~~l~~~l~---~~~~~~l  157 (197)
                      +++.|++++|||++. ..++.++ +..+. +... ..  +..+.....     ...... ....+..++.   ..++++|
T Consensus       167 ~~~~riI~lSATl~n-~~~la~w-l~~~~-~~~~-~r--~vpl~~~i~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~vL  240 (674)
T PRK01172        167 NPDARILALSATVSN-ANELAQW-LNASL-IKSN-FR--PVPLKLGILYRKRLILDGYERSQVDINSLIKETVNDGGQVL  240 (674)
T ss_pred             CcCCcEEEEeCccCC-HHHHHHH-hCCCc-cCCC-CC--CCCeEEEEEecCeeeecccccccccHHHHHHHHHhCCCcEE
Confidence            568899999999974 4555543 33221 1110 01  111111111     111111 1111222222   3457999


Q ss_pred             EEecccccHHHHHHHHHhCC-------------------------CCeEeecCCCChhhhhhhhC
Q psy7789         158 IFAEKKQDVDAIHEYLLLKG-------------------------KPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       158 IF~~s~~~~~~l~~~L~~~~-------------------------~~~~~~h~~~~~~~R~~i~~  197 (197)
                      |||+|++.|+.++..|.+..                         ..+..+||+|++++|+.+++
T Consensus       241 VF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~  305 (674)
T PRK01172        241 VFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEE  305 (674)
T ss_pred             EEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHH
Confidence            99999999999999886531                         24788999999999998863

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.82  E-value=7.4e-19  Score=154.95  Aligned_cols=174  Identities=13%  Similarity=0.076  Sum_probs=125.8

Q ss_pred             CCeeEEEEEcCCChHHhH---HHHhc-CCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhc
Q psy7789          11 IPLRTCLAIGGVPMNQSL---DVIKK-GCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF   86 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~---~~l~~-~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~   86 (197)
                      .++++..++|+.+..++.   +.+.. .+||+||||.    ++ .+.+.+++++++||||+|++     +......++.+
T Consensus       527 ~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~----ll-~~~v~f~~L~llVIDEahrf-----gv~~~~~L~~~  596 (926)
T TIGR00580       527 FPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHK----LL-QKDVKFKDLGLLIIDEEQRF-----GVKQKEKLKEL  596 (926)
T ss_pred             CCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHH----Hh-hCCCCcccCCEEEeeccccc-----chhHHHHHHhc
Confidence            479999999988755443   33444 5999999994    23 35567899999999999995     33345566777


Q ss_pred             cCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecccccH
Q psy7789          87 RGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDV  166 (197)
Q Consensus        87 ~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~  166 (197)
                      +++.|+++||||..+..........+++..+...+..  +..+.+++.......-...+...+. .+++++||||+++++
T Consensus       597 ~~~~~vL~~SATpiprtl~~~l~g~~d~s~I~~~p~~--R~~V~t~v~~~~~~~i~~~i~~el~-~g~qv~if~n~i~~~  673 (926)
T TIGR00580       597 RTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPED--RLPVRTFVMEYDPELVREAIRRELL-RGGQVFYVHNRIESI  673 (926)
T ss_pred             CCCCCEEEEecCCCHHHHHHHHhcCCCcEEEecCCCC--ccceEEEEEecCHHHHHHHHHHHHH-cCCeEEEEECCcHHH
Confidence            7889999999998877776666666777777655433  2235554433222221223333333 346899999999999


Q ss_pred             HHHHHHHHhC--CCCeEeecCCCChhhhhhhhC
Q psy7789         167 DAIHEYLLLK--GKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       167 ~~l~~~L~~~--~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      +.+++.|++.  ++++..+||+|++++|+++++
T Consensus       674 e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~  706 (926)
T TIGR00580       674 EKLATQLRELVPEARIAIAHGQMTENELEEVML  706 (926)
T ss_pred             HHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHH
Confidence            9999999985  789999999999999998863

All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transacribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families.

>KOG0344|consensus

Probab=99.81  E-value=6.5e-20  Score=149.74  Aligned_cols=163  Identities=23%  Similarity=0.363  Sum_probs=148.1

Q ss_pred             CCcEEEeCchHHHHHHhcCC--ccCCCccEEEeehhhhhhcC-CCHHHHHHHHhhccC-CceEEEEeecCChhHHHHHHH
Q psy7789          34 GCHMMVATPGRLMDMLDKKM--VSLDVCRYLCLDEADRMVDM-GFEEDVRTIFSFFRG-QRQTLLFSATMPKKIQNFARS  109 (197)
Q Consensus        34 ~~~Ili~TP~~l~~~l~~~~--~~l~~l~~vViDEad~l~~~-~~~~~i~~i~~~~~~-~~q~i~~SAT~~~~~~~~~~~  109 (197)
                      .+||+|+||.++...+..+.  +++..+.++|+||||.+++. .|..++..|++.+.+ +..+-+||||++.++.++++.
T Consensus       262 k~dili~TP~ri~~~~~~~~~~idl~~V~~lV~dEaD~lfe~~~f~~Qla~I~sac~s~~i~~a~FSat~~~~VEE~~~~  341 (593)
T KOG0344|consen  262 KYDILISTPMRIVGLLGLGKLNIDLSKVEWLVVDEADLLFEPEFFVEQLADIYSACQSPDIRVALFSATISVYVEEWAEL  341 (593)
T ss_pred             HHHHHhcCHHHHHHHhcCCCccchhheeeeEeechHHhhhChhhHHHHHHHHHHHhcCcchhhhhhhccccHHHHHHHHH
Confidence            48999999999999998765  78999999999999999998 899999999988864 557779999999999999999


Q ss_pred             hcCCCeEEEeCCCCccCcceeEEEEEcC-chhhHHHHHHHhhcC-CCCEEEEecccccHHHHHHHH-HhCCCCeEeecCC
Q psy7789         110 ALVKPITINVGRAGAASMNVVQEVEYVK-QEAKIVYLLECLQKT-EPPVLIFAEKKQDVDAIHEYL-LLKGKPFFTLKSL  186 (197)
Q Consensus       110 ~~~~~~~i~~~~~~~~~~~i~~~~~~~~-~~~k~~~l~~~l~~~-~~~~lIF~~s~~~~~~l~~~L-~~~~~~~~~~h~~  186 (197)
                      ...++..+.++..++....+.|..++|. +..|+..+..++... .+|++||+.+.++|.+|++.| .-.++++..+||+
T Consensus       342 i~~~~~~vivg~~~sa~~~V~QelvF~gse~~K~lA~rq~v~~g~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e  421 (593)
T KOG0344|consen  342 IKSDLKRVIVGLRNSANETVDQELVFCGSEKGKLLALRQLVASGFKPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGE  421 (593)
T ss_pred             hhccceeEEEecchhHhhhhhhhheeeecchhHHHHHHHHHhccCCCCeEEEEecHHHHHHHHHHhhhccCcceeeEecc
Confidence            9999999999988888889999999995 567999999999875 679999999999999999999 7779999999999


Q ss_pred             CChhhhhhhh
Q psy7789         187 KEDQNNQTLE  196 (197)
Q Consensus       187 ~~~~~R~~i~  196 (197)
                      .++.+|++.+
T Consensus       422 ~~~~qrde~~  431 (593)
T KOG0344|consen  422 RSQKQRDETM  431 (593)
T ss_pred             cchhHHHHHH
Confidence            9999999865

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.79  E-value=3.7e-18  Score=146.10  Aligned_cols=167  Identities=13%  Similarity=0.191  Sum_probs=118.2

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhcc-CCc
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFR-GQR   90 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~-~~~   90 (197)
                      |+.+...+||.+. .+......+.+|+++||+.       ....++++++||+||||.....+  +.+..+++..+ ..+
T Consensus       253 g~~v~v~~Gg~~~-~~~~t~~k~~~Ilv~T~~L-------~l~~L~~v~~VVIDEaHEr~~~~--DllL~llk~~~~~~r  322 (675)
T PHA02653        253 GSPISLKYGSIPD-ELINTNPKPYGLVFSTHKL-------TLNKLFDYGTVIIDEVHEHDQIG--DIIIAVARKHIDKIR  322 (675)
T ss_pred             CceEEEEECCcch-HHhhcccCCCCEEEEeCcc-------cccccccCCEEEccccccCccch--hHHHHHHHHhhhhcC
Confidence            6788899999872 2222233368999999852       11247899999999999987653  44555554443 346


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcC----------chhhHHHHHHHhh----cCCCCE
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVK----------QEAKIVYLLECLQ----KTEPPV  156 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~----------~~~k~~~l~~~l~----~~~~~~  156 (197)
                      |+++||||+++++..+ ..++++|..+.+...  ....+.+++....          +.++.. +...+.    ..++++
T Consensus       323 q~ILmSATl~~dv~~l-~~~~~~p~~I~I~gr--t~~pV~~~yi~~~~~~~~~~~y~~~~k~~-~l~~L~~~~~~~~g~i  398 (675)
T PHA02653        323 SLFLMTATLEDDRDRI-KEFFPNPAFVHIPGG--TLFPISEVYVKNKYNPKNKRAYIEEEKKN-IVTALKKYTPPKGSSG  398 (675)
T ss_pred             EEEEEccCCcHhHHHH-HHHhcCCcEEEeCCC--cCCCeEEEEeecCcccccchhhhHHHHHH-HHHHHHHhhcccCCcE
Confidence            9999999999888776 578889988887532  2345666655332          122222 223332    234689


Q ss_pred             EEEecccccHHHHHHHHHhC--CCCeEeecCCCChhhh
Q psy7789         157 LIFAEKKQDVDAIHEYLLLK--GKPFFTLKSLKEDQNN  192 (197)
Q Consensus       157 lIF~~s~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~R  192 (197)
                      |||++++.+|+.+++.|.+.  ++++..+||+|++.++
T Consensus       399 LVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~eq  436 (675)
T PHA02653        399 IVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVPNIDE  436 (675)
T ss_pred             EEEECcHHHHHHHHHHHHhhcCCceEEeccCCcCHHHH
Confidence            99999999999999999987  7999999999998643

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.78  E-value=1.1e-18  Score=141.01  Aligned_cols=159  Identities=13%  Similarity=0.124  Sum_probs=106.0

Q ss_pred             CcEEEeCchHHHHHHhcC----CccCC--CccEEEeehhhhhhcCCCHHHHHHHHhhcc-CCceEEEEeecCChhHHHHH
Q psy7789          35 CHMMVATPGRLMDMLDKK----MVSLD--VCRYLCLDEADRMVDMGFEEDVRTIFSFFR-GQRQTLLFSATMPKKIQNFA  107 (197)
Q Consensus        35 ~~Ili~TP~~l~~~l~~~----~~~l~--~l~~vViDEad~l~~~~~~~~i~~i~~~~~-~~~q~i~~SAT~~~~~~~~~  107 (197)
                      ++|+++||+++...+...    ...+.  ..+++|+||+|.+.++++.. +..+++.++ .+.|++++|||+++.+.++.
T Consensus        95 ~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~~~~~-l~~~l~~l~~~~~~~i~~SATlp~~l~~~~  173 (358)
T TIGR01587        95 DPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYTLAL-ILAVLEVLKDNDVPILLMSATLPKFLKEYA  173 (358)
T ss_pred             CCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHHHHHH-HHHHHHHHHHcCCCEEEEecCchHHHHHHH
Confidence            689999999999877641    11122  23799999999998764333 555555554 47899999999997777776


Q ss_pred             HHhcCCCeEEEeCCCCccCcceeEEEEEc--CchhhHHHHHHHhhc--CCCCEEEEecccccHHHHHHHHHhCCC--CeE
Q psy7789         108 RSALVKPITINVGRAGAASMNVVQEVEYV--KQEAKIVYLLECLQK--TEPPVLIFAEKKQDVDAIHEYLLLKGK--PFF  181 (197)
Q Consensus       108 ~~~~~~~~~i~~~~~~~~~~~i~~~~~~~--~~~~k~~~l~~~l~~--~~~~~lIF~~s~~~~~~l~~~L~~~~~--~~~  181 (197)
                      ..+...+.......... .....+.+..+  ....+...+.++++.  .++++||||||++.|+.+++.|++.+.  ++.
T Consensus       174 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~lVf~~t~~~~~~~~~~L~~~~~~~~~~  252 (358)
T TIGR01587       174 EKIGYVEFNEPLDLKEE-RRFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIM  252 (358)
T ss_pred             hcCCCcccccCCCCccc-cccccccceeeccccccCHHHHHHHHHHhhCCCeEEEEECCHHHHHHHHHHHHhhcCCCeEE
Confidence            66544322111111100 00112222222  223445555555543  346899999999999999999998876  599


Q ss_pred             eecCCCChhhhhhh
Q psy7789         182 TLKSLKEDQNNQTL  195 (197)
Q Consensus       182 ~~h~~~~~~~R~~i  195 (197)
                      .+||+|++.+|+++
T Consensus       253 ~~h~~~~~~~r~~~  266 (358)
T TIGR01587       253 LLHSRFTEKDRAKK  266 (358)
T ss_pred             EEECCCCHHHHHHH
Confidence            99999999999764

This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.77  E-value=1.2e-17  Score=149.51  Aligned_cols=157  Identities=15%  Similarity=0.234  Sum_probs=112.4

Q ss_pred             hcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhh-hhhcCCCHHH-HHHHHhhccCCceEEEEeecCChhHHHHHHH
Q psy7789          32 KKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEAD-RMVDMGFEED-VRTIFSFFRGQRQTLLFSATMPKKIQNFARS  109 (197)
Q Consensus        32 ~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad-~l~~~~~~~~-i~~i~~~~~~~~q~i~~SAT~~~~~~~~~~~  109 (197)
                      +.+++|+++|||+|+..+..... +++++++|+|||| +.++.+|... +..++.. .++.|+++||||++.+  .+.+.
T Consensus       161 s~~t~I~v~TpG~LL~~l~~d~~-Ls~~~~IIIDEAHERsLn~DfLLg~Lk~lL~~-rpdlKvILmSATid~e--~fs~~  236 (1294)
T PRK11131        161 SDNTMVKLMTDGILLAEIQQDRL-LMQYDTIIIDEAHERSLNIDFILGYLKELLPR-RPDLKVIITSATIDPE--RFSRH  236 (1294)
T ss_pred             CCCCCEEEEChHHHHHHHhcCCc-cccCcEEEecCccccccccchHHHHHHHhhhc-CCCceEEEeeCCCCHH--HHHHH
Confidence            45699999999999999876554 8999999999999 5777776643 4444333 2478999999999753  55555


Q ss_pred             hcCCCeEEEeCCCCccCcceeEEEEEcCc------hhhHHHHHHHh----hcCCCCEEEEecccccHHHHHHHHHhCCCC
Q psy7789         110 ALVKPITINVGRAGAASMNVVQEVEYVKQ------EAKIVYLLECL----QKTEPPVLIFAEKKQDVDAIHEYLLLKGKP  179 (197)
Q Consensus       110 ~~~~~~~i~~~~~~~~~~~i~~~~~~~~~------~~k~~~l~~~l----~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~  179 (197)
                      +...| .+.+.....   .+.+.+..+..      .+.+..+.+.+    ....+++|||+++..+++.+++.|++.+++
T Consensus       237 F~~ap-vI~V~Gr~~---pVei~y~p~~~~~~~~~~d~l~~ll~~V~~l~~~~~GdILVFLpg~~EIe~lae~L~~~~~~  312 (1294)
T PRK11131        237 FNNAP-IIEVSGRTY---PVEVRYRPIVEEADDTERDQLQAIFDAVDELGREGPGDILIFMSGEREIRDTADALNKLNLR  312 (1294)
T ss_pred             cCCCC-EEEEcCccc---cceEEEeecccccchhhHHHHHHHHHHHHHHhcCCCCCEEEEcCCHHHHHHHHHHHHhcCCC
Confidence            55455 455553321   24555554432      12333333332    233568999999999999999999988764


Q ss_pred             ---eEeecCCCChhhhhhhh
Q psy7789         180 ---FFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       180 ---~~~~h~~~~~~~R~~i~  196 (197)
                         +..+||+|++++|+++.
T Consensus       313 ~~~VlpLhg~Ls~~eQ~~Vf  332 (1294)
T PRK11131        313 HTEILPLYARLSNSEQNRVF  332 (1294)
T ss_pred             cceEeecccCCCHHHHHHHh
Confidence               77899999999999875

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.77  E-value=3.1e-17  Score=142.05  Aligned_cols=174  Identities=13%  Similarity=0.099  Sum_probs=112.9

Q ss_pred             CCeeEEEEEcCCChHHh---HHHHhc-CCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhc
Q psy7789          11 IPLRTCLAIGGVPMNQS---LDVIKK-GCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF   86 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~---~~~l~~-~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~   86 (197)
                      .|+++..++||.+..+.   .+.+.. .++|+||||+.+.+     ...+++++++|+||+|++..     .....+...
T Consensus       337 ~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~v~~~~l~lvVIDE~Hrfg~-----~qr~~l~~~  406 (681)
T PRK10917        337 LGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQD-----DVEFHNLGLVIIDEQHRFGV-----EQRLALREK  406 (681)
T ss_pred             cCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcc-----cchhcccceEEEechhhhhH-----HHHHHHHhc
Confidence            47999999999885443   344544 59999999977643     34578999999999999632     222333344


Q ss_pred             cCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhH-HHHHHHhhcCCCCEEEEeccc--
Q psy7789          87 RGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKI-VYLLECLQKTEPPVLIFAEKK--  163 (197)
Q Consensus        87 ~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~-~~l~~~l~~~~~~~lIF~~s~--  163 (197)
                      ...+++++||||..+...........+...+..  ....+..+.+.+......++. ..+.+.+ ..+.+++|||+++  
T Consensus       407 ~~~~~iL~~SATp~prtl~~~~~g~~~~s~i~~--~p~~r~~i~~~~~~~~~~~~~~~~i~~~~-~~g~q~~v~~~~ie~  483 (681)
T PRK10917        407 GENPHVLVMTATPIPRTLAMTAYGDLDVSVIDE--LPPGRKPITTVVIPDSRRDEVYERIREEI-AKGRQAYVVCPLIEE  483 (681)
T ss_pred             CCCCCEEEEeCCCCHHHHHHHHcCCCceEEEec--CCCCCCCcEEEEeCcccHHHHHHHHHHHH-HcCCcEEEEEccccc
Confidence            557899999999776654433221122222222  222223355544433332222 2333333 3456999999964  


Q ss_pred             ------ccHHHHHHHHHhC--CCCeEeecCCCChhhhhhhhC
Q psy7789         164 ------QDVDAIHEYLLLK--GKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       164 ------~~~~~l~~~L~~~--~~~~~~~h~~~~~~~R~~i~~  197 (197)
                            ..++++++.|.+.  ++++..+||+|++++|+++++
T Consensus       484 s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~  525 (681)
T PRK10917        484 SEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMA  525 (681)
T ss_pred             ccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHH
Confidence                  4566788888876  578999999999999999874

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.77  E-value=5.3e-17  Score=130.93  Aligned_cols=162  Identities=13%  Similarity=0.076  Sum_probs=108.1

Q ss_pred             cCCcEEEeCchHHHHHHhcC-----Cc---cCCCccEEEeehhhhhhcCCC-----HHHHHHHHhhccCCceEEEEeecC
Q psy7789          33 KGCHMMVATPGRLMDMLDKK-----MV---SLDVCRYLCLDEADRMVDMGF-----EEDVRTIFSFFRGQRQTLLFSATM   99 (197)
Q Consensus        33 ~~~~Ili~TP~~l~~~l~~~-----~~---~l~~l~~vViDEad~l~~~~~-----~~~i~~i~~~~~~~~q~i~~SAT~   99 (197)
                      ..|+|+++||+.+..++...     ..   .+..++++|+||+|.+..++.     ......+++......+++++|||+
T Consensus       112 ~~p~illT~p~~l~~llr~~~~~~~~~~~~~~~~~~~iV~DE~H~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~lSAT~  191 (357)
T TIGR03158       112 STPIILLTNPDIFVYLTRFAYIDRGDIAAGFYTKFSTVIFDEFHLYDAKQLVGMLFLLAYMQLIRFFECRRKFVFLSATP  191 (357)
T ss_pred             CCCCEEEecHHHHHHHHhhhccCcccchhhhhcCCCEEEEecccccCcccchhhhhhhHHHHHHHhhhcCCcEEEEecCC
Confidence            46999999999998776431     11   257899999999999865321     122334444444467999999999


Q ss_pred             ChhHHHHHHHh--cCCCeEEEeCCCC------------------ccCcceeEEEEEcCchhhHHHHH---HHh----hc-
Q psy7789         100 PKKIQNFARSA--LVKPITINVGRAG------------------AASMNVVQEVEYVKQEAKIVYLL---ECL----QK-  151 (197)
Q Consensus       100 ~~~~~~~~~~~--~~~~~~i~~~~~~------------------~~~~~i~~~~~~~~~~~k~~~l~---~~l----~~-  151 (197)
                      ++.+.+.....  ++.+.....+...                  ...+.+.+.++. ....|...+.   +.+    +. 
T Consensus       192 ~~~~~~~l~~~~~~~~~~~~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~-~~~~~~~~l~~l~~~i~~~~~~~  270 (357)
T TIGR03158       192 DPALILRLQNAKQAGVKIAPIDGEKYQFPDNPELEADNKTQSFRPVLPPVELELIP-APDFKEEELSELAEEVIERFRQL  270 (357)
T ss_pred             CHHHHHHHHhccccCceeeeecCcccccCCChhhhccccccccceeccceEEEEEe-CCchhHHHHHHHHHHHHHHHhcc
Confidence            99888877765  4554433222200                  011245554444 3333433332   222    22 


Q ss_pred             CCCCEEEEecccccHHHHHHHHHhCC--CCeEeecCCCChhhhhhh
Q psy7789         152 TEPPVLIFAEKKQDVDAIHEYLLLKG--KPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       152 ~~~~~lIF~~s~~~~~~l~~~L~~~~--~~~~~~h~~~~~~~R~~i  195 (197)
                      .++++||||||++.|+.+++.|++.|  +.+..+||.+++++|+++
T Consensus       271 ~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~~~~R~~~  316 (357)
T TIGR03158       271 PGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAPKKDRERA  316 (357)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCCHHHHHHh
Confidence            24589999999999999999999865  578899999999999865

subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system.

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.77  E-value=2.8e-18  Score=148.69  Aligned_cols=185  Identities=15%  Similarity=0.157  Sum_probs=132.2

Q ss_pred             CCCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccC
Q psy7789           9 LPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRG   88 (197)
Q Consensus         9 ~~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~   88 (197)
                      ...|+||...+|+.+...+  .+. +++|+|+|||++..++++.......+++||+||+|.+.+...++.+..|+...+.
T Consensus       100 ~~~GirV~~~TgD~~~~~~--~l~-~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~~RG~~lE~iv~r~~~  176 (766)
T COG1204         100 EELGIRVGISTGDYDLDDE--RLA-RYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRTRGPVLESIVARMRR  176 (766)
T ss_pred             HhcCCEEEEecCCcccchh--hhc-cCCEEEEchHHhhHhhhcCcchhhcccEEEEeeeeecCCcccCceehhHHHHHHh
Confidence            3569999999999875552  232 4999999999999999988888999999999999999887777777777666643


Q ss_pred             ---CceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccC-cceeEEEEEcCchhh---------HHHHHHHhhcCCCC
Q psy7789          89 ---QRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAAS-MNVVQEVEYVKQEAK---------IVYLLECLQKTEPP  155 (197)
Q Consensus        89 ---~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~-~~i~~~~~~~~~~~k---------~~~l~~~l~~~~~~  155 (197)
                         ..|++.+|||++ +..+++.+.-.++......+..... ....+.+.......|         ...++...-..+++
T Consensus       177 ~~~~~rivgLSATlp-N~~evA~wL~a~~~~~~~rp~~l~~~v~~~~~~~~~~~~~k~~~~~~~~~~~~~v~~~~~~~~q  255 (766)
T COG1204         177 LNELIRIVGLSATLP-NAEEVADWLNAKLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNLALELVLESLAEGGQ  255 (766)
T ss_pred             hCcceEEEEEeeecC-CHHHHHHHhCCcccccCCCCcccccCCccceEEEEecCccccccccchHHHHHHHHHHHhcCCe
Confidence               479999999997 5677776666665543444333322 223333333332221         22222222234579


Q ss_pred             EEEEecccccHHHHHHHHHhC---------------------C----------------CCeEeecCCCChhhhhhhhC
Q psy7789         156 VLIFAEKKQDVDAIHEYLLLK---------------------G----------------KPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       156 ~lIF~~s~~~~~~l~~~L~~~---------------------~----------------~~~~~~h~~~~~~~R~~i~~  197 (197)
                      +||||+|++.+...|..|++.                     +                ..++.+|+||+.++|.-+++
T Consensus       256 vLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHhAGL~~~~R~~vE~  334 (766)
T COG1204         256 VLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPREDRQLVED  334 (766)
T ss_pred             EEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccccccCCCHHHHHHHHH
Confidence            999999999999999999730                     0                12678999999999998763

>COG1205 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]

Probab=99.75  E-value=4.8e-17  Score=142.70  Aligned_cols=189  Identities=18%  Similarity=0.227  Sum_probs=137.7

Q ss_pred             cccCCCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhc-C---CccCCCccEEEeehhhhhhcCCCHHHHHH
Q psy7789           6 ISALPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDK-K---MVSLDVCRYLCLDEADRMVDMGFEEDVRT   81 (197)
Q Consensus         6 ~~~~~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~-~---~~~l~~l~~vViDEad~l~~~~~~~~i~~   81 (197)
                      .+..+.++++...+|+...++....+.++||||+++|.+|..++-. .   .+.++++++||+||+|.+-.. |+.++..
T Consensus       139 ~~~~~~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYrGv-~GS~vA~  217 (851)
T COG1205         139 ISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGV-QGSEVAL  217 (851)
T ss_pred             HHhCCCcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceecccc-chhHHHH
Confidence            3455557999999999988888788889999999999999996532 2   334788999999999998654 6666665


Q ss_pred             HHhhc-------cCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEc-----------CchhhHH
Q psy7789          82 IFSFF-------RGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYV-----------KQEAKIV  143 (197)
Q Consensus        82 i~~~~-------~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~-----------~~~~k~~  143 (197)
                      +++++       +..+|+++.|||+... .+++..+........+.......+......+.-           +...-..
T Consensus       218 llRRL~~~~~~~~~~~q~i~~SAT~~np-~e~~~~l~~~~f~~~v~~~g~~~~~~~~~~~~p~~~~~~~~~r~s~~~~~~  296 (851)
T COG1205         218 LLRRLLRRLRRYGSPLQIICTSATLANP-GEFAEELFGRDFEVPVDEDGSPRGLRYFVRREPPIRELAESIRRSALAELA  296 (851)
T ss_pred             HHHHHHHHHhccCCCceEEEEeccccCh-HHHHHHhcCCcceeeccCCCCCCCceEEEEeCCcchhhhhhcccchHHHHH
Confidence            55544       4588999999999755 556666666655554554444444444444433           1122334


Q ss_pred             HHHHHhhcCCCCEEEEecccccHHHHH----HHHHhCC----CCeEeecCCCChhhhhhhh
Q psy7789         144 YLLECLQKTEPPVLIFAEKKQDVDAIH----EYLLLKG----KPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       144 ~l~~~l~~~~~~~lIF~~s~~~~~~l~----~~L~~~~----~~~~~~h~~~~~~~R~~i~  196 (197)
                      .+...+-.++-++|+|+.+++.++.++    ..+...+    ..+..++|+|..++|.+|+
T Consensus       297 ~~~~~~~~~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie  357 (851)
T COG1205         297 TLAALLVRNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIE  357 (851)
T ss_pred             HHHHHHHHcCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHH
Confidence            555555566779999999999999998    4444445    6789999999999999876

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.73  E-value=2.7e-16  Score=135.28  Aligned_cols=173  Identities=12%  Similarity=0.086  Sum_probs=109.1

Q ss_pred             CCeeEEEEEcCCChHHhH---HHHh-cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhc
Q psy7789          11 IPLRTCLAIGGVPMNQSL---DVIK-KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF   86 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~---~~l~-~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~   86 (197)
                      .|+++++++||.+..+..   +.+. +.++|+|+||+.+.+     ...+++++++|+||+|++... .+   ..+....
T Consensus       311 ~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~-----~~~~~~l~lvVIDEaH~fg~~-qr---~~l~~~~  381 (630)
T TIGR00643       311 LGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE-----KVEFKRLALVIIDEQHRFGVE-QR---KKLREKG  381 (630)
T ss_pred             cCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc-----cccccccceEEEechhhccHH-HH---HHHHHhc
Confidence            489999999998765533   3443 358999999987653     355789999999999996322 12   2222232


Q ss_pred             c--CCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhc---CCCCEEEEec
Q psy7789          87 R--GQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQK---TEPPVLIFAE  161 (197)
Q Consensus        87 ~--~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~  161 (197)
                      .  ..+|++++|||..+.......  ..+.....+.........+...+..  ...+ ..+.+.+..   .+.+++|||+
T Consensus       382 ~~~~~~~~l~~SATp~prtl~l~~--~~~l~~~~i~~~p~~r~~i~~~~~~--~~~~-~~~~~~i~~~l~~g~q~~v~~~  456 (630)
T TIGR00643       382 QGGFTPHVLVMSATPIPRTLALTV--YGDLDTSIIDELPPGRKPITTVLIK--HDEK-DIVYEFIEEEIAKGRQAYVVYP  456 (630)
T ss_pred             ccCCCCCEEEEeCCCCcHHHHHHh--cCCcceeeeccCCCCCCceEEEEeC--cchH-HHHHHHHHHHHHhCCcEEEEEc
Confidence            2  268999999997665443321  1221111111111112234443332  2222 333443332   3568999998


Q ss_pred             cc--------ccHHHHHHHHHhC--CCCeEeecCCCChhhhhhhhC
Q psy7789         162 KK--------QDVDAIHEYLLLK--GKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       162 s~--------~~~~~l~~~L~~~--~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      ..        ..++.+++.|.+.  ++++..+||+|++++|+++++
T Consensus       457 ~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~  502 (630)
T TIGR00643       457 LIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVME  502 (630)
T ss_pred             cccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHH
Confidence            76        4566788888764  788999999999999998864

>KOG0351|consensus

Probab=99.73  E-value=4.9e-17  Score=142.46  Aligned_cols=184  Identities=14%  Similarity=0.181  Sum_probs=136.0

Q ss_pred             CCCCeeEEEEEcCCChHHhHHH---Hh-c--CCcEEEeCchHHHHHH--hcCCccCCC---ccEEEeehhhhhhcCC--C
Q psy7789           9 LPIPLRTCLAIGGVPMNQSLDV---IK-K--GCHMMVATPGRLMDML--DKKMVSLDV---CRYLCLDEADRMVDMG--F   75 (197)
Q Consensus         9 ~~~~i~~~~~~gg~~~~~~~~~---l~-~--~~~Ili~TP~~l~~~l--~~~~~~l~~---l~~vViDEad~l~~~~--~   75 (197)
                      ...+|+...+.++.....+...   +. +  ..+|+..|||++...-  .....++..   +.++||||||++.+|+  |
T Consensus       325 ~~~~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWgHdF  404 (941)
T KOG0351|consen  325 SKKGIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWGHDF  404 (941)
T ss_pred             hhcCcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhhcccc
Confidence            4668999999999887655533   33 3  4799999999998642  333334444   8899999999999996  8


Q ss_pred             HHHHHHHH---hhccCCceEEEEeecCChhHHHHHHHhcC--CCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhh
Q psy7789          76 EEDVRTIF---SFFRGQRQTLLFSATMPKKIQNFARSALV--KPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQ  150 (197)
Q Consensus        76 ~~~i~~i~---~~~~~~~q~i~~SAT~~~~~~~~~~~~~~--~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~  150 (197)
                      ++.++.+.   ..++ ...+++++||.+..+++-+-..++  ++.++   .....++++...+..-........+.+.++
T Consensus       405 Rp~Yk~l~~l~~~~~-~vP~iALTATAT~~v~~DIi~~L~l~~~~~~---~~sfnR~NL~yeV~~k~~~~~~~~~~~~~~  480 (941)
T KOG0351|consen  405 RPSYKRLGLLRIRFP-GVPFIALTATATERVREDVIRSLGLRNPELF---KSSFNRPNLKYEVSPKTDKDALLDILEESK  480 (941)
T ss_pred             cHHHHHHHHHHhhCC-CCCeEEeehhccHHHHHHHHHHhCCCCccee---cccCCCCCceEEEEeccCccchHHHHHHhh
Confidence            88877653   3333 478999999999998887666654  55433   233444555555444433444455555555


Q ss_pred             cC--CCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         151 KT--EPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       151 ~~--~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      ..  ...+||||.++++|+.++..|+..|+++..+|+||++.+|+.|+
T Consensus       481 ~~~~~~s~IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq  528 (941)
T KOG0351|consen  481 LRHPDQSGIIYCLSRKECEQVSAVLRSLGKSAAFYHAGLPPKERETVQ  528 (941)
T ss_pred             hcCCCCCeEEEeCCcchHHHHHHHHHHhchhhHhhhcCCCHHHHHHHH
Confidence            44  34799999999999999999999999999999999999999885

>cd00268 DEADc DEAD-box helicases

Probab=99.71  E-value=2.1e-16  Score=117.86  Aligned_cols=107  Identities=46%  Similarity=0.849  Sum_probs=98.1

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .++++..++||.+..+....+.++++|+|+||+++.+.+.+....+++++++|+||+|.+.+.++...+..++..++...
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~l~~lIvDE~h~~~~~~~~~~~~~~~~~l~~~~  175 (203)
T cd00268          96 TNLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDR  175 (203)
T ss_pred             CCceEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCCChhhCCEEEEeChHHhhccChHHHHHHHHHhCCccc
Confidence            37899999999988877777777899999999999999988888899999999999999998889999999999999899


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEE
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITI  117 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i  117 (197)
                      |++++|||+++++......++.+|..+
T Consensus       176 ~~~~~SAT~~~~~~~~~~~~~~~~~~~  202 (203)
T cd00268         176 QTLLFSATMPKEVRDLARKFLRNPVRI  202 (203)
T ss_pred             EEEEEeccCCHHHHHHHHHHCCCCEEe
Confidence            999999999999999999999998765

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.

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.68  E-value=1.2e-15  Score=137.27  Aligned_cols=157  Identities=17%  Similarity=0.219  Sum_probs=111.8

Q ss_pred             hcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhh-hhhcCCCHHH-HHHHHhhccCCceEEEEeecCChhHHHHHHH
Q psy7789          32 KKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEAD-RMVDMGFEED-VRTIFSFFRGQRQTLLFSATMPKKIQNFARS  109 (197)
Q Consensus        32 ~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad-~l~~~~~~~~-i~~i~~~~~~~~q~i~~SAT~~~~~~~~~~~  109 (197)
                      +.+.+|.++|||.|+..+.... .++++++||||||| +.++.++... +..++... ++.|+++||||++.  ..+.+.
T Consensus       154 s~~T~I~~~TdGiLLr~l~~d~-~L~~~~~IIIDEaHERsL~~D~LL~lLk~il~~r-pdLKlIlmSATld~--~~fa~~  229 (1283)
T TIGR01967       154 SSNTLVKLMTDGILLAETQQDR-FLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRR-PDLKIIITSATIDP--ERFSRH  229 (1283)
T ss_pred             CCCceeeeccccHHHHHhhhCc-ccccCcEEEEcCcchhhccchhHHHHHHHHHhhC-CCCeEEEEeCCcCH--HHHHHH
Confidence            3468999999999999987655 47999999999999 5777776654 56665444 57899999999974  345555


Q ss_pred             hcCCCeEEEeCCCCccCcceeEEEEEcCc------hhhHHHHHHHh----hcCCCCEEEEecccccHHHHHHHHHhCC--
Q psy7789         110 ALVKPITINVGRAGAASMNVVQEVEYVKQ------EAKIVYLLECL----QKTEPPVLIFAEKKQDVDAIHEYLLLKG--  177 (197)
Q Consensus       110 ~~~~~~~i~~~~~~~~~~~i~~~~~~~~~------~~k~~~l~~~l----~~~~~~~lIF~~s~~~~~~l~~~L~~~~--  177 (197)
                      +...| .+.+.....   .+...+.....      .++...+.+.+    ....+++|||+++..+++.+++.|.+.+  
T Consensus       230 F~~ap-vI~V~Gr~~---PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~~~~GdILVFLpg~~EI~~l~~~L~~~~~~  305 (1283)
T TIGR01967       230 FNNAP-IIEVSGRTY---PVEVRYRPLVEEQEDDDLDQLEAILDAVDELFAEGPGDILIFLPGEREIRDAAEILRKRNLR  305 (1283)
T ss_pred             hcCCC-EEEECCCcc---cceeEEecccccccchhhhHHHHHHHHHHHHHhhCCCCEEEeCCCHHHHHHHHHHHHhcCCC
Confidence            54445 455543221   23333333321      12333333333    3445789999999999999999999875  


Q ss_pred             -CCeEeecCCCChhhhhhhh
Q psy7789         178 -KPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       178 -~~~~~~h~~~~~~~R~~i~  196 (197)
                       +.+..+||+|++++|+++.
T Consensus       306 ~~~VlpLhg~Ls~~eQ~~vf  325 (1283)
T TIGR01967       306 HTEILPLYARLSNKEQQRVF  325 (1283)
T ss_pred             CcEEEeccCCCCHHHHHHHh
Confidence             4588999999999998874

This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.67  E-value=4.7e-16  Score=130.67  Aligned_cols=169  Identities=8%  Similarity=0.074  Sum_probs=106.8

Q ss_pred             eeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceE
Q psy7789          13 LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQT   92 (197)
Q Consensus        13 i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~   92 (197)
                      ..+..+.||....       .+++|+|+||+++.....   ..+++++++|+||||++...    .+..++..+++.+|+
T Consensus       187 ~~~~~i~~g~~~~-------~~~~I~VaT~qsl~~~~~---~~~~~~~~iIvDEaH~~~~~----~~~~il~~~~~~~~~  252 (501)
T PHA02558        187 EAMHKIYSGTAKD-------TDAPIVVSTWQSAVKQPK---EWFDQFGMVIVDECHLFTGK----SLTSIITKLDNCKFK  252 (501)
T ss_pred             cceeEEecCcccC-------CCCCEEEeeHHHHhhchh---hhccccCEEEEEchhcccch----hHHHHHHhhhccceE
Confidence            3444566665432       247999999999876432   24689999999999999653    456777778778899


Q ss_pred             EEEeecCChhHHHH--HHHhcCCCeEEEeCC---------------------CCccCcceeEE-----E-EEcCchhhHH
Q psy7789          93 LLFSATMPKKIQNF--ARSALVKPITINVGR---------------------AGAASMNVVQE-----V-EYVKQEAKIV  143 (197)
Q Consensus        93 i~~SAT~~~~~~~~--~~~~~~~~~~i~~~~---------------------~~~~~~~i~~~-----~-~~~~~~~k~~  143 (197)
                      +++|||.+......  ...++. |+...+..                     ...........     + ..+..+.+..
T Consensus       253 lGLTATp~~~~~~~~~~~~~fG-~i~~~v~~~~li~~g~l~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~l~~~~~Rn~  331 (501)
T PHA02558        253 FGLTGSLRDGKANILQYVGLFG-DIFKPVTTSQLMEEGQVTDLKINSIFLRYPDEDRVKLKGEDYQEEIKYITSHTKRNK  331 (501)
T ss_pred             EEEeccCCCccccHHHHHHhhC-CceEEecHHHHHhCCCcCCceEEEEeccCCHHHhhhhcccchHHHHHHHhccHHHHH
Confidence            99999986432111  111111 11111110                     00000000000     0 0112223444


Q ss_pred             HHHHHhh---cCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         144 YLLECLQ---KTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       144 ~l~~~l~---~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .+.+++.   ..+.+++|||++.++++.+++.|++.|.++..+||+|++++|++++
T Consensus       332 ~I~~~~~~~~~~~~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~  387 (501)
T PHA02558        332 WIANLALKLAKKGENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMK  387 (501)
T ss_pred             HHHHHHHHHHhcCCCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHH
Confidence            4444432   3456899999999999999999999999999999999999999865

>KOG0952|consensus

Probab=99.63  E-value=2.3e-15  Score=130.10  Aligned_cols=186  Identities=18%  Similarity=0.170  Sum_probs=129.6

Q ss_pred             cccccC-CCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcC---CccCCCccEEEeehhhhhhcCCCHHHH
Q psy7789           4 PFISAL-PIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKK---MVSLDVCRYLCLDEADRMVDMGFEEDV   79 (197)
Q Consensus         4 ~~~~~~-~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~---~~~l~~l~~vViDEad~l~~~~~~~~i   79 (197)
                      +|.+++ ++||+|.-+||+....+-.  +. .++|||+|||+.--..++.   .--++.+++|||||+|.|-+. .++.+
T Consensus       183 ~~~kkl~~~gi~v~ELTGD~ql~~te--i~-~tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHlLhd~-RGpvl  258 (1230)
T KOG0952|consen  183 KFSKKLAPLGISVRELTGDTQLTKTE--IA-DTQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHLLHDD-RGPVL  258 (1230)
T ss_pred             HHhhhcccccceEEEecCcchhhHHH--HH-hcCEEEecccceeeeeeeeccchhhhhheeeEEeeeehhhcCc-ccchH
Confidence            344444 4799999999997654333  22 2999999999975444332   223688999999999998665 77777


Q ss_pred             HHHHhhcc-------CCceEEEEeecCChhHHHHHHHhcC-C-CeEEEeCCCCccCcceeEEEEEcCch---h-------
Q psy7789          80 RTIFSFFR-------GQRQTLLFSATMPKKIQNFARSALV-K-PITINVGRAGAASMNVVQEVEYVKQE---A-------  140 (197)
Q Consensus        80 ~~i~~~~~-------~~~q~i~~SAT~~~~~~~~~~~~~~-~-~~~i~~~~~~~~~~~i~~~~~~~~~~---~-------  140 (197)
                      +.|..++.       ...+++++|||+| +..+.+ .|++ | +..+...+..-.+..+.+.++.....   .       
T Consensus       259 EtiVaRtlr~vessqs~IRivgLSATlP-N~eDvA-~fL~vn~~~glfsFd~~yRPvpL~~~~iG~k~~~~~~~~~~~d~  336 (1230)
T KOG0952|consen  259 ETIVARTLRLVESSQSMIRIVGLSATLP-NYEDVA-RFLRVNPYAGLFSFDQRYRPVPLTQGFIGIKGKKNRQQKKNIDE  336 (1230)
T ss_pred             HHHHHHHHHHHHhhhhheEEEEeeccCC-CHHHHH-HHhcCCCccceeeecccccccceeeeEEeeecccchhhhhhHHH
Confidence            77765552       4568999999997 444444 4554 3 35666666666677788888776543   1       


Q ss_pred             -hHHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhC----C-------------------CCeEeecCCCChhhhhhhh
Q psy7789         141 -KIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLK----G-------------------KPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       141 -k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~----~-------------------~~~~~~h~~~~~~~R~~i~  196 (197)
                       ..+.+.+.+.+ +.+++|||.++..+...|+.|.+.    |                   ...+.+|+||..++|.-++
T Consensus       337 ~~~~kv~e~~~~-g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~l~E  415 (1230)
T KOG0952|consen  337 VCYDKVVEFLQE-GHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQLVE  415 (1230)
T ss_pred             HHHHHHHHHHHc-CCeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHHHHH
Confidence             22344444443 469999999999999999988643    1                   1256889999999998665

>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases

Probab=99.59  E-value=1.3e-14  Score=104.94  Aligned_cols=95  Identities=23%  Similarity=0.492  Sum_probs=80.0

Q ss_pred             CCeeEEEEEcCCChH-HhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccC-
Q psy7789          11 IPLRTCLAIGGVPMN-QSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRG-   88 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~-~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~-   88 (197)
                      .++++..++||.+.. .+...+.++++|+|+||+++.+++.....++.+++++|+||+|.+..+++...+..+++.+.. 
T Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~iViDE~h~l~~~~~~~~~~~i~~~~~~~  150 (169)
T PF00270_consen   71 TNVRVVLLHGGQSISEDQREVLSNQADILVTTPEQLLDLISNGKINISRLSLIVIDEAHHLSDETFRAMLKSILRRLKRF  150 (169)
T ss_dssp             TTSSEEEESTTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSSTGTTESEEEEETHHHHHHTTHHHHHHHHHHHSHTT
T ss_pred             cccccccccccccccccccccccccccccccCcchhhccccccccccccceeeccCcccccccccHHHHHHHHHHHhcCC
Confidence            468999999998865 455566677999999999999999876557788999999999999998888889999888743 


Q ss_pred             -CceEEEEeecCChhHHH
Q psy7789          89 -QRQTLLFSATMPKKIQN  105 (197)
Q Consensus        89 -~~q~i~~SAT~~~~~~~  105 (197)
                       +.|++++|||+++.+..
T Consensus       151 ~~~~~i~~SAT~~~~~~~  168 (169)
T PF00270_consen  151 KNIQIILLSATLPSNVEK  168 (169)
T ss_dssp             TTSEEEEEESSSTHHHHH
T ss_pred             CCCcEEEEeeCCChhHhh
Confidence             58999999999955543

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. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....

>PRK13766 Hef nuclease; Provisional

Probab=99.55  E-value=3.6e-13  Score=118.89  Aligned_cols=86  Identities=20%  Similarity=0.151  Sum_probs=65.7

Q ss_pred             eeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceE
Q psy7789          13 LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQT   92 (197)
Q Consensus        13 i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~   92 (197)
                      .++..++|+.+.....+.+ ..++|+|+||+.+...+..+.+.+.+++++|+||||++.+......+........+.+++
T Consensus        87 ~~v~~~~g~~~~~~r~~~~-~~~~iiv~T~~~l~~~l~~~~~~~~~~~liVvDEaH~~~~~~~~~~i~~~~~~~~~~~~i  165 (773)
T PRK13766         87 EKIVVFTGEVSPEKRAELW-EKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKNPLV  165 (773)
T ss_pred             ceEEEEeCCCCHHHHHHHH-hCCCEEEECHHHHHHHHHcCCCChhhCcEEEEECCccccccccHHHHHHHHHhcCCCCEE
Confidence            4788888887766444334 458999999999998887788889999999999999987654444444444444457789


Q ss_pred             EEEeecC
Q psy7789          93 LLFSATM   99 (197)
Q Consensus        93 i~~SAT~   99 (197)
                      +++|||.
T Consensus       166 l~lTaTP  172 (773)
T PRK13766        166 LGLTASP  172 (773)
T ss_pred             EEEEcCC
Confidence            9999996

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.55  E-value=1.5e-13  Score=119.06  Aligned_cols=64  Identities=20%  Similarity=0.259  Sum_probs=55.5

Q ss_pred             EEEcCchhhHHHHHHHhhc---CCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         133 VEYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       133 ~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .+++..++|...+.+.+..   .+.|+||||+|++.++.+++.|.+.|+++..+||++++++|..+.
T Consensus       405 ~i~~~~~~K~~al~~~i~~~~~~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~~~~~~~e~~~i~  471 (790)
T PRK09200        405 KVFVTLDEKYKAVIEEVKERHETGRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKNAAKEAQIIA  471 (790)
T ss_pred             eEEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCccHHHHHHHH
Confidence            4456778899999988865   356899999999999999999999999999999999998887653

>KOG0947|consensus

Probab=99.54  E-value=5.7e-14  Score=120.70  Aligned_cols=88  Identities=20%  Similarity=0.233  Sum_probs=77.9

Q ss_pred             EEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEe
Q psy7789          17 LAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFS   96 (197)
Q Consensus        17 ~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~S   96 (197)
                      ++||+..+...       +.++|+|.|.|.+|+.++.--.+++++||+||+|.+.+...+-.+++++-++|...++|++|
T Consensus       369 LlTGDvqinPe-------AsCLIMTTEILRsMLYrgadliRDvE~VIFDEVHYiND~eRGvVWEEViIMlP~HV~~IlLS  441 (1248)
T KOG0947|consen  369 LLTGDVQINPE-------ASCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYINDVERGVVWEEVIIMLPRHVNFILLS  441 (1248)
T ss_pred             eeecceeeCCC-------cceEeehHHHHHHHHhcccchhhccceEEEeeeeecccccccccceeeeeeccccceEEEEe
Confidence            78887765544       88999999999999998877789999999999999999889999999999999999999999


Q ss_pred             ecCChhHHHHHHHhcC
Q psy7789          97 ATMPKKIQNFARSALV  112 (197)
Q Consensus        97 AT~~~~~~~~~~~~~~  112 (197)
                      ||.| +..+++.+..+
T Consensus       442 ATVP-N~~EFA~WIGR  456 (1248)
T KOG0947|consen  442 ATVP-NTLEFADWIGR  456 (1248)
T ss_pred             ccCC-ChHHHHHHhhh
Confidence            9997 55677777665

>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]

Probab=99.54  E-value=3e-13  Score=113.54  Aligned_cols=174  Identities=13%  Similarity=0.094  Sum_probs=122.4

Q ss_pred             CCeeEEEEEcCCChHH---hHHHHhcC-CcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhc
Q psy7789          11 IPLRTCLAIGGVPMNQ---SLDVIKKG-CHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF   86 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~---~~~~l~~~-~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~   86 (197)
                      .||+++.++|......   ..+.+.+| .||+|||     +.+.+....++++.++|+||-|++     +-.-+..+..-
T Consensus       338 ~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGT-----HALiQd~V~F~~LgLVIiDEQHRF-----GV~QR~~L~~K  407 (677)
T COG1200         338 LGIRVALLTGSLKGKARKEILEQLASGEIDIVVGT-----HALIQDKVEFHNLGLVIIDEQHRF-----GVHQRLALREK  407 (677)
T ss_pred             cCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEc-----chhhhcceeecceeEEEEeccccc-----cHHHHHHHHHh
Confidence            4899999999975333   33445444 9999999     777778889999999999999995     65555666555


Q ss_pred             cC-CceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhh-HHHHHHHhhcCCCCEEEEecccc
Q psy7789          87 RG-QRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAK-IVYLLECLQKTEPPVLIFAEKKQ  164 (197)
Q Consensus        87 ~~-~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k-~~~l~~~l~~~~~~~lIF~~s~~  164 (197)
                      .. .+..++||||-  -.+..+-..+.+...-.++.-+.-+..|...++.....++ ...+...+. .+.|+.+-|+-++
T Consensus       408 G~~~Ph~LvMTATP--IPRTLAlt~fgDldvS~IdElP~GRkpI~T~~i~~~~~~~v~e~i~~ei~-~GrQaY~VcPLIe  484 (677)
T COG1200         408 GEQNPHVLVMTATP--IPRTLALTAFGDLDVSIIDELPPGRKPITTVVIPHERRPEVYERIREEIA-KGRQAYVVCPLIE  484 (677)
T ss_pred             CCCCCcEEEEeCCC--chHHHHHHHhccccchhhccCCCCCCceEEEEeccccHHHHHHHHHHHHH-cCCEEEEEecccc
Confidence            55 68899999993  3455555666665444444444444556666665433222 233333333 4568999997654


Q ss_pred             --------cHHHHHHHHHhC--CCCeEeecCCCChhhhhhhhC
Q psy7789         165 --------DVDAIHEYLLLK--GKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       165 --------~~~~l~~~L~~~--~~~~~~~h~~~~~~~R~~i~~  197 (197)
                              .|+++++.|+..  ++++..+||.|+.+++++||.
T Consensus       485 ESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~  527 (677)
T COG1200         485 ESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVME  527 (677)
T ss_pred             ccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHH
Confidence                    566778888854  678999999999999999873

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.53  E-value=6.5e-13  Score=114.43  Aligned_cols=64  Identities=22%  Similarity=0.300  Sum_probs=56.0

Q ss_pred             EEEcCchhhHHHHHHHhhcC---CCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         133 VEYVKQEAKIVYLLECLQKT---EPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       133 ~~~~~~~~k~~~l~~~l~~~---~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .+++...+|...+.+.+++.   +.|+||||+|++.++.++..|.+.|+++..+||++++++|..+.
T Consensus       401 ~i~~~~~~K~~ai~~~i~~~~~~~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~~~E~~ii~  467 (762)
T TIGR03714       401 KIYATLPEKLMATLEDVKEYHETGQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNAAKEAQIIA  467 (762)
T ss_pred             eEEECHHHHHHHHHHHHHHHhhCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCChHHHHHHHH
Confidence            56677888999999888652   45899999999999999999999999999999999999887653

Members of this protein family are homologous to SecA and part of the accessory Sec system. This system, including both five core proteins for export and a variable number of proteins for glycosylation, operates in certain Gram-positive pathogens for the maturation and delivery of serine-rich glycoproteins such as the cell surface glycoprotein GspB in Streptococcus gordonii.

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.52  E-value=6.3e-13  Score=115.60  Aligned_cols=64  Identities=16%  Similarity=0.237  Sum_probs=55.7

Q ss_pred             EEEcCchhhHHHHHHHhhc---CCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         133 VEYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       133 ~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .++....+|...+.+.+.+   .+.|+||||+|++.++.++..|.+.|++...+||++++.+|+.|.
T Consensus       421 ~v~~t~~~k~~av~~~i~~~~~~g~PVLVgt~Sie~sE~ls~~L~~~gi~h~vLnak~~q~Ea~iia  487 (896)
T PRK13104        421 LVYLTQADKFQAIIEDVRECGVRKQPVLVGTVSIEASEFLSQLLKKENIKHQVLNAKFHEKEAQIIA  487 (896)
T ss_pred             eEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHHHHHHcCCCeEeecCCCChHHHHHHH
Confidence            4556677888888877753   356899999999999999999999999999999999999998875

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.51  E-value=3.8e-13  Score=114.44  Aligned_cols=103  Identities=12%  Similarity=0.133  Sum_probs=82.4

Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcC---CCCEEEEecccccHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKT---EPPVLIFAEKKQDVD  167 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~---~~~~lIF~~s~~~~~  167 (197)
                      ++..||||.+.+..++...|..+++.|....  .......+.++++...+|...+.+.++..   +.++||||+|++.++
T Consensus       410 kl~GmTGTa~~~~~El~~~y~l~vv~IPt~k--p~~r~~~~~~v~~t~~~K~~aL~~~i~~~~~~~~pvLIft~t~~~se  487 (656)
T PRK12898        410 RLAGMTGTAREVAGELWSVYGLPVVRIPTNR--PSQRRHLPDEVFLTAAAKWAAVAARVRELHAQGRPVLVGTRSVAASE  487 (656)
T ss_pred             HHhcccCcChHHHHHHHHHHCCCeEEeCCCC--CccceecCCEEEeCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHH
Confidence            4567999999888888888888866654432  22333555567788889999999999763   468999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCChhhhhhh
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~R~~i  195 (197)
                      .+++.|.+.|+++..+||++++.++..+
T Consensus       488 ~L~~~L~~~gi~~~~Lhg~~~~rE~~ii  515 (656)
T PRK12898        488 RLSALLREAGLPHQVLNAKQDAEEAAIV  515 (656)
T ss_pred             HHHHHHHHCCCCEEEeeCCcHHHHHHHH
Confidence            9999999999999999999877776544

>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]

Probab=99.50  E-value=9.2e-13  Score=106.95  Aligned_cols=106  Identities=21%  Similarity=0.149  Sum_probs=83.4

Q ss_pred             eeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceE
Q psy7789          13 LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQT   92 (197)
Q Consensus        13 i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~   92 (197)
                      -.++.++|..+.++....|.. .+|+|+||+-+..-+..+.++++++.++||||||+-.+++..-.+..-.-...+++.+
T Consensus        87 ~~i~~ltGev~p~~R~~~w~~-~kVfvaTPQvveNDl~~Grid~~dv~~lifDEAHRAvGnyAYv~Va~~y~~~~k~~~i  165 (542)
T COG1111          87 DEIAALTGEVRPEEREELWAK-KKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHRAVGNYAYVFVAKEYLRSAKNPLI  165 (542)
T ss_pred             hheeeecCCCChHHHHHHHhh-CCEEEeccHHHHhHHhcCccChHHceEEEechhhhccCcchHHHHHHHHHHhccCceE
Confidence            467789999998888888876 7899999999999999999999999999999999988876666666554555578899


Q ss_pred             EEEeecCCh---hHHHHHHHhcCCCeEEEe
Q psy7789          93 LLFSATMPK---KIQNFARSALVKPITINV  119 (197)
Q Consensus        93 i~~SAT~~~---~~~~~~~~~~~~~~~i~~  119 (197)
                      +++|||-..   .+.++++.+.-+.+.+..
T Consensus       166 lgLTASPGs~~ekI~eV~~nLgIe~vevrT  195 (542)
T COG1111         166 LGLTASPGSDLEKIQEVVENLGIEKVEVRT  195 (542)
T ss_pred             EEEecCCCCCHHHHHHHHHhCCcceEEEec
Confidence            999999643   355556555544444444

>KOG0352|consensus

Probab=99.49  E-value=1.8e-14  Score=114.67  Aligned_cols=159  Identities=17%  Similarity=0.166  Sum_probs=112.7

Q ss_pred             CCcEEEeCchHHHHHHhc----CCccCCCccEEEeehhhhhhcCC--CHHHHHHHHhhc--cCCceEEEEeecCChhHHH
Q psy7789          34 GCHMMVATPGRLMDMLDK----KMVSLDVCRYLCLDEADRMVDMG--FEEDVRTIFSFF--RGQRQTLLFSATMPKKIQN  105 (197)
Q Consensus        34 ~~~Ili~TP~~l~~~l~~----~~~~l~~l~~vViDEad~l~~~~--~~~~i~~i~~~~--~~~~q~i~~SAT~~~~~~~  105 (197)
                      +..++.-|||....-..+    ...+-.-+.|+|+||||++.+||  |++++..+-..-  -+....++++||.++++.+
T Consensus       113 ~~K~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHCVSQWGHDFRPDYL~LG~LRS~~~~vpwvALTATA~~~VqE  192 (641)
T KOG0352|consen  113 TIKMLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHCVSQWGHDFRPDYLTLGSLRSVCPGVPWVALTATANAKVQE  192 (641)
T ss_pred             ceeEEEEchhhhhhhhHHHHHHHHhhhceeeeEEechhhhHhhhccccCcchhhhhhHHhhCCCCceEEeecccChhHHH
Confidence            468999999987654322    33345678899999999999996  888776653222  2477899999999999888


Q ss_pred             HH--HHhcCCCeEEEeCCCCccCcceeEEEEEcC----chhhHHHHHHHhhc----------C----CCCEEEEeccccc
Q psy7789         106 FA--RSALVKPITINVGRAGAASMNVVQEVEYVK----QEAKIVYLLECLQK----------T----EPPVLIFAEKKQD  165 (197)
Q Consensus       106 ~~--~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~----~~~k~~~l~~~l~~----------~----~~~~lIF~~s~~~  165 (197)
                      -+  ..-+++|+-+...+.-  +.+   .|+.+.    -++-+..|.++-..          .    .+..||||.|+..
T Consensus       193 Di~~qL~L~~PVAiFkTP~F--R~N---LFYD~~~K~~I~D~~~~LaDF~~~~LG~~~~~~~~~K~~~GCGIVYCRTR~~  267 (641)
T KOG0352|consen  193 DIAFQLKLRNPVAIFKTPTF--RDN---LFYDNHMKSFITDCLTVLADFSSSNLGKHEKASQNKKTFTGCGIVYCRTRNE  267 (641)
T ss_pred             HHHHHHhhcCcHHhccCcch--hhh---hhHHHHHHHHhhhHhHhHHHHHHHhcCChhhhhcCCCCcCcceEEEeccHHH
Confidence            54  4455677665443222  121   222221    12334444444321          1    2358999999999


Q ss_pred             HHHHHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         166 VDAIHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       166 ~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      ||.++-.|..+|+++..+|+||...||.+|+|
T Consensus       268 cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe  299 (641)
T KOG0352|consen  268 CEQVAIMLEIAGIPAMAYHAGLKKKERTEVQE  299 (641)
T ss_pred             HHHHHHHhhhcCcchHHHhcccccchhHHHHH
Confidence            99999999999999999999999999999874

>PRK09694 helicase Cas3; Provisional

Probab=99.47  E-value=9.7e-13  Score=115.78  Aligned_cols=161  Identities=11%  Similarity=0.048  Sum_probs=96.1

Q ss_pred             CcEEEeCchHHHHHHhcC-CccCCCc----cEEEeehhhhhhcCCCHHHHHHHHhhcc-CCceEEEEeecCChhHHHHHH
Q psy7789          35 CHMMVATPGRLMDMLDKK-MVSLDVC----RYLCLDEADRMVDMGFEEDVRTIFSFFR-GQRQTLLFSATMPKKIQNFAR  108 (197)
Q Consensus        35 ~~Ili~TP~~l~~~l~~~-~~~l~~l----~~vViDEad~l~~~~~~~~i~~i~~~~~-~~~q~i~~SAT~~~~~~~~~~  108 (197)
                      .+|+|||+.+++..+-.. ...++.+    +.|||||+|.+-. .....+..+++.+. ....+|++|||+|+..++...
T Consensus       411 api~V~TiDQlL~a~l~~kh~~lR~~~La~svvIiDEVHAyD~-ym~~lL~~~L~~l~~~g~~vIllSATLP~~~r~~L~  489 (878)
T PRK09694        411 GQIGVCTIDQVLISVLPVKHRFIRGFGLGRSVLIVDEVHAYDA-YMYGLLEAVLKAQAQAGGSVILLSATLPATLKQKLL  489 (878)
T ss_pred             CCEEEcCHHHHHHHHHccchHHHHHHhhccCeEEEechhhCCH-HHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHH
Confidence            699999999999654322 1122222    4899999999833 34445566666553 356799999999988765443


Q ss_pred             H-hcCC-C--------eEEE----------eCCCCc---cCcceeEEEEEcCc-hhhHHHHHHHhh--cCCCCEEEEecc
Q psy7789         109 S-ALVK-P--------ITIN----------VGRAGA---ASMNVVQEVEYVKQ-EAKIVYLLECLQ--KTEPPVLIFAEK  162 (197)
Q Consensus       109 ~-~~~~-~--------~~i~----------~~~~~~---~~~~i~~~~~~~~~-~~k~~~l~~~l~--~~~~~~lIF~~s  162 (197)
                      . +... +        ....          ......   .+..+.-....... ......+..+++  ..+++++|||||
T Consensus       490 ~a~~~~~~~~~~~~YPlvt~~~~~~~~~~~~~~~~~~~~~~~~v~v~~~~~~~~~~~~~~l~~i~~~~~~g~~vLVf~NT  569 (878)
T PRK09694        490 DTYGGHDPVELSSAYPLITWRGVNGAQRFDLSAHPEQLPARFTIQLEPICLADMLPDLTLLQRMIAAANAGAQVCLICNL  569 (878)
T ss_pred             HHhccccccccccccccccccccccceeeeccccccccCcceEEEEEeeccccccCHHHHHHHHHHHHhcCCEEEEEECC
Confidence            3 3211 0        0000          000000   00001100111111 111222222322  234689999999


Q ss_pred             cccHHHHHHHHHhCC---CCeEeecCCCChhhhhhhh
Q psy7789         163 KQDVDAIHEYLLLKG---KPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       163 ~~~~~~l~~~L~~~~---~~~~~~h~~~~~~~R~~i~  196 (197)
                      ++.|+++++.|++.+   .++..+||.+++.+|++++
T Consensus       570 V~~Aq~ly~~L~~~~~~~~~v~llHsrf~~~dR~~~E  606 (878)
T PRK09694        570 VDDAQKLYQRLKELNNTQVDIDLFHARFTLNDRREKE  606 (878)
T ss_pred             HHHHHHHHHHHHhhCCCCceEEEEeCCCCHHHHHHHH
Confidence            999999999999875   6899999999999997654

>KOG0951|consensus

Probab=99.46  E-value=5.3e-13  Score=117.49  Aligned_cols=184  Identities=15%  Similarity=0.161  Sum_probs=125.8

Q ss_pred             cCCCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCC--ccCCCccEEEeehhhhhhcCCCHHHHHHHHhh
Q psy7789           8 ALPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKM--VSLDVCRYLCLDEADRMVDMGFEEDVRTIFSF   85 (197)
Q Consensus         8 ~~~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~--~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~   85 (197)
                      ..+.||+|+-.+|+.....+.  + .+..|+++|||+--...+++.  --..-++++|+||.|.+-++ .++.++.|..+
T Consensus       388 la~~GI~V~ElTgD~~l~~~q--i-eeTqVIV~TPEK~DiITRk~gdraY~qlvrLlIIDEIHLLhDd-RGpvLESIVaR  463 (1674)
T KOG0951|consen  388 LAPLGITVLELTGDSQLGKEQ--I-EETQVIVTTPEKWDIITRKSGDRAYEQLVRLLIIDEIHLLHDD-RGPVLESIVAR  463 (1674)
T ss_pred             ccccCcEEEEecccccchhhh--h-hcceeEEeccchhhhhhcccCchhHHHHHHHHhhhhhhhcccc-cchHHHHHHHH
Confidence            445799999999987644332  1 148899999999755554321  11345678999999988654 67777666544


Q ss_pred             c-------cCCceEEEEeecCChhHHHHHHHhcC-CCeEEEeCCCCccCcceeEEEEEcCchh---hHHHHHHHh-----
Q psy7789          86 F-------RGQRQTLLFSATMPKKIQNFARSALV-KPITINVGRAGAASMNVVQEVEYVKQEA---KIVYLLECL-----  149 (197)
Q Consensus        86 ~-------~~~~q~i~~SAT~~~~~~~~~~~~~~-~~~~i~~~~~~~~~~~i~~~~~~~~~~~---k~~~l~~~l-----  149 (197)
                      +       ....+.+.+|||+|.. .+ +..|++ ++..+.-.+..-.+..+.|+++.+.+..   +++.+.+..     
T Consensus       464 t~r~ses~~e~~RlVGLSATLPNy-~D-V~~Fl~v~~~glf~fd~syRpvPL~qq~Igi~ek~~~~~~qamNe~~yeKVm  541 (1674)
T KOG0951|consen  464 TFRRSESTEEGSRLVGLSATLPNY-ED-VASFLRVDPEGLFYFDSSYRPVPLKQQYIGITEKKPLKRFQAMNEACYEKVL  541 (1674)
T ss_pred             HHHHhhhcccCceeeeecccCCch-hh-hHHHhccCcccccccCcccCcCCccceEeccccCCchHHHHHHHHHHHHHHH
Confidence            4       2367899999999843 22 334444 3344445555566677999999886543   333333332     


Q ss_pred             hcC-CCCEEEEecccccHHHHHHHHHh-------------------------------------CCCCeEeecCCCChhh
Q psy7789         150 QKT-EPPVLIFAEKKQDVDAIHEYLLL-------------------------------------KGKPFFTLKSLKEDQN  191 (197)
Q Consensus       150 ~~~-~~~~lIF~~s~~~~~~l~~~L~~-------------------------------------~~~~~~~~h~~~~~~~  191 (197)
                      +.- +.|+|||+.+++++-+.|..+++                                     .-+.++.+|+||+..+
T Consensus       542 ~~agk~qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLpygfaIHhAGl~R~d  621 (1674)
T KOG0951|consen  542 EHAGKNQVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLPYGFAIHHAGLNRKD  621 (1674)
T ss_pred             HhCCCCcEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhhccceeeccCCCcch
Confidence            322 35899999999999888888762                                     0245889999999999


Q ss_pred             hhhhhC
Q psy7789         192 NQTLEN  197 (197)
Q Consensus       192 R~~i~~  197 (197)
                      |+.+++
T Consensus       622 R~~~Ed  627 (1674)
T KOG0951|consen  622 RELVED  627 (1674)
T ss_pred             HHHHHH
Confidence            998864

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.46  E-value=2.1e-12  Score=110.79  Aligned_cols=61  Identities=16%  Similarity=0.285  Sum_probs=49.5

Q ss_pred             EEEcCchhhHHHHHHHhh---cCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhh
Q psy7789         133 VEYVKQEAKIVYLLECLQ---KTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       133 ~~~~~~~~k~~~l~~~l~---~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i  195 (197)
                      .++....+|...+.+.+.   ..+.|+||||+|+..++.++..|.+.|++...+||+  +.+|++.
T Consensus       382 ~i~~t~~~k~~ai~~~i~~~~~~grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna~--q~~rEa~  445 (745)
T TIGR00963       382 LVYKTEEEKWKAVVDEIKERHAKGQPVLVGTTSVEKSELLSNLLKERGIPHNVLNAK--NHEREAE  445 (745)
T ss_pred             eEEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeCC--hHHHHHH
Confidence            345566778888877664   335689999999999999999999999999999999  6666653

The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus.

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.46  E-value=2.4e-12  Score=111.78  Aligned_cols=61  Identities=16%  Similarity=0.265  Sum_probs=51.6

Q ss_pred             EEEcCchhhHHHHHHHhhc---CCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhh
Q psy7789         133 VEYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       133 ~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i  195 (197)
                      .++....+|...+.+.+.+   .+.|+||||+|+..++.++..|.+.|+++..+||+  +.+|++.
T Consensus       407 ~i~~t~~~K~~aI~~~I~~~~~~grpVLIft~Si~~se~Ls~~L~~~gi~~~vLnak--q~eREa~  470 (830)
T PRK12904        407 LIYKTEKEKFDAVVEDIKERHKKGQPVLVGTVSIEKSELLSKLLKKAGIPHNVLNAK--NHEREAE  470 (830)
T ss_pred             eEEECHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCceEeccCc--hHHHHHH
Confidence            4556778899999988865   34589999999999999999999999999999996  6667654

>KOG0948|consensus

Probab=99.40  E-value=8.2e-13  Score=111.38  Aligned_cols=153  Identities=17%  Similarity=0.196  Sum_probs=108.0

Q ss_pred             EEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEE
Q psy7789          15 TCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLL   94 (197)
Q Consensus        15 ~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~   94 (197)
                      |.+.+|+..+.       ..+..+|+|.|.|.+|+.++.--++.+..||+||+|.+-+...+-.|++-+-.+|++.+.++
T Consensus       199 VGLMTGDVTIn-------P~ASCLVMTTEILRsMLYRGSEvmrEVaWVIFDEIHYMRDkERGVVWEETIIllP~~vr~VF  271 (1041)
T KOG0948|consen  199 VGLMTGDVTIN-------PDASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDKERGVVWEETIILLPDNVRFVF  271 (1041)
T ss_pred             cceeecceeeC-------CCCceeeeHHHHHHHHHhccchHhheeeeEEeeeehhccccccceeeeeeEEeccccceEEE
Confidence            44556655443       23889999999999999999888999999999999999998888889988899999999999


Q ss_pred             EeecCChhHHHHHHHhc---CCCeEEEeCCCCccCcceeEEEEEc---------Cc-----hhhH---------------
Q psy7789          95 FSATMPKKIQNFARSAL---VKPITINVGRAGAASMNVVQEVEYV---------KQ-----EAKI---------------  142 (197)
Q Consensus        95 ~SAT~~~~~~~~~~~~~---~~~~~i~~~~~~~~~~~i~~~~~~~---------~~-----~~k~---------------  142 (197)
                      +|||+| +..+++++..   +.|-.+.-.+-.  +-.+.|+.+..         .+     ++.+               
T Consensus       272 LSATiP-NA~qFAeWI~~ihkQPcHVVYTdyR--PTPLQHyifP~ggdGlylvVDek~~FrednF~~am~~l~~~~~~~~  348 (1041)
T KOG0948|consen  272 LSATIP-NARQFAEWICHIHKQPCHVVYTDYR--PTPLQHYIFPAGGDGLYLVVDEKGKFREDNFQKAMSVLRKAGESDG  348 (1041)
T ss_pred             EeccCC-CHHHHHHHHHHHhcCCceEEeecCC--CCcceeeeecCCCCeeEEEEecccccchHHHHHHHHHhhccCCCcc
Confidence            999997 4566666654   455444433322  22234432221         11     1112               


Q ss_pred             -----------------------HHHHHHhhc-CCCCEEEEecccccHHHHHHHHHhCC
Q psy7789         143 -----------------------VYLLECLQK-TEPPVLIFAEKKQDVDAIHEYLLLKG  177 (197)
Q Consensus       143 -----------------------~~l~~~l~~-~~~~~lIF~~s~~~~~~l~~~L~~~~  177 (197)
                                             ..++..+.. .-.|+|||+-|+++|+.+|..+.+..
T Consensus       349 ~~~~~~k~~kG~~~~~~~~~s~i~kiVkmi~~~~~~PVIvFSFSkkeCE~~Alqm~kld  407 (1041)
T KOG0948|consen  349 KKKANKKGRKGGTGGKGPGDSDIYKIVKMIMERNYLPVIVFSFSKKECEAYALQMSKLD  407 (1041)
T ss_pred             ccccccccccCCcCCCCCCcccHHHHHHHHHhhcCCceEEEEecHhHHHHHHHhhccCc
Confidence                                   222222222 23489999999999999999886543

>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]

Probab=99.29  E-value=3.4e-11  Score=106.24  Aligned_cols=97  Identities=23%  Similarity=0.276  Sum_probs=78.6

Q ss_pred             EEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEE
Q psy7789          16 CLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLF   95 (197)
Q Consensus        16 ~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~   95 (197)
                      .+++|+.+++       +++.++|+|.|.|.+|+..+...+..+..||+||+|.+.+...+..++.++-++|...|++++
T Consensus       194 GL~TGDv~IN-------~~A~clvMTTEILRnMlyrg~~~~~~i~~ViFDEvHyi~D~eRG~VWEE~Ii~lP~~v~~v~L  266 (1041)
T COG4581         194 GLMTGDVSIN-------PDAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIGDRERGVVWEEVIILLPDHVRFVFL  266 (1041)
T ss_pred             cceecceeeC-------CCCceEEeeHHHHHHHhccCcccccccceEEEEeeeeccccccchhHHHHHHhcCCCCcEEEE
Confidence            4566655444       348999999999999999998999999999999999999988999999999999999999999


Q ss_pred             eecCChhHHHHHHHhc---CCCeEEEeC
Q psy7789          96 SATMPKKIQNFARSAL---VKPITINVG  120 (197)
Q Consensus        96 SAT~~~~~~~~~~~~~---~~~~~i~~~  120 (197)
                      |||++.. .++..++.   ..|..+...
T Consensus       267 SATv~N~-~EF~~Wi~~~~~~~~~vv~t  293 (1041)
T COG4581         267 SATVPNA-EEFAEWIQRVHSQPIHVVST  293 (1041)
T ss_pred             eCCCCCH-HHHHHHHHhccCCCeEEEee
Confidence            9999743 45444444   344444443

>KOG0353|consensus

Probab=99.29  E-value=1.6e-11  Score=96.98  Aligned_cols=182  Identities=14%  Similarity=0.200  Sum_probs=128.3

Q ss_pred             CCeeEEEEEcCCChHHhH---HHHhc---CCcEEEeCchHHHHH---Hh--cCCccCCCccEEEeehhhhhhcCC--CHH
Q psy7789          11 IPLRTCLAIGGVPMNQSL---DVIKK---GCHMMVATPGRLMDM---LD--KKMVSLDVCRYLCLDEADRMVDMG--FEE   77 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~---~~l~~---~~~Ili~TP~~l~~~---l~--~~~~~l~~l~~vViDEad~l~~~~--~~~   77 (197)
                      +||...++-...+.++-.   ..+.+   ...++..||+++...   +.  .+.+....++++.+||+|+-.+||  |++
T Consensus       157 lgi~as~lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~~~iaidevhccsqwghdfr~  236 (695)
T KOG0353|consen  157 LGIDASMLNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLIAIDEVHCCSQWGHDFRP  236 (695)
T ss_pred             hCcchhhccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhcceeEEEeecceeehhhhCcccCc
Confidence            466666666555544322   22322   378999999998742   22  256677899999999999999986  777


Q ss_pred             HHH--HHHhhccCCceEEEEeecCChhHHHHHHHhcC--CCeEEEeCCCCccCcceeEEEEEcC--chhhHHHHHHHhhc
Q psy7789          78 DVR--TIFSFFRGQRQTLLFSATMPKKIQNFARSALV--KPITINVGRAGAASMNVVQEVEYVK--QEAKIVYLLECLQK  151 (197)
Q Consensus        78 ~i~--~i~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~--~~~~i~~~~~~~~~~~i~~~~~~~~--~~~k~~~l~~~l~~  151 (197)
                      .+.  .|+++.-++..++.++||.+..+..-++..+.  ....+.   ..-.+++++..+...+  +++=...+..+++.
T Consensus       237 dy~~l~ilkrqf~~~~iigltatatn~vl~d~k~il~ie~~~tf~---a~fnr~nl~yev~qkp~n~dd~~edi~k~i~~  313 (695)
T KOG0353|consen  237 DYKALGILKRQFKGAPIIGLTATATNHVLDDAKDILCIEAAFTFR---AGFNRPNLKYEVRQKPGNEDDCIEDIAKLIKG  313 (695)
T ss_pred             chHHHHHHHHhCCCCceeeeehhhhcchhhHHHHHHhHHhhheee---cccCCCCceeEeeeCCCChHHHHHHHHHHhcc
Confidence            665  45666667889999999999887776665543  112221   2233455665555443  33445666666664


Q ss_pred             C--CCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhh
Q psy7789         152 T--EPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       152 ~--~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i  195 (197)
                      .  +...||||-|+++|+.++..|+++|+.+..+|+.|.+++|..+
T Consensus       314 ~f~gqsgiiyc~sq~d~ekva~alkn~gi~a~~yha~lep~dks~~  359 (695)
T KOG0353|consen  314 DFAGQSGIIYCFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGA  359 (695)
T ss_pred             ccCCCcceEEEeccccHHHHHHHHHhcCccccccccccCccccccc
Confidence            3  3468999999999999999999999999999999999998754

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.28  E-value=3.6e-10  Score=98.21  Aligned_cols=175  Identities=13%  Similarity=0.114  Sum_probs=107.0

Q ss_pred             CeeEEEEEcCCChHHhHHHH----hcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCC-----C-HHHHHH
Q psy7789          12 PLRTCLAIGGVPMNQSLDVI----KKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMG-----F-EEDVRT   81 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l----~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~-----~-~~~i~~   81 (197)
                      |.++..++||.+..++.+.+    .+.++|+||||+.++       ..+++++++|+||+|....++     | ...+. 
T Consensus       215 g~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~-------~p~~~l~liVvDEeh~~s~~~~~~p~y~~r~va-  286 (679)
T PRK05580        215 GAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF-------LPFKNLGLIIVDEEHDSSYKQQEGPRYHARDLA-  286 (679)
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc-------ccccCCCEEEEECCCccccccCcCCCCcHHHHH-
Confidence            67899999998876655443    245899999998764       347899999999999875332     1 11222 


Q ss_pred             HHhhccCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchh-------hHHHHHHHhhc---
Q psy7789          82 IFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEA-------KIVYLLECLQK---  151 (197)
Q Consensus        82 i~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~-------k~~~l~~~l~~---  151 (197)
                      +.+....+.|++++|||.+.+....+..  .....+...............++......       -...+.+.+++   
T Consensus       287 ~~ra~~~~~~~il~SATps~~s~~~~~~--g~~~~~~l~~r~~~~~~p~v~~id~~~~~~~~~~~~ls~~l~~~i~~~l~  364 (679)
T PRK05580        287 VVRAKLENIPVVLGSATPSLESLANAQQ--GRYRLLRLTKRAGGARLPEVEIIDMRELLRGENGSFLSPPLLEAIKQRLE  364 (679)
T ss_pred             HHHhhccCCCEEEEcCCCCHHHHHHHhc--cceeEEEeccccccCCCCeEEEEechhhhhhcccCCCCHHHHHHHHHHHH
Confidence            2333446889999999987665554421  12233333322211111111222221110       11334444443   


Q ss_pred             CCCCEEEEeccc------------------------------------------------------------ccHHHHHH
Q psy7789         152 TEPPVLIFAEKK------------------------------------------------------------QDVDAIHE  171 (197)
Q Consensus       152 ~~~~~lIF~~s~------------------------------------------------------------~~~~~l~~  171 (197)
                      .+.|+|+|+|++                                                            ..++.+++
T Consensus       365 ~g~qvll~~nrrGy~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~l~~~g~G~e~~~e  444 (679)
T PRK05580        365 RGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGSTDLVPVGPGTERLEE  444 (679)
T ss_pred             cCCeEEEEEcCCCCCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCCeeEEeeccHHHHHH
Confidence            345899998852                                                            26778899


Q ss_pred             HHHhC--CCCeEeecCCCCh--hhhhhhh
Q psy7789         172 YLLLK--GKPFFTLKSLKED--QNNQTLE  196 (197)
Q Consensus       172 ~L~~~--~~~~~~~h~~~~~--~~R~~i~  196 (197)
                      .|++.  +.++..+|+++.+  ++|++++
T Consensus       445 ~l~~~fp~~~v~~~~~d~~~~~~~~~~~l  473 (679)
T PRK05580        445 ELAELFPEARILRIDRDTTRRKGALEQLL  473 (679)
T ss_pred             HHHHhCCCCcEEEEeccccccchhHHHHH
Confidence            99887  8899999999974  4566553

>TIGR00595 priA primosomal protein N'

Probab=99.28  E-value=3.7e-10  Score=94.95  Aligned_cols=171  Identities=12%  Similarity=0.114  Sum_probs=104.2

Q ss_pred             CeeEEEEEcCCChHHhHHHHh----cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCC-----C-HHHHHH
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIK----KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMG-----F-EEDVRT   81 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~----~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~-----~-~~~i~~   81 (197)
                      |.+++.++|+.+..+..+.+.    +.++|+|||+..++       ..+++++++||||.|....++     | ...+..
T Consensus        50 ~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsalf-------~p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a~  122 (505)
T TIGR00595        50 GSQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRSALF-------LPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAV  122 (505)
T ss_pred             CCcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChHHHc-------CcccCCCEEEEECCCccccccccCCCCcHHHHHH
Confidence            567889999987655544432    45899999997664       246889999999999886432     1 122333


Q ss_pred             HHhhccCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchh----hHHHHHHHhhc---CCC
Q psy7789          82 IFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEA----KIVYLLECLQK---TEP  154 (197)
Q Consensus        82 i~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~----k~~~l~~~l~~---~~~  154 (197)
                      .... ..+.+++++|||.+.+....+..  +....+...............++....+.    -...+++.+++   .++
T Consensus       123 ~ra~-~~~~~vil~SATPsles~~~~~~--g~~~~~~l~~r~~~~~~p~v~vid~~~~~~~~~ls~~l~~~i~~~l~~g~  199 (505)
T TIGR00595       123 YRAK-KFNCPVVLGSATPSLESYHNAKQ--KAYRLLVLTRRVSGRKPPEVKLIDMRKEPRQSFLSPELITAIEQTLAAGE  199 (505)
T ss_pred             HHHH-hcCCCEEEEeCCCCHHHHHHHhc--CCeEEeechhhhcCCCCCeEEEEecccccccCCccHHHHHHHHHHHHcCC
Confidence            3333 35889999999976554443321  12223333221111111122222222221    12334444432   246


Q ss_pred             CEEEEeccccc------------------------------------------------------------HHHHHHHHH
Q psy7789         155 PVLIFAEKKQD------------------------------------------------------------VDAIHEYLL  174 (197)
Q Consensus       155 ~~lIF~~s~~~------------------------------------------------------------~~~l~~~L~  174 (197)
                      ++|||+|++..                                                            ++.+++.|+
T Consensus       200 qvLvflnrrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~~l~~~g~Gte~~~e~l~  279 (505)
T TIGR00595       200 QSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELA  279 (505)
T ss_pred             cEEEEEeCCcCCCeeEhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCCeeEeecccHHHHHHHHH
Confidence            89999887643                                                            588899998


Q ss_pred             hC--CCCeEeecCCCChhhh
Q psy7789         175 LK--GKPFFTLKSLKEDQNN  192 (197)
Q Consensus       175 ~~--~~~~~~~h~~~~~~~R  192 (197)
                      +.  +.++..+|++++..++
T Consensus       280 ~~fp~~~v~~~d~d~~~~~~  299 (505)
T TIGR00595       280 KLFPGARIARIDSDTTSRKG  299 (505)
T ss_pred             hhCCCCcEEEEecccccCcc
Confidence            87  7899999999988765

All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]

Probab=99.25  E-value=2.2e-10  Score=100.15  Aligned_cols=156  Identities=13%  Similarity=0.125  Sum_probs=111.9

Q ss_pred             CCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhh-hhcCCCHH-HHHHHHhhccCCceEEEEeecCChhHHHHHHHhc
Q psy7789          34 GCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADR-MVDMGFEE-DVRTIFSFFRGQRQTLLFSATMPKKIQNFARSAL  111 (197)
Q Consensus        34 ~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~-l~~~~~~~-~i~~i~~~~~~~~q~i~~SAT~~~~~~~~~~~~~  111 (197)
                      ...|-++|.|.|+..+.+..+ |+.++++||||||. .++.++.- .+..++...+++.++|+||||+.   .+....++
T Consensus       139 ~Trik~mTdGiLlrei~~D~~-Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DLKiIimSATld---~~rfs~~f  214 (845)
T COG1643         139 RTRIKVMTDGILLREIQNDPL-LSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLIIMSATLD---AERFSAYF  214 (845)
T ss_pred             CceeEEeccHHHHHHHhhCcc-cccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCceEEEEecccC---HHHHHHHc
Confidence            467999999999999986665 79999999999995 34433332 34566677777899999999998   44455677


Q ss_pred             CCCeEEEeCCCCccCcceeEEEEEcC-chh-hHH----HHHHHhhcCCCCEEEEecccccHHHHHHHHHh----CCCCeE
Q psy7789         112 VKPITINVGRAGAASMNVVQEVEYVK-QEA-KIV----YLLECLQKTEPPVLIFAEKKQDVDAIHEYLLL----KGKPFF  181 (197)
Q Consensus       112 ~~~~~i~~~~~~~~~~~i~~~~~~~~-~~~-k~~----~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~----~~~~~~  181 (197)
                      .+.-.+.+....-   .+..+|.... .++ -..    .+...+.+..+.+|||.+-..+.+.+++.|.+    ....+.
T Consensus       215 ~~apvi~i~GR~f---PVei~Y~~~~~~d~~l~~ai~~~v~~~~~~~~GdILvFLpG~~EI~~~~~~L~~~~l~~~~~i~  291 (845)
T COG1643         215 GNAPVIEIEGRTY---PVEIRYLPEAEADYILLDAIVAAVDIHLREGSGSILVFLPGQREIERTAEWLEKAELGDDLEIL  291 (845)
T ss_pred             CCCCEEEecCCcc---ceEEEecCCCCcchhHHHHHHHHHHHhccCCCCCEEEECCcHHHHHHHHHHHHhccccCCcEEe
Confidence            7665665543321   2444443332 223 222    33333445567899999999999999999998    357899


Q ss_pred             eecCCCChhhhhhhh
Q psy7789         182 TLKSLKEDQNNQTLE  196 (197)
Q Consensus       182 ~~h~~~~~~~R~~i~  196 (197)
                      ++||.|+.++..++.
T Consensus       292 PLy~~L~~~eQ~rvF  306 (845)
T COG1643         292 PLYGALSAEEQVRVF  306 (845)
T ss_pred             eccccCCHHHHHhhc
Confidence            999999999988874

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.21  E-value=3.1e-10  Score=99.01  Aligned_cols=64  Identities=11%  Similarity=0.241  Sum_probs=54.6

Q ss_pred             EEEcCchhhHHHHHHHhhc---CCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         133 VEYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       133 ~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .++....+|...+.+-+.+   .+.|+||||+|+..++.++..|...|++...+|+++++.+|+.|.
T Consensus       426 ~iy~t~~~K~~Aii~ei~~~~~~GrpVLV~t~sv~~se~ls~~L~~~gi~~~vLnak~~~~Ea~ii~  492 (908)
T PRK13107        426 LVYLTADEKYQAIIKDIKDCRERGQPVLVGTVSIEQSELLARLMVKEKIPHEVLNAKFHEREAEIVA  492 (908)
T ss_pred             cEEeCHHHHHHHHHHHHHHHHHcCCCEEEEeCcHHHHHHHHHHHHHCCCCeEeccCcccHHHHHHHH
Confidence            3445667788887777764   356899999999999999999999999999999999999998875

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.18  E-value=8.5e-10  Score=80.91  Aligned_cols=108  Identities=32%  Similarity=0.578  Sum_probs=87.9

Q ss_pred             eEEEEEcCCChHHhHHHHhcCC-cEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceE
Q psy7789          14 RTCLAIGGVPMNQSLDVIKKGC-HMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQT   92 (197)
Q Consensus        14 ~~~~~~gg~~~~~~~~~l~~~~-~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~   92 (197)
                      ......++.........+..+. +++++||+.+.+.+.........++++|+||+|.+....+...+..++..+++..++
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~~~~~~~~~iIiDE~h~~~~~~~~~~~~~~~~~~~~~~~~  163 (201)
T smart00487       84 KVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQL  163 (201)
T ss_pred             EEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCCcCHhHCCEEEEECHHHHhcCCcHHHHHHHHHhCCccceE
Confidence            3444555555455555565555 999999999999998777778899999999999998766888999999988889999


Q ss_pred             EEEeecCChhHHHHHHHhcCCCeEEEeCC
Q psy7789          93 LLFSATMPKKIQNFARSALVKPITINVGR  121 (197)
Q Consensus        93 i~~SAT~~~~~~~~~~~~~~~~~~i~~~~  121 (197)
                      +++|||.++........++.+...+....
T Consensus       164 v~~saT~~~~~~~~~~~~~~~~~~~~~~~  192 (201)
T smart00487      164 LLLSATPPEEIENLLELFLNDPVFIDVGP  192 (201)
T ss_pred             EEEecCCchhHHHHHHHhcCCCEEEeCCc
Confidence            99999999999999999988777666554

>KOG0950|consensus

Probab=99.16  E-value=1e-10  Score=101.23  Aligned_cols=86  Identities=17%  Similarity=0.179  Sum_probs=64.0

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhc--CCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhc---
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDK--KMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF---   86 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~--~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~---   86 (197)
                      |+.+...+|+.+.....+.    -++-|||.|+-..+++.  +.-.+..+.+||+||.|.+.+.+.+..++.++..+   
T Consensus       297 G~~ve~y~g~~~p~~~~k~----~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~~rg~~lE~~l~k~~y~  372 (1008)
T KOG0950|consen  297 GFPVEEYAGRFPPEKRRKR----ESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDKGRGAILELLLAKILYE  372 (1008)
T ss_pred             CCcchhhcccCCCCCcccc----eeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeeccccchHHHHHHHHHHHh
Confidence            5555555566655544433    67999999999887753  23346889999999999999998888887776554   


Q ss_pred             --cCCceEEEEeecCCh
Q psy7789          87 --RGQRQTLLFSATMPK  101 (197)
Q Consensus        87 --~~~~q~i~~SAT~~~  101 (197)
                        ....|+|.+|||++.
T Consensus       373 ~~~~~~~iIGMSATi~N  389 (1008)
T KOG0950|consen  373 NLETSVQIIGMSATIPN  389 (1008)
T ss_pred             ccccceeEeeeecccCC
Confidence              234579999999973

>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]

Probab=99.15  E-value=1.8e-09  Score=95.86  Aligned_cols=176  Identities=15%  Similarity=0.101  Sum_probs=131.8

Q ss_pred             CCCCeeEEEEEcCCChHHhHHHHh----cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHh
Q psy7789           9 LPIPLRTCLAIGGVPMNQSLDVIK----KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFS   84 (197)
Q Consensus         9 ~~~~i~~~~~~gg~~~~~~~~~l~----~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~   84 (197)
                      .|.+|++..+.-=.+..++.+.++    +..||||||     +-+-++.+.++++.++||||=|++     +-.-++-++
T Consensus       668 ~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGT-----HrLL~kdv~FkdLGLlIIDEEqRF-----GVk~KEkLK  737 (1139)
T COG1197         668 AGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGT-----HRLLSKDVKFKDLGLLIIDEEQRF-----GVKHKEKLK  737 (1139)
T ss_pred             cCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEec-----hHhhCCCcEEecCCeEEEechhhc-----CccHHHHHH
Confidence            456899988877777666665443    358999999     566667888999999999999995     555556666


Q ss_pred             hccCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecccc
Q psy7789          85 FFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQ  164 (197)
Q Consensus        85 ~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~  164 (197)
                      .+..+.-++-+|||-=|....+.-.-+++...|..++...  -.+..++..-+..--...+.+-+.. ++|+..-.|.++
T Consensus       738 ~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R--~pV~T~V~~~d~~~ireAI~REl~R-gGQvfYv~NrV~  814 (1139)
T COG1197         738 ELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDR--LPVKTFVSEYDDLLIREAILRELLR-GGQVFYVHNRVE  814 (1139)
T ss_pred             HHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCCC--cceEEEEecCChHHHHHHHHHHHhc-CCEEEEEecchh
Confidence            7778889999999987888888888888877776665543  2344443322333333444444333 468888889999


Q ss_pred             cHHHHHHHHHhC--CCCeEeecCCCChhhhhhhhC
Q psy7789         165 DVDAIHEYLLLK--GKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       165 ~~~~l~~~L~~~--~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      +.+.+++.|+..  ..++.+.||.|+..+=++||+
T Consensus       815 ~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~  849 (1139)
T COG1197         815 SIEKKAERLRELVPEARIAVAHGQMRERELEEVML  849 (1139)
T ss_pred             hHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHH
Confidence            999999999988  678999999999999888863

>PF06862 DUF1253: Protein of unknown function (DUF1253); InterPro: IPR010678 This family is defined by a C-terminal region of approximately 500 residues, Digestive organ expansion factor (DEF) is thought to Regulate the p53 pathway to control the expansion growth of digestive organs and is required for the expansion growth of intestine, liver and exocrine pancreas, but not endocrine pancreas [, ]

Probab=99.14  E-value=2.9e-09  Score=87.09  Aligned_cols=159  Identities=17%  Similarity=0.214  Sum_probs=113.8

Q ss_pred             CCcEEEeCchHHHHHHhc------CCccCCCccEEEeehhhhhhc--CCCHHHHHHHHhhccC-----------------
Q psy7789          34 GCHMMVATPGRLMDMLDK------KMVSLDVCRYLCLDEADRMVD--MGFEEDVRTIFSFFRG-----------------   88 (197)
Q Consensus        34 ~~~Ili~TP~~l~~~l~~------~~~~l~~l~~vViDEad~l~~--~~~~~~i~~i~~~~~~-----------------   88 (197)
                      ++|||||+|-.|...+..      ..--|+.+..+|+|.||.++.  |.....+-.-+...|+                 
T Consensus       131 ~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~MQNW~Hv~~v~~~lN~~P~~~~~~DfsRVR~w~Ldg  210 (442)
T PF06862_consen  131 SSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLLMQNWEHVLHVFEHLNLQPKKSHDTDFSRVRPWYLDG  210 (442)
T ss_pred             cCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHHHhhHHHHHHHHHHhccCCCCCCCCCHHHHHHHHHcC
Confidence            489999999999988874      122389999999999999874  4333333344444442                 


Q ss_pred             ----CceEEEEeecCChhHHHHHHHhcCCC-eEEEe--CCC-----CccCcceeEEEEEcCc-------hhhHHHHHH-H
Q psy7789          89 ----QRQTLLFSATMPKKIQNFARSALVKP-ITINV--GRA-----GAASMNVVQEVEYVKQ-------EAKIVYLLE-C  148 (197)
Q Consensus        89 ----~~q~i~~SAT~~~~~~~~~~~~~~~~-~~i~~--~~~-----~~~~~~i~~~~~~~~~-------~~k~~~l~~-~  148 (197)
                          -+|++++|+..++++..+....+.|. ..+.+  ...     ......+.|.|...+.       +.+++++.. +
T Consensus       211 ~a~~~RQtii~S~~~~pe~~slf~~~~~N~~G~v~~~~~~~~~g~i~~v~~~v~Q~F~r~~~~s~~~~~d~Rf~yF~~~i  290 (442)
T PF06862_consen  211 QAKYYRQTIIFSSFQTPEINSLFNRHCQNYAGKVRLKPPYEASGVISQVVVQVRQVFQRFDCSSPADDPDARFKYFTKKI  290 (442)
T ss_pred             cchheeEeEEecCCCCHHHHHHHHhhCcCccceEEEeeccccceeeeccccCCceEEEEecCCCcchhhhHHHHHHHHHH
Confidence                15999999999999999999877664 22232  222     2345667787776432       334444443 2


Q ss_pred             ---hh--cCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhh
Q psy7789         149 ---LQ--KTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNN  192 (197)
Q Consensus       149 ---l~--~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R  192 (197)
                         +.  ...+.+|||++|.-+-..+.++|++.++++..+|...++.+-
T Consensus       291 LP~l~~~~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~i  339 (442)
T PF06862_consen  291 LPQLKRDSKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSDI  339 (442)
T ss_pred             HHHhhhccCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHHH
Confidence               22  223689999999999999999999999999999988888773

; GO: 0005634 nucleus

>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]

Probab=99.11  E-value=4.9e-09  Score=81.98  Aligned_cols=160  Identities=19%  Similarity=0.131  Sum_probs=99.5

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCce
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQ   91 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q   91 (197)
                      ++.+.+++|+++..-+       .+++|+|..+|+..-       +..++++|||+|.+.-..-......+-+....+.-
T Consensus       170 ~~~I~~Lyg~S~~~fr-------~plvVaTtHQLlrFk-------~aFD~liIDEVDAFP~~~d~~L~~Av~~ark~~g~  235 (441)
T COG4098         170 NCDIDLLYGDSDSYFR-------APLVVATTHQLLRFK-------QAFDLLIIDEVDAFPFSDDQSLQYAVKKARKKEGA  235 (441)
T ss_pred             cCCeeeEecCCchhcc-------ccEEEEehHHHHHHH-------hhccEEEEeccccccccCCHHHHHHHHHhhcccCc
Confidence            5777788887665433       679999998888763       34569999999998533222222233334445677


Q ss_pred             EEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCc-ceeEEEEEcCchhhH------HHHHHHhhc---CCCCEEEEec
Q psy7789          92 TLLFSATMPKKIQNFARSALVKPITINVGRAGAASM-NVVQEVEYVKQEAKI------VYLLECLQK---TEPPVLIFAE  161 (197)
Q Consensus        92 ~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~-~i~~~~~~~~~~~k~------~~l~~~l~~---~~~~~lIF~~  161 (197)
                      +|++|||-+++...-+..-  +-..+.++......+ .+..++|.-+...++      ..|...++.   .+.|++||++
T Consensus       236 ~IylTATp~k~l~r~~~~g--~~~~~klp~RfH~~pLpvPkf~w~~~~~k~l~r~kl~~kl~~~lekq~~~~~P~liF~p  313 (441)
T COG4098         236 TIYLTATPTKKLERKILKG--NLRILKLPARFHGKPLPVPKFVWIGNWNKKLQRNKLPLKLKRWLEKQRKTGRPVLIFFP  313 (441)
T ss_pred             eEEEecCChHHHHHHhhhC--CeeEeecchhhcCCCCCCCceEEeccHHHHhhhccCCHHHHHHHHHHHhcCCcEEEEec
Confidence            8999999887766544333  222333433222222 233334433333222      245555543   3468999999


Q ss_pred             ccccHHHHHHHHHhC-C-CCeEeecCCC
Q psy7789         162 KKQDVDAIHEYLLLK-G-KPFFTLKSLK  187 (197)
Q Consensus       162 s~~~~~~l~~~L~~~-~-~~~~~~h~~~  187 (197)
                      ++...+.+++.|++. + ..+..+|+..
T Consensus       314 ~I~~~eq~a~~lk~~~~~~~i~~Vhs~d  341 (441)
T COG4098         314 EIETMEQVAAALKKKLPKETIASVHSED  341 (441)
T ss_pred             chHHHHHHHHHHHhhCCccceeeeeccC
Confidence            999999999999654 3 3557788754

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=98.99  E-value=1.1e-08  Score=91.33  Aligned_cols=57  Identities=12%  Similarity=0.158  Sum_probs=50.1

Q ss_pred             hhHHHHHHHhhcC-CCCEEEEecccccHHHHHHHHH-hCCCCeEeecCCCChhhhhhhh
Q psy7789         140 AKIVYLLECLQKT-EPPVLIFAEKKQDVDAIHEYLL-LKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       140 ~k~~~l~~~l~~~-~~~~lIF~~s~~~~~~l~~~L~-~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .|..+|.++++.. +.|+||||+++..+..+++.|+ ..|+++..+||+|++.+|+++.
T Consensus       479 ~Ki~~L~~~L~~~~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~  537 (956)
T PRK04914        479 PRVEWLIDFLKSHRSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAA  537 (956)
T ss_pred             HHHHHHHHHHHhcCCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHH
Confidence            4667888888866 4689999999999999999995 6699999999999999999875

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=98.99  E-value=2.1e-09  Score=94.33  Aligned_cols=161  Identities=20%  Similarity=0.162  Sum_probs=99.4

Q ss_pred             CcEEEeCchHHHHHHhc-CCcc---CCCccEEEeehhhhhhcCCCHHHHHHHHhhcc-CCceEEEEeecCChhHHHHHHH
Q psy7789          35 CHMMVATPGRLMDMLDK-KMVS---LDVCRYLCLDEADRMVDMGFEEDVRTIFSFFR-GQRQTLLFSATMPKKIQNFARS  109 (197)
Q Consensus        35 ~~Ili~TP~~l~~~l~~-~~~~---l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~-~~~q~i~~SAT~~~~~~~~~~~  109 (197)
                      ..+.++||......... ....   .=-...+|+||+|.+.+......+..++..+. -...++++|||+|+...+....
T Consensus       311 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~~~~~~~~~l~~~i~~l~~~g~~ill~SATlP~~~~~~l~~  390 (733)
T COG1203         311 LALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLYADETMLAALLALLEALAEAGVPVLLMSATLPPFLKEKLKK  390 (733)
T ss_pred             ccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHhhcccchHHHHHHHHHHHHhCCCCEEEEecCCCHHHHHHHHH
Confidence            45666666665552211 1111   11235889999999987633333333333332 3778999999999999998888


Q ss_pred             hcCCCeEEEeCCCCc---cCcceeEEEEEcCchhhH-HHHHHHhh---cCCCCEEEEecccccHHHHHHHHHhCCCCeEe
Q psy7789         110 ALVKPITINVGRAGA---ASMNVVQEVEYVKQEAKI-VYLLECLQ---KTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFT  182 (197)
Q Consensus       110 ~~~~~~~i~~~~~~~---~~~~i~~~~~~~~~~~k~-~~l~~~l~---~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~  182 (197)
                      .+.+...+.......   .-..+.+.. .....+.. ........   ..+++++|-|||+..|.++++.|+..+.++..
T Consensus       391 ~~~~~~~~~~~~~~~~~~~e~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~~v~L  469 (733)
T COG1203         391 ALGKGREVVENAKFCPKEDEPGLKRKE-RVDVEDGPQEELIELISEEVKEGKKVLVIVNTVDRAIELYEKLKEKGPKVLL  469 (733)
T ss_pred             HHhcccceecccccccccccccccccc-chhhhhhhhHhhhhcchhhhccCCcEEEEEecHHHHHHHHHHHHhcCCCEEE
Confidence            877655544432100   001111110 01111110 01111111   23468999999999999999999999888999


Q ss_pred             ecCCCChhhhhhhh
Q psy7789         183 LKSLKEDQNNQTLE  196 (197)
Q Consensus       183 ~h~~~~~~~R~~i~  196 (197)
                      +||.+...+|.+.+
T Consensus       470 lHSRf~~~dR~~ke  483 (733)
T COG1203         470 LHSRFTLKDREEKE  483 (733)
T ss_pred             EecccchhhHHHHH
Confidence            99999999999876

>KOG0354|consensus

Probab=98.97  E-value=5.9e-09  Score=89.26  Aligned_cols=91  Identities=18%  Similarity=0.192  Sum_probs=66.4

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCcc-CCCccEEEeehhhhhhcCC-CHHHHHHHHhhccCC
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVS-LDVCRYLCLDEADRMVDMG-FEEDVRTIFSFFRGQ   89 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~-l~~l~~vViDEad~l~~~~-~~~~i~~i~~~~~~~   89 (197)
                      +-++....||.........+-..++|+|+||..|...+...... ++++.++||||||+-.... |-..++..+..-...
T Consensus       132 ~~~~T~~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra~kn~~Y~~Vmr~~l~~k~~~  211 (746)
T KOG0354|consen  132 PYSVTGQLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRTSKNHPYNNIMREYLDLKNQG  211 (746)
T ss_pred             cccceeeccCccCCCchhhhhcccceEEeChHhhhhhcccccccccceEEEEEEcccccccccccHHHHHHHHHHhhhcc
Confidence            44666677774444444455556999999999999988765444 6999999999999988765 444555665555556


Q ss_pred             ceEEEEeecCChh
Q psy7789          90 RQTLLFSATMPKK  102 (197)
Q Consensus        90 ~q~i~~SAT~~~~  102 (197)
                      .|++++|||....
T Consensus       212 ~qILgLTASpG~~  224 (746)
T KOG0354|consen  212 NQILGLTASPGSK  224 (746)
T ss_pred             ccEEEEecCCCcc
Confidence            6999999997644

>TIGR00603 rad25 DNA repair helicase rad25

Probab=98.96  E-value=1.7e-09  Score=93.46  Aligned_cols=153  Identities=12%  Similarity=0.069  Sum_probs=90.1

Q ss_pred             CCcEEEeCchHHHHHHhcC--------CccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEeecCChhHH-
Q psy7789          34 GCHMMVATPGRLMDMLDKK--------MVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQ-  104 (197)
Q Consensus        34 ~~~Ili~TP~~l~~~l~~~--------~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SAT~~~~~~-  104 (197)
                      ..+|+|+|...+.....+.        .+.-....++|+||||++..    .....++..+ .....+++|||...+-. 
T Consensus       343 ~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lpA----~~fr~il~~l-~a~~RLGLTATP~ReD~~  417 (732)
T TIGR00603       343 EAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPA----AMFRRVLTIV-QAHCKLGLTATLVREDDK  417 (732)
T ss_pred             CCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccccH----HHHHHHHHhc-CcCcEEEEeecCcccCCc
Confidence            3789999998775432211        12234678999999999854    3344555555 34567999999752211 


Q ss_pred             -HHHHHhcCCCeEEEeCCC------CccCcceeEEEE---------------------EcCchhhHHHHHHHhhcC---C
Q psy7789         105 -NFARSALVKPITINVGRA------GAASMNVVQEVE---------------------YVKQEAKIVYLLECLQKT---E  153 (197)
Q Consensus       105 -~~~~~~~~~~~~i~~~~~------~~~~~~i~~~~~---------------------~~~~~~k~~~l~~~l~~~---~  153 (197)
                       .....++. |......-.      ...+......+.                     ......|+..+..+++.+   +
T Consensus       418 ~~~L~~LiG-P~vye~~~~eLi~~G~LA~~~~~ev~v~~t~~~~~~yl~~~~~~k~~l~~~np~K~~~~~~Li~~he~~g  496 (732)
T TIGR00603       418 ITDLNFLIG-PKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSRKRMLLYVMNPNKFRACQFLIRFHEQRG  496 (732)
T ss_pred             hhhhhhhcC-CeeeecCHHHHHhCCccccceEEEEEecCCHHHHHHHHHhcchhhhHHhhhChHHHHHHHHHHHHHhhcC
Confidence             11222222 222222110      011100101111                     112334666666666543   4


Q ss_pred             CCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         154 PPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       154 ~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      .++||||++...++.++..|   +  +..+||++++.+|+++.+
T Consensus       497 ~kiLVF~~~~~~l~~~a~~L---~--~~~I~G~ts~~ER~~il~  535 (732)
T TIGR00603       497 DKIIVFSDNVFALKEYAIKL---G--KPFIYGPTSQQERMQILQ  535 (732)
T ss_pred             CeEEEEeCCHHHHHHHHHHc---C--CceEECCCCHHHHHHHHH
Confidence            58999999999999888877   3  467999999999999863

All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=98.96  E-value=6.9e-09  Score=90.79  Aligned_cols=174  Identities=17%  Similarity=0.226  Sum_probs=110.7

Q ss_pred             ccccCC-CCeeEEEEEcCCChHH---hHHHHh-cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCC-----
Q psy7789           5 FISALP-IPLRTCLAIGGVPMNQ---SLDVIK-KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMG-----   74 (197)
Q Consensus         5 ~~~~~~-~~i~~~~~~gg~~~~~---~~~~l~-~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~-----   74 (197)
                      |.+..+ ..+++. .+|..+..+   -.+.+. +..||+|+|..-|...+..  +.-.+.+++.+|++|.++..+     
T Consensus       148 ~~e~~~~~~~~~~-yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~--L~~~kFdfifVDDVDA~LkaskNvDr  224 (1187)
T COG1110         148 FAEDAGSLDVLVV-YHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEE--LSKLKFDFIFVDDVDAILKASKNVDR  224 (1187)
T ss_pred             HHhhcCCcceeee-eccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHH--hcccCCCEEEEccHHHHHhccccHHH
Confidence            444444 334444 555544333   335554 4699999998776665542  111367799999999998532     


Q ss_pred             ------CHHH-------HHHHHhhc------------------------cCCceEEEEeecCChhHHHHHHHhcCCCeEE
Q psy7789          75 ------FEED-------VRTIFSFF------------------------RGQRQTLLFSATMPKKIQNFARSALVKPITI  117 (197)
Q Consensus        75 ------~~~~-------i~~i~~~~------------------------~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i  117 (197)
                            |-+.       +..+...+                        .+..++++.|||..+.-.  -...++.-.-+
T Consensus       225 iL~LlGf~eE~i~~a~~~~~lr~~~~~~~~~~~~~e~~~~~e~~~~~~r~k~g~LvvsSATg~~rg~--R~~LfReLlgF  302 (1187)
T COG1110         225 LLRLLGFSEEVIESAYELIKLRRKLYGEKRAERVREELREVEREREKKRRKLGILVVSSATGKPRGS--RLKLFRELLGF  302 (1187)
T ss_pred             HHHHcCCCHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhccCCceEEEeeccCCCCCc--hHHHHHHHhCC
Confidence                  2111       11111111                        134689999999875532  11233333345


Q ss_pred             EeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecc---cccHHHHHHHHHhCCCCeEeecCC
Q psy7789         118 NVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEK---KQDVDAIHEYLLLKGKPFFTLKSL  186 (197)
Q Consensus       118 ~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s---~~~~~~l~~~L~~~~~~~~~~h~~  186 (197)
                      .++.......++...+...   +-...+.++++..+.-+|||++.   ++.++++++.|+++|+++..+|++
T Consensus       303 evG~~~~~LRNIvD~y~~~---~~~e~~~elvk~lG~GgLIfV~~d~G~e~aeel~e~Lr~~Gi~a~~~~a~  371 (1187)
T COG1110         303 EVGSGGEGLRNIVDIYVES---ESLEKVVELVKKLGDGGLIFVPIDYGREKAEELAEYLRSHGINAELIHAE  371 (1187)
T ss_pred             ccCccchhhhheeeeeccC---ccHHHHHHHHHHhCCCeEEEEEcHHhHHHHHHHHHHHHhcCceEEEeecc
Confidence            5555556667777766555   44555666667776679999999   999999999999999999999985

>KOG0922|consensus

Probab=98.93  E-value=5.9e-08  Score=81.67  Aligned_cols=153  Identities=14%  Similarity=0.127  Sum_probs=102.4

Q ss_pred             CcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhh-hcCC-CHHHHHHHHhhccCCceEEEEeecCChhHHHHHHHhcC
Q psy7789          35 CHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRM-VDMG-FEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALV  112 (197)
Q Consensus        35 ~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l-~~~~-~~~~i~~i~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~  112 (197)
                      ..|.+.|.|.|++-+.... .++..+.+|+||||.= +..+ ..-.++.+++. +++.++|++|||++   .+....|+.
T Consensus       141 TrikymTDG~LLRE~l~Dp-~LskYsvIIlDEAHERsl~TDiLlGlLKki~~~-R~~LklIimSATld---a~kfS~yF~  215 (674)
T KOG0922|consen  141 TRIKYMTDGMLLREILKDP-LLSKYSVIILDEAHERSLHTDILLGLLKKILKK-RPDLKLIIMSATLD---AEKFSEYFN  215 (674)
T ss_pred             eeEEEecchHHHHHHhcCC-ccccccEEEEechhhhhhHHHHHHHHHHHHHhc-CCCceEEEEeeeec---HHHHHHHhc
Confidence            5799999999998776554 3689999999999952 2211 22233343333 34679999999998   556667887


Q ss_pred             CCeEEEeCCCCccCcceeEEEEEcCchhhHHH----HHHHhh-cCCCCEEEEecccccHHHHHHHHHhC----CC----C
Q psy7789         113 KPITINVGRAGAASMNVVQEVEYVKQEAKIVY----LLECLQ-KTEPPVLIFAEKKQDVDAIHEYLLLK----GK----P  179 (197)
Q Consensus       113 ~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~----l~~~l~-~~~~~~lIF~~s~~~~~~l~~~L~~~----~~----~  179 (197)
                      +...+.+....-   .+...|..-+..+-++.    ++++-. +.++-+|||-...++.+.+++.|.+.    +.    -
T Consensus       216 ~a~i~~i~GR~f---PVei~y~~~p~~dYv~a~~~tv~~Ih~~E~~GDILvFLtGqeEIe~~~~~l~e~~~~~~~~~~~~  292 (674)
T KOG0922|consen  216 NAPILTIPGRTF---PVEILYLKEPTADYVDAALITVIQIHLTEPPGDILVFLTGQEEIEAACELLRERAKSLPEDCPEL  292 (674)
T ss_pred             CCceEeecCCCC---ceeEEeccCCchhhHHHHHHHHHHHHccCCCCCEEEEeCCHHHHHHHHHHHHHHhhhccccCcce
Confidence            766666653332   24444444344333322    222222 23457999999999999999999775    22    2


Q ss_pred             eEeecCCCChhhhhhh
Q psy7789         180 FFTLKSLKEDQNNQTL  195 (197)
Q Consensus       180 ~~~~h~~~~~~~R~~i  195 (197)
                      +.++||.|+.++..+|
T Consensus       293 ~lply~aL~~e~Q~rv  308 (674)
T KOG0922|consen  293 ILPLYGALPSEEQSRV  308 (674)
T ss_pred             eeeecccCCHHHhhcc
Confidence            5789999999998876

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=98.88  E-value=2.3e-08  Score=69.09  Aligned_cols=88  Identities=34%  Similarity=0.482  Sum_probs=66.5

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCce
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQ   91 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q   91 (197)
                      ++.+..+.++.....+......+++|+++|++.+..............+++|+||+|.+....................+
T Consensus        57 ~~~~~~~~~~~~~~~~~~~~~~~~~i~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~~~~~~~~~~~  136 (144)
T cd00046          57 GIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLPKDRQ  136 (144)
T ss_pred             CcEEEEEecCcchhHHHHHhcCCCCEEEECcHHHHHHHHcCCcchhcCCEEEEeCHHHHhhcchHHHHHHHHhhCCccce
Confidence            57778888877666555555667999999999999888766555678999999999999876544432233444567889


Q ss_pred             EEEEeecC
Q psy7789          92 TLLFSATM   99 (197)
Q Consensus        92 ~i~~SAT~   99 (197)
                      ++++|||.
T Consensus       137 ~i~~saTp  144 (144)
T cd00046         137 VLLLSATP  144 (144)
T ss_pred             EEEEeccC
Confidence            99999994

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]

Probab=98.83  E-value=1.4e-08  Score=84.41  Aligned_cols=156  Identities=17%  Similarity=0.116  Sum_probs=93.3

Q ss_pred             cEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEeecCChhH---HHHHHHhcC
Q psy7789          36 HMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKI---QNFARSALV  112 (197)
Q Consensus        36 ~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SAT~~~~~---~~~~~~~~~  112 (197)
                      .|.|+|-..+...-....+..++..++|+||||++....+......    +.....++++|||.+..-   .......+.
T Consensus       124 ~i~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~~a~~~~~~~~~----~~~~~~~LGLTATp~R~D~~~~~~l~~~~g  199 (442)
T COG1061         124 KVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAPSYRRILEL----LSAAYPRLGLTATPEREDGGRIGDLFDLIG  199 (442)
T ss_pred             cEEEEEhHHHhhhhhhhhhcccccCEEEEEccccCCcHHHHHHHHh----hhcccceeeeccCceeecCCchhHHHHhcC
Confidence            6999998887775211233345788999999999977655543333    322222899999964211   111111111


Q ss_pred             CCeEEEeCCCC------ccCcceeEEEE------------------------------------EcCchhhHHHHHHHhh
Q psy7789         113 KPITINVGRAG------AASMNVVQEVE------------------------------------YVKQEAKIVYLLECLQ  150 (197)
Q Consensus       113 ~~~~i~~~~~~------~~~~~i~~~~~------------------------------------~~~~~~k~~~l~~~l~  150 (197)
                       +.........      ..+........                                    ....+.+...+..++.
T Consensus       200 -~~vy~~~~~~li~~g~Lap~~~~~i~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  278 (442)
T COG1061         200 -PIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKESARFRELLRARGTLRAENEARRIAIASERKIAAVRGLLL  278 (442)
T ss_pred             -CeEeecCHHHHHhCCCccceEEEEEEeccchHHHHHhhhhhhhhhhhhhhhhhhhHHHHHHHHhhccHHHHHHHHHHHH
Confidence             2222222110      01100000000                                    0011233444444454


Q ss_pred             cC--CCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         151 KT--EPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       151 ~~--~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      .+  ..+++|||.+...+..++..+...|. +..+.|+.++++|+++.+
T Consensus       279 ~~~~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~  326 (442)
T COG1061         279 KHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILE  326 (442)
T ss_pred             HhcCCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHH
Confidence            43  45899999999999999999999888 999999999999998863

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=98.62  E-value=6.3e-08  Score=85.18  Aligned_cols=60  Identities=18%  Similarity=0.419  Sum_probs=51.6

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHH-HHHHhcCCccCC-------CccEEEeehhhhhhc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRL-MDMLDKKMVSLD-------VCRYLCLDEADRMVD   72 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l-~~~l~~~~~~l~-------~l~~vViDEad~l~~   72 (197)
                      .|+++..++||.+...+.+.+  +|||+||||++| +++++.+.+.++       .++++|+||||.++-
T Consensus       162 lGLsV~~i~GG~~~~eq~~~y--~~DIVygTPgRLgfDyLrd~~~~~~~~~~vqr~~~~~IIDEADsmLi  229 (970)
T PRK12899        162 LGLTTGVLVSGSPLEKRKEIY--QCDVVYGTASEFGFDYLRDNSIATRKEEQVGRGFYFAIIDEVDSILI  229 (970)
T ss_pred             cCCeEEEEeCCCCHHHHHHHc--CCCEEEECCChhHHHHhhCCCCCcCHHHhhcccccEEEEechhhhhh
Confidence            479999999999998887665  499999999999 999988766655       558999999999873

>KOG0920|consensus

Probab=98.61  E-value=9.6e-07  Score=77.91  Aligned_cols=157  Identities=15%  Similarity=0.143  Sum_probs=103.2

Q ss_pred             CcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhh-hcCCCHHHHHHHHhhccCCceEEEEeecCChhHHHHHHHhcCC
Q psy7789          35 CHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRM-VDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVK  113 (197)
Q Consensus        35 ~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l-~~~~~~~~i~~i~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~  113 (197)
                      ..++.||-|.|+..+.. .-.+..+..+|+||+|.= .+.+|.-.+...+-..+++.++|+||||+.   .+....|+..
T Consensus       265 t~L~fcTtGvLLr~L~~-~~~l~~vthiivDEVHER~i~~DflLi~lk~lL~~~p~LkvILMSAT~d---ae~fs~YF~~  340 (924)
T KOG0920|consen  265 TRLLFCTTGVLLRRLQS-DPTLSGVTHIIVDEVHERSINTDFLLILLKDLLPRNPDLKVILMSATLD---AELFSDYFGG  340 (924)
T ss_pred             eeEEEecHHHHHHHhcc-CcccccCceeeeeeEEEccCCcccHHHHHHHHhhhCCCceEEEeeeecc---hHHHHHHhCC
Confidence            67999999999999986 445799999999999964 344455554444444457999999999998   5555677766


Q ss_pred             CeEEEeCCCCc----------------cCcceeEEE-----------EEc-CchhhHHHHHHHhh---c--CCCCEEEEe
Q psy7789         114 PITINVGRAGA----------------ASMNVVQEV-----------EYV-KQEAKIVYLLECLQ---K--TEPPVLIFA  160 (197)
Q Consensus       114 ~~~i~~~~~~~----------------~~~~i~~~~-----------~~~-~~~~k~~~l~~~l~---~--~~~~~lIF~  160 (197)
                      ...+++....-                ......+..           ..+ ..+.....+.+++.   .  ..+.+|||-
T Consensus       341 ~pvi~i~grtfpV~~~fLEDil~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~id~~Li~~li~~I~~~~~~GaILVFL  420 (924)
T KOG0920|consen  341 CPVITIPGRTFPVKEYFLEDILSKTGYVSEDDSARSGPERSQLRLARLKLWEPEIDYDLIEDLIEYIDEREFEGAILVFL  420 (924)
T ss_pred             CceEeecCCCcchHHHHHHHHHHHhcccccccccccccccCccccccchhccccccHHHHHHHHHhcccCCCCceEEEEc
Confidence            66666643110                000000000           000 01112222333332   2  246799999


Q ss_pred             cccccHHHHHHHHHhC-------CCCeEeecCCCChhhhhhh
Q psy7789         161 EKKQDVDAIHEYLLLK-------GKPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       161 ~s~~~~~~l~~~L~~~-------~~~~~~~h~~~~~~~R~~i  195 (197)
                      +.......+++.|...       .+-+.++|+.|+..+.+.|
T Consensus       421 PG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~V  462 (924)
T KOG0920|consen  421 PGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAV  462 (924)
T ss_pred             CCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHh
Confidence            9999999999999643       2568899999999887765

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=98.52  E-value=1.6e-06  Score=75.17  Aligned_cols=58  Identities=17%  Similarity=0.200  Sum_probs=49.0

Q ss_pred             hhhHHHHHHHhhc---CCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         139 EAKIVYLLECLQK---TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       139 ~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      ..++..+.+.++.   .+.+++|||+|++.++.+++.|.+.|+++..+||++++.+|.+++
T Consensus       425 ~~qi~~Ll~eI~~~~~~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l  485 (655)
T TIGR00631       425 DGQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEII  485 (655)
T ss_pred             cchHHHHHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHH
Confidence            3455566666653   345899999999999999999999999999999999999998875

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University)

>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]

Probab=98.46  E-value=3.2e-06  Score=70.04  Aligned_cols=101  Identities=18%  Similarity=0.106  Sum_probs=67.8

Q ss_pred             CceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhc---CCCCEEEEeccccc
Q psy7789          89 QRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQD  165 (197)
Q Consensus        89 ~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~  165 (197)
                      ..|++++|||-.+.-.+   ....+-+.-.+.+....-+.+.    .-+.....+.|++-++.   .+.++||=+-|++.
T Consensus       386 ~~q~i~VSATPg~~E~e---~s~~~vveQiIRPTGLlDP~ie----vRp~~~QvdDL~~EI~~r~~~~eRvLVTtLTKkm  458 (663)
T COG0556         386 IPQTIYVSATPGDYELE---QSGGNVVEQIIRPTGLLDPEIE----VRPTKGQVDDLLSEIRKRVAKNERVLVTTLTKKM  458 (663)
T ss_pred             cCCEEEEECCCChHHHH---hccCceeEEeecCCCCCCCcee----eecCCCcHHHHHHHHHHHHhcCCeEEEEeehHHH
Confidence            45999999996543222   2222222222233332222221    12334456666666553   34689999999999


Q ss_pred             HHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         166 VDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       166 ~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      |+.|+++|.+.|+++..+|++...-+|-+|+
T Consensus       459 AEdLT~Yl~e~gikv~YlHSdidTlER~eIi  489 (663)
T COG0556         459 AEDLTEYLKELGIKVRYLHSDIDTLERVEII  489 (663)
T ss_pred             HHHHHHHHHhcCceEEeeeccchHHHHHHHH
Confidence            9999999999999999999999999998875

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=98.38  E-value=5.2e-06  Score=74.91  Aligned_cols=57  Identities=21%  Similarity=0.422  Sum_probs=48.0

Q ss_pred             hhHHHHHHHhh---cCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         140 AKIVYLLECLQ---KTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       140 ~k~~~l~~~l~---~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .|+..|..++.   ..+.++|||+.-......|.+.|...|++...++|+++.++|.+++
T Consensus       471 gKl~lLdkLL~~Lk~~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~I  530 (1033)
T PLN03142        471 GKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASI  530 (1033)
T ss_pred             hHHHHHHHHHHHHHhcCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHH
Confidence            45555555554   3456999999999999999999999999999999999999998875

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=98.37  E-value=2.3e-06  Score=74.47  Aligned_cols=57  Identities=19%  Similarity=0.182  Sum_probs=48.2

Q ss_pred             hhHHHHHHHhhc---CCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         140 AKIVYLLECLQK---TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       140 ~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .++..+.+.++.   .+.+++|||+|++.++.+++.|.+.|+++..+||++++.+|.+++
T Consensus       430 ~q~~~L~~~L~~~~~~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l  489 (652)
T PRK05298        430 GQVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEII  489 (652)
T ss_pred             ccHHHHHHHHHHHHhCCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHH
Confidence            445556665553   346899999999999999999999999999999999999998875

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=98.31  E-value=4.9e-06  Score=72.86  Aligned_cols=104  Identities=12%  Similarity=0.153  Sum_probs=76.5

Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhc---CCCCEEEEecccccHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQDVD  167 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~  167 (197)
                      ++.+||.|...+..++.+.|.-+  .+.++........-..-.++....+|...+.+.+..   .+.|+||||+|+..++
T Consensus       377 kl~GmTGTa~~e~~Ef~~iY~l~--vv~IPtnkp~~r~d~~d~i~~t~~~K~~al~~~i~~~~~~g~pvLI~t~si~~se  454 (796)
T PRK12906        377 KLSGMTGTAKTEEEEFREIYNME--VITIPTNRPVIRKDSPDLLYPTLDSKFNAVVKEIKERHAKGQPVLVGTVAIESSE  454 (796)
T ss_pred             hhhccCCCCHHHHHHHHHHhCCC--EEEcCCCCCeeeeeCCCeEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHH
Confidence            56778899877766676666444  444443332211112234566778899899888854   3468999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .++..|.+.|++...+||++.+.+++.|.
T Consensus       455 ~ls~~L~~~gi~~~~Lna~~~~~Ea~ii~  483 (796)
T PRK12906        455 RLSHLLDEAGIPHAVLNAKNHAKEAEIIM  483 (796)
T ss_pred             HHHHHHHHCCCCeeEecCCcHHHHHHHHH
Confidence            99999999999999999999988887663

>KOG0923|consensus

Probab=98.28  E-value=3.4e-05  Score=65.59  Aligned_cols=154  Identities=16%  Similarity=0.118  Sum_probs=102.6

Q ss_pred             CcEEEeCchHHHHHHhcCCccCCCccEEEeehhhh-hhcCC-CHHHHHHHHhhccCCceEEEEeecCChhHHHHHHHhcC
Q psy7789          35 CHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADR-MVDMG-FEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALV  112 (197)
Q Consensus        35 ~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~-l~~~~-~~~~i~~i~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~  112 (197)
                      .-|-++|.|.|+.-+... .+|...+.+||||||. -+..+ ....+..| .+++++..+++.|||++   .+....|+.
T Consensus       356 TvlKYMTDGmLlREfL~e-pdLasYSViiiDEAHERTL~TDILfgLvKDI-ar~RpdLKllIsSAT~D---AekFS~fFD  430 (902)
T KOG0923|consen  356 TVLKYMTDGMLLREFLSE-PDLASYSVIIVDEAHERTLHTDILFGLVKDI-ARFRPDLKLLISSATMD---AEKFSAFFD  430 (902)
T ss_pred             eeeeeecchhHHHHHhcc-ccccceeEEEeehhhhhhhhhhHHHHHHHHH-HhhCCcceEEeeccccC---HHHHHHhcc
Confidence            346689999998776533 3578999999999995 23322 23334444 34457889999999998   445667777


Q ss_pred             CCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHH-HhhcC----CCCEEEEecccccHHHHHHHHHh----CC-----C
Q psy7789         113 KPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLE-CLQKT----EPPVLIFAEKKQDVDAIHEYLLL----KG-----K  178 (197)
Q Consensus       113 ~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~-~l~~~----~~~~lIF~~s~~~~~~l~~~L~~----~~-----~  178 (197)
                      +.-++.++...   -.+..+|-..++.+-++.-+. +++-+    .+-+|||..-.+..+...+.|.+    .|     +
T Consensus       431 dapIF~iPGRR---yPVdi~Yt~~PEAdYldAai~tVlqIH~tqp~GDILVFltGQeEIEt~~e~l~~~~~~LGski~el  507 (902)
T KOG0923|consen  431 DAPIFRIPGRR---YPVDIFYTKAPEADYLDAAIVTVLQIHLTQPLGDILVFLTGQEEIETVKENLKERCRRLGSKIREL  507 (902)
T ss_pred             CCcEEeccCcc---cceeeecccCCchhHHHHHHhhheeeEeccCCccEEEEeccHHHHHHHHHHHHHHHHHhccccceE
Confidence            76666665333   335566666677665544333 33322    34699999887777666666643    33     3


Q ss_pred             CeEeecCCCChhhhhhhh
Q psy7789         179 PFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       179 ~~~~~h~~~~~~~R~~i~  196 (197)
                      =+.++|+.||.+.+.+|-
T Consensus       508 iv~PiYaNLPselQakIF  525 (902)
T KOG0923|consen  508 IVLPIYANLPSELQAKIF  525 (902)
T ss_pred             EEeeccccCChHHHHhhc
Confidence            477999999999887764

>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional

Probab=98.20  E-value=2.9e-05  Score=71.11  Aligned_cols=65  Identities=18%  Similarity=0.242  Sum_probs=47.6

Q ss_pred             CCcEEEeCchHHHHHHhc-----CCccCCCccEEEeehhhhhhc------C---------CCHHHHHHHHhhccCCceEE
Q psy7789          34 GCHMMVATPGRLMDMLDK-----KMVSLDVCRYLCLDEADRMVD------M---------GFEEDVRTIFSFFRGQRQTL   93 (197)
Q Consensus        34 ~~~Ili~TP~~l~~~l~~-----~~~~l~~l~~vViDEad~l~~------~---------~~~~~i~~i~~~~~~~~q~i   93 (197)
                      ..+|+|+|..++...+..     ....+.+.++||+||||+...      .         .+...++.++.++  +.-.+
T Consensus       511 ~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs~~~d~~~~~~~~~~~~~~~~~~~yr~iL~yF--dA~~I  588 (1123)
T PRK11448        511 ETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGYTLDKEMSEGELQFRDQLDYVSKYRRVLDYF--DAVKI  588 (1123)
T ss_pred             CCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCCCccccccccchhccchhhhHHHHHHHHHhhc--CccEE
Confidence            478999999998876532     124578899999999999631      0         1245677888876  35679


Q ss_pred             EEeecCC
Q psy7789          94 LFSATMP  100 (197)
Q Consensus        94 ~~SAT~~  100 (197)
                      +||||-.
T Consensus       589 GLTATP~  595 (1123)
T PRK11448        589 GLTATPA  595 (1123)
T ss_pred             EEecCCc
Confidence            9999964

>KOG0385|consensus

Probab=98.19  E-value=3.3e-05  Score=66.64  Aligned_cols=55  Identities=22%  Similarity=0.392  Sum_probs=44.1

Q ss_pred             HHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         142 IVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       142 ~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      ++.|+.-|+..+.+||||..=...-.-|-++..-+||....+-|.++.++|..-+
T Consensus       476 LDkLL~~Lk~~GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI  530 (971)
T KOG0385|consen  476 LDKLLPKLKEQGHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAI  530 (971)
T ss_pred             HHHHHHHHHhCCCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCCcHHHHHHH
Confidence            4555556667778999999877777777777778899999999999999998643

>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

Probab=98.18  E-value=1.1e-05  Score=55.30  Aligned_cols=59  Identities=25%  Similarity=0.329  Sum_probs=51.5

Q ss_pred             chhhHHHHHHHhhcC---CCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         138 QEAKIVYLLECLQKT---EPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       138 ~~~k~~~l~~~l~~~---~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .+.|...+.+++...   ++++||||++...++.+++.|.+.+..+..+||++++.+|..+.
T Consensus        10 ~~~k~~~i~~~i~~~~~~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   71 (131)
T cd00079          10 EDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVL   71 (131)
T ss_pred             CHHHHHHHHHHHHhcccCCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHH
Confidence            347888888888755   46899999999999999999999899999999999999998764

>COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=98.05  E-value=4.7e-05  Score=66.26  Aligned_cols=152  Identities=18%  Similarity=0.237  Sum_probs=87.0

Q ss_pred             CcEEEeCchHHHHHHhcC-----CccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEeecCChhHHHHHHH
Q psy7789          35 CHMMVATPGRLMDMLDKK-----MVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARS  109 (197)
Q Consensus        35 ~~Ili~TP~~l~~~l~~~-----~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SAT~~~~~~~~~~~  109 (197)
                      ++|.++|-..+...+...     .+.....+++||||||+-    .....+.|+.++....|.+  +||.......-.-.
T Consensus       257 ~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRg----i~~~~~~I~dYFdA~~~gL--TATP~~~~d~~T~~  330 (875)
T COG4096         257 SEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRG----IYSEWSSILDYFDAATQGL--TATPKETIDRSTYG  330 (875)
T ss_pred             eeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhhh----HHhhhHHHHHHHHHHHHhh--ccCccccccccccc
Confidence            689999999998887654     566788999999999994    5555567777774333333  77765422222222


Q ss_pred             hc-CC------------------C--eEEEe--CCCCccCcc-----------e--eEEEEEcCc-----------hhhH
Q psy7789         110 AL-VK------------------P--ITINV--GRAGAASMN-----------V--VQEVEYVKQ-----------EAKI  142 (197)
Q Consensus       110 ~~-~~------------------~--~~i~~--~~~~~~~~~-----------i--~~~~~~~~~-----------~~k~  142 (197)
                      ++ ..                  +  +.+.+  ......+..           +  ..+.+...+           +.-.
T Consensus       331 ~F~g~Pt~~YsleeAV~DGfLvpy~vi~i~~~~~~~G~~~~~~serek~~g~~i~~dd~~~~~~d~dr~~v~~~~~~~V~  410 (875)
T COG4096         331 FFNGEPTYAYSLEEAVEDGFLVPYKVIRIDTDFDLDGWKPDAGSEREKLQGEAIDEDDQNFEARDFDRTLVIPFRTETVA  410 (875)
T ss_pred             ccCCCcceeecHHHHhhccccCCCCceEEeeeccccCcCcCccchhhhhhccccCcccccccccccchhccccchHHHHH
Confidence            22 22                  2  22222  111111110           1  001110000           1112


Q ss_pred             HHHHHHhhc--C---CCCEEEEecccccHHHHHHHHHhC-----CCCeEeecCCCChhhh
Q psy7789         143 VYLLECLQK--T---EPPVLIFAEKKQDVDAIHEYLLLK-----GKPFFTLKSLKEDQNN  192 (197)
Q Consensus       143 ~~l~~~l~~--~---~~~~lIF~~s~~~~~~l~~~L~~~-----~~~~~~~h~~~~~~~R  192 (197)
                      ..+.+.+..  .   .+|+||||.+..+|+.+.+.|.+.     |--|..+.|+-.+.++
T Consensus       411 r~~~~~l~~~~~g~~~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT~d~~~~q~  470 (875)
T COG4096         411 RELTEYLKRGATGDEIGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITGDAEQAQA  470 (875)
T ss_pred             HHHHHHhccccCCCccCceEEEeeCcHHHHHHHHHHHHhCccccCceEEEEeccchhhHH
Confidence            344444544  2   258999999999999999999765     2336667777665554

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=98.03  E-value=4e-05  Score=68.29  Aligned_cols=101  Identities=10%  Similarity=0.119  Sum_probs=73.7

Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcC---CCCEEEEecccccHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKT---EPPVLIFAEKKQDVD  167 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~---~~~~lIF~~s~~~~~  167 (197)
                      ++-+||.|...+..++...|--+  ++.++........-..-.++....+|...+.+.+...   +.|+||||+|++.++
T Consensus       535 kLaGMTGTA~te~~Ef~~iY~L~--Vv~IPTnrP~~R~D~~d~vy~t~~eK~~Ali~~I~~~~~~grpVLIft~Sve~sE  612 (1025)
T PRK12900        535 KLAGMTGTAETEASEFFEIYKLD--VVVIPTNKPIVRKDMDDLVYKTRREKYNAIVLKVEELQKKGQPVLVGTASVEVSE  612 (1025)
T ss_pred             hhcccCCCChhHHHHHHHHhCCc--EEECCCCCCcceecCCCeEecCHHHHHHHHHHHHHHHhhCCCCEEEEeCcHHHHH
Confidence            45678888887777887777544  3444433322221222355678888999999988643   568999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCChhhhhhh
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~R~~i  195 (197)
                      .++..|...|++...+|+  .+.+|++.
T Consensus       613 ~Ls~~L~~~gI~h~vLna--kq~~REa~  638 (1025)
T PRK12900        613 TLSRMLRAKRIAHNVLNA--KQHDREAE  638 (1025)
T ss_pred             HHHHHHHHcCCCceeecC--CHHHhHHH
Confidence            999999999999999997  45566653

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=97.99  E-value=0.00017  Score=63.75  Aligned_cols=54  Identities=19%  Similarity=0.172  Sum_probs=44.5

Q ss_pred             EEEcCchhhHHHHHHHhhc---CCCCEEEEecccccHHHHHHHHHhCCCCeEeecCC
Q psy7789         133 VEYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSL  186 (197)
Q Consensus       133 ~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~  186 (197)
                      .++....+|...+.+-+.+   .+.|+||-|.|++.++.++..|.+.|++..++++.
T Consensus       416 ~vy~t~~~K~~Ai~~ei~~~~~~GrPVLIgT~SVe~SE~ls~~L~~~gi~h~vLNAk  472 (939)
T PRK12902        416 QVYKTEIAKWRAVANETAEMHKQGRPVLVGTTSVEKSELLSALLQEQGIPHNLLNAK  472 (939)
T ss_pred             eEEcCHHHHHHHHHHHHHHHHhCCCCEEEeeCCHHHHHHHHHHHHHcCCchheeeCC
Confidence            3445667788888776653   35689999999999999999999999998888886

>KOG0925|consensus

Probab=97.97  E-value=0.00015  Score=59.94  Aligned_cols=138  Identities=12%  Similarity=0.081  Sum_probs=87.7

Q ss_pred             EeCchHHHHHHhcC--------CccCCCccEEEeehhhhh-hcC-CCHHHHHHHHhhccCCceEEEEeecCChhHHHHHH
Q psy7789          39 VATPGRLMDMLDKK--------MVSLDVCRYLCLDEADRM-VDM-GFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFAR  108 (197)
Q Consensus        39 i~TP~~l~~~l~~~--------~~~l~~l~~vViDEad~l-~~~-~~~~~i~~i~~~~~~~~q~i~~SAT~~~~~~~~~~  108 (197)
                      .+||..++.++..+        .-.++..+.+|+||||.= +.. -..-.++.++..- ++.+++++|||+.   ....+
T Consensus       132 C~~~~T~Lky~tDgmLlrEams~p~l~~y~viiLDeahERtlATDiLmGllk~v~~~r-pdLk~vvmSatl~---a~Kfq  207 (699)
T KOG0925|consen  132 CTSPNTLLKYCTDGMLLREAMSDPLLGRYGVIILDEAHERTLATDILMGLLKEVVRNR-PDLKLVVMSATLD---AEKFQ  207 (699)
T ss_pred             cCChhHHHHHhcchHHHHHHhhCcccccccEEEechhhhhhHHHHHHHHHHHHHHhhC-CCceEEEeecccc---hHHHH
Confidence            45677777655432        122788999999999952 221 1333455555554 4889999999987   45566


Q ss_pred             HhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHH----hh-cCCCCEEEEecccccHHHHHHHHHhC----C--
Q psy7789         109 SALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLEC----LQ-KTEPPVLIFAEKKQDVDAIHEYLLLK----G--  177 (197)
Q Consensus       109 ~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~----l~-~~~~~~lIF~~s~~~~~~l~~~L~~~----~--  177 (197)
                      .|+.++-.+.++..+  +  +..+|....+.+.+..-+..    -. +.++-+++|....++.+...+.+...    |  
T Consensus       208 ~yf~n~Pll~vpg~~--P--vEi~Yt~e~erDylEaairtV~qih~~ee~GDilvFLtgeeeIe~aC~~i~re~~~L~~~  283 (699)
T KOG0925|consen  208 RYFGNAPLLAVPGTH--P--VEIFYTPEPERDYLEAAIRTVLQIHMCEEPGDILVFLTGEEEIEDACRKISREVDNLGPQ  283 (699)
T ss_pred             HHhCCCCeeecCCCC--c--eEEEecCCCChhHHHHHHHHHHHHHhccCCCCEEEEecCHHHHHHHHHHHHHHHHhhccc
Confidence            888888888887622  2  33355545555544433333    22 23568999999987777777766532    2  


Q ss_pred             ---CCeEeec
Q psy7789         178 ---KPFFTLK  184 (197)
Q Consensus       178 ---~~~~~~h  184 (197)
                         .+|.++|
T Consensus       284 ~g~l~v~PLy  293 (699)
T KOG0925|consen  284 VGPLKVVPLY  293 (699)
T ss_pred             cCCceEEecC
Confidence               4677777

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=97.93  E-value=0.0002  Score=63.54  Aligned_cols=59  Identities=15%  Similarity=0.252  Sum_probs=47.4

Q ss_pred             EEEcCchhhHHHHHHHhhc---CCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhh
Q psy7789         133 VEYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQN  191 (197)
Q Consensus       133 ~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~  191 (197)
                      .++....+|...+.+-+..   .+.|+||-+.|++.++.++..|++.|++..++++.-...|
T Consensus       426 ~vy~t~~eK~~Ai~~ei~~~~~~GrPVLVGT~SVe~SE~ls~~L~~~gi~h~VLNAk~~~~E  487 (913)
T PRK13103        426 LVYLTAEEKYAAIITDIKECMALGRPVLVGTATIETSEHMSNLLKKEGIEHKVLNAKYHEKE  487 (913)
T ss_pred             eEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCCHHHHHHHHHHHHHcCCcHHHhccccchhH
Confidence            4566777888888877764   3568999999999999999999999998877777654443

>KOG0924|consensus

Probab=97.90  E-value=0.00046  Score=59.25  Aligned_cols=153  Identities=15%  Similarity=0.128  Sum_probs=88.2

Q ss_pred             CcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhh-hcCC-CHHHHHHHHhhccCCceEEEEeecCChhHHHHHHHhcC
Q psy7789          35 CHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRM-VDMG-FEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALV  112 (197)
Q Consensus        35 ~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l-~~~~-~~~~i~~i~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~  112 (197)
                      ..|-..|.|.|+.-.-.. -.|.+...+|+||||.= ++.+ ..-.++.++.. +.+..+|+.|||+.  .+. ...|+.
T Consensus       446 T~IkymTDGiLLrEsL~d-~~L~kYSviImDEAHERslNtDilfGllk~~lar-RrdlKliVtSATm~--a~k-f~nfFg  520 (1042)
T KOG0924|consen  446 TKIKYMTDGILLRESLKD-RDLDKYSVIIMDEAHERSLNTDILFGLLKKVLAR-RRDLKLIVTSATMD--AQK-FSNFFG  520 (1042)
T ss_pred             eeEEEeccchHHHHHhhh-hhhhheeEEEechhhhcccchHHHHHHHHHHHHh-hccceEEEeecccc--HHH-HHHHhC
Confidence            457788998888644322 23678899999999953 3322 12222333222 35889999999997  333 445555


Q ss_pred             CCeEEEeCCCCccCcceeEEEEEcCchhhH-HHHHHHhhc----CCCCEEEEecccccHHHHHHHHHh----C------C
Q psy7789         113 KPITINVGRAGAASMNVVQEVEYVKQEAKI-VYLLECLQK----TEPPVLIFAEKKQDVDAIHEYLLL----K------G  177 (197)
Q Consensus       113 ~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~-~~l~~~l~~----~~~~~lIF~~s~~~~~~l~~~L~~----~------~  177 (197)
                      +.-.+.++...-   .+...+...+-++-+ ..+-..+.-    ..+-.|||..-.+..+-....++.    .      +
T Consensus       521 n~p~f~IpGRTy---PV~~~~~k~p~eDYVeaavkq~v~Ihl~~~~GdilIfmtGqediE~t~~~i~~~l~ql~~~~~~~  597 (1042)
T KOG0924|consen  521 NCPQFTIPGRTY---PVEIMYTKTPVEDYVEAAVKQAVQIHLSGPPGDILIFMTGQEDIECTCDIIKEKLEQLDSAPTTD  597 (1042)
T ss_pred             CCceeeecCCcc---ceEEEeccCchHHHHHHHHhhheEeeccCCCCCEEEecCCCcchhHHHHHHHHHHHhhhcCCCCc
Confidence            433333332221   122222223323222 222233321    135699999887766665555432    2      5


Q ss_pred             CCeEeecCCCChhhhhhh
Q psy7789         178 KPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       178 ~~~~~~h~~~~~~~R~~i  195 (197)
                      ..+.++++.|+++-+.+|
T Consensus       598 L~vlpiYSQLp~dlQ~ki  615 (1042)
T KOG0924|consen  598 LAVLPIYSQLPADLQAKI  615 (1042)
T ss_pred             eEEEeehhhCchhhhhhh
Confidence            789999999999877665

>KOG4150|consensus

Probab=97.87  E-value=0.00016  Score=60.85  Aligned_cols=175  Identities=5%  Similarity=-0.063  Sum_probs=110.3

Q ss_pred             EcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcC----CccCCCccEEEeehhhhhhcCCCHHHHH----HHHhhc----
Q psy7789          19 IGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKK----MVSLDVCRYLCLDEADRMVDMGFEEDVR----TIFSFF----   86 (197)
Q Consensus        19 ~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~----~~~l~~l~~vViDEad~l~~~~~~~~i~----~i~~~~----   86 (197)
                      +.|.+-.........+..++.+.|..+....--+    ...+-++.++++||+|.+... +....+    .+.+.+    
T Consensus       369 ~D~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~~-~~~~~~~~~R~L~~L~~~F~  447 (1034)
T KOG4150|consen  369 SDKLSETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLFP-TKALAQDQLRALSDLIKGFE  447 (1034)
T ss_pred             ccCCCchhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeeecc-hhhHHHHHHHHHHHHHHHHH
Confidence            3444455555566778999999998888765322    222566789999999988654 444333    333332    


Q ss_pred             -cCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEE-EEcC-----c---hhhHHHHHHHh---hcCC
Q psy7789          87 -RGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEV-EYVK-----Q---EAKIVYLLECL---QKTE  153 (197)
Q Consensus        87 -~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~-~~~~-----~---~~k~~~l~~~l---~~~~  153 (197)
                       ..+.|++-.|||+...++-....+.-+-..+...+...  ..-++.+ |.-+     +   +.+....-+++   -.++
T Consensus       448 ~~~~~~~~~~~~~~K~~~~~~~~~~~~~E~~Li~~DGSP--s~~K~~V~WNP~~~P~~~~~~~~~i~E~s~~~~~~i~~~  525 (1034)
T KOG4150|consen  448 ASINMGVYDGDTPYKDRTRLRSELANLSELELVTIDGSP--SSEKLFVLWNPSAPPTSKSEKSSKVVEVSHLFAEMVQHG  525 (1034)
T ss_pred             hhcCcceEeCCCCcCCHHHHHHHhcCCcceEEEEecCCC--CccceEEEeCCCCCCcchhhhhhHHHHHHHHHHHHHHcC
Confidence             34779999999998888887777766554433332222  2223322 2211     1   22222222222   2345


Q ss_pred             CCEEEEecccccHHHHHHHHHhC----CC----CeEeecCCCChhhhhhhh
Q psy7789         154 PPVLIFAEKKQDVDAIHEYLLLK----GK----PFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       154 ~~~lIF~~s~~~~~~l~~~L~~~----~~----~~~~~h~~~~~~~R~~i~  196 (197)
                      -++|.||++++-|+-+....++.    |-    .+..+.||-+.++|.+|+
T Consensus       526 ~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE  576 (1034)
T KOG4150|consen  526 LRCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIE  576 (1034)
T ss_pred             CcEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHH
Confidence            69999999999999877665442    31    466788999999999986

>KOG2340|consensus

Probab=97.87  E-value=1.8e-05  Score=65.61  Aligned_cols=155  Identities=20%  Similarity=0.282  Sum_probs=100.2

Q ss_pred             CCcEEEeCchHHHHHHhcC-----Ccc-CCCccEEEeehhhhhhcCCCHHHHHHHHhhc---cCC---------------
Q psy7789          34 GCHMMVATPGRLMDMLDKK-----MVS-LDVCRYLCLDEADRMVDMGFEEDVRTIFSFF---RGQ---------------   89 (197)
Q Consensus        34 ~~~Ili~TP~~l~~~l~~~-----~~~-l~~l~~vViDEad~l~~~~~~~~i~~i~~~~---~~~---------------   89 (197)
                      ..|||||+|-.|.-++.+.     .++ ++.+.++|||.||.++..+ -+++..|+..+   |..               
T Consensus       385 ~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l~QN-wEhl~~ifdHLn~~P~k~h~~DfSRVR~wyL~  463 (698)
T KOG2340|consen  385 KSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIMLMQN-WEHLLHIFDHLNLQPSKQHDVDFSRVRMWYLD  463 (698)
T ss_pred             ccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHHHhh-HHHHHHHHHHhhcCcccccCCChhheehheec
Confidence            4899999999998888632     222 7889999999999997532 23444444443   322               


Q ss_pred             ------ceEEEEeecCChhHHHHHHHhcCCCeE-EEeCC------CCccCcceeEEEEE--cC-----chhhHHHHHHHh
Q psy7789          90 ------RQTLLFSATMPKKIQNFARSALVKPIT-INVGR------AGAASMNVVQEVEY--VK-----QEAKIVYLLECL  149 (197)
Q Consensus        90 ------~q~i~~SAT~~~~~~~~~~~~~~~~~~-i~~~~------~~~~~~~i~~~~~~--~~-----~~~k~~~l~~~l  149 (197)
                            +|+++||+-..+....+...++.|... +....      -....-.+.|.|..  +.     ...++.++.+-+
T Consensus       464 ~qsr~~rQtl~Fs~y~~~~~nS~fn~~c~N~~Gkv~~~~~~~~gsi~~v~~~l~Qvf~ri~~~si~~~~D~RFkyFv~~I  543 (698)
T KOG2340|consen  464 GQSRYFRQTLLFSRYSHPLFNSLFNQYCQNMAGKVKARNLQSGGSISNVGIPLCQVFQRIEVKSIIETPDARFKYFVDKI  543 (698)
T ss_pred             cHHHHHHHHHHHHhhccHHHHHHHHHhhhhhcceeeeccccCCCchhhccchhhhhhhheeccCcccCchHHHHHHHHhh
Confidence                  388999998888888888888876532 21111      11111223333322  21     245666666554


Q ss_pred             h-cCC----CCEEEEecccccHHHHHHHHHhCCCCeEeecCCCCh
Q psy7789         150 Q-KTE----PPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKED  189 (197)
Q Consensus       150 ~-~~~----~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~  189 (197)
                      . +..    ..+|||.++..+-..+.+++++.+++...+|.-.++
T Consensus       544 mPq~~k~t~s~~LiyIPSYfDFVRvRNy~K~e~i~F~~i~EYssk  588 (698)
T KOG2340|consen  544 MPQLIKRTESGILIYIPSYFDFVRVRNYMKKEEISFVMINEYSSK  588 (698)
T ss_pred             chhhcccccCceEEEecchhhHHHHHHHhhhhhcchHHHhhhhhH
Confidence            3 332    357999999999999999999988776666644433

>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family

Probab=97.75  E-value=0.001  Score=58.34  Aligned_cols=61  Identities=15%  Similarity=0.141  Sum_probs=39.3

Q ss_pred             CcEEEeCchHHHHHHhcC--CccCCCcc-EEEeehhhhhhcCCCHHHHHHHH-hhccCCceEEEEeecCC
Q psy7789          35 CHMMVATPGRLMDMLDKK--MVSLDVCR-YLCLDEADRMVDMGFEEDVRTIF-SFFRGQRQTLLFSATMP  100 (197)
Q Consensus        35 ~~Ili~TP~~l~~~l~~~--~~~l~~l~-~vViDEad~l~~~~~~~~i~~i~-~~~~~~~q~i~~SAT~~  100 (197)
                      .+|+|+|..++...+...  .+...+-+ +||+||||+....    .+...+ +.+ ++..+++||||--
T Consensus       339 ~~iivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHrs~~~----~~~~~l~~~~-p~a~~lGfTaTP~  403 (667)
T TIGR00348       339 GGIIITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHRSQYG----ELAKNLKKAL-KNASFFGFTGTPI  403 (667)
T ss_pred             CCEEEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCccccch----HHHHHHHhhC-CCCcEEEEeCCCc
Confidence            689999999998754321  11111122 8999999997432    233333 445 4678999999963

Members of this family are assumed to differ from each other in DNA site specificity.

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3

Probab=97.54  E-value=0.00028  Score=51.15  Aligned_cols=64  Identities=16%  Similarity=0.109  Sum_probs=45.0

Q ss_pred             hcCCcEEEeCchHHHHHHhcC-----------CccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEeecCC
Q psy7789          32 KKGCHMMVATPGRLMDMLDKK-----------MVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMP  100 (197)
Q Consensus        32 ~~~~~Ili~TP~~l~~~l~~~-----------~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SAT~~  100 (197)
                      ....++++.|..++.......           .......+++|+||||++....   .++.++.  .+...++.+|||..
T Consensus       109 ~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI~DEaH~~~~~~---~~~~i~~--~~~~~~l~lTATp~  183 (184)
T PF04851_consen  109 NNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVIIDEAHHYPSDS---SYREIIE--FKAAFILGLTATPF  183 (184)
T ss_dssp             BSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEEEEETGGCTHHHH---HHHHHHH--SSCCEEEEEESS-S
T ss_pred             cccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEEEEehhhhcCCHH---HHHHHHc--CCCCeEEEEEeCcc
Confidence            346899999999999886531           1234577899999999985432   1455555  46778999999964

1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B ....

>KOG0951|consensus

Probab=97.51  E-value=0.0011  Score=60.47  Aligned_cols=151  Identities=12%  Similarity=0.231  Sum_probs=93.3

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHH------HHHHHHh
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEE------DVRTIFS   84 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~------~i~~i~~   84 (197)
                      .|+++..++|..+..-..   ....+|+|+||++.-.+ .    +...++++|.||+|.+.+. ++.      .++.|-.
T Consensus      1214 ~G~~~~~l~ge~s~~lkl---~~~~~vii~tpe~~d~l-q----~iQ~v~l~i~d~lh~igg~-~g~v~evi~S~r~ia~ 1284 (1674)
T KOG0951|consen 1214 LGLRIVKLTGETSLDLKL---LQKGQVIISTPEQWDLL-Q----SIQQVDLFIVDELHLIGGV-YGAVYEVICSMRYIAS 1284 (1674)
T ss_pred             cCceEEecCCccccchHH---hhhcceEEechhHHHHH-h----hhhhcceEeeehhhhhccc-CCceEEEEeeHHHHHH
Confidence            589999999987765432   22378999999998766 2    5678899999999999753 221      1666667


Q ss_pred             hccCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCC-ccCcceeEEEEEcC-chhhHHHHH----HHhh---cCCCC
Q psy7789          85 FFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAG-AASMNVVQEVEYVK-QEAKIVYLL----ECLQ---KTEPP  155 (197)
Q Consensus        85 ~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~-~~~~~i~~~~~~~~-~~~k~~~l~----~~l~---~~~~~  155 (197)
                      .+-+..+++++|..+.. .+..  ..+.....+...+.. ..|-.+.-+.+... .+.....+.    ..+.   ..+++
T Consensus      1285 q~~k~ir~v~ls~~lan-a~d~--ig~s~~~v~Nf~p~~R~~Pl~i~i~~~~~~~~~~~~~am~~~~~~ai~~~a~~~k~ 1361 (1674)
T KOG0951|consen 1285 QLEKKIRVVALSSSLAN-ARDL--IGASSSGVFNFSPSVRPVPLEIHIQSVDISHFESRMLAMTKPTYTAIVRHAGNRKP 1361 (1674)
T ss_pred             HHHhheeEEEeehhhcc-chhh--ccccccceeecCcccCCCceeEEEEEeccchhHHHHHHhhhhHHHHHHHHhcCCCC
Confidence            77778899999988763 2333  222333333333332 22222222222222 222222211    1222   23568


Q ss_pred             EEEEecccccHHHHHHHH
Q psy7789         156 VLIFAEKKQDVDAIHEYL  173 (197)
Q Consensus       156 ~lIF~~s~~~~~~l~~~L  173 (197)
                      ++||+++++.|..++.-|
T Consensus      1362 ~~vf~p~rk~~~~~a~~~ 1379 (1674)
T KOG0951|consen 1362 AIVFLPTRKHARLVAVDL 1379 (1674)
T ss_pred             eEEEeccchhhhhhhhcc
Confidence            999999999999988755

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=97.50  E-value=0.0042  Score=54.72  Aligned_cols=153  Identities=13%  Similarity=0.188  Sum_probs=95.2

Q ss_pred             CcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCH-------HHHHHHHhhccCCceEEEEeecCChhHHHHH
Q psy7789          35 CHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFE-------EDVRTIFSFFRGQRQTLLFSATMPKKIQNFA  107 (197)
Q Consensus        35 ~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~-------~~i~~i~~~~~~~~q~i~~SAT~~~~~~~~~  107 (197)
                      .+-++++.++|.....   -.+++.+.||+||+...+..-|.       +.+..+...+.+...+|++-|+++...-++.
T Consensus       122 ~~rLivqIdSL~R~~~---~~l~~yDvVIIDEv~svL~qL~S~Tm~~~~~v~~~L~~lI~~ak~VI~~DA~ln~~tvdFl  198 (824)
T PF02399_consen  122 YDRLIVQIDSLHRLDG---SLLDRYDVVIIDEVMSVLNQLFSPTMRQREEVDNLLKELIRNAKTVIVMDADLNDQTVDFL  198 (824)
T ss_pred             cCeEEEEehhhhhccc---ccccccCEEEEehHHHHHHHHhHHHHhhHHHHHHHHHHHHHhCCeEEEecCCCCHHHHHHH
Confidence            5778888888866642   24677899999999988753222       2222334445667899999999999999999


Q ss_pred             HHhcCCC-eEEEeCCCCccCcceeEEEEEcC------------------------------------chhhHHHHHHHhh
Q psy7789         108 RSALVKP-ITINVGRAGAASMNVVQEVEYVK------------------------------------QEAKIVYLLECLQ  150 (197)
Q Consensus       108 ~~~~~~~-~~i~~~~~~~~~~~i~~~~~~~~------------------------------------~~~k~~~l~~~l~  150 (197)
                      +.+..+. +.+.+. +...+.-.......++                                    ..+....+-.++.
T Consensus       199 ~~~Rp~~~i~vI~n-~y~~~~fs~R~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tF~~~L~~  277 (824)
T PF02399_consen  199 ASCRPDENIHVIVN-TYASPGFSNRRCTFLRSLGTDTLAAALNPEDENADTSPTPKHSPDPTATAAISNDETTFFSELLA  277 (824)
T ss_pred             HHhCCCCcEEEEEe-eeecCCcccceEEEecccCcHHHHHHhCCcccccccCCCcCCCCccccccccccchhhHHHHHHH
Confidence            8876543 333332 2211111100111000                                    0011122222222


Q ss_pred             --cCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhh
Q psy7789         151 --KTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQN  191 (197)
Q Consensus       151 --~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~  191 (197)
                        ..++++-||++|...++.++++.+..+.++..++|+-+..+
T Consensus       278 ~L~~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~d  320 (824)
T PF02399_consen  278 RLNAGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLED  320 (824)
T ss_pred             HHhCCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCccc
Confidence              23457889999999999999999999999998888765553

It functions as a docking protein to recruit essential components of the viral replication machinery to viral DNA origins. In the presence of the major DNA-binding protein, it opens dsDNA which leads to a conformational change in the origin that facilitates DNA unwinding and subsequent replication [].; GO: 0003688 DNA replication origin binding, 0005524 ATP binding, 0006260 DNA replication

>KOG0926|consensus

Probab=97.49  E-value=0.00041  Score=60.48  Aligned_cols=137  Identities=18%  Similarity=0.227  Sum_probs=78.7

Q ss_pred             CCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhh-cC----CCHHHHHHHHhhccC------CceEEEEeecCChh
Q psy7789          34 GCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMV-DM----GFEEDVRTIFSFFRG------QRQTLLFSATMPKK  102 (197)
Q Consensus        34 ~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~-~~----~~~~~i~~i~~~~~~------~~q~i~~SAT~~~~  102 (197)
                      ...|.++|.|-|+.-+.+ .+.|...+.+|+||||.=. ..    |....+-.+.+.+..      ...+|+||||+.  
T Consensus       349 ~T~IkFMTDGVLLrEi~~-DflL~kYSvIIlDEAHERSvnTDILiGmLSRiV~LR~k~~ke~~~~kpLKLIIMSATLR--  425 (1172)
T KOG0926|consen  349 DTSIKFMTDGVLLREIEN-DFLLTKYSVIILDEAHERSVNTDILIGMLSRIVPLRQKYYKEQCQIKPLKLIIMSATLR--  425 (1172)
T ss_pred             CceeEEecchHHHHHHHH-hHhhhhceeEEechhhhccchHHHHHHHHHHHHHHHHHHhhhhcccCceeEEEEeeeEE--
Confidence            468999999999988874 4557889999999999632 11    112222222222222      347899999985  


Q ss_pred             HHHH--HHHhcC-CCeEEEeCCCCccCcceeEEEE-EcCchhh---HHHHHHHhhcCC-CCEEEEecccccHHHHHHHHH
Q psy7789         103 IQNF--ARSALV-KPITINVGRAGAASMNVVQEVE-YVKQEAK---IVYLLECLQKTE-PPVLIFAEKKQDVDAIHEYLL  174 (197)
Q Consensus       103 ~~~~--~~~~~~-~~~~i~~~~~~~~~~~i~~~~~-~~~~~~k---~~~l~~~l~~~~-~~~lIF~~s~~~~~~l~~~L~  174 (197)
                      +.++  .++++. .|-.+.+....  -+ +.-+|- ..+.+.-   +...+.+-+..+ +-.|||+....+++.|.+.|+
T Consensus       426 VsDFtenk~LFpi~pPlikVdARQ--fP-VsIHF~krT~~DYi~eAfrKtc~IH~kLP~G~ILVFvTGQqEV~qL~~kLR  502 (1172)
T KOG0926|consen  426 VSDFTENKRLFPIPPPLIKVDARQ--FP-VSIHFNKRTPDDYIAEAFRKTCKIHKKLPPGGILVFVTGQQEVDQLCEKLR  502 (1172)
T ss_pred             ecccccCceecCCCCceeeeeccc--Cc-eEEEeccCCCchHHHHHHHHHHHHhhcCCCCcEEEEEeChHHHHHHHHHHH
Confidence            2222  233343 23344443221  11 222222 1222222   222333333332 469999999999999999999


Q ss_pred             hC
Q psy7789         175 LK  176 (197)
Q Consensus       175 ~~  176 (197)
                      +.
T Consensus       503 K~  504 (1172)
T KOG0926|consen  503 KR  504 (1172)
T ss_pred             hh
Confidence            86

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=97.47  E-value=0.00021  Score=54.86  Aligned_cols=56  Identities=25%  Similarity=0.448  Sum_probs=46.2

Q ss_pred             eeEEEEEcC-CChHHhHHHHhc-CCcEEEeCchHHHHHHhcCCccCCCccEEEeehhh
Q psy7789          13 LRTCLAIGG-VPMNQSLDVIKK-GCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEAD   68 (197)
Q Consensus        13 i~~~~~~gg-~~~~~~~~~l~~-~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad   68 (197)
                      .+|+-+++. ...++|...+.. ..+|.||||+|+..++..+.+.+++++++|+|--|
T Consensus       154 ~~v~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~~~L~l~~l~~ivlD~s~  211 (252)
T PF14617_consen  154 CKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLENGALSLSNLKRIVLDWSY  211 (252)
T ss_pred             chHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHcCCCCcccCeEEEEcCCc
Confidence            444445555 367888888874 68999999999999999999999999999999754

>KOG0949|consensus

Probab=97.46  E-value=0.00021  Score=63.37  Aligned_cols=67  Identities=18%  Similarity=0.242  Sum_probs=51.8

Q ss_pred             CCcEEEeCchHHHHHHhc---CCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEeecCChh
Q psy7789          34 GCHMMVATPGRLMDMLDK---KMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKK  102 (197)
Q Consensus        34 ~~~Ili~TP~~l~~~l~~---~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SAT~~~~  102 (197)
                      +|+|+|+-|+++-+++..   ..-+..+++++|+||+|.+....-...+..++-..  .+.++++|||+.+.
T Consensus       605 nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~ed~l~~Eqll~li--~CP~L~LSATigN~  674 (1330)
T KOG0949|consen  605 NCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNEEDGLLWEQLLLLI--PCPFLVLSATIGNP  674 (1330)
T ss_pred             hceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhccccccchHHHHHHHhc--CCCeeEEecccCCH
Confidence            599999999999999976   44568999999999999997654343444444443  56799999999643

>KOG1123|consensus

Probab=97.31  E-value=0.0014  Score=54.63  Aligned_cols=154  Identities=14%  Similarity=0.179  Sum_probs=80.6

Q ss_pred             CCcEEEeCchHHHHHHhcC--------CccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEeecCChhHHH
Q psy7789          34 GCHMMVATPGRLMDMLDKK--------MVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQN  105 (197)
Q Consensus        34 ~~~Ili~TP~~l~~~l~~~--------~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SAT~~~~~~~  105 (197)
                      ++.|+|+|=..+..--++.        .+.-..+.++++||+|.+....|+..+.-+-..     -.+.++||+-.+-..
T Consensus       390 ~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvvPA~MFRRVlsiv~aH-----cKLGLTATLvREDdK  464 (776)
T KOG1123|consen  390 GAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVVPAKMFRRVLSIVQAH-----CKLGLTATLVREDDK  464 (776)
T ss_pred             CCcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccchHHHHHHHHHHHHHH-----hhccceeEEeecccc
Confidence            5889999964333211111        122466789999999999877677555444222     246788887422111


Q ss_pred             HHHH-hcCCC-----eEEEeCCCCc----------------------cCcceeEEEEEcCchhhHH---HHHHHhhcCCC
Q psy7789         106 FARS-ALVKP-----ITINVGRAGA----------------------ASMNVVQEVEYVKQEAKIV---YLLECLQKTEP  154 (197)
Q Consensus       106 ~~~~-~~~~~-----~~i~~~~~~~----------------------~~~~i~~~~~~~~~~~k~~---~l~~~l~~~~~  154 (197)
                      +... |+-.|     .|.++.....                      .-..-+....++=++.|+.   .|++.-++.+-
T Consensus       465 I~DLNFLIGPKlYEAnWmdL~~kGhIA~VqCaEVWCpMt~eFy~eYL~~~t~kr~lLyvMNP~KFraCqfLI~~HE~RgD  544 (776)
T KOG1123|consen  465 ITDLNFLIGPKLYEANWMDLQKKGHIAKVQCAEVWCPMTPEFYREYLRENTRKRMLLYVMNPNKFRACQFLIKFHERRGD  544 (776)
T ss_pred             ccccceeecchhhhccHHHHHhCCceeEEeeeeeecCCCHHHHHHHHhhhhhhhheeeecCcchhHHHHHHHHHHHhcCC
Confidence            1111 11111     1111111000                      0000111222333444543   44444445556


Q ss_pred             CEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         155 PVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       155 ~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      ++|||..+.-...+.|   -+.|-  ..++|..++.+|.+|++
T Consensus       545 KiIVFsDnvfALk~YA---ikl~K--pfIYG~Tsq~ERm~ILq  582 (776)
T KOG1123|consen  545 KIIVFSDNVFALKEYA---IKLGK--PFIYGPTSQNERMKILQ  582 (776)
T ss_pred             eEEEEeccHHHHHHHH---HHcCC--ceEECCCchhHHHHHHH
Confidence            8999997655444444   34443  37899999999999874

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=97.31  E-value=0.0012  Score=57.87  Aligned_cols=148  Identities=17%  Similarity=0.171  Sum_probs=85.6

Q ss_pred             ccccCCCCeeEEEEEcCCChHHhHHHHh----cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhc---CC---
Q psy7789           5 FISALPIPLRTCLAIGGVPMNQSLDVIK----KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD---MG---   74 (197)
Q Consensus         5 ~~~~~~~~i~~~~~~gg~~~~~~~~~l~----~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~---~~---   74 (197)
                      |...+  |.+++.+++|.+..+..+.|.    +...|+|||=--++       ..++++.++|+||=|.-.-   ++   
T Consensus       265 f~~rF--g~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF-------~Pf~~LGLIIvDEEHD~sYKq~~~prY  335 (730)
T COG1198         265 FKARF--GAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALF-------LPFKNLGLIIVDEEHDSSYKQEDGPRY  335 (730)
T ss_pred             HHHHh--CCChhhhcccCChHHHHHHHHHHhcCCceEEEEechhhc-------CchhhccEEEEeccccccccCCcCCCc
Confidence            44455  478889999988666665553    46999999942222       2378999999999997642   11   


Q ss_pred             CHHHHHHHHhhccCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCch-hhH-----HHHHHH
Q psy7789          75 FEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQE-AKI-----VYLLEC  148 (197)
Q Consensus        75 ~~~~i~~i~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~-~k~-----~~l~~~  148 (197)
                      ...++....... .+.++|+-|||-+-+....+  .-.....+.+..............+.+..+ .+.     ..|++.
T Consensus       336 hARdvA~~Ra~~-~~~pvvLgSATPSLES~~~~--~~g~y~~~~L~~R~~~a~~p~v~iiDmr~e~~~~~~~lS~~Ll~~  412 (730)
T COG1198         336 HARDVAVLRAKK-ENAPVVLGSATPSLESYANA--ESGKYKLLRLTNRAGRARLPRVEIIDMRKEPLETGRSLSPALLEA  412 (730)
T ss_pred             CHHHHHHHHHHH-hCCCEEEecCCCCHHHHHhh--hcCceEEEEccccccccCCCcceEEeccccccccCccCCHHHHHH
Confidence            223344333333 58899999999664433333  222233444433332111122223333221 111     456666


Q ss_pred             hhc---CCCCEEEEecccc
Q psy7789         149 LQK---TEPPVLIFAEKKQ  164 (197)
Q Consensus       149 l~~---~~~~~lIF~~s~~  164 (197)
                      +++   .+.|+|+|.|.+-
T Consensus       413 i~~~l~~geQ~llflnRRG  431 (730)
T COG1198         413 IRKTLERGEQVLLFLNRRG  431 (730)
T ss_pred             HHHHHhcCCeEEEEEccCC
Confidence            653   3569999999863

>KOG0952|consensus

Probab=97.13  E-value=9.2e-05  Score=65.89  Aligned_cols=176  Identities=12%  Similarity=0.119  Sum_probs=97.2

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHh--cCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhc---
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLD--KKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF---   86 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~--~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~---   86 (197)
                      |+++.-++|+...+  ...+. .++++|+||++.....+  +..--+.+++.+|+||.|++.+. +++.+..+....   
T Consensus      1001 g~k~ie~tgd~~pd--~~~v~-~~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg~~-rgPVle~ivsr~n~~ 1076 (1230)
T KOG0952|consen 1001 GIKVIELTGDVTPD--VKAVR-EADIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLGED-RGPVLEVIVSRMNYI 1076 (1230)
T ss_pred             CceeEeccCccCCC--hhhee-cCceEEcccccccCccccccchhhhccccceeecccccccCC-CcceEEEEeeccccC
Confidence            78888888876544  22222 38999999999887775  44555789999999999998654 444444332222   


Q ss_pred             ----cCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEE-------EEEcC-chhhHHHHHHHhhcCC-
Q psy7789          87 ----RGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQE-------VEYVK-QEAKIVYLLECLQKTE-  153 (197)
Q Consensus        87 ----~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~-------~~~~~-~~~k~~~l~~~l~~~~-  153 (197)
                          ++..|.+.+|.- ......+..+....+. ...  ..+..+.-...       .++|+ -..+..--...++.++ 
T Consensus      1077 s~~t~~~vr~~glsta-~~na~dla~wl~~~~~-~nf--~~svrpvp~~~~i~gfp~~~~cprm~smnkpa~qaik~~sp 1152 (1230)
T KOG0952|consen 1077 SSQTEEPVRYLGLSTA-LANANDLADWLNIKDM-YNF--RPSVRPVPLEVHIDGFPGQHYCPRMMSMNKPAFQAIKTHSP 1152 (1230)
T ss_pred             ccccCcchhhhhHhhh-hhccHHHHHHhCCCCc-CCC--CcccccCCceEeecCCCchhcchhhhhcccHHHHHHhcCCC
Confidence                223355555332 2334444444433322 101  01111110000       11222 2233344445566654 


Q ss_pred             -CCEEEEecccccHHHHHHHHHh----------------------------------CCCCeEeecCCCChhhhhhh
Q psy7789         154 -PPVLIFAEKKQDVDAIHEYLLL----------------------------------KGKPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       154 -~~~lIF~~s~~~~~~l~~~L~~----------------------------------~~~~~~~~h~~~~~~~R~~i  195 (197)
                       .+++||+.+++.....+.-|-.                                  .++-+..+|+++...+|..+
T Consensus      1153 ~~p~lifv~srrqtrlta~~li~~~~~~~~p~~fl~~de~e~e~~~~~~~d~~Lk~tl~Fgi~lhhagl~~~dr~~~ 1229 (1230)
T KOG0952|consen 1153 IKPVLIFVSSRRQTRLTALDLIASCATEDNPKQFLNMDELELEIIMSKVRDTNLKLTLPFGIGLHHAGLIENDRKIV 1229 (1230)
T ss_pred             CCceEEEeecccccccchHhHHhhccCCCCchhccCCCHHHHHHHHHHhcccchhhhhhhhhhhhhhhccccccccC
Confidence             4899999887654444433311                                  13446778889988888754

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=97.07  E-value=0.0047  Score=55.17  Aligned_cols=88  Identities=11%  Similarity=0.077  Sum_probs=69.9

Q ss_pred             CcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEeecCC------hhHHHHHH
Q psy7789          35 CHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMP------KKIQNFAR  108 (197)
Q Consensus        35 ~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SAT~~------~~~~~~~~  108 (197)
                      ..|+++||..|..-+-.+.++++.+..+||||||++.+......+..+.+.-.+..=+.+|||.-.      ..+.++++
T Consensus         8 ggi~~~T~rIl~~DlL~~ri~~~~itgiiv~~Ahr~~~~~~eaFI~rlyr~~n~~gfIkafSdsP~~~~~g~~~l~~vmk   87 (814)
T TIGR00596         8 GGIFSITSRILVVDLLTGIIPPELITGILVLRADRIIESSQEAFILRLYRQKNKTGFIKAFSDNPEAFTMGFSPLETKMR   87 (814)
T ss_pred             CCEEEEechhhHhHHhcCCCCHHHccEEEEeecccccccccHHHHHHHHHHhCCCcceEEecCCCcccccchHHHHHHHH
Confidence            579999999998777778899999999999999999888777778888777777778899999865      35666777


Q ss_pred             HhcCCCeEEEeCCC
Q psy7789         109 SALVKPITINVGRA  122 (197)
Q Consensus       109 ~~~~~~~~i~~~~~  122 (197)
                      .++-..+.+.....
T Consensus        88 ~L~i~~v~l~prf~  101 (814)
T TIGR00596        88 NLFLRHVYLWPRFH  101 (814)
T ss_pred             HhCcCeEEEeCCCc
Confidence            76666555544433

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit

>KOG0384|consensus

Probab=96.99  E-value=0.011  Score=53.99  Aligned_cols=52  Identities=33%  Similarity=0.438  Sum_probs=44.6

Q ss_pred             HHHHhhcCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         145 LLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       145 l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      |+.-|+..+.+||||..=++.-.-|+++|..++|+.--+-|.+..+-|++-+
T Consensus       691 LL~rLk~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AI  742 (1373)
T KOG0384|consen  691 LLPRLKEGGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAI  742 (1373)
T ss_pred             HHHHHhcCCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHHHHHH
Confidence            3333445566899999999999999999999999999999999999998754

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=96.94  E-value=0.0012  Score=59.66  Aligned_cols=161  Identities=15%  Similarity=0.067  Sum_probs=91.2

Q ss_pred             CcEEEeCchHHHHHHh--c-CCccCC--C--ccEEEeehhhhhhcCCCHHHHHHHHhhcc-CCceEEEEeecCChhHHHH
Q psy7789          35 CHMMVATPGRLMDMLD--K-KMVSLD--V--CRYLCLDEADRMVDMGFEEDVRTIFSFFR-GQRQTLLFSATMPKKIQNF  106 (197)
Q Consensus        35 ~~Ili~TP~~l~~~l~--~-~~~~l~--~--l~~vViDEad~l~~~~~~~~i~~i~~~~~-~~~q~i~~SAT~~~~~~~~  106 (197)
                      ++++|||++.++....  + +...+.  .  =+.|||||+|.+-.. ....+..++.... -...++++|||+|+.+...
T Consensus       563 apv~V~TIDQlL~a~~~~r~~~~~l~ll~La~svlVlDEVHaYD~~-~~~~L~rlL~w~~~lG~~VlLmSATLP~~l~~~  641 (1110)
T TIGR02562       563 APVLVCTIDHLIPATESHRGGHHIAPMLRLMSSDLILDEPDDYEPE-DLPALLRLVQLAGLLGSRVLLSSATLPPALVKT  641 (1110)
T ss_pred             CCeEEecHHHHHHHhhhcccchhHHHHHHhcCCCEEEECCccCCHH-HHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHH
Confidence            7899999999998762  2 111111  1  247899999998433 2333444444332 2678999999999876653


Q ss_pred             HHH-hc----------CC---C--eEEEeCCCCc-----------------------------cCcceeEEEEEcCch--
Q psy7789         107 ARS-AL----------VK---P--ITINVGRAGA-----------------------------ASMNVVQEVEYVKQE--  139 (197)
Q Consensus       107 ~~~-~~----------~~---~--~~i~~~~~~~-----------------------------~~~~i~~~~~~~~~~--  139 (197)
                      ... |.          ..   +  +.-...++..                             .+....-....++..  
T Consensus       642 L~~Ay~~G~~~~q~~~g~~~~~~~i~CaW~DE~~~~~~~~~~~~~F~~~H~~Fv~~R~~~L~~~p~~R~a~i~~~~~~~~  721 (1110)
T TIGR02562       642 LFRAYEAGRQMYQALYGQPKKPLNICCAWVDEPQVWQADCNQKSEFIQRHQDFLRDRAVQLAKKPVRRLAELLSLSSLPR  721 (1110)
T ss_pred             HHHHHHHHHHHHHHhcCCCCCCcceeEEeecccCchhhhhcCHHHHHHHHHHHHHHHHHHHhcCcccceEEEeecCCccc
Confidence            332 21          11   1  1111111110                             111112223333322  


Q ss_pred             ---hhHHHHHHHhh--------cC-------CCC---EEEEecccccHHHHHHHHHhC----C--CCeEeecCCCChhhh
Q psy7789         140 ---AKIVYLLECLQ--------KT-------EPP---VLIFAEKKQDVDAIHEYLLLK----G--KPFFTLKSLKEDQNN  192 (197)
Q Consensus       140 ---~k~~~l~~~l~--------~~-------~~~---~lIF~~s~~~~~~l~~~L~~~----~--~~~~~~h~~~~~~~R  192 (197)
                         .....+.+.+.        .+       +++   .+|=+++++.+..+|..|...    +  +.+.+|||..+...|
T Consensus       722 ~~~~~~~~~a~~i~~~~~~LH~~h~~~~~~sgk~VSfGliR~anI~p~V~~A~~L~~~~~~~~~~i~~~~yHSr~~l~~R  801 (1110)
T TIGR02562       722 ENESTYLALAQSLLEGALRLHQAHAQTDPKSEKKVSVGLIRVANIDPLIRLAQFLYALLAEEKYQIHLCCYHAQDPLLLR  801 (1110)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHhCccCCCCCeEEEEEEEEEcCchHHHHHHHHHHhhccccCCceeEEEecccChHHHH
Confidence               12222222221        11       122   688889999999999988754    3  357789999999999


Q ss_pred             hhhh
Q psy7789         193 QTLE  196 (197)
Q Consensus       193 ~~i~  196 (197)
                      ..+|
T Consensus       802 s~~E  805 (1110)
T TIGR02562       802 SYIE  805 (1110)
T ss_pred             HHHH
Confidence            8876

The helicase in many CRISPR-associated (cas) gene clusters is designated Cas3, and most Cas3 proteins are described by model TIGR01587. Members of this family are considerably larger, show a number of motifs in common with TIGR01587 sequences, and replace Cas3 in some CRISPR/cas loci in a number of Proteobacteria, including Yersinia pestis, Chromobacterium violaceum, Erwinia carotovora subsp. atroseptica SCRI1043, Photorhabdus luminescens subsp. laumondii TTO1, Legionella pneumophila, etc.

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=96.62  E-value=0.02  Score=50.23  Aligned_cols=99  Identities=13%  Similarity=0.110  Sum_probs=70.2

Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhc---CCCCEEEEecccccHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQDVD  167 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~  167 (197)
                      .+..||.|...+..++.+.|.-+  .+.+++.......-..-.++....+|...+.+-+.+   .+.|+||.|.|+..++
T Consensus       364 kLsGMTGTa~t~~~Ef~~iY~l~--Vv~IPtnkp~~R~d~~d~iy~t~~~k~~Aii~ei~~~~~~GrPVLVgt~sI~~SE  441 (764)
T PRK12326        364 TVCGMTGTAVAAGEQLRQFYDLG--VSVIPPNKPNIREDEADRVYATAAEKNDAIVEHIAEVHETGQPVLVGTHDVAESE  441 (764)
T ss_pred             hheeecCCChhHHHHHHHHhCCc--EEECCCCCCceeecCCCceEeCHHHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHH
Confidence            56789999987777777666544  444443322211111224566778888888877754   3568999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCChhh
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQN  191 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~  191 (197)
                      .++..|.+.|++...+++.-..+|
T Consensus       442 ~ls~~L~~~gI~h~vLNAk~~~~E  465 (764)
T PRK12326        442 ELAERLRAAGVPAVVLNAKNDAEE  465 (764)
T ss_pred             HHHHHHHhCCCcceeeccCchHhH
Confidence            999999999999999998744433

>PF00176 SNF2_N: SNF2 family N-terminal domain; InterPro: IPR000330 This domain is found in proteins involved in a variety of processes including transcription regulation (e

Probab=96.57  E-value=0.003  Score=49.49  Aligned_cols=85  Identities=18%  Similarity=0.112  Sum_probs=46.3

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHh---cCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccC
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLD---KKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRG   88 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~---~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~   88 (197)
                      .+++..+.|+..............+++|+|.+.+...-.   ...+.--+.++||+||+|.+-+. ..... ..+..+. 
T Consensus        85 ~~~v~~~~~~~~~~~~~~~~~~~~~vvi~ty~~~~~~~~~~~~~~l~~~~~~~vIvDEaH~~k~~-~s~~~-~~l~~l~-  161 (299)
T PF00176_consen   85 SLRVIIYDGDSERRRLSKNQLPKYDVVITTYETLRKARKKKDKEDLKQIKWDRVIVDEAHRLKNK-DSKRY-KALRKLR-  161 (299)
T ss_dssp             TS-EEEESSSCHHHHTTSSSCCCSSEEEEEHHHHH--TSTHTTHHHHTSEEEEEEETTGGGGTTT-TSHHH-HHHHCCC-
T ss_pred             cccccccccccccccccccccccceeeeccccccccccccccccccccccceeEEEecccccccc-ccccc-ccccccc-
Confidence            456666666551222222222458999999998881110   01122234889999999999433 22222 3333353 


Q ss_pred             CceEEEEeecC
Q psy7789          89 QRQTLLFSATM   99 (197)
Q Consensus        89 ~~q~i~~SAT~   99 (197)
                      ....+++|||.
T Consensus       162 ~~~~~lLSgTP  172 (299)
T PF00176_consen  162 ARYRWLLSGTP  172 (299)
T ss_dssp             ECEEEEE-SS-
T ss_pred             cceEEeecccc
Confidence            66778899994

g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1) [, ]. SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilises energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. Proteins that contain this domain appear to be distantly related to the DEAX box helicases IPR001410 from INTERPRO, however no helicase activity has ever been demonstrated for these proteins. ; GO: 0003677 DNA binding, 0005524 ATP binding; PDB: 1Z63_B 1Z3I_X 3DMQ_A 3MWY_W.

>PRK14873 primosome assembly protein PriA; Provisional

Probab=96.46  E-value=0.051  Score=47.77  Aligned_cols=93  Identities=8%  Similarity=0.004  Sum_probs=59.4

Q ss_pred             ccccCCCCeeEEEEEcCCChHHhHHHHh----cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhc-C--CCH-
Q psy7789           5 FISALPIPLRTCLAIGGVPMNQSLDVIK----KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD-M--GFE-   76 (197)
Q Consensus         5 ~~~~~~~~i~~~~~~gg~~~~~~~~~l~----~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~-~--~~~-   76 (197)
                      |.+.++ +-.++.++++.+..+..+.+.    +.++|+|||-.-++       .-+.++.++|+||=|.-.- .  +-+ 
T Consensus       208 l~~~f~-~~~v~~lhS~l~~~~R~~~w~~~~~G~~~IViGtRSAvF-------aP~~~LgLIIvdEEhd~sykq~~~p~y  279 (665)
T PRK14873        208 LRALLG-AGDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSAVF-------APVEDLGLVAIWDDGDDLLAEPRAPYP  279 (665)
T ss_pred             HHHHcC-CCcEEEECCCCCHHHHHHHHHHHhCCCCcEEEEcceeEE-------eccCCCCEEEEEcCCchhhcCCCCCCc
Confidence            344444 356888999988766665543    34899999953222       2378999999999886532 1  111 


Q ss_pred             --HHHHHHHhhccCCceEEEEeecCChhHHHH
Q psy7789          77 --EDVRTIFSFFRGQRQTLLFSATMPKKIQNF  106 (197)
Q Consensus        77 --~~i~~i~~~~~~~~q~i~~SAT~~~~~~~~  106 (197)
                        .++...... ..+..+++-|||-+-+....
T Consensus       280 haRdvA~~Ra~-~~~~~lvLgSaTPSles~~~  310 (665)
T PRK14873        280 HAREVALLRAH-QHGCALLIGGHARTAEAQAL  310 (665)
T ss_pred             cHHHHHHHHHH-HcCCcEEEECCCCCHHHHHH
Confidence              223332222 35888999999987665543

>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain

Probab=96.44  E-value=0.0081  Score=42.11  Aligned_cols=64  Identities=16%  Similarity=0.144  Sum_probs=31.5

Q ss_pred             EEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhcc--CCceEEEEeecCChhH
Q psy7789          37 MMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFR--GQRQTLLFSATMPKKI  103 (197)
Q Consensus        37 Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~--~~~q~i~~SAT~~~~~  103 (197)
                      |-++|-..+...+.+ .....+.+++|+||||..--.. -. ....+..+.  ....++++|||-|...
T Consensus        75 i~vMc~at~~~~~~~-p~~~~~yd~II~DEcH~~Dp~s-IA-~rg~l~~~~~~g~~~~i~mTATPPG~~  140 (148)
T PF07652_consen   75 IDVMCHATYGHFLLN-PCRLKNYDVIIMDECHFTDPTS-IA-ARGYLRELAESGEAKVIFMTATPPGSE  140 (148)
T ss_dssp             EEEEEHHHHHHHHHT-SSCTTS-SEEEECTTT--SHHH-HH-HHHHHHHHHHTTS-EEEEEESS-TT--
T ss_pred             ccccccHHHHHHhcC-cccccCccEEEEeccccCCHHH-Hh-hheeHHHhhhccCeeEEEEeCCCCCCC
Confidence            344444444444433 3446889999999999862211 11 111122222  2458999999977543

The domain is related to the DEAD/DEAH box helicase domain which is found in a large family of ATPases.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity, 0019079 viral genome replication; PDB: 2QEQ_A 2V6J_A 2V6I_A 8OHM_A 4A92_B 1JR6_A 1HEI_A 1ONB_A 1A1V_A 1YMF_A ....

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=96.43  E-value=0.021  Score=50.98  Aligned_cols=97  Identities=16%  Similarity=0.176  Sum_probs=67.6

Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhc---CCCCEEEEecccccHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQDVD  167 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~  167 (197)
                      ++.+||.|...+..++...|.-+  .+.++........-..-.++.....|...+.+-+..   .+.|+||.|.|++.++
T Consensus       363 kLsGMTGTA~te~~Ef~~iY~l~--Vv~IPTnkP~~R~D~~d~iy~t~~~K~~Aii~ei~~~~~~gqPVLVgT~SIe~SE  440 (925)
T PRK12903        363 KLSGMTGTAKTEEQEFIDIYNMR--VNVVPTNKPVIRKDEPDSIFGTKHAKWKAVVKEVKRVHKKGQPILIGTAQVEDSE  440 (925)
T ss_pred             hhhccCCCCHHHHHHHHHHhCCC--EEECCCCCCeeeeeCCCcEEEcHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHH
Confidence            46778888877777777666444  444443222111111124566778888888877664   3458999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCCh
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKED  189 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~  189 (197)
                      .++..|.+.|++...+++.-..
T Consensus       441 ~ls~~L~~~gi~h~vLNAk~~e  462 (925)
T PRK12903        441 TLHELLLEANIPHTVLNAKQNA  462 (925)
T ss_pred             HHHHHHHHCCCCceeecccchh
Confidence            9999999999998888886443

>PF07517 SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011115 SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane

Probab=96.22  E-value=0.015  Score=45.27  Aligned_cols=59  Identities=10%  Similarity=0.137  Sum_probs=41.4

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHH-HHhcC----Cc--cCCCccEEEeehhhhhh
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMD-MLDKK----MV--SLDVCRYLCLDEADRMV   71 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~-~l~~~----~~--~l~~l~~vViDEad~l~   71 (197)
                      .|+++..++++.+.+...+...  +||+.+|...+.- .++..    ..  -.....++||||+|.++
T Consensus       145 LGlsv~~~~~~~~~~~r~~~Y~--~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  145 LGLSVGIITSDMSSEERREAYA--ADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSIL  210 (266)
T ss_dssp             TT--EEEEETTTEHHHHHHHHH--SSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHT
T ss_pred             hhhccccCccccCHHHHHHHHh--CcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEE
Confidence            3899999999988665444444  7899999988874 44321    11  15788999999999886

SecA protein achieves this translocation, in association with SecY protein, in an ATP-dependent manner [,]. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the IPR0011545 from INTERPRO.; GO: 0005524 ATP binding, 0017038 protein import, 0016020 membrane; PDB: 1NL3_B 1NKT_B 3DIN_B 3JUX_A 2FSG_B 2VDA_A 2FSH_A 2FSF_A 2FSI_A 3BXZ_A ....

>KOG1000|consensus

Probab=96.17  E-value=0.2  Score=42.15  Aligned_cols=41  Identities=12%  Similarity=0.130  Sum_probs=37.9

Q ss_pred             CCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhh
Q psy7789         154 PPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQT  194 (197)
Q Consensus       154 ~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~  194 (197)
                      .|.+|||.-...-+.+..++.++++....+.|..+..+|..
T Consensus       493 ~KflVFaHH~~vLd~Iq~~~~~r~vg~IRIDGst~s~~R~l  533 (689)
T KOG1000|consen  493 RKFLVFAHHQIVLDTIQVEVNKRKVGSIRIDGSTPSHRRTL  533 (689)
T ss_pred             ceEEEEehhHHHHHHHHHHHHHcCCCeEEecCCCCchhHHH
Confidence            48999999999999999999999999999999999999874

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=95.81  E-value=0.068  Score=47.88  Aligned_cols=95  Identities=12%  Similarity=0.086  Sum_probs=65.6

Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhc---CCCCEEEEecccccHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQDVD  167 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~  167 (197)
                      .+.+||.|...+-.++...|.-+  .+.+++.......-..-.++....+|...+.+-+..   .+.|+||-|.|++.++
T Consensus       361 kL~GMTGTa~te~~Ef~~iY~l~--vv~IPtnkp~~R~d~~d~v~~t~~~K~~AI~~ei~~~~~~grPVLIgT~SIe~SE  438 (870)
T CHL00122        361 KLSGMTGTAKTEELEFEKIYNLE--VVCIPTHRPMLRKDLPDLIYKDELSKWRAIADECLQMHQTGRPILIGTTTIEKSE  438 (870)
T ss_pred             hhcccCCCCHHHHHHHHHHhCCC--EEECCCCCCccceeCCCeEEeCHHHHHHHHHHHHHHHHhcCCCEEEeeCCHHHHH
Confidence            46778888876666666666444  333443332221112234566777787777766553   3568999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCC
Q psy7789         168 AIHEYLLLKGKPFFTLKSLK  187 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~  187 (197)
                      .++..|.+.|++..++++.-
T Consensus       439 ~ls~~L~~~gi~h~vLNAk~  458 (870)
T CHL00122        439 LLSQLLKEYRLPHQLLNAKP  458 (870)
T ss_pred             HHHHHHHHcCCccceeeCCC
Confidence            99999999999988888863

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative

Probab=95.50  E-value=0.085  Score=47.91  Aligned_cols=41  Identities=20%  Similarity=0.277  Sum_probs=29.5

Q ss_pred             hcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhc
Q psy7789          32 KKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD   72 (197)
Q Consensus        32 ~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~   72 (197)
                      ...+||||+.-.-|++-+.....-+..-+++||||||.+.+
T Consensus       414 a~~AdivItNHa~L~~~~~~~~~ilp~~~~lIiDEAH~L~d  454 (850)
T TIGR01407       414 AEQAQILITNHAYLITRLVDNPELFPSFRDLIIDEAHHLPD  454 (850)
T ss_pred             HhcCCEEEecHHHHHHHhhcccccCCCCCEEEEECcchHHH
Confidence            34699999998877776543322234557999999999963

This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.

>cd01524 RHOD_Pyr_redox Member of the Rhodanese Homology Domain superfamily

Probab=95.11  E-value=0.16  Score=32.35  Aligned_cols=37  Identities=8%  Similarity=0.040  Sum_probs=32.6

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCCh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKED  189 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~  189 (197)
                      ..++++||++-..+...+..|+..|+++..+.||++.
T Consensus        51 ~~~vvl~c~~g~~a~~~a~~L~~~G~~v~~l~GG~~~   87 (90)
T cd01524          51 DKEIIVYCAVGLRGYIAARILTQNGFKVKNLDGGYKT   87 (90)
T ss_pred             CCcEEEEcCCChhHHHHHHHHHHCCCCEEEecCCHHH
Confidence            3589999998888999999999999999999999864

Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar rhodanese-like domains found C-terminal of the pyridine nucleotide-disulphide oxidoreductase (Pyr-redox) domain and the Pyr-redox dimerization domain.

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=95.04  E-value=0.16  Score=45.96  Aligned_cols=99  Identities=12%  Similarity=0.074  Sum_probs=68.2

Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcC---CCCEEEEecccccHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKT---EPPVLIFAEKKQDVD  167 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~---~~~~lIF~~s~~~~~  167 (197)
                      ++.+||.|...+..++...|.-+  .+.++........-..-.++....+|...+.+-+.+.   +.|+||-|.|+...+
T Consensus       505 kl~GmTGTa~~e~~Ef~~iY~l~--v~~iPt~kp~~r~d~~d~iy~t~~~k~~ai~~ei~~~~~~grPvLigt~si~~se  582 (970)
T PRK12899        505 KLAGMTGTAITESREFKEIYNLY--VLQVPTFKPCLRIDHNDEFYMTEREKYHAIVAEIASIHRKGNPILIGTESVEVSE  582 (970)
T ss_pred             hhcccCCCCHHHHHHHHHHhCCC--EEECCCCCCceeeeCCCcEecCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHH
Confidence            56789999877767766666443  3444433221111111235667778888887776543   458999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCChhh
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQN  191 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~  191 (197)
                      .++..|.+.|++...+++.-...|
T Consensus       583 ~ls~~L~~~gi~h~vLNak~~~~E  606 (970)
T PRK12899        583 KLSRILRQNRIEHTVLNAKNHAQE  606 (970)
T ss_pred             HHHHHHHHcCCcceecccchhhhH
Confidence            999999999999888888744433

>KOG0387|consensus

Probab=95.00  E-value=0.79  Score=40.78  Aligned_cols=56  Identities=25%  Similarity=0.404  Sum_probs=45.5

Q ss_pred             hHHHHHHHh---hcCCCCEEEEecccccHHHHHHHHH-hCCCCeEeecCCCChhhhhhhh
Q psy7789         141 KIVYLLECL---QKTEPPVLIFAEKKQDVDAIHEYLL-LKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       141 k~~~l~~~l---~~~~~~~lIF~~s~~~~~~l~~~L~-~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      |...+..++   ...+.++|.|..|+..-.-+-.+|. ..||.+..+.|..+...|..+.
T Consensus       531 Km~vl~~ll~~W~kqg~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~~~~R~~lV  590 (923)
T KOG0387|consen  531 KMKVLAKLLKDWKKQGDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTPAALRQKLV  590 (923)
T ss_pred             hHHHHHHHHHHHhhCCCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCccchhhHHH
Confidence            444444444   4455689999999999999999999 6899999999999999998653

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=94.94  E-value=0.12  Score=47.14  Aligned_cols=101  Identities=11%  Similarity=0.135  Sum_probs=71.3

Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcC---CCCEEEEecccccHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKT---EPPVLIFAEKKQDVD  167 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~---~~~~lIF~~s~~~~~  167 (197)
                      .+-+||.|...+..++...|.-+  ++.++........-..-.++....+|..++.+-+...   +.|+||=+.|++.++
T Consensus       565 kLsGMTGTA~tea~Ef~~IY~L~--Vv~IPTnrP~~R~D~~D~vy~t~~eK~~Aii~ei~~~~~~GrPVLVGT~SVe~SE  642 (1112)
T PRK12901        565 KLAGMTGTAETEAGEFWDIYKLD--VVVIPTNRPIARKDKEDLVYKTKREKYNAVIEEITELSEAGRPVLVGTTSVEISE  642 (1112)
T ss_pred             hhcccCCCCHHHHHHHHHHhCCC--EEECCCCCCcceecCCCeEecCHHHHHHHHHHHHHHHHHCCCCEEEEeCcHHHHH
Confidence            45678888877777777777555  4444433222221122355677788888888777643   568999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCChhhhh
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQNNQ  193 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~R~  193 (197)
                      .++..|+..|++..++++.....|-+
T Consensus       643 ~lS~~L~~~gI~H~VLNAK~h~~EAe  668 (1112)
T PRK12901        643 LLSRMLKMRKIPHNVLNAKLHQKEAE  668 (1112)
T ss_pred             HHHHHHHHcCCcHHHhhccchhhHHH
Confidence            99999999999888888876555443

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4

Probab=94.41  E-value=0.041  Score=48.01  Aligned_cols=40  Identities=23%  Similarity=0.223  Sum_probs=31.1

Q ss_pred             cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhc
Q psy7789          33 KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD   72 (197)
Q Consensus        33 ~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~   72 (197)
                      ..+||+|++..-|+..+....-.+-..+++||||||.+.+
T Consensus       181 ~~AdivItNHalL~~~~~~~~~iLP~~~~lIiDEAH~L~d  220 (636)
T TIGR03117       181 RRCRILFCTHAMLGLAFRDKWGLLPQPDILIVDEAHLFEQ  220 (636)
T ss_pred             ccCCEEEECHHHHHHHhhhhcCCCCCCCEEEEeCCcchHH
Confidence            4589999999888876654322356689999999999963

Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome.

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=94.30  E-value=0.043  Score=33.74  Aligned_cols=29  Identities=14%  Similarity=0.097  Sum_probs=25.7

Q ss_pred             HHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .+++.|++.++.+..+||+|++++|.+++
T Consensus         2 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~   30 (82)
T smart00490        2 ELAELLKELGIKVARLHGGLSQEEREEIL   30 (82)
T ss_pred             HHHHHHHHCCCeEEEEECCCCHHHHHHHH
Confidence            57788888899999999999999998765

>PF00271 Helicase_C: Helicase conserved C-terminal domain; InterPro: IPR001650 The domain, which defines this group of proteins is found in a wide variety of helicases and helicase related proteins

Probab=94.25  E-value=0.035  Score=34.27  Aligned_cols=26  Identities=15%  Similarity=0.188  Sum_probs=23.6

Q ss_pred             HHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         171 EYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       171 ~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      ++|+..|+++..+||+|++++|++++
T Consensus         1 ~~L~~~~~~~~~i~~~~~~~~r~~~~   26 (78)
T PF00271_consen    1 KFLEKKGIKVAIIHGDMSQKERQEIL   26 (78)
T ss_dssp             HHHHHTTSSEEEESTTSHHHHHHHHH
T ss_pred             CChHHCCCcEEEEECCCCHHHHHHHH
Confidence            36889999999999999999999876

It may be that this is not an autonomously folding unit, but an integral part of the helicase. The eukaryotic translation initiation factor 4A (eIF4A) is a member of the DEA(D/H)-box RNA helicase family This is a diverse group of proteins that couples an ATPase activity to RNA binding and unwinding. The structure of the carboxyl-terminal domain of eIF4A has been determined to 1.75 A resolution; it has a parallel alpha-beta topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases [].; GO: 0003676 nucleic acid binding, 0004386 helicase activity, 0005524 ATP binding; PDB: 2Z83_A 2JGN_C 2I4I_A 2BMF_A 2BHR_B 1WP9_E 2WAX_C 2WAY_C 3JUX_A 3DIN_B ....

>cd01533 4RHOD_Repeat_2 Member of the Rhodanese Homology Domain superfamily, repeat 2

Probab=94.05  E-value=0.35  Score=31.96  Aligned_cols=38  Identities=13%  Similarity=0.177  Sum_probs=31.9

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCCC--eEeecCCCChh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGKP--FFTLKSLKEDQ  190 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~~--~~~~h~~~~~~  190 (197)
                      ..++++||.+-.++...+..|+..|++  +..+.|||+.=
T Consensus        66 ~~~ivv~C~~G~rs~~a~~~L~~~G~~~~v~~l~gG~~~W  105 (109)
T cd01533          66 RTPIVVNCAGRTRSIIGAQSLINAGLPNPVAALRNGTQGW  105 (109)
T ss_pred             CCeEEEECCCCchHHHHHHHHHHCCCCcceeEecCCHHHH
Confidence            457999999988888889999999994  88899998653

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 2nd repeat which does contain the putative catalytic Cys residue.

>cd01534 4RHOD_Repeat_3 Member of the Rhodanese Homology Domain superfamily, repeat 3

Probab=93.92  E-value=0.29  Score=31.47  Aligned_cols=36  Identities=11%  Similarity=0.166  Sum_probs=31.1

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCC
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKE  188 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~  188 (197)
                      ..++++||.+-.++...+..|+..|+++..+.||+.
T Consensus        56 ~~~iv~~c~~G~rs~~aa~~L~~~G~~v~~l~GG~~   91 (95)
T cd01534          56 GARIVLADDDGVRADMTASWLAQMGWEVYVLEGGLA   91 (95)
T ss_pred             CCeEEEECCCCChHHHHHHHHHHcCCEEEEecCcHH
Confidence            457999999988888899999999999888889874

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 3rd repeat which does not contain the putative catalytic Cys residue.

>KOG0389|consensus

Probab=93.42  E-value=0.13  Score=45.50  Aligned_cols=87  Identities=20%  Similarity=0.253  Sum_probs=50.0

Q ss_pred             cCCCCeeEEEEEcCCChHHhHHH-Hhc---CCcEEEeCchHHHHHH-hcCCccCCCccEEEeehhhhhhcCCCHHHHHHH
Q psy7789           8 ALPIPLRTCLAIGGVPMNQSLDV-IKK---GCHMMVATPGRLMDML-DKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTI   82 (197)
Q Consensus         8 ~~~~~i~~~~~~gg~~~~~~~~~-l~~---~~~Ili~TP~~l~~~l-~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i   82 (197)
                      -+| .++|...+|....+++.+. +..   .+||+++|=.....-= .++-+.-.+++++|+||+|.|=+.+ .+.++.+
T Consensus       470 wCP-sl~Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmLKN~~-SeRy~~L  547 (941)
T KOG0389|consen  470 WCP-SLKVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLKNRT-SERYKHL  547 (941)
T ss_pred             hCC-ceEEEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHHHHHHHhccccEEEecchhhhhccc-hHHHHHh
Confidence            344 5888888887655544433 332   5899999942222100 1122334667799999999986542 2333333


Q ss_pred             HhhccCCceEEEEeec
Q psy7789          83 FSFFRGQRQTLLFSAT   98 (197)
Q Consensus        83 ~~~~~~~~q~i~~SAT   98 (197)
                      +. + +..+.++++.|
T Consensus       548 M~-I-~An~RlLLTGT  561 (941)
T KOG0389|consen  548 MS-I-NANFRLLLTGT  561 (941)
T ss_pred             cc-c-cccceEEeeCC
Confidence            22 2 24456666666

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=93.32  E-value=0.09  Score=46.34  Aligned_cols=59  Identities=15%  Similarity=0.167  Sum_probs=41.8

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHH-HHHhcC------CccCCCccEEEeehhhhhh
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLM-DMLDKK------MVSLDVCRYLCLDEADRMV   71 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~-~~l~~~------~~~l~~l~~vViDEad~l~   71 (197)
                      +|++|+.++++.+..+.....  .+||+.+|..-+- ++++..      ..-.+.+.+.||||+|.++
T Consensus       146 LGLsvg~i~~~~~~~err~aY--~~DItYgTn~e~gFDyLRDnm~~~~~~~v~R~~~faIVDEvDSiL  211 (764)
T PRK12326        146 LGLTVGWITEESTPEERRAAY--ACDVTYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEADSVL  211 (764)
T ss_pred             cCCEEEEECCCCCHHHHHHHH--cCCCEEcCCcccccccchhhhccChHhhcCCccceeeecchhhhe
Confidence            489999999988766544444  3899999987654 233321      1224678899999999876

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=93.24  E-value=0.22  Score=40.38  Aligned_cols=131  Identities=11%  Similarity=0.143  Sum_probs=65.4

Q ss_pred             CCeeEEEEEcCCChHHhH-HHHhcCC-----cEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcC-------CCHH
Q psy7789          11 IPLRTCLAIGGVPMNQSL-DVIKKGC-----HMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDM-------GFEE   77 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~-~~l~~~~-----~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~-------~~~~   77 (197)
                      .+-++..+++..+..... ..+....     ...+..|..+..............+.+||||||++...       ....
T Consensus        30 ~~~~~~~l~~n~~l~~~l~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~DviivDEAqrl~~~~~~~~~~~~~~  109 (352)
T PF09848_consen   30 EGKKVLYLCGNHPLRNKLREQLAKKYNPKLKKSDFRKPTSFINNYSESDKEKNKYDVIIVDEAQRLRTKGDQYNNFSEPN  109 (352)
T ss_pred             cCCceEEEEecchHHHHHHHHHhhhcccchhhhhhhhhHHHHhhcccccccCCcCCEEEEehhHhhhhccccccccccHH
Confidence            355666666665544422 3333322     33344444443333222234578899999999999873       1346


Q ss_pred             HHHHHHhhcc------CCceEEEEeecCChh-HHHHHHHhcCCCeEEEeCCCCccCc-ceeEEEEEcCchhhHHHHHHHh
Q psy7789          78 DVRTIFSFFR------GQRQTLLFSATMPKK-IQNFARSALVKPITINVGRAGAASM-NVVQEVEYVKQEAKIVYLLECL  149 (197)
Q Consensus        78 ~i~~i~~~~~------~~~q~i~~SAT~~~~-~~~~~~~~~~~~~~i~~~~~~~~~~-~i~~~~~~~~~~~k~~~l~~~l  149 (197)
                      ++..+++.-.      ...|.+--+...+.+ ..+....+-...          ... .+..++......+-..++..++
T Consensus       110 ~L~~i~~~~kv~v~f~D~~Q~i~~~e~~~~~~l~~~~~~~~~~~----------~~~~~L~~q~R~~~~~~~~~wI~~ll  179 (352)
T PF09848_consen  110 QLDEIIKRAKVVVFFYDENQSIRPSEIGTLENLEEIAENLGIEV----------RHFFELKTQFRCHGSKEYIDWIDNLL  179 (352)
T ss_pred             HHHHHHhcCCEEEEEEccccEeecccCCCHHHHHHHHHhcCCcc----------ccCcCcCcceecCCCHHHHHHHHHHH
Confidence            6777766621      123444444433333 233333321111          001 3444555445566667777777


Q ss_pred             hc
Q psy7789         150 QK  151 (197)
Q Consensus       150 ~~  151 (197)
                      ..
T Consensus       180 ~~  181 (352)
T PF09848_consen  180 DN  181 (352)
T ss_pred             hc
Confidence            53

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=93.03  E-value=0.3  Score=44.98  Aligned_cols=73  Identities=15%  Similarity=0.243  Sum_probs=47.7

Q ss_pred             ChHHhHHHHhcC-CcEEEeCchHHHHHHhcC-CccCCCcc-EEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEeecC
Q psy7789          23 PMNQSLDVIKKG-CHMMVATPGRLMDMLDKK-MVSLDVCR-YLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATM   99 (197)
Q Consensus        23 ~~~~~~~~l~~~-~~Ili~TP~~l~~~l~~~-~~~l~~l~-~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SAT~   99 (197)
                      +.....+.+.++ -.|+|+|-.++....... .....+-. .||+||||+.   +++..-..+-..++ ++..++|+.|-
T Consensus       338 s~~~Lk~~l~~~~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHRS---Q~G~~~~~~~~~~~-~a~~~gFTGTP  413 (962)
T COG0610         338 STSELKELLEDGKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRS---QYGELAKLLKKALK-KAIFIGFTGTP  413 (962)
T ss_pred             CHHHHHHHHhcCCCcEEEEEecccchhhhcccccccCCCcEEEEEechhhc---cccHHHHHHHHHhc-cceEEEeeCCc
Confidence            444445566654 489999999999988654 11122322 6789999997   34444444444453 48889999884

>cd01523 RHOD_Lact_B Member of the Rhodanese Homology Domain superfamily

Probab=92.94  E-value=0.18  Score=32.72  Aligned_cols=37  Identities=16%  Similarity=0.141  Sum_probs=32.8

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCCh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKED  189 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~  189 (197)
                      ..+++++|.+-.++...+..|+..|+++..+.||+..
T Consensus        61 ~~~ivv~C~~G~rs~~aa~~L~~~G~~~~~l~GG~~~   97 (100)
T cd01523          61 DQEVTVICAKEGSSQFVAELLAERGYDVDYLAGGMKA   97 (100)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHcCceeEEeCCcHHh
Confidence            3579999999889999999999999998889999864

This CD includes predicted proteins with rhodanese-like domains found N-terminal of the metallo-beta-lactamase domain.

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=92.83  E-value=0.096  Score=41.31  Aligned_cols=44  Identities=16%  Similarity=0.162  Sum_probs=29.2

Q ss_pred             EEEeehhhhhhcCCC--------HHHHHHHHhhccCCceEEEEeecCChhHHH
Q psy7789          61 YLCLDEADRMVDMGF--------EEDVRTIFSFFRGQRQTLLFSATMPKKIQN  105 (197)
Q Consensus        61 ~vViDEad~l~~~~~--------~~~i~~i~~~~~~~~q~i~~SAT~~~~~~~  105 (197)
                      .+|+||||..-+...        ...+..+-+.+| +.+++++|||--.+..+
T Consensus       175 vivfDEcH~akn~~~~~~~~sk~g~avl~LQ~~LP-~ARvvY~SATgasep~N  226 (303)
T PF13872_consen  175 VIVFDECHKAKNLSSGSKKPSKTGIAVLELQNRLP-NARVVYASATGASEPRN  226 (303)
T ss_pred             eEEeccchhcCCCCccCccccHHHHHHHHHHHhCC-CCcEEEecccccCCCce
Confidence            889999999865322        123444445554 66699999997655444

>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin

Probab=92.68  E-value=0.075  Score=38.51  Aligned_cols=40  Identities=20%  Similarity=0.169  Sum_probs=26.3

Q ss_pred             cCCcEEEeCchHHHHHHhcCCcc--CCCccEEEeehhhhhhc
Q psy7789          33 KGCHMMVATPGRLMDMLDKKMVS--LDVCRYLCLDEADRMVD   72 (197)
Q Consensus        33 ~~~~Ili~TP~~l~~~l~~~~~~--l~~l~~vViDEad~l~~   72 (197)
                      ..+||+|++=.-|++......+.  ..+-..|||||||.+.+
T Consensus       118 ~~adivi~~y~yl~~~~~~~~~~~~~~~~~ivI~DEAHNL~~  159 (174)
T PF06733_consen  118 KNADIVICNYNYLFDPSIRKSLFGIDLKDNIVIFDEAHNLED  159 (174)
T ss_dssp             GG-SEEEEETHHHHSHHHHHHHCT--CCCEEEEETTGGGCGG
T ss_pred             ccCCEEEeCHHHHhhHHHHhhhccccccCcEEEEecccchHH
Confidence            45999999987777654332221  12336899999999865

RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast [].; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 3CRV_A 3CRW_1 2VL7_A 4A15_A 2VSF_A.

>KOG3089|consensus

Probab=92.58  E-value=0.23  Score=37.19  Aligned_cols=40  Identities=25%  Similarity=0.523  Sum_probs=32.7

Q ss_pred             hHHHHhc-CCcEEEeCchHHHHHHhcCCccCCCccEEEeeh
Q psy7789          27 SLDVIKK-GCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDE   66 (197)
Q Consensus        27 ~~~~l~~-~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDE   66 (197)
                      +.+...+ ..++-||||+|+..++....++++.++++|+|=
T Consensus       188 ~~k~~k~~~v~~gIgTp~Ri~~lv~~~~f~~~~lk~iIlD~  228 (271)
T KOG3089|consen  188 QVKLLKKRVVHLGIGTPGRIKELVKQGGFNLSPLKFIILDW  228 (271)
T ss_pred             HHHHHhhcceeEeecCcHHHHHHHHhcCCCCCcceeEEeec
Confidence            4444433 378889999999999999889999999999873

>cd01526 RHOD_ThiF Member of the Rhodanese Homology Domain superfamily

Probab=92.57  E-value=0.69  Score=31.29  Aligned_cols=38  Identities=11%  Similarity=0.075  Sum_probs=33.3

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCC--CeEeecCCCChh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGK--PFFTLKSLKEDQ  190 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~--~~~~~h~~~~~~  190 (197)
                      ..++++||++-.++...+..|+..|+  ++..+.||+..=
T Consensus        72 ~~~ivv~C~~G~rs~~aa~~L~~~G~~~~v~~l~GG~~~W  111 (122)
T cd01526          72 DSPIYVVCRRGNDSQTAVRKLKELGLERFVRDIIGGLKAW  111 (122)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHcCCccceeeecchHHHH
Confidence            45799999998899999999999999  699999998654

This CD includes several putative molybdopterin synthase sulfurylases including the molybdenum cofactor biosynthetic protein (CnxF) of Aspergillus nidulans and the molybdenum cofactor synthesis protein 3 (MOCS3) of Homo sapiens. These rhodanese-like domains are found C-terminal of the ThiF and MoeZ_MoeB domains.

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=92.51  E-value=0.13  Score=45.96  Aligned_cols=59  Identities=19%  Similarity=0.321  Sum_probs=42.0

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHH-HHHhcC------CccCCCccEEEeehhhhhh
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLM-DMLDKK------MVSLDVCRYLCLDEADRMV   71 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~-~~l~~~------~~~l~~l~~vViDEad~l~   71 (197)
                      +|++|+.++|+.+.....+..  .+||+.+|...+- ++++..      ..-.+.+.+.||||+|.++
T Consensus       148 LGl~vg~i~~~~~~~~r~~~y--~~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~~~aIvDEvDSiL  213 (796)
T PRK12906        148 LGLTVGLNLNSMSPDEKRAAY--NCDITYSTNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEVDSIL  213 (796)
T ss_pred             cCCeEEEeCCCCCHHHHHHHh--cCCCeecCCccccccchhhccccchhhhhccCcceeeeccchhee
Confidence            489999999987766554444  3899999997765 344321      1124678899999999875

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=92.14  E-value=0.65  Score=42.73  Aligned_cols=34  Identities=12%  Similarity=0.108  Sum_probs=27.2

Q ss_pred             HHHHHHhhcCCCCEEEEecccccHHHHHHHHHhC
Q psy7789         143 VYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLK  176 (197)
Q Consensus       143 ~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~  176 (197)
                      ..+.+++...++++|||++|.+..+.+++.|...
T Consensus       742 ~~i~~l~~~~~g~~LVLFtSy~~l~~v~~~l~~~  775 (928)
T PRK08074        742 AYIAKIAKATKGRMLVLFTSYEMLKKTYYNLKNE  775 (928)
T ss_pred             HHHHHHHHhCCCCEEEEECCHHHHHHHHHHHhhc
Confidence            3444555566789999999999999999999764

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative

Probab=91.86  E-value=0.27  Score=44.69  Aligned_cols=32  Identities=19%  Similarity=0.330  Sum_probs=26.2

Q ss_pred             HHHHHhhcCCCCEEEEecccccHHHHHHHHHh
Q psy7789         144 YLLECLQKTEPPVLIFAEKKQDVDAIHEYLLL  175 (197)
Q Consensus       144 ~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~  175 (197)
                      .+.+++...++++|||++|.+..+.+++.|..
T Consensus       665 ~i~~l~~~~~g~~LVlftS~~~l~~v~~~L~~  696 (850)
T TIGR01407       665 YIIEITAITSPKILVLFTSYEMLHMVYDMLNE  696 (850)
T ss_pred             HHHHHHHhcCCCEEEEeCCHHHHHHHHHHHhh
Confidence            44455555677999999999999999999976

This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.

>KOG0391|consensus

Probab=91.80  E-value=0.23  Score=46.02  Aligned_cols=82  Identities=17%  Similarity=0.249  Sum_probs=51.6

Q ss_pred             CeeEEEEEcCCChHH-hHHHHhc-C-CcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccC
Q psy7789          12 PLRTCLAIGGVPMNQ-SLDVIKK-G-CHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRG   88 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~-~~~~l~~-~-~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~   88 (197)
                      |+++.+.+|.-.-++ ....|.+ + .||.|++=..++.-  ...+.-++++|+|+||||.+-++ -...++.++..  +
T Consensus       690 glKILTYyGs~kErkeKRqgW~kPnaFHVCItSYklv~qd--~~AFkrkrWqyLvLDEaqnIKnf-ksqrWQAllnf--n  764 (1958)
T KOG0391|consen  690 GLKILTYYGSHKERKEKRQGWAKPNAFHVCITSYKLVFQD--LTAFKRKRWQYLVLDEAQNIKNF-KSQRWQALLNF--N  764 (1958)
T ss_pred             cceEeeecCCHHHHHHHhhcccCCCeeEEeehhhHHHHhH--HHHHHhhccceeehhhhhhhcch-hHHHHHHHhcc--c
Confidence            899999999644322 3333533 3 68888885333322  23445577889999999998665 33456666554  3


Q ss_pred             CceEEEEeec
Q psy7789          89 QRQTLLFSAT   98 (197)
Q Consensus        89 ~~q~i~~SAT   98 (197)
                      ..|.++++.|
T Consensus       765 sqrRLLLtgT  774 (1958)
T KOG0391|consen  765 SQRRLLLTGT  774 (1958)
T ss_pred             hhheeeecCC
Confidence            4455666666

>cd00158 RHOD Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein

Probab=91.69  E-value=0.93  Score=28.14  Aligned_cols=36  Identities=11%  Similarity=0.255  Sum_probs=30.8

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCC-CeEeecCCCC
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGK-PFFTLKSLKE  188 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~-~~~~~h~~~~  188 (197)
                      ..++++||++...+...+..|+..|+ ++..+-||+.
T Consensus        50 ~~~vv~~c~~~~~a~~~~~~l~~~G~~~v~~l~gG~~   86 (89)
T cd00158          50 DKPIVVYCRSGNRSARAAKLLRKAGGTNVYNLEGGML   86 (89)
T ss_pred             CCeEEEEeCCCchHHHHHHHHHHhCcccEEEecCChh
Confidence            35799999999999999999999976 6778888875

The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins.

>smart00450 RHOD Rhodanese Homology Domain

Probab=91.67  E-value=0.46  Score=30.10  Aligned_cols=38  Identities=13%  Similarity=0.168  Sum_probs=33.0

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCCC-eEeecCCCChh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGKP-FFTLKSLKEDQ  190 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~~-~~~~h~~~~~~  190 (197)
                      ..++++||.+-..+..++..|+..|++ +..+.|++..=
T Consensus        56 ~~~iv~~c~~g~~a~~~~~~l~~~G~~~v~~l~GG~~~w   94 (100)
T smart00450       56 DKPVVVYCRSGNRSAKAAWLLRELGFKNVYLLDGGYKEW   94 (100)
T ss_pred             CCeEEEEeCCCcHHHHHHHHHHHcCCCceEEecCCHHHH
Confidence            357999999999999999999999997 88999998653

An alpha beta fold found duplicated in the Rhodanese protein. The the Cysteine containing enzymatically active version of the domain is also found in the CDC25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and stress proteins such as Senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions with a loss of the cysteine are also seen in Dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases. These are likely to play a role in protein interactions.

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=91.37  E-value=0.18  Score=45.36  Aligned_cols=59  Identities=20%  Similarity=0.215  Sum_probs=41.0

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHH-HHHhcC------CccCCCccEEEeehhhhhh
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLM-DMLDKK------MVSLDVCRYLCLDEADRMV   71 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~-~~l~~~------~~~l~~l~~vViDEad~l~   71 (197)
                      +|+.|..+.++.+..+..+...  +||+.+|..-+- ++++..      ..-.+.+.+.||||+|.++
T Consensus       144 LGLsvg~i~~~~~~~err~aY~--~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvDSiL  209 (870)
T CHL00122        144 LGLTVGLIQEGMSSEERKKNYL--KDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVDSIL  209 (870)
T ss_pred             cCCceeeeCCCCChHHHHHhcC--CCCEecCCccccccchhhccCcChHHhhccccceeeeecchhhe
Confidence            3788988888877765544444  899999986443 333321      1124778899999999875

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=91.34  E-value=0.19  Score=39.67  Aligned_cols=39  Identities=18%  Similarity=0.187  Sum_probs=28.2

Q ss_pred             cCCcEEEeCchHHHHHHhcCC--ccCCCccEEEeehhhhhhc
Q psy7789          33 KGCHMMVATPGRLMDMLDKKM--VSLDVCRYLCLDEADRMVD   72 (197)
Q Consensus        33 ~~~~Ili~TP~~l~~~l~~~~--~~l~~l~~vViDEad~l~~   72 (197)
                      ..+||||++-.-|++......  ..+ .-.+|||||||.+.+
T Consensus       210 ~~Adivi~ny~yll~~~~r~~~~~~l-~~~~lIiDEAHnL~d  250 (289)
T smart00488      210 EFANVVVLPYQYLLDPKIRQALSIEL-KDSIVIFDEAHNLDN  250 (289)
T ss_pred             hcCCEEEECHHHHhcHHHHHHhcccc-cccEEEEeCccChHH
Confidence            459999999888876553222  233 367999999999854

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=91.34  E-value=0.19  Score=39.67  Aligned_cols=39  Identities=18%  Similarity=0.187  Sum_probs=28.2

Q ss_pred             cCCcEEEeCchHHHHHHhcCC--ccCCCccEEEeehhhhhhc
Q psy7789          33 KGCHMMVATPGRLMDMLDKKM--VSLDVCRYLCLDEADRMVD   72 (197)
Q Consensus        33 ~~~~Ili~TP~~l~~~l~~~~--~~l~~l~~vViDEad~l~~   72 (197)
                      ..+||||++-.-|++......  ..+ .-.+|||||||.+.+
T Consensus       210 ~~Adivi~ny~yll~~~~r~~~~~~l-~~~~lIiDEAHnL~d  250 (289)
T smart00489      210 EFANVVVLPYQYLLDPKIRQALSIEL-KDSIVIFDEAHNLDN  250 (289)
T ss_pred             hcCCEEEECHHHHhcHHHHHHhcccc-cccEEEEeCccChHH
Confidence            459999999888876553222  233 367999999999854

>cd01529 4RHOD_Repeats Member of the Rhodanese Homology Domain superfamily

Probab=91.14  E-value=0.47  Score=30.48  Aligned_cols=36  Identities=14%  Similarity=0.068  Sum_probs=31.3

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCC-CeEeecCCCC
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGK-PFFTLKSLKE  188 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~-~~~~~h~~~~  188 (197)
                      ..++++||++-..+...+..|+..|+ ++..+.|+|.
T Consensus        56 ~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~l~GG~~   92 (96)
T cd01529          56 ATRYVLTCDGSLLARFAAQELLALGGKPVALLDGGTS   92 (96)
T ss_pred             CCCEEEEeCChHHHHHHHHHHHHcCCCCEEEeCCCHH
Confidence            35799999998888999999999998 6888999885

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. Only the second and most of the fourth repeats contain the putative catalytic Cys residue. This CD aligns the 1st , 2nd, 3rd, and 4th repeats.

>PRK05642 DNA replication initiation factor; Validated

Probab=90.97  E-value=0.5  Score=36.05  Aligned_cols=89  Identities=19%  Similarity=0.297  Sum_probs=53.8

Q ss_pred             eEEEEEcCCC--hHHhHHHH-----hcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcC-CCHHHHHHHHhh
Q psy7789          14 RTCLAIGGVP--MNQSLDVI-----KKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDM-GFEEDVRTIFSF   85 (197)
Q Consensus        14 ~~~~~~gg~~--~~~~~~~l-----~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~-~~~~~i~~i~~~   85 (197)
                      +...++|...  ...-...+     ..+..+++.+.+.+......-.-.+.+.+++++|++|.+... .....+-.++..
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~~~~~~~~~~~~~~~~~~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~  125 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPLAELLDRGPELLDNLEQYELVCLDDLDVIAGKADWEEALFHLFNR  125 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEeeHHHHHhhhHHHHHhhhhCCEEEEechhhhcCChHHHHHHHHHHHH
Confidence            5667888753  33333332     246788888887776543211113567789999999988543 234556777766


Q ss_pred             ccCCceEEEEeecCChh
Q psy7789          86 FRGQRQTLLFSATMPKK  102 (197)
Q Consensus        86 ~~~~~q~i~~SAT~~~~  102 (197)
                      +..+...++++++.++.
T Consensus       126 ~~~~g~~ilits~~~p~  142 (234)
T PRK05642        126 LRDSGRRLLLAASKSPR  142 (234)
T ss_pred             HHhcCCEEEEeCCCCHH
Confidence            65544456666665543

>cd01532 4RHOD_Repeat_1 Member of the Rhodanese Homology Domain superfamily, repeat 1

Probab=90.56  E-value=1  Score=28.72  Aligned_cols=36  Identities=14%  Similarity=0.173  Sum_probs=28.9

Q ss_pred             CCCEEEEecc--cccHHHHHHHHHhCCC-CeEeecCCCC
Q psy7789         153 EPPVLIFAEK--KQDVDAIHEYLLLKGK-PFFTLKSLKE  188 (197)
Q Consensus       153 ~~~~lIF~~s--~~~~~~l~~~L~~~~~-~~~~~h~~~~  188 (197)
                      ..++++||.+  +..+...+..|+..|+ ++..+.|||.
T Consensus        50 ~~~ivl~c~~G~~~~s~~aa~~L~~~G~~~v~~l~GG~~   88 (92)
T cd01532          50 DTPIVVYGEGGGEDLAPRAARRLSELGYTDVALLEGGLQ   88 (92)
T ss_pred             CCeEEEEeCCCCchHHHHHHHHHHHcCccCEEEccCCHH
Confidence            4579999988  3447788889999997 6888889875

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 1st repeat which does not contain the putative catalytic Cys residue.

>KOG0391|consensus

Probab=90.45  E-value=0.38  Score=44.69  Aligned_cols=65  Identities=20%  Similarity=0.280  Sum_probs=58.2

Q ss_pred             EEEcCchhhHHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         133 VEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       133 ~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      -+.|+.-.+++.|+.-|+.++.++|||+.=.+.-+-|-.+|+.+||--..+.|..+-++|.+.++
T Consensus      1256 qyDcGKLQtLAiLLqQLk~eghRvLIfTQMtkmLDVLeqFLnyHgylY~RLDg~t~vEqRQaLme 1320 (1958)
T KOG0391|consen 1256 QYDCGKLQTLAILLQQLKSEGHRVLIFTQMTKMLDVLEQFLNYHGYLYVRLDGNTSVEQRQALME 1320 (1958)
T ss_pred             ecccchHHHHHHHHHHHHhcCceEEehhHHHHHHHHHHHHHhhcceEEEEecCCccHHHHHHHHH
Confidence            34677778888888888889899999999999999999999999999999999999999998763

>KOG0921|consensus

Probab=90.21  E-value=0.77  Score=41.58  Aligned_cols=42  Identities=19%  Similarity=0.241  Sum_probs=32.6

Q ss_pred             CCEEEEecccccHHHHHHHHHhC-------CCCeEeecCCCChhhhhhh
Q psy7789         154 PPVLIFAEKKQDVDAIHEYLLLK-------GKPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       154 ~~~lIF~~s~~~~~~l~~~L~~~-------~~~~~~~h~~~~~~~R~~i  195 (197)
                      +-+++|.+-......|..+|..+       .+++...|+....++..+|
T Consensus       644 gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~ilp~Hsq~~~~eqrkv  692 (1282)
T KOG0921|consen  644 GAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHSQLTSQEQRKV  692 (1282)
T ss_pred             cceeeecCchHHhhhhhhhhhhhhhhccchhcccccchhhcccHhhhhc
Confidence            46899999999999999988654       4678889987776665544

>cd01528 RHOD_2 Member of the Rhodanese Homology Domain superfamily, subgroup 2

Probab=89.94  E-value=1.1  Score=29.05  Aligned_cols=38  Identities=11%  Similarity=0.255  Sum_probs=32.5

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCC-CeEeecCCCChh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGK-PFFTLKSLKEDQ  190 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~-~~~~~h~~~~~~  190 (197)
                      ..++++||++-.++...+..|.+.|+ ++..+.||+..=
T Consensus        58 ~~~vv~~c~~g~rs~~~~~~l~~~G~~~v~~l~GG~~~w   96 (101)
T cd01528          58 DKDIVVLCHHGGRSMQVAQWLLRQGFENVYNLQGGIDAW   96 (101)
T ss_pred             CCeEEEEeCCCchHHHHHHHHHHcCCccEEEecCCHHHH
Confidence            45899999998899999999999998 488899997653

Subgroup 2 includes uncharacterized putative rhodanese-related domains.

>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

Probab=89.82  E-value=3.1  Score=36.71  Aligned_cols=50  Identities=18%  Similarity=0.143  Sum_probs=36.6

Q ss_pred             hHHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCCC-eEeecCCCChh
Q psy7789         141 KIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKP-FFTLKSLKEDQ  190 (197)
Q Consensus       141 k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~-~~~~h~~~~~~  190 (197)
                      ....+..+++..+++++||++|.+..+.+++.+...... ....+|..+.+
T Consensus       467 ~~~~i~~~~~~~~~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~~~~~  517 (654)
T COG1199         467 LAAYLREILKASPGGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGEDERE  517 (654)
T ss_pred             HHHHHHHHHhhcCCCEEEEeccHHHHHHHHHHHhhcCccceeeecCCCcHH
Confidence            345666667777789999999999999999999987642 33445544443

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=89.67  E-value=0.34  Score=44.50  Aligned_cols=40  Identities=18%  Similarity=0.223  Sum_probs=30.0

Q ss_pred             cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhc
Q psy7789          33 KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD   72 (197)
Q Consensus        33 ~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~   72 (197)
                      ..+||+|+.-.-|+.-+....--+...+++||||||++.+
T Consensus       430 ~~AdivItNHalLl~dl~~~~~ilp~~~~lViDEAH~l~d  469 (928)
T PRK08074        430 KFADLVITNHALLLTDLTSEEPLLPSYEHIIIDEAHHFEE  469 (928)
T ss_pred             hcCCEEEECHHHHHHHHhhhcccCCCCCeEEEECCchHHH
Confidence            4599999998877766533222346679999999999964

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=89.50  E-value=0.4  Score=43.24  Aligned_cols=59  Identities=15%  Similarity=0.223  Sum_probs=41.3

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHH-HHHhcC------CccCCCccEEEeehhhhhh
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLM-DMLDKK------MVSLDVCRYLCLDEADRMV   71 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~-~~l~~~------~~~l~~l~~vViDEad~l~   71 (197)
                      +|+.|+.+..+.+.........  +||..+|..-+- ++++..      ..-.+.+.+.||||+|.++
T Consensus       146 LGLsvG~i~~~~~~~~rr~aY~--~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEVDSIL  211 (925)
T PRK12903        146 LGLSVGINKANMDPNLKREAYA--CDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEVDSIL  211 (925)
T ss_pred             hCCceeeeCCCCChHHHHHhcc--CCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccchhee
Confidence            3788888888776665444443  899999987654 344432      1124778899999999886

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=89.48  E-value=1.7  Score=32.29  Aligned_cols=36  Identities=17%  Similarity=0.249  Sum_probs=21.9

Q ss_pred             hcCCcEEEeCchHHHHHHhcCCcc-C-CCccEEEeehhhhhh
Q psy7789          32 KKGCHMMVATPGRLMDMLDKKMVS-L-DVCRYLCLDEADRMV   71 (197)
Q Consensus        32 ~~~~~Ili~TP~~l~~~l~~~~~~-l-~~l~~vViDEad~l~   71 (197)
                      -+.++|+++|+......    .+. . ..++++|||||-.+.
T Consensus       168 l~~~~vi~~T~~~~~~~----~~~~~~~~~d~vIvDEAsq~~  205 (236)
T PF13086_consen  168 LKEADVIFTTLSSAASP----FLSNFKEKFDVVIVDEASQIT  205 (236)
T ss_dssp             HHT-SEEEEETCGGG-C----CGTT-----SEEEETTGGGS-
T ss_pred             cccccccccccccchhh----HhhhhcccCCEEEEeCCCCcc
Confidence            34699999999776222    222 2 278899999998874

>PF02463 SMC_N: RecF/RecN/SMC N terminal domain; InterPro: IPR003395 This domain is found at the N terminus of structural maintenance of chromosomes (SMC) proteins, which function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression []

Probab=89.46  E-value=0.31  Score=36.56  Aligned_cols=43  Identities=19%  Similarity=0.264  Sum_probs=32.3

Q ss_pred             CCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEeec
Q psy7789          56 LDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSAT   98 (197)
Q Consensus        56 l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SAT   98 (197)
                      .....++++||+|.-++......+..++....+..|+++.|..
T Consensus       156 ~~~~p~~ilDEvd~~LD~~~~~~l~~~l~~~~~~~Q~ii~Th~  198 (220)
T PF02463_consen  156 YKPSPFLILDEVDAALDEQNRKRLADLLKELSKQSQFIITTHN  198 (220)
T ss_dssp             CS--SEEEEESTTTTS-HHHHHHHHHHHHHHTTTSEEEEE-S-
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccc
Confidence            3556799999999999877788888888888888999988643

The domain is also found in RecF and RecN proteins, which are involved in DNA metabolism and recombination.; PDB: 3HTK_A 1W1W_C 2WD5_A 3L51_A 1XEW_Y 3KTA_B 3NWC_B 1XEX_A 1GXL_C 1GXK_A ....

>cd01518 RHOD_YceA Member of the Rhodanese Homology Domain superfamily

Probab=89.13  E-value=0.49  Score=30.74  Aligned_cols=37  Identities=19%  Similarity=0.241  Sum_probs=31.0

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCCC-eEeecCCCCh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGKP-FFTLKSLKED  189 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~~-~~~~h~~~~~  189 (197)
                      ..+++|||.+-.++...+..|+..|++ +..+.||+..
T Consensus        61 ~~~ivvyC~~G~rs~~a~~~L~~~G~~~v~~l~GG~~~   98 (101)
T cd01518          61 GKKVLMYCTGGIRCEKASAYLKERGFKNVYQLKGGILK   98 (101)
T ss_pred             CCEEEEECCCchhHHHHHHHHHHhCCcceeeechhHHH
Confidence            357999999888888889999999994 8889998753

This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins.

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=89.11  E-value=0.96  Score=34.16  Aligned_cols=92  Identities=14%  Similarity=0.206  Sum_probs=55.2

Q ss_pred             CeeEEEEEcCCC--hHHhHHHH-------hcCCcEEEeCchHHHHHH----hcCC-----ccCCCccEEEeehhhhhhcC
Q psy7789          12 PLRTCLAIGGVP--MNQSLDVI-------KKGCHMMVATPGRLMDML----DKKM-----VSLDVCRYLCLDEADRMVDM   73 (197)
Q Consensus        12 ~i~~~~~~gg~~--~~~~~~~l-------~~~~~Ili~TP~~l~~~l----~~~~-----~~l~~l~~vViDEad~l~~~   73 (197)
                      ...+..++|+..  ...-...+       ..+..|+..+.+.+...+    ..+.     -.+...+++++|++|.+.+.
T Consensus        33 ~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~~~f~~~~~~~~~~~~~~~~~~~~~~~DlL~iDDi~~l~~~  112 (219)
T PF00308_consen   33 RYNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSAEEFIREFADALRDGEIEEFKDRLRSADLLIIDDIQFLAGK  112 (219)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEHHHHHHHHHHHHHTTSHHHHHHHHCTSSEEEEETGGGGTTH
T ss_pred             CCCceEEECCCCCCHHHHHHHHHHHHHhccccccceeecHHHHHHHHHHHHHcccchhhhhhhhcCCEEEEecchhhcCc
Confidence            456778999864  33322222       135789998888776543    2222     13688999999999998653


Q ss_pred             C-CHHHHHHHHhhcc-CCceEEEEeecCChhH
Q psy7789          74 G-FEEDVRTIFSFFR-GQRQTLLFSATMPKKI  103 (197)
Q Consensus        74 ~-~~~~i~~i~~~~~-~~~q~i~~SAT~~~~~  103 (197)
                      . ..+.+-.++..+. ...|+++.|...|.+.
T Consensus       113 ~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l  144 (219)
T PF00308_consen  113 QRTQEELFHLFNRLIESGKQLILTSDRPPSEL  144 (219)
T ss_dssp             HHHHHHHHHHHHHHHHTTSEEEEEESS-TTTT
T ss_pred             hHHHHHHHHHHHHHHhhCCeEEEEeCCCCccc
Confidence            1 2344555555553 3567777776665543

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=89.03  E-value=1  Score=30.47  Aligned_cols=35  Identities=23%  Similarity=0.375  Sum_probs=20.4

Q ss_pred             cEEEeehhhhhhcCCCHHHHHHHHhhcc-CCceEEEEee
Q psy7789          60 RYLCLDEADRMVDMGFEEDVRTIFSFFR-GQRQTLLFSA   97 (197)
Q Consensus        60 ~~vViDEad~l~~~~~~~~i~~i~~~~~-~~~q~i~~SA   97 (197)
                      .++|+||+|.+..   .+.+..+..... ...++++++.
T Consensus        89 ~~lviDe~~~l~~---~~~l~~l~~l~~~~~~~vvl~G~  124 (131)
T PF13401_consen   89 VLLVIDEADHLFS---DEFLEFLRSLLNESNIKVVLVGT  124 (131)
T ss_dssp             EEEEEETTHHHHT---HHHHHHHHHHTCSCBEEEEEEES
T ss_pred             eEEEEeChHhcCC---HHHHHHHHHHHhCCCCeEEEEEC
Confidence            6899999999751   444444433333 3445555543

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=88.98  E-value=3.3  Score=37.02  Aligned_cols=34  Identities=15%  Similarity=0.141  Sum_probs=26.7

Q ss_pred             HHHHHhhcCCCCEEEEecccccHHHHHHHHHhCC
Q psy7789         144 YLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKG  177 (197)
Q Consensus       144 ~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~  177 (197)
                      .+.++++..++.+|||++|...-+.+++.+.+.|
T Consensus       513 ~i~~~~~~~pgg~lvfFpSy~~l~~v~~~~~~~~  546 (705)
T TIGR00604       513 LLVEFSKIIPDGIVVFFPSYSYLENIVSTWKEMG  546 (705)
T ss_pred             HHHHHhhcCCCcEEEEccCHHHHHHHHHHHHhcC
Confidence            3445555567789999999999999999887654

All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>cd01520 RHOD_YbbB Member of the Rhodanese Homology Domain superfamily

Probab=88.91  E-value=0.71  Score=31.57  Aligned_cols=37  Identities=16%  Similarity=0.147  Sum_probs=31.0

Q ss_pred             CCCEEEEec-ccccHHHHHHHHHhCCCCeEeecCCCCh
Q psy7789         153 EPPVLIFAE-KKQDVDAIHEYLLLKGKPFFTLKSLKED  189 (197)
Q Consensus       153 ~~~~lIF~~-s~~~~~~l~~~L~~~~~~~~~~h~~~~~  189 (197)
                      ..++++||+ +-.++...+..|+..|+++..+.||++.
T Consensus        86 ~~~vvvyC~~~G~rs~~a~~~L~~~G~~v~~L~GG~~a  123 (128)
T cd01520          86 DPKLLIYCARGGMRSQSLAWLLESLGIDVPLLEGGYKA  123 (128)
T ss_pred             CCeEEEEeCCCCccHHHHHHHHHHcCCceeEeCCcHHH
Confidence            357999997 5677888888898899999999999865

This CD includes several putative ATP /GTP binding proteins including E. coli YbbB.

>cd01527 RHOD_YgaP Member of the Rhodanese Homology Domain superfamily

Probab=88.87  E-value=0.92  Score=29.23  Aligned_cols=37  Identities=8%  Similarity=0.065  Sum_probs=31.3

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCC-CeEeecCCCCh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGK-PFFTLKSLKED  189 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~-~~~~~h~~~~~  189 (197)
                      ..++++||++-.++...+..|.+.|+ ++..+.|++..
T Consensus        54 ~~~iv~~c~~g~~s~~~~~~L~~~g~~~v~~l~gG~~~   91 (99)
T cd01527          54 ANAIIFHCRSGMRTQQNAERLAAISAGEAYVLEGGLDA   91 (99)
T ss_pred             CCcEEEEeCCCchHHHHHHHHHHcCCccEEEeeCCHHH
Confidence            35899999998888899999999888 68889998754

This CD includes Escherichia coli YgaP, and similar uncharacterized putative rhodanese-related sulfurtransferases.

>PF13173 AAA_14: AAA domain

Probab=88.86  E-value=0.88  Score=31.01  Aligned_cols=40  Identities=15%  Similarity=0.274  Sum_probs=28.2

Q ss_pred             CccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEeecCC
Q psy7789          58 VCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMP  100 (197)
Q Consensus        58 ~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SAT~~  100 (197)
                      .-.++++||+|.+-+  +...++.+.... ++.++++.+....
T Consensus        61 ~~~~i~iDEiq~~~~--~~~~lk~l~d~~-~~~~ii~tgS~~~  100 (128)
T PF13173_consen   61 GKKYIFIDEIQYLPD--WEDALKFLVDNG-PNIKIILTGSSSS  100 (128)
T ss_pred             CCcEEEEehhhhhcc--HHHHHHHHHHhc-cCceEEEEccchH
Confidence            567999999999865  467777776654 4567777665543

>TIGR02981 phageshock_pspE phage shock operon rhodanese PspE

Probab=88.80  E-value=1.6  Score=28.61  Aligned_cols=36  Identities=11%  Similarity=0.080  Sum_probs=28.8

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCC
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKE  188 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~  188 (197)
                      ..++++||++-.++...+..|++.|+.....-||+.
T Consensus        58 ~~~vvlyC~~G~rS~~aa~~L~~~G~~~v~~~GG~~   93 (101)
T TIGR02981        58 NDTVKLYCNAGRQSGMAKDILLDMGYTHAENAGGIK   93 (101)
T ss_pred             CCeEEEEeCCCHHHHHHHHHHHHcCCCeEEecCCHH
Confidence            457899999988999999999999986444457764

Members of this very narrowly defined protein family are proteins active as rhodanese (EC 2.8.1.1) and found in the extended variants of the phage shock protein (psp operon) in Escherichia coli and a few closely related species. Note that the designation phage shock protein PspE has been applied, incorrectly, in many instances where the genome lacks the phage shock regulon entirely.

>cd01521 RHOD_PspE2 Member of the Rhodanese Homology Domain superfamily

Probab=88.59  E-value=0.94  Score=29.98  Aligned_cols=39  Identities=10%  Similarity=0.020  Sum_probs=31.9

Q ss_pred             CCCEEEEeccc--ccHHHHHHHHHhCCCCeEeecCCCChhh
Q psy7789         153 EPPVLIFAEKK--QDVDAIHEYLLLKGKPFFTLKSLKEDQN  191 (197)
Q Consensus       153 ~~~~lIF~~s~--~~~~~l~~~L~~~~~~~~~~h~~~~~~~  191 (197)
                      ..++++||++-  ..+...+..|+..|+++..+.|++..=.
T Consensus        64 ~~~vvvyc~~g~~~~s~~~a~~l~~~G~~v~~l~GG~~~W~  104 (110)
T cd01521          64 EKLFVVYCDGPGCNGATKAALKLAELGFPVKEMIGGLDWWK  104 (110)
T ss_pred             CCeEEEEECCCCCchHHHHHHHHHHcCCeEEEecCCHHHHH
Confidence            35799999875  4788899999999999999999986543

This CD includes the putative rhodanese-like protein, Psp2, of Yersinia pestis biovar Medievalis and other similar uncharacterized proteins.

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=88.43  E-value=0.75  Score=41.73  Aligned_cols=39  Identities=13%  Similarity=0.315  Sum_probs=29.9

Q ss_pred             cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhc
Q psy7789          33 KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD   72 (197)
Q Consensus        33 ~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~   72 (197)
                      ..+||+|+.-.-|+..+.... .+...+++||||||.+.+
T Consensus       412 ~~AdivItNHall~~~~~~~~-~~p~~~~lIiDEAH~l~~  450 (820)
T PRK07246        412 KTARLLITNHAYFLTRVQDDK-DFARNKVLVFDEAQKLML  450 (820)
T ss_pred             HhCCEEEEchHHHHHHHhhcc-CCCCCCEEEEECcchhHH
Confidence            459999999887776654332 256789999999999963

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=88.12  E-value=0.92  Score=40.40  Aligned_cols=60  Identities=17%  Similarity=0.141  Sum_probs=51.0

Q ss_pred             cCchhhHHHHHHHhhcC---CCCEEEEecccccHHHHHHHHHhC-CCCeEeecCCCChhhhhhh
Q psy7789         136 VKQEAKIVYLLECLQKT---EPPVLIFAEKKQDVDAIHEYLLLK-GKPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       136 ~~~~~k~~~l~~~l~~~---~~~~lIF~~s~~~~~~l~~~L~~~-~~~~~~~h~~~~~~~R~~i  195 (197)
                      +....|.+.+++++.+.   ++++||-++.+.-...+.+.|+.+ |.++..+||+|++.+|..+
T Consensus       225 vTGSGKTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~  288 (730)
T COG1198         225 VTGSGKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRV  288 (730)
T ss_pred             CCCCcHHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHH
Confidence            45567888888887753   568999999999999999999887 8999999999999999764

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=88.02  E-value=3.9  Score=34.43  Aligned_cols=94  Identities=11%  Similarity=0.199  Sum_probs=55.2

Q ss_pred             CeeEEEEEcCCC--hHHhHHHH-----hcCCcEEEeCchHHHHHHh----cCCc-----cCCCccEEEeehhhhhhcCC-
Q psy7789          12 PLRTCLAIGGVP--MNQSLDVI-----KKGCHMMVATPGRLMDMLD----KKMV-----SLDVCRYLCLDEADRMVDMG-   74 (197)
Q Consensus        12 ~i~~~~~~gg~~--~~~~~~~l-----~~~~~Ili~TP~~l~~~l~----~~~~-----~l~~l~~vViDEad~l~~~~-   74 (197)
                      ..+...++|+..  ...-...+     ..+..++..+.+.+...+.    .+..     .+.+.+++++||+|.+.... 
T Consensus       140 ~~npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~~~f~~~~~~~l~~~~~~~f~~~~~~~dvLiIDDiq~l~~k~~  219 (445)
T PRK12422        140 PFNPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRSELFTEHLVSAIRSGEMQRFRQFYRNVDALFIEDIEVFSGKGA  219 (445)
T ss_pred             CCceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeHHHHHHHHHHHHhcchHHHHHHHcccCCEEEEcchhhhcCChh
Confidence            356788998864  33322222     2468899888877654432    2111     15778999999999986532 


Q ss_pred             CHHHHHHHHhhc-cCCceEEEEeecCChhHHH
Q psy7789          75 FEEDVRTIFSFF-RGQRQTLLFSATMPKKIQN  105 (197)
Q Consensus        75 ~~~~i~~i~~~~-~~~~q~i~~SAT~~~~~~~  105 (197)
                      ..+.+..++..+ ....|+++.|.+.+.+...
T Consensus       220 ~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~  251 (445)
T PRK12422        220 TQEEFFHTFNSLHTEGKLIVISSTCAPQDLKA  251 (445)
T ss_pred             hHHHHHHHHHHHHHCCCcEEEecCCCHHHHhh
Confidence            344444555433 2355666666555554443

>PRK06893 DNA replication initiation factor; Validated

Probab=87.92  E-value=1.2  Score=33.85  Aligned_cols=89  Identities=15%  Similarity=0.213  Sum_probs=47.4

Q ss_pred             EEEEEcCCC--hHHhHHHH-----hcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcC-CCHHHHHHHHhhc
Q psy7789          15 TCLAIGGVP--MNQSLDVI-----KKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDM-GFEEDVRTIFSFF   86 (197)
Q Consensus        15 ~~~~~gg~~--~~~~~~~l-----~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~-~~~~~i~~i~~~~   86 (197)
                      ...++|...  ...-...+     ..+..+.+.+..........-.-.+.+.+++++||+|.+... .....+..++...
T Consensus        41 ~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~  120 (229)
T PRK06893         41 FFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPLSKSQYFSPAVLENLEQQDLVCLDDLQAVIGNEEWELAIFDLFNRI  120 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeHHHhhhhhHHHHhhcccCCEEEEeChhhhcCChHHHHHHHHHHHHH
Confidence            346666643  33332222     234566666654322211111113567889999999998643 2233455555554


Q ss_pred             cC-CceEEEEeecCChhH
Q psy7789          87 RG-QRQTLLFSATMPKKI  103 (197)
Q Consensus        87 ~~-~~q~i~~SAT~~~~~  103 (197)
                      .. ..+++++|++.++..
T Consensus       121 ~~~~~~illits~~~p~~  138 (229)
T PRK06893        121 KEQGKTLLLISADCSPHA  138 (229)
T ss_pred             HHcCCcEEEEeCCCChHH
Confidence            43 446678888876543

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=87.90  E-value=0.57  Score=37.09  Aligned_cols=38  Identities=16%  Similarity=0.218  Sum_probs=27.8

Q ss_pred             CCCccEEEeehhhhhhcCCCH--HHHHHHHhhccCCceEE
Q psy7789          56 LDVCRYLCLDEADRMVDMGFE--EDVRTIFSFFRGQRQTL   93 (197)
Q Consensus        56 l~~l~~vViDEad~l~~~~~~--~~i~~i~~~~~~~~q~i   93 (197)
                      --.++++||||+|.++..+..  ..+.+.++++.+..++-
T Consensus       143 ~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ip  182 (302)
T PF05621_consen  143 RLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIP  182 (302)
T ss_pred             HcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCC
Confidence            456889999999999875533  34667788887766653

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=87.88  E-value=1.5  Score=37.01  Aligned_cols=89  Identities=15%  Similarity=0.105  Sum_probs=52.1

Q ss_pred             CeeEEEEEcCCC--hHHhHHHH-------hcCCcEEEeCchHHHHHHhc------CCc-----cCCCccEEEeehhhhhh
Q psy7789          12 PLRTCLAIGGVP--MNQSLDVI-------KKGCHMMVATPGRLMDMLDK------KMV-----SLDVCRYLCLDEADRMV   71 (197)
Q Consensus        12 ~i~~~~~~gg~~--~~~~~~~l-------~~~~~Ili~TP~~l~~~l~~------~~~-----~l~~l~~vViDEad~l~   71 (197)
                      .-+...++|+..  ...-...+       ..+..++..|++.+...+..      +.+     .+.+.++||+||+|.+.
T Consensus       140 ~~npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~~~f~~~~~~~l~~~~~~~~~~~~~~~~~dvLiIDDiq~l~  219 (450)
T PRK14087        140 SYNPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSGDEFARKAVDILQKTHKEIEQFKNEICQNDVLIIDDVQFLS  219 (450)
T ss_pred             ccCceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHHHHHHhhhHHHHHHHHhccCCEEEEecccccc
Confidence            346778898754  33322222       13578888888887765421      111     25778999999999885


Q ss_pred             cC-CCHHHHHHHHhhccC-CceEEEEeecCC
Q psy7789          72 DM-GFEEDVRTIFSFFRG-QRQTLLFSATMP  100 (197)
Q Consensus        72 ~~-~~~~~i~~i~~~~~~-~~q~i~~SAT~~  100 (197)
                      .. ...+.+..++..+.. ..|+++.|-..|
T Consensus       220 ~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P  250 (450)
T PRK14087        220 YKEKTNEIFFTIFNNFIENDKQLFFSSDKSP  250 (450)
T ss_pred             CCHHHHHHHHHHHHHHHHcCCcEEEECCCCH
Confidence            42 234455555555433 446665555443

>cd01444 GlpE_ST GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily

Probab=87.74  E-value=1.1  Score=28.56  Aligned_cols=36  Identities=17%  Similarity=0.194  Sum_probs=31.3

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCC-CeEeecCCCC
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGK-PFFTLKSLKE  188 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~-~~~~~h~~~~  188 (197)
                      ..+++++|++-.++...+..|+..|+ ++..+.|++.
T Consensus        56 ~~~ivv~c~~g~~s~~a~~~l~~~G~~~v~~l~gG~~   92 (96)
T cd01444          56 DRPVVVYCYHGNSSAQLAQALREAGFTDVRSLAGGFE   92 (96)
T ss_pred             CCCEEEEeCCCChHHHHHHHHHHcCCceEEEcCCCHH
Confidence            35899999999999999999999998 5888888874

Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a catalytically active cysteine.

>KOG0392|consensus

Probab=87.71  E-value=1.7  Score=40.79  Aligned_cols=87  Identities=15%  Similarity=0.213  Sum_probs=52.1

Q ss_pred             eeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHH---HHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCC
Q psy7789          13 LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMD---MLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        13 i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~---~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~   89 (197)
                      +++...+|+-..+...+.=-++.+|+|++=+-+..   .+.+     .+..|+|+||-|.+-+.  ...+-...+.+..+
T Consensus      1057 L~v~~yvg~p~~r~~lR~q~~~~~iiVtSYDv~RnD~d~l~~-----~~wNYcVLDEGHVikN~--ktkl~kavkqL~a~ 1129 (1549)
T KOG0392|consen 1057 LKVLQYVGPPAERRELRDQYKNANIIVTSYDVVRNDVDYLIK-----IDWNYCVLDEGHVIKNS--KTKLTKAVKQLRAN 1129 (1549)
T ss_pred             hhhhhhcCChHHHHHHHhhccccceEEeeHHHHHHHHHHHHh-----cccceEEecCcceecch--HHHHHHHHHHHhhc
Confidence            67777777644333322222348999999765552   2232     34459999999998553  55555666666656


Q ss_pred             ceEEEEeecCChhHHHH
Q psy7789          90 RQTLLFSATMPKKIQNF  106 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~  106 (197)
                      .++|+....+...+.+.
T Consensus      1130 hRLILSGTPIQNnvleL 1146 (1549)
T KOG0392|consen 1130 HRLILSGTPIQNNVLEL 1146 (1549)
T ss_pred             ceEEeeCCCcccCHHHH
Confidence            66665555555444443

>cd01525 RHOD_Kc Member of the Rhodanese Homology Domain superfamily

Probab=87.41  E-value=1.5  Score=28.48  Aligned_cols=37  Identities=14%  Similarity=0.219  Sum_probs=31.4

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCCC-eEeecCCCCh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGKP-FFTLKSLKED  189 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~~-~~~~h~~~~~  189 (197)
                      ..++++||.+-..+...+..|+..|+. +..+.||+..
T Consensus        65 ~~~vv~~c~~g~~s~~~a~~L~~~G~~~v~~l~GG~~a  102 (105)
T cd01525          65 GKIIVIVSHSHKHAALFAAFLVKCGVPRVCILDGGINA  102 (105)
T ss_pred             CCeEEEEeCCCccHHHHHHHHHHcCCCCEEEEeCcHHH
Confidence            457999999888888999999999985 8889998853

Included in this CD are the rhodanese-like domains found C-terminal of the serine/threonine protein kinases catalytic (S_TKc) domain and the Tre-2, BUB2p, Cdc16p (TBC) domain. The putative active site Cys residue is not present in this CD.

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=87.19  E-value=0.87  Score=40.58  Aligned_cols=40  Identities=23%  Similarity=0.231  Sum_probs=27.8

Q ss_pred             cCCcEEEeCchHHHHHHhc-CCccCC--CccEEEeehhhhhhc
Q psy7789          33 KGCHMMVATPGRLMDMLDK-KMVSLD--VCRYLCLDEADRMVD   72 (197)
Q Consensus        33 ~~~~Ili~TP~~l~~~l~~-~~~~l~--~l~~vViDEad~l~~   72 (197)
                      ..+||||+.-.-|+.-+.. ..--+.  +-+++||||||++.+
T Consensus       218 ~~AdivVtNH~LLladl~~~~~~iLp~~~~~~lViDEAH~L~d  260 (697)
T PRK11747        218 DEADVVVANHDLVLADLELGGGVVLPDPENLLYVLDEGHHLPD  260 (697)
T ss_pred             hhCCEEEECcHHHHhhhhccCCcccCCCCCCEEEEECccchHH
Confidence            4599999998777755532 111233  467899999999963

>PRK14873 primosome assembly protein PriA; Provisional

Probab=87.06  E-value=1.7  Score=38.52  Aligned_cols=57  Identities=16%  Similarity=0.085  Sum_probs=47.1

Q ss_pred             hhhHHHHHHHhhc---CCCCEEEEecccccHHHHHHHHHhC-C-CCeEeecCCCChhhhhhh
Q psy7789         139 EAKIVYLLECLQK---TEPPVLIFAEKKQDVDAIHEYLLLK-G-KPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       139 ~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~~L~~~-~-~~~~~~h~~~~~~~R~~i  195 (197)
                      ..|...+++++..   .++++||-++++..+..+.+.|++. | .++..+||++++.+|.+.
T Consensus       171 SGKTevyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~  232 (665)
T PRK14873        171 EDWARRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRR  232 (665)
T ss_pred             CcHHHHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHH
Confidence            4677777776654   3568999999999999999999876 4 679999999999999763

>KOG0964|consensus

Probab=86.83  E-value=1.2  Score=40.41  Aligned_cols=94  Identities=12%  Similarity=0.159  Sum_probs=65.0

Q ss_pred             CeeEEEEEcC-CChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          12 PLRTCLAIGG-VPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        12 ~i~~~~~~gg-~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      ||.+..-+.| ..-...+..|++|-.=+||-- -++.+=.-.+..     +-++||+|.-++.+++..+..+++.+..+.
T Consensus      1078 GIsI~VSFnskq~E~~~m~QLSGGQKsvvALa-LIFaIQrcDPAP-----FYlfDEIDAaLDaQyR~aVa~lIkelS~~a 1151 (1200)
T KOG0964|consen 1078 GISIKVSFNSKQGETLEMEQLSGGQKSVVALA-LIFAIQRCDPAP-----FYLFDEIDAALDAQYRTAVADLIKELSDSA 1151 (1200)
T ss_pred             ceeEEEEeecCccHHHHHHHhcCchHHHHHHH-HHHHHHhcCCcc-----hhhHhHHhhhccHHHHHHHHHHHHHHhhcc
Confidence            4555554443 444445577887765555432 111111112222     779999999999999999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcCC
Q psy7789          91 QTLLFSATMPKKIQNFARSALVK  113 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~  113 (197)
                      |+|+  .|+-|++...+..|++-
T Consensus      1152 QFI~--TTFRpEll~vAdKfygV 1172 (1200)
T KOG0964|consen 1152 QFIT--TTFRPELLSVADKFYGV 1172 (1200)
T ss_pred             ceEe--ecccHHHHHHHHhhhce
Confidence            9886  57889999999998864

>PRK10287 thiosulfate:cyanide sulfurtransferase; Provisional

Probab=86.51  E-value=3  Score=27.49  Aligned_cols=36  Identities=14%  Similarity=0.083  Sum_probs=29.5

Q ss_pred             CCEEEEecccccHHHHHHHHHhCCCCeEeecCCCCh
Q psy7789         154 PPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKED  189 (197)
Q Consensus       154 ~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~  189 (197)
                      .++++||++-.++...+..|...|++....-||+..
T Consensus        61 ~~IVlyC~~G~rS~~aa~~L~~~G~~~v~~~GG~~~   96 (104)
T PRK10287         61 DTVKLYCNAGRQSGQAKEILSEMGYTHAENAGGLKD   96 (104)
T ss_pred             CeEEEEeCCChHHHHHHHHHHHcCCCeEEecCCHHH
Confidence            469999999889999999999999875555687654

>cd01447 Polysulfide_ST Polysulfide-sulfurtransferase - Rhodanese Homology Domain

Probab=86.36  E-value=0.84  Score=29.49  Aligned_cols=37  Identities=11%  Similarity=0.164  Sum_probs=31.0

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCCC-eEeecCCCCh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGKP-FFTLKSLKED  189 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~~-~~~~h~~~~~  189 (197)
                      ..+++|||.+-.++...+..|...|++ +..+-|++..
T Consensus        61 ~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~l~Gg~~~   98 (103)
T cd01447          61 DKPFVFYCASGWRSALAGKTLQDMGLKPVYNIEGGFKD   98 (103)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHcChHHhEeecCcHHH
Confidence            357999998878888889999999986 8888888754

This domain is believed to serve as a polysulfide binding and transferase domain in anaerobic gram-negative bacteria, functioning in oxidative phosphorylation with polysulfide-sulfur as a terminal electron acceptor. The active site contains the same conserved cysteine that is the catalytic residue in other Rhodanese Homology Domain proteins.

>PRK08727 hypothetical protein; Validated

Probab=86.16  E-value=1.7  Score=33.12  Aligned_cols=88  Identities=13%  Similarity=0.022  Sum_probs=46.9

Q ss_pred             eEEEEEcCCC--hHHhHHH-----HhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCC-CHHHHHHHHhh
Q psy7789          14 RTCLAIGGVP--MNQSLDV-----IKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMG-FEEDVRTIFSF   85 (197)
Q Consensus        14 ~~~~~~gg~~--~~~~~~~-----l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~-~~~~i~~i~~~   85 (197)
                      ....++|+..  ...-...     ...+..+++.+...+...+....-.+.+.++||+||+|.+..+. ....+-.++..
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~l~~~dlLiIDDi~~l~~~~~~~~~lf~l~n~  121 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPLQAAAGRLRDALEALEGRSLVALDGLESIAGQREDEVALFDFHNR  121 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEeHHHhhhhHHHHHHHHhcCCEEEEeCcccccCChHHHHHHHHHHHH
Confidence            4567787753  3322222     23467777766655554333222245677899999999886542 22233344444


Q ss_pred             ccC-CceEEEEeecCCh
Q psy7789          86 FRG-QRQTLLFSATMPK  101 (197)
Q Consensus        86 ~~~-~~q~i~~SAT~~~  101 (197)
                      ... ..++++.|...+.
T Consensus       122 ~~~~~~~vI~ts~~~p~  138 (233)
T PRK08727        122 ARAAGITLLYTARQMPD  138 (233)
T ss_pred             HHHcCCeEEEECCCChh
Confidence            332 3345555544333

>KOG0953|consensus

Probab=85.91  E-value=2.5  Score=36.36  Aligned_cols=156  Identities=11%  Similarity=0.016  Sum_probs=84.5

Q ss_pred             CCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHH-HHhhccC
Q psy7789          10 PIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRT-IFSFFRG   88 (197)
Q Consensus        10 ~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~-i~~~~~~   88 (197)
                      ..||.|-+++|..-....-+  .+.+..+=||-|...-        -...+..||||.-.+-+.+.+-.+-. ++.....
T Consensus       237 a~gipCdL~TGeE~~~~~~~--~~~a~hvScTVEM~sv--------~~~yeVAViDEIQmm~Dp~RGwAWTrALLGl~Ad  306 (700)
T KOG0953|consen  237 ALGIPCDLLTGEERRFVLDN--GNPAQHVSCTVEMVSV--------NTPYEVAVIDEIQMMRDPSRGWAWTRALLGLAAD  306 (700)
T ss_pred             hcCCCccccccceeeecCCC--CCcccceEEEEEEeec--------CCceEEEEehhHHhhcCcccchHHHHHHHhhhhh
Confidence            35788888888532222111  1236666677533221        13456899999999988766544443 3333333


Q ss_pred             CceEEEEeecCChhHHHHHHHhcCC---CeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcC-CCCEEEEecccc
Q psy7789          89 QRQTLLFSATMPKKIQNFARSALVK---PITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKT-EPPVLIFAEKKQ  164 (197)
Q Consensus        89 ~~q~i~~SAT~~~~~~~~~~~~~~~---~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~-~~~~lIF~~s~~  164 (197)
                      +..+..=     +.+...++..+..   ...+.             .|-....-.-.+.++.-+... ++-++| |-|++
T Consensus       307 EiHLCGe-----psvldlV~~i~k~TGd~vev~-------------~YeRl~pL~v~~~~~~sl~nlk~GDCvV-~FSkk  367 (700)
T KOG0953|consen  307 EIHLCGE-----PSVLDLVRKILKMTGDDVEVR-------------EYERLSPLVVEETALGSLSNLKPGDCVV-AFSKK  367 (700)
T ss_pred             hhhccCC-----chHHHHHHHHHhhcCCeeEEE-------------eecccCcceehhhhhhhhccCCCCCeEE-Eeehh
Confidence            3333221     3344444444432   11111             111111111112333334433 344554 55788


Q ss_pred             cHHHHHHHHHhCCCC-eEeecCCCChhhhhh
Q psy7789         165 DVDAIHEYLLLKGKP-FFTLKSLKEDQNNQT  194 (197)
Q Consensus       165 ~~~~l~~~L~~~~~~-~~~~h~~~~~~~R~~  194 (197)
                      ..-.+...+.+.|.. +++++|+++++.|.+
T Consensus       368 ~I~~~k~kIE~~g~~k~aVIYGsLPPeTr~a  398 (700)
T KOG0953|consen  368 DIFTVKKKIEKAGNHKCAVIYGSLPPETRLA  398 (700)
T ss_pred             hHHHHHHHHHHhcCcceEEEecCCCCchhHH
Confidence            888888888888664 999999999998864

>KOG0347|consensus

Probab=85.88  E-value=0.83  Score=39.12  Aligned_cols=42  Identities=14%  Similarity=0.106  Sum_probs=37.9

Q ss_pred             EEEEecccccHHHHHHHHHh----CCCCeEeecCCCChhhhhhhhC
Q psy7789         156 VLIFAEKKQDVDAIHEYLLL----KGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       156 ~lIF~~s~~~~~~l~~~L~~----~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      +|||++|++-|..+.+.|..    .|+++..+.|||+....+++++
T Consensus       266 ~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~  311 (731)
T KOG0347|consen  266 ALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLN  311 (731)
T ss_pred             eEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHh
Confidence            89999999999999998865    3899999999999999988764

>cd01519 RHOD_HSP67B2 Member of the Rhodanese Homology Domain superfamily

Probab=85.87  E-value=1  Score=29.28  Aligned_cols=37  Identities=11%  Similarity=0.021  Sum_probs=31.1

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCC-CeEeecCCCCh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGK-PFFTLKSLKED  189 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~-~~~~~h~~~~~  189 (197)
                      ..++++||++-.++...+..|...|+ ++..+.|++..
T Consensus        66 ~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~~~Gg~~~  103 (106)
T cd01519          66 DKELIFYCKAGVRSKAAAELARSLGYENVGNYPGSWLD  103 (106)
T ss_pred             CCeEEEECCCcHHHHHHHHHHHHcCCccceecCCcHHH
Confidence            35799999998888899999999998 48888888753

This CD includes the heat shock protein 67B2 of Drosophila melanogaster and other similar proteins, many of which are uncharacterized.

>PF11019 DUF2608: Protein of unknown function (DUF2608); InterPro: IPR022565 This family is conserved in Bacteria

Probab=85.38  E-value=13  Score=28.85  Aligned_cols=60  Identities=17%  Similarity=0.247  Sum_probs=47.0

Q ss_pred             cceeEEEEEcCchhhHHHHHHHhhcCC--CCEEEEe-cccccHHHHHHHHHhCCCCeEeecCC
Q psy7789         127 MNVVQEVEYVKQEAKIVYLLECLQKTE--PPVLIFA-EKKQDVDAIHEYLLLKGKPFFTLKSL  186 (197)
Q Consensus       127 ~~i~~~~~~~~~~~k~~~l~~~l~~~~--~~~lIF~-~s~~~~~~l~~~L~~~~~~~~~~h~~  186 (197)
                      +....-+.+++..+|-..|..++...+  ++.|||+ ++.+....+-+.+++.|+....+|-.
T Consensus       149 ~~~~~GIlft~~~~KG~~L~~fL~~~~~~pk~IIfIDD~~~nl~sv~~a~k~~~I~f~G~~Yt  211 (252)
T PF11019_consen  149 PSFYDGILFTGGQDKGEVLKYFLDKINQSPKKIIFIDDNKENLKSVEKACKKSGIDFIGFHYT  211 (252)
T ss_pred             ceeecCeEEeCCCccHHHHHHHHHHcCCCCCeEEEEeCCHHHHHHHHHHHhhCCCcEEEEEEc
Confidence            334455667788888888888888654  4678888 77889999999999999988888743

The function is not known.

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=85.36  E-value=9.8  Score=34.08  Aligned_cols=42  Identities=12%  Similarity=0.192  Sum_probs=29.5

Q ss_pred             HHHHHHhhcCCCCEEEEecccccHHHHHHHHHhC-CCCeEeecCC
Q psy7789         143 VYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLK-GKPFFTLKSL  186 (197)
Q Consensus       143 ~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~-~~~~~~~h~~  186 (197)
                      ..+.+++. .++.++||++|.+..+.+++.|... ++++ ..+|.
T Consensus       525 ~~i~~l~~-~~gg~LVlFtSy~~l~~v~~~l~~~~~~~l-l~Q~~  567 (697)
T PRK11747        525 EFLPELLE-KHKGSLVLFASRRQMQKVADLLPRDLRLML-LVQGD  567 (697)
T ss_pred             HHHHHHHh-cCCCEEEEeCcHHHHHHHHHHHHHhcCCcE-EEeCC
Confidence            34445555 5567999999999999999999753 4443 34554

>PF00271 Helicase_C: Helicase conserved C-terminal domain; InterPro: IPR001650 The domain, which defines this group of proteins is found in a wide variety of helicases and helicase related proteins

Probab=85.15  E-value=2.1  Score=26.07  Aligned_cols=51  Identities=12%  Similarity=0.261  Sum_probs=37.0

Q ss_pred             CCeeEEEEEcCCChHHhHHHHh----cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehh
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIK----KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEA   67 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~----~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEa   67 (197)
                      .|+++..++|+.+..+..+.+.    +..+|+|+|-     .+ ...+++..++.+|+-+.
T Consensus         6 ~~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli~t~-----~~-~~Gid~~~~~~vi~~~~   60 (78)
T PF00271_consen    6 KGIKVAIIHGDMSQKERQEILKKFNSGEIRVLIATD-----IL-GEGIDLPDASHVIFYDP   60 (78)
T ss_dssp             TTSSEEEESTTSHHHHHHHHHHHHHTTSSSEEEESC-----GG-TTSSTSTTESEEEESSS
T ss_pred             CCCcEEEEECCCCHHHHHHHHHHhhccCceEEEeec-----cc-ccccccccccccccccc
Confidence            3799999999988666554443    3589999993     33 34566788889987655

It may be that this is not an autonomously folding unit, but an integral part of the helicase. The eukaryotic translation initiation factor 4A (eIF4A) is a member of the DEA(D/H)-box RNA helicase family This is a diverse group of proteins that couples an ATPase activity to RNA binding and unwinding. The structure of the carboxyl-terminal domain of eIF4A has been determined to 1.75 A resolution; it has a parallel alpha-beta topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases [].; GO: 0003676 nucleic acid binding, 0004386 helicase activity, 0005524 ATP binding; PDB: 2Z83_A 2JGN_C 2I4I_A 2BMF_A 2BHR_B 1WP9_E 2WAX_C 2WAY_C 3JUX_A 3DIN_B ....

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=85.01  E-value=3.3  Score=29.68  Aligned_cols=54  Identities=19%  Similarity=0.236  Sum_probs=43.2

Q ss_pred             cCCCccEEEeehhhhhhcCCC--HHHHHHHHhhccCCceEEEEeecCChhHHHHHH
Q psy7789          55 SLDVCRYLCLDEADRMVDMGF--EEDVRTIFSFFRGQRQTLLFSATMPKKIQNFAR  108 (197)
Q Consensus        55 ~l~~l~~vViDEad~l~~~~~--~~~i~~i~~~~~~~~q~i~~SAT~~~~~~~~~~  108 (197)
                      .....++||+||+=..++.++  .+.+..+++.-|...-+|+.+-..|+++.+.+.
T Consensus        92 ~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p~~l~e~AD  147 (159)
T cd00561          92 ASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAPKELIEAAD  147 (159)
T ss_pred             hcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhCc
Confidence            356789999999988877663  567778888888888899998888888777653

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>KOG0390|consensus

Probab=85.00  E-value=1.4  Score=39.43  Aligned_cols=58  Identities=17%  Similarity=0.207  Sum_probs=39.1

Q ss_pred             hhHHHHHHHhhcCCCCEEEEe---cccccHHHHHHHH-HhCCCCeEeecCCCChhhhhhhhC
Q psy7789         140 AKIVYLLECLQKTEPPVLIFA---EKKQDVDAIHEYL-LLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       140 ~k~~~l~~~l~~~~~~~lIF~---~s~~~~~~l~~~L-~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      .|+..|..++.....++++|+   ...+...++.+.+ +-+|+.+..+||.|+..+|+.+.+
T Consensus       578 ~kl~~L~~ll~~~~ek~~~~~v~Isny~~tldl~e~~~~~~g~~~~rLdG~~~~~qRq~~vd  639 (776)
T KOG0390|consen  578 GKLLVLVFLLEVIREKLLVKSVLISNYTQTLDLFEQLCRWRGYEVLRLDGKTSIKQRQKLVD  639 (776)
T ss_pred             hHHHHHHHHHHHHhhhcceEEEEeccHHHHHHHHHHHHhhcCceEEEEcCCCchHHHHHHHH
Confidence            356666666654444555555   4445555554444 445999999999999999998863

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=84.97  E-value=3  Score=30.36  Aligned_cols=54  Identities=17%  Similarity=0.241  Sum_probs=43.5

Q ss_pred             CCCccEEEeehhhhhhcCCC--HHHHHHHHhhccCCceEEEEeecCChhHHHHHHH
Q psy7789          56 LDVCRYLCLDEADRMVDMGF--EEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARS  109 (197)
Q Consensus        56 l~~l~~vViDEad~l~~~~~--~~~i~~i~~~~~~~~q~i~~SAT~~~~~~~~~~~  109 (197)
                      -...++||+||+-..++.++  .+.+..+++.-|+..-+|+..-..|+++.+.+..
T Consensus        95 ~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~p~~l~e~AD~  150 (173)
T TIGR00708        95 DPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGCPQDLLELADL  150 (173)
T ss_pred             cCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhCce
Confidence            46789999999998888764  4577788888888888999988888887776643

Alternate name: corrinoid adenosyltransferase.

>PF05872 DUF853: Bacterial protein of unknown function (DUF853); InterPro: IPR008571 Members of this family have a P-loop containing nucleotide triphosphate hydrolases fold

Probab=84.47  E-value=2.3  Score=35.73  Aligned_cols=44  Identities=14%  Similarity=0.312  Sum_probs=31.2

Q ss_pred             cCCCccEE-EeehhhhhhcCC---CHHHHHHHHhhccCC-ceEEEEeec
Q psy7789          55 SLDVCRYL-CLDEADRMVDMG---FEEDVRTIFSFFRGQ-RQTLLFSAT   98 (197)
Q Consensus        55 ~l~~l~~v-ViDEad~l~~~~---~~~~i~~i~~~~~~~-~q~i~~SAT   98 (197)
                      ++++.++| .|||||.++++-   +.+.+..+.+.+++. .=+.++|-+
T Consensus       251 D~dkPklVfFfDEAHLLF~da~kall~~ieqvvrLIRSKGVGv~fvTQ~  299 (502)
T PF05872_consen  251 DLDKPKLVFFFDEAHLLFNDAPKALLDKIEQVVRLIRSKGVGVYFVTQN  299 (502)
T ss_pred             CCCCceEEEEEechhhhhcCCCHHHHHHHHHHHHHhhccCceEEEEeCC
Confidence            46778875 599999999764   667777777777653 345555554

This family is restricted to bacterial proteins, none of which have currently been characterised.

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=84.45  E-value=0.82  Score=41.89  Aligned_cols=59  Identities=14%  Similarity=0.179  Sum_probs=39.1

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHH-HHHhcC------CccCCCccEEEeehhhhhh
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLM-DMLDKK------MVSLDVCRYLCLDEADRMV   71 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~-~~l~~~------~~~l~~l~~vViDEad~l~   71 (197)
                      .|++|.++..+.+.+...+..  .+||..||..-+- ++|+..      ..-.+.+.|.||||+|.++
T Consensus       206 lGLtVg~i~~~~~~~~Rr~aY--~~DItYgTn~EfGFDYLRDnma~~~~~~vqR~~~faIVDEvDSvL  271 (1025)
T PRK12900        206 HGLSVGVILNTMRPEERREQY--LCDITYGTNNEFGFDYLRDNMAGTPEEMVQRDFYFAIVDEVDSVL  271 (1025)
T ss_pred             hCCeeeeeCCCCCHHHHHHhC--CCcceecCCCccccccchhccccchhhhhccCCceEEEechhhhh
Confidence            378888887766555443332  3899999986543 344321      1124778899999999875

>cd01449 TST_Repeat_2 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain

Probab=83.99  E-value=2  Score=28.60  Aligned_cols=36  Identities=14%  Similarity=0.113  Sum_probs=30.5

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCC-CeEeecCCCC
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGK-PFFTLKSLKE  188 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~-~~~~~h~~~~  188 (197)
                      ..++++||++-..+...+..|+..|+ ++..+-|++.
T Consensus        78 ~~~iv~yc~~g~~s~~~~~~l~~~G~~~v~~l~GG~~  114 (118)
T cd01449          78 DKPVIVYCGSGVTACVLLLALELLGYKNVRLYDGSWS  114 (118)
T ss_pred             CCCEEEECCcHHHHHHHHHHHHHcCCCCeeeeCChHH
Confidence            45799999998888899999999998 5888888874

TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue.

>cd01448 TST_Repeat_1 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain

Probab=83.98  E-value=2.8  Score=28.05  Aligned_cols=37  Identities=11%  Similarity=0.020  Sum_probs=30.9

Q ss_pred             CCCEEEEecc-cccHHHHHHHHHhCCCC-eEeecCCCCh
Q psy7789         153 EPPVLIFAEK-KQDVDAIHEYLLLKGKP-FFTLKSLKED  189 (197)
Q Consensus       153 ~~~~lIF~~s-~~~~~~l~~~L~~~~~~-~~~~h~~~~~  189 (197)
                      ..++++||++ -..+...+..|+..|++ +..+-|++..
T Consensus        79 ~~~vv~~c~~g~~~a~~~~~~l~~~G~~~v~~l~GG~~~  117 (122)
T cd01448          79 DDTVVVYDDGGGFFAARAWWTLRYFGHENVRVLDGGLQA  117 (122)
T ss_pred             CCEEEEECCCCCccHHHHHHHHHHcCCCCEEEecCCHHH
Confidence            3579999998 58888889999999975 8888898854

TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it is believed to be involved in protein interaction.

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=83.89  E-value=2  Score=30.74  Aligned_cols=65  Identities=11%  Similarity=0.203  Sum_probs=40.1

Q ss_pred             CCcEEEeCchHH-----HH----HHh---cCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEeecCC
Q psy7789          34 GCHMMVATPGRL-----MD----MLD---KKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMP  100 (197)
Q Consensus        34 ~~~Ili~TP~~l-----~~----~l~---~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SAT~~  100 (197)
                      .||+.+..|+.-     .+    +..   .... -...+.+||||||.|... ....+.+.+..-|.+..+++++....
T Consensus        67 ~~d~~~~~~~~~~~~i~i~~ir~i~~~~~~~~~-~~~~KviiI~~ad~l~~~-a~NaLLK~LEepp~~~~fiL~t~~~~  143 (162)
T PF13177_consen   67 HPDFIIIKPDKKKKSIKIDQIREIIEFLSLSPS-EGKYKVIIIDEADKLTEE-AQNALLKTLEEPPENTYFILITNNPS  143 (162)
T ss_dssp             CTTEEEEETTTSSSSBSHHHHHHHHHHCTSS-T-TSSSEEEEEETGGGS-HH-HHHHHHHHHHSTTTTEEEEEEES-GG
T ss_pred             CcceEEEecccccchhhHHHHHHHHHHHHHHHh-cCCceEEEeehHhhhhHH-HHHHHHHHhcCCCCCEEEEEEECChH
Confidence            488888887643     12    221   1222 267889999999998543 45566666666666667777665543

...

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=83.79  E-value=2.6  Score=35.43  Aligned_cols=89  Identities=16%  Similarity=0.269  Sum_probs=48.5

Q ss_pred             CeeEEEEEcCCC--hHHhHHHH-----hc--CCcEEEeCchHHHHHH----hcCC-----ccCCCccEEEeehhhhhhcC
Q psy7789          12 PLRTCLAIGGVP--MNQSLDVI-----KK--GCHMMVATPGRLMDML----DKKM-----VSLDVCRYLCLDEADRMVDM   73 (197)
Q Consensus        12 ~i~~~~~~gg~~--~~~~~~~l-----~~--~~~Ili~TP~~l~~~l----~~~~-----~~l~~l~~vViDEad~l~~~   73 (197)
                      ..+..+++|+..  ...-...+     ..  +..++..|.+.+...+    ....     -.+.+.++|++||+|.+...
T Consensus       147 ~~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~~  226 (450)
T PRK00149        147 AYNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTSEKFTNDFVNALRNNTMEEFKEKYRSVDVLLIDDIQFLAGK  226 (450)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHHHHHcCcHHHHHHHHhcCCEEEEehhhhhcCC
Confidence            346678888754  33322222     12  4678877777665432    1111     12457889999999998653


Q ss_pred             C-CHHHHHHHHhhcc-CCceEEEEeecCCh
Q psy7789          74 G-FEEDVRTIFSFFR-GQRQTLLFSATMPK  101 (197)
Q Consensus        74 ~-~~~~i~~i~~~~~-~~~q~i~~SAT~~~  101 (197)
                      . ..+.+..++..+- ...++++ +++.++
T Consensus       227 ~~~~~~l~~~~n~l~~~~~~iii-ts~~~p  255 (450)
T PRK00149        227 ERTQEEFFHTFNALHEAGKQIVL-TSDRPP  255 (450)
T ss_pred             HHHHHHHHHHHHHHHHCCCcEEE-ECCCCH
Confidence            2 2234444444443 3445555 455443

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=83.52  E-value=2.8  Score=37.73  Aligned_cols=39  Identities=8%  Similarity=0.035  Sum_probs=24.1

Q ss_pred             CCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEe
Q psy7789          57 DVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFS   96 (197)
Q Consensus        57 ~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~S   96 (197)
                      .+.+.+||||+|.|.... .+.+.++++.-+....+|+.+
T Consensus       118 gr~KVIIIDEah~LT~~A-~NALLKtLEEPP~~v~FILaT  156 (830)
T PRK07003        118 ARFKVYMIDEVHMLTNHA-FNAMLKTLEEPPPHVKFILAT  156 (830)
T ss_pred             CCceEEEEeChhhCCHHH-HHHHHHHHHhcCCCeEEEEEE
Confidence            567899999999985532 333444555544444555543

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=83.43  E-value=3.1  Score=34.40  Aligned_cols=89  Identities=15%  Similarity=0.258  Sum_probs=48.0

Q ss_pred             eeEEEEEcCCC--hHHhHHH----H-hc--CCcEEEeCchHHHHHHh----cCC-----ccCCCccEEEeehhhhhhcCC
Q psy7789          13 LRTCLAIGGVP--MNQSLDV----I-KK--GCHMMVATPGRLMDMLD----KKM-----VSLDVCRYLCLDEADRMVDMG   74 (197)
Q Consensus        13 i~~~~~~gg~~--~~~~~~~----l-~~--~~~Ili~TP~~l~~~l~----~~~-----~~l~~l~~vViDEad~l~~~~   74 (197)
                      -+..+++|+..  ...-...    + ..  +..++..|.+.+...+.    .+.     -.+.+.++|++||+|.+....
T Consensus       136 ~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~~~  215 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSSEKFTNDFVNALRNNKMEEFKEKYRSVDLLLIDDIQFLAGKE  215 (405)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEHHHHHHHHHHHHHcCCHHHHHHHHHhCCEEEEehhhhhcCCH
Confidence            35677888753  3322222    2 12  46788888776654321    111     124567899999999886532


Q ss_pred             -CHHHHHHHHhhc-cCCceEEEEeecCChh
Q psy7789          75 -FEEDVRTIFSFF-RGQRQTLLFSATMPKK  102 (197)
Q Consensus        75 -~~~~i~~i~~~~-~~~~q~i~~SAT~~~~  102 (197)
                       ....+..++..+ ..+.++++ +++.++.
T Consensus       216 ~~~~~l~~~~n~~~~~~~~iii-ts~~~p~  244 (405)
T TIGR00362       216 RTQEEFFHTFNALHENGKQIVL-TSDRPPK  244 (405)
T ss_pred             HHHHHHHHHHHHHHHCCCCEEE-ecCCCHH
Confidence             223344444443 23456555 4554433

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>PRK08762 molybdopterin biosynthesis protein MoeB; Validated

Probab=83.43  E-value=4.7  Score=33.13  Aligned_cols=38  Identities=5%  Similarity=-0.022  Sum_probs=31.7

Q ss_pred             CCCCEEEEecccccHHHHHHHHHhCCC-CeEeecCCCCh
Q psy7789         152 TEPPVLIFAEKKQDVDAIHEYLLLKGK-PFFTLKSLKED  189 (197)
Q Consensus       152 ~~~~~lIF~~s~~~~~~l~~~L~~~~~-~~~~~h~~~~~  189 (197)
                      ...++++||++-.++...+..|+..|+ ++..+.|++..
T Consensus        56 ~~~~IvvyC~~G~rs~~aa~~L~~~G~~~v~~l~GG~~~   94 (376)
T PRK08762         56 RDREIVLICASGTRSAHAAATLRELGYTRVASVAGGFSA   94 (376)
T ss_pred             CCCeEEEEcCCCcHHHHHHHHHHHcCCCceEeecCcHHH
Confidence            345799999998888889999999998 58888888754

>cd01522 RHOD_1 Member of the Rhodanese Homology Domain superfamily, subgroup 1

Probab=83.40  E-value=3.9  Score=27.40  Aligned_cols=39  Identities=18%  Similarity=0.181  Sum_probs=32.4

Q ss_pred             CCCCEEEEecccccHHHHHHHHHhCCCC-eEeecCCCChh
Q psy7789         152 TEPPVLIFAEKKQDVDAIHEYLLLKGKP-FFTLKSLKEDQ  190 (197)
Q Consensus       152 ~~~~~lIF~~s~~~~~~l~~~L~~~~~~-~~~~h~~~~~~  190 (197)
                      ...++++||++-.++...+..|+..|+. +..+.|++..-
T Consensus        63 ~~~~ivv~C~~G~rs~~aa~~L~~~G~~~v~~l~gG~~~~  102 (117)
T cd01522          63 KDRPVLLLCRSGNRSIAAAEAAAQAGFTNVYNVLEGFEGD  102 (117)
T ss_pred             CCCeEEEEcCCCccHHHHHHHHHHCCCCeEEECcCceecC
Confidence            3457999999989999999999999984 77788887653

This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins.

>PRK05580 primosome assembly protein PriA; Validated

Probab=83.29  E-value=3.4  Score=36.78  Aligned_cols=56  Identities=14%  Similarity=0.153  Sum_probs=43.0

Q ss_pred             hhhHHHHHHHhh---cCCCCEEEEecccccHHHHHHHHHhC-CCCeEeecCCCChhhhhh
Q psy7789         139 EAKIVYLLECLQ---KTEPPVLIFAEKKQDVDAIHEYLLLK-GKPFFTLKSLKEDQNNQT  194 (197)
Q Consensus       139 ~~k~~~l~~~l~---~~~~~~lIF~~s~~~~~~l~~~L~~~-~~~~~~~h~~~~~~~R~~  194 (197)
                      ..|.......+.   ..++++||-++++.-+..+++.|++. |.++..+||+++..+|.+
T Consensus       173 SGKT~v~l~~i~~~l~~g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~  232 (679)
T PRK05580        173 SGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLD  232 (679)
T ss_pred             ChHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHH
Confidence            345544433332   23568999999999999999999875 889999999999988764

>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

Probab=83.25  E-value=1.1  Score=39.47  Aligned_cols=40  Identities=18%  Similarity=0.240  Sum_probs=30.3

Q ss_pred             cCCcEEEeCchHHHHHHhcCCcc--CCCccEEEeehhhhhhc
Q psy7789          33 KGCHMMVATPGRLMDMLDKKMVS--LDVCRYLCLDEADRMVD   72 (197)
Q Consensus        33 ~~~~Ili~TP~~l~~~l~~~~~~--l~~l~~vViDEad~l~~   72 (197)
                      ..++++|+++..+..-.......  +-.-+.+|+||||++.+
T Consensus       193 ~~ad~vv~nh~~~~~~~~~~~~~~~~p~~~v~v~DEAH~l~d  234 (654)
T COG1199         193 ENADLVVTNHALLLADVALEESRILLPENDVVVFDEAHNLPD  234 (654)
T ss_pred             hhCCEEEEccHHHHhHHHhhhhhccCCcccEEEEeccccchH
Confidence            45999999998888755433322  45677999999999976

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=83.17  E-value=3.5  Score=37.22  Aligned_cols=97  Identities=15%  Similarity=0.213  Sum_probs=62.2

Q ss_pred             EEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhc---CCCCEEEEecccccHHHH
Q psy7789          93 LLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQDVDAI  169 (197)
Q Consensus        93 i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l  169 (197)
                      ..++.|...+..++...|.-+-..+-..... .+.. ....++.....|+..+++.+..   .+.|+||-+.+++.++.+
T Consensus       368 ~gmTGTa~te~~EF~~iY~l~vv~iPTnrp~-~R~D-~~D~vy~t~~~K~~Aiv~~I~~~~~~gqPvLvgT~sie~SE~l  445 (822)
T COG0653         368 AGMTGTADTEEEEFDVIYGLDVVVIPTNRPI-IRLD-EPDLVYKTEEEKFKAIVEDIKERHEKGQPVLVGTVSIEKSELL  445 (822)
T ss_pred             cCCCCcchhhhhhhhhccCCceeeccCCCcc-cCCC-CccccccchHHHHHHHHHHHHHHHhcCCCEEEcCcceecchhH
Confidence            4566666666666665554443333222111 1111 1223455677888888877764   356999999999999999


Q ss_pred             HHHHHhCCCCeEeecCCCChhh
Q psy7789         170 HEYLLLKGKPFFTLKSLKEDQN  191 (197)
Q Consensus       170 ~~~L~~~~~~~~~~h~~~~~~~  191 (197)
                      .+.|++.|++-..+.+.-...+
T Consensus       446 s~~L~~~~i~h~VLNAk~h~~E  467 (822)
T COG0653         446 SKLLRKAGIPHNVLNAKNHARE  467 (822)
T ss_pred             HHHHHhcCCCceeeccccHHHH
Confidence            9999999988767776655444

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=82.82  E-value=3.7  Score=35.98  Aligned_cols=92  Identities=15%  Similarity=0.190  Sum_probs=53.4

Q ss_pred             CeeEEEEEcCCC--hHHhHHHHh-------cCCcEEEeCchHHHHHHh----cCC-----ccCCCccEEEeehhhhhhcC
Q psy7789          12 PLRTCLAIGGVP--MNQSLDVIK-------KGCHMMVATPGRLMDMLD----KKM-----VSLDVCRYLCLDEADRMVDM   73 (197)
Q Consensus        12 ~i~~~~~~gg~~--~~~~~~~l~-------~~~~Ili~TP~~l~~~l~----~~~-----~~l~~l~~vViDEad~l~~~   73 (197)
                      .-+..+++|+..  .......+.       .+..++..|.+.+...+.    .+.     -.+.++++|+|||+|.+...
T Consensus       313 ~~NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yitaeef~~el~~al~~~~~~~f~~~y~~~DLLlIDDIq~l~gk  392 (617)
T PRK14086        313 AYNPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSSEEFTNEFINSIRDGKGDSFRRRYREMDILLVDDIQFLEDK  392 (617)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHHHHHHHHHHHhccHHHHHHHhhcCCEEEEehhccccCC
Confidence            345678888753  333332221       257888888877664332    111     12567899999999988653


Q ss_pred             C-CHHHHHHHHhhccC-CceEEEEeecCChhH
Q psy7789          74 G-FEEDVRTIFSFFRG-QRQTLLFSATMPKKI  103 (197)
Q Consensus        74 ~-~~~~i~~i~~~~~~-~~q~i~~SAT~~~~~  103 (197)
                      . ....+..++..+.. +.|+++.|-..+.+.
T Consensus       393 e~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL  424 (617)
T PRK14086        393 ESTQEEFFHTFNTLHNANKQIVLSSDRPPKQL  424 (617)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEecCCChHhh
Confidence            2 23445555555543 567776555544443

>KOG4439|consensus

Probab=82.79  E-value=1.3  Score=39.11  Aligned_cols=60  Identities=18%  Similarity=0.187  Sum_probs=35.0

Q ss_pred             eeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHH----HHhc----CCccCCCccEEEeehhhhhhcC
Q psy7789          13 LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMD----MLDK----KMVSLDVCRYLCLDEADRMVDM   73 (197)
Q Consensus        13 i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~----~l~~----~~~~l~~l~~vViDEad~l~~~   73 (197)
                      ++|.+.+|....+-..+.+.. +||+|+|=.-+-.    -...    ..+.-=....||+||||.+-+.
T Consensus       411 LsV~~~HG~n~r~i~~~~L~~-YDvViTTY~lva~~~~~e~~~~~~~spL~~I~W~RVILDEAH~IrN~  478 (901)
T KOG4439|consen  411 LSVYLYHGPNKREISAKELRK-YDVVITTYNLVANKPDDELEEGKNSSPLARIAWSRVILDEAHNIRNS  478 (901)
T ss_pred             eEEEEecCCccccCCHHHHhh-cceEEEeeeccccCCchhhhcccCccHHHHhhHHHhhhhhhhhhccc
Confidence            777777776544434455554 9999999522222    0000    1111123558999999998664

>PRK06835 DNA replication protein DnaC; Validated

Probab=82.30  E-value=8.8  Score=31.00  Aligned_cols=87  Identities=14%  Similarity=0.177  Sum_probs=50.8

Q ss_pred             eEEEEEcCCC--hHHhH-----HHHhcCCcEEEeCchHHHHHHhcC-----------CccCCCccEEEeehhhhhhcCC-
Q psy7789          14 RTCLAIGGVP--MNQSL-----DVIKKGCHMMVATPGRLMDMLDKK-----------MVSLDVCRYLCLDEADRMVDMG-   74 (197)
Q Consensus        14 ~~~~~~gg~~--~~~~~-----~~l~~~~~Ili~TP~~l~~~l~~~-----------~~~l~~l~~vViDEad~l~~~~-   74 (197)
                      ...+++|...  .....     ..+..+..|+..|-..+...+...           .-.+.++++||||+........ 
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t~~~l~~~l~~~~~~~~~~~~~~~~~l~~~DLLIIDDlG~e~~t~~  263 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRTADELIEILREIRFNNDKELEEVYDLLINCDLLIIDDLGTEKITEF  263 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEEHHHHHHHHHHHHhccchhHHHHHHHhccCCEEEEeccCCCCCCHH
Confidence            5677888643  33322     223457889988888887765321           1235788999999998764332 


Q ss_pred             CHHHHHHHHhhccC-CceEEEEeecCCh
Q psy7789          75 FEEDVRTIFSFFRG-QRQTLLFSATMPK  101 (197)
Q Consensus        75 ~~~~i~~i~~~~~~-~~q~i~~SAT~~~  101 (197)
                      ....+-.++...-. ...+ ++|+.+++
T Consensus       264 ~~~~Lf~iin~R~~~~k~t-IiTSNl~~  290 (329)
T PRK06835        264 SKSELFNLINKRLLRQKKM-IISTNLSL  290 (329)
T ss_pred             HHHHHHHHHHHHHHCCCCE-EEECCCCH
Confidence            23345555554433 3444 45555543

>TIGR00595 priA primosomal protein N'

Probab=82.17  E-value=4.5  Score=34.70  Aligned_cols=44  Identities=14%  Similarity=0.117  Sum_probs=38.2

Q ss_pred             CCCCEEEEecccccHHHHHHHHHhC-CCCeEeecCCCChhhhhhh
Q psy7789         152 TEPPVLIFAEKKQDVDAIHEYLLLK-GKPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       152 ~~~~~lIF~~s~~~~~~l~~~L~~~-~~~~~~~h~~~~~~~R~~i  195 (197)
                      .++++|+-++++.-+..+++.|++. |.++..+||+++..+|.++
T Consensus        24 ~g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~   68 (505)
T TIGR00595        24 LGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQA   68 (505)
T ss_pred             cCCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHH
Confidence            3568999999999999999999875 7789999999999988654

All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=82.01  E-value=4.7  Score=29.82  Aligned_cols=55  Identities=16%  Similarity=0.257  Sum_probs=44.0

Q ss_pred             CCCccEEEeehhhhhhcCCC--HHHHHHHHhhccCCceEEEEeecCChhHHHHHHHh
Q psy7789          56 LDVCRYLCLDEADRMVDMGF--EEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSA  110 (197)
Q Consensus        56 l~~l~~vViDEad~l~~~~~--~~~i~~i~~~~~~~~q~i~~SAT~~~~~~~~~~~~  110 (197)
                      -...++||+||+-..++.++  .+.+..+++.-|...-+|+..-..|+++.+.+...
T Consensus       113 ~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~p~~Lie~ADlV  169 (191)
T PRK05986        113 DESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGAPRELIEAADLV  169 (191)
T ss_pred             CCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhCchh
Confidence            36788999999998888774  55788888888888888888888888877766443

>cd01535 4RHOD_Repeat_4 Member of the Rhodanese Homology Domain superfamily, repeat 4

Probab=81.97  E-value=4.8  Score=28.23  Aligned_cols=36  Identities=11%  Similarity=-0.000  Sum_probs=31.2

Q ss_pred             CCEEEEecccccHHHHHHHHHhCCC-CeEeecCCCCh
Q psy7789         154 PPVLIFAEKKQDVDAIHEYLLLKGK-PFFTLKSLKED  189 (197)
Q Consensus       154 ~~~lIF~~s~~~~~~l~~~L~~~~~-~~~~~h~~~~~  189 (197)
                      .+++|+|.+-..+...+..|+..|+ ++..+.||+..
T Consensus        50 ~~vVv~c~~g~~a~~aa~~L~~~G~~~v~~L~GG~~a   86 (145)
T cd01535          50 ERYVLTCGSSLLARFAAADLAALTVKPVFVLEGGTAA   86 (145)
T ss_pred             CCEEEEeCCChHHHHHHHHHHHcCCcCeEEecCcHHH
Confidence            5799999998888888999999988 79999998754

This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 4th repeat which, in general, contains the putative catalytic Cys residue.

>PRK08084 DNA replication initiation factor; Provisional

Probab=81.87  E-value=3.1  Score=31.70  Aligned_cols=88  Identities=8%  Similarity=0.117  Sum_probs=45.1

Q ss_pred             eeEEEEEcCCC--hHHhHHHH-----hcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcC-CCHHHHHHHHh
Q psy7789          13 LRTCLAIGGVP--MNQSLDVI-----KKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDM-GFEEDVRTIFS   84 (197)
Q Consensus        13 i~~~~~~gg~~--~~~~~~~l-----~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~-~~~~~i~~i~~   84 (197)
                      .....++|...  ...-...+     ..+..+...+.+........-.-.+...+++++||+|.+... .....+..++.
T Consensus        45 ~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~~~~~~~~~~~~~~~~~~dlliiDdi~~~~~~~~~~~~lf~l~n  124 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPLDKRAWFVPEVLEGMEQLSLVCIDNIECIAGDELWEMAIFDLYN  124 (235)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEHHHHhhhhHHHHHHhhhCCEEEEeChhhhcCCHHHHHHHHHHHH
Confidence            35667777643  33222222     235667776665533222111112345679999999998643 23445555555


Q ss_pred             hccC-C-ceEEEEeecCCh
Q psy7789          85 FFRG-Q-RQTLLFSATMPK  101 (197)
Q Consensus        85 ~~~~-~-~q~i~~SAT~~~  101 (197)
                      .... . .++++ |++.++
T Consensus       125 ~~~e~g~~~li~-ts~~~p  142 (235)
T PRK08084        125 RILESGRTRLLI-TGDRPP  142 (235)
T ss_pred             HHHHcCCCeEEE-eCCCCh
Confidence            5433 2 34554 555443

>PRK04296 thymidine kinase; Provisional

Probab=81.55  E-value=4.6  Score=29.67  Aligned_cols=54  Identities=11%  Similarity=0.188  Sum_probs=31.6

Q ss_pred             EeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEeecC
Q psy7789          39 VATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATM   99 (197)
Q Consensus        39 i~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SAT~   99 (197)
                      +..+..++..+..   .-.+.++||+||++.+-    .+++..+++.+.+....+++++--
T Consensus        62 ~~~~~~~~~~~~~---~~~~~dvviIDEaq~l~----~~~v~~l~~~l~~~g~~vi~tgl~  115 (190)
T PRK04296         62 VSSDTDIFELIEE---EGEKIDCVLIDEAQFLD----KEQVVQLAEVLDDLGIPVICYGLD  115 (190)
T ss_pred             eCChHHHHHHHHh---hCCCCCEEEEEccccCC----HHHHHHHHHHHHHcCCeEEEEecC
Confidence            4455555555543   23577899999997641    344666666654444455554443

>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated

Probab=81.43  E-value=5.3  Score=29.20  Aligned_cols=52  Identities=19%  Similarity=0.294  Sum_probs=42.7

Q ss_pred             CCCccEEEeehhhhhhcCCC--HHHHHHHHhhccCCceEEEEeecCChhHHHHH
Q psy7789          56 LDVCRYLCLDEADRMVDMGF--EEDVRTIFSFFRGQRQTLLFSATMPKKIQNFA  107 (197)
Q Consensus        56 l~~l~~vViDEad~l~~~~~--~~~i~~i~~~~~~~~q~i~~SAT~~~~~~~~~  107 (197)
                      -...+++|+||+-..++.++  .+.+..+++.-|+..-+|+..-..|+++.+.+
T Consensus       113 ~~~~dlvVLDEi~~Al~~gli~~eeVl~~L~~rp~~~evILTGR~~p~~Lie~A  166 (178)
T PRK07414        113 EGRYSLVVLDELSLAIQFGLIPETEVLEFLEKRPSHVDVILTGPEMPESLLAIA  166 (178)
T ss_pred             CCCCCEEEEehhHHHHHCCCccHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhC
Confidence            36789999999998888774  45788888888888889998888888877755

>PRK00162 glpE thiosulfate sulfurtransferase; Validated

Probab=81.31  E-value=3.1  Score=27.28  Aligned_cols=38  Identities=18%  Similarity=0.369  Sum_probs=32.0

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCCC-eEeecCCCChh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGKP-FFTLKSLKEDQ  190 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~~-~~~~h~~~~~~  190 (197)
                      ..+++++|.+-.++...+..|+..|+. +..+.|++..=
T Consensus        58 ~~~ivv~c~~g~~s~~a~~~L~~~G~~~v~~l~GG~~~w   96 (108)
T PRK00162         58 DTPVMVMCYHGNSSQGAAQYLLQQGFDVVYSIDGGFEAW   96 (108)
T ss_pred             CCCEEEEeCCCCCHHHHHHHHHHCCchheEEecCCHHHH
Confidence            457999999988999999999999985 88888988653

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=81.17  E-value=2.3  Score=37.59  Aligned_cols=41  Identities=7%  Similarity=0.038  Sum_probs=25.4

Q ss_pred             CCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEee
Q psy7789          56 LDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSA   97 (197)
Q Consensus        56 l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SA   97 (197)
                      ..+.+.+||||+|.|.... .+.+.+.++.-+....+|+.|.
T Consensus       122 ~gr~KViIIDEah~Ls~~A-aNALLKTLEEPP~~v~FILaTt  162 (700)
T PRK12323        122 AGRFKVYMIDEVHMLTNHA-FNAMLKTLEEPPEHVKFILATT  162 (700)
T ss_pred             cCCceEEEEEChHhcCHHH-HHHHHHhhccCCCCceEEEEeC
Confidence            4678899999999995532 2333444444444555666543

>PRK06526 transposase; Provisional

Probab=81.03  E-value=7.1  Score=30.24  Aligned_cols=68  Identities=16%  Similarity=0.081  Sum_probs=39.6

Q ss_pred             hcCCcEEEeCchHHHHHHhc----CC-----ccCCCccEEEeehhhhhhcCC-CHHHHHHHHhhccCCceEEEEeecC
Q psy7789          32 KKGCHMMVATPGRLMDMLDK----KM-----VSLDVCRYLCLDEADRMVDMG-FEEDVRTIFSFFRGQRQTLLFSATM   99 (197)
Q Consensus        32 ~~~~~Ili~TP~~l~~~l~~----~~-----~~l~~l~~vViDEad~l~~~~-~~~~i~~i~~~~~~~~q~i~~SAT~   99 (197)
                      ..|..+++.|...+...+..    +.     ..+...+++|+||+|.+.... -...+..++...-....+++.|..-
T Consensus       124 ~~g~~v~f~t~~~l~~~l~~~~~~~~~~~~l~~l~~~dlLIIDD~g~~~~~~~~~~~L~~li~~r~~~~s~IitSn~~  201 (254)
T PRK06526        124 QAGHRVLFATAAQWVARLAAAHHAGRLQAELVKLGRYPLLIVDEVGYIPFEPEAANLFFQLVSSRYERASLIVTSNKP  201 (254)
T ss_pred             HCCCchhhhhHHHHHHHHHHHHhcCcHHHHHHHhccCCEEEEcccccCCCCHHHHHHHHHHHHHHHhcCCEEEEcCCC
Confidence            45788888888777765531    11     135678899999999874321 1223444443322234466655553

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=80.98  E-value=6  Score=32.88  Aligned_cols=92  Identities=17%  Similarity=0.229  Sum_probs=59.5

Q ss_pred             CeeEEEEEcCCC--hHHhHHHHh-----c--CCcEEEeCchHHHHHHhc-----C----CccCCCccEEEeehhhhhhcC
Q psy7789          12 PLRTCLAIGGVP--MNQSLDVIK-----K--GCHMMVATPGRLMDMLDK-----K----MVSLDVCRYLCLDEADRMVDM   73 (197)
Q Consensus        12 ~i~~~~~~gg~~--~~~~~~~l~-----~--~~~Ili~TP~~l~~~l~~-----~----~~~l~~l~~vViDEad~l~~~   73 (197)
                      .-++..++||..  ...-...+.     .  ++.++..|.+.+..-+-.     +    .-.. ++++++||+++.+...
T Consensus       112 ~~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~se~f~~~~v~a~~~~~~~~Fk~~y-~~dlllIDDiq~l~gk  190 (408)
T COG0593         112 AYNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTNDFVKALRDNEMEKFKEKY-SLDLLLIDDIQFLAGK  190 (408)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEeccHHHHHHHHHHHHHhhhHHHHHHhh-ccCeeeechHhHhcCC
Confidence            467889999975  333333332     2  358899999887643321     1    1124 7999999999998764


Q ss_pred             -CCHHHHHHHHhhccC-CceEEEEeecCChhHH
Q psy7789          74 -GFEEDVRTIFSFFRG-QRQTLLFSATMPKKIQ  104 (197)
Q Consensus        74 -~~~~~i~~i~~~~~~-~~q~i~~SAT~~~~~~  104 (197)
                       ...+.+-.++..+.. +.|+++.|...|.++.
T Consensus       191 ~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~  223 (408)
T COG0593         191 ERTQEEFFHTFNALLENGKQIVLTSDRPPKELN  223 (408)
T ss_pred             hhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhc
Confidence             345556666666654 4488888877776544

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=80.97  E-value=6.7  Score=34.63  Aligned_cols=54  Identities=17%  Similarity=0.303  Sum_probs=40.5

Q ss_pred             CCeeEEEEEcCCChHHhHHHH---h-cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhh
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVI---K-KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRM   70 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l---~-~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l   70 (197)
                      .++++..++|+.+..++.+.+   . +..+|+|||.     .+. ..+++.+++++|+..++.+
T Consensus       481 ~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~-----vie-~GvDiP~v~~VIi~~~~r~  538 (630)
T TIGR00643       481 PKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATT-----VIE-VGVDVPNATVMVIEDAERF  538 (630)
T ss_pred             CCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECc-----eee-cCcccCCCcEEEEeCCCcC
Confidence            478999999998765554433   3 3589999994     443 4567889999999888874

>PRK10689 transcription-repair coupling factor; Provisional

Probab=80.55  E-value=3.5  Score=38.99  Aligned_cols=53  Identities=13%  Similarity=0.313  Sum_probs=40.9

Q ss_pred             CeeEEEEEcCCChHHhHHHHh----cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhh
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIK----KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRM   70 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~----~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l   70 (197)
                      ++++..++|+.+.++..+.+.    +..+|+|||     +.+. ..+++.+++++|++.+|.+
T Consensus       835 ~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaT-----dIie-rGIDIP~v~~VIi~~ad~f  891 (1147)
T PRK10689        835 EARIAIGHGQMRERELERVMNDFHHQRFNVLVCT-----TIIE-TGIDIPTANTIIIERADHF  891 (1147)
T ss_pred             CCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEEC-----chhh-cccccccCCEEEEecCCCC
Confidence            688999999988665544432    469999999     4554 4567899999999999875

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	197
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	6e-80
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	1e-77
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	4e-56
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	1e-53
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	2e-48
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	4e-44
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	5e-43
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	2e-42
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	1e-41
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	7e-41
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	2e-40
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	3e-40
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	5e-40
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	1e-39
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	2e-39
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	4e-39
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	4e-39
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	8e-39
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	3e-37
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	1e-36
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	2e-36
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	2e-36
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	3e-36
3bor_A	237	Human initiation factor 4A-II; translation initiat	8e-35
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	7e-34
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	2e-33
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	2e-33
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	2e-32
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	4e-32
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	5e-32
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	2e-31
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	1e-24
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	9e-22
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-06
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	3e-05

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  243 bits (622), Expect = 6e-80
 Identities = 72/173 (41%), Positives = 110/173 (63%), Gaps = 6/173 (3%)

Query: 13  LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
           +R C+  GG  + Q +  +++GCH++VATPGRL+DM+++  + LD C+YL LDEADRM+D
Sbjct: 130 VRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLD 189

Query: 73  MGFEEDVRTIFSFF----RGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMN 128
           MGFE  +R I        +G R T++FSAT PK+IQ  AR  L + I + VGR G+ S N
Sbjct: 190 MGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSEN 249

Query: 129 VVQEVEYVKQEAKIVYLLECLQKTEPP--VLIFAEKKQDVDAIHEYLLLKGKP 179
           + Q+V +V++  K  +LL+ L  T      L+F E K+  D++ ++L  +G  
Sbjct: 250 ITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYA 302

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster} Length = 434

 Score =  237 bits (608), Expect = 1e-77
 Identities = 62/169 (36%), Positives = 97/169 (57%), Gaps = 2/169 (1%)

Query: 13  LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
           L+  +  GG       + I +GCH+++ATPGRL+D +D+  ++ +  R++ LDEADRM+D
Sbjct: 158 LKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLD 217

Query: 73  MGFEEDVRTIFSF--FRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVV 130
           MGF ED+R I +    R + QTL+FSAT P++IQ  A   L   + + +G  G A  +V 
Sbjct: 218 MGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVK 277

Query: 131 QEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKP 179
           Q +  V + AK   L+E L +     ++F E K+  D +  +L  K  P
Sbjct: 278 QTIYEVNKYAKRSKLIEILSEQADGTIVFVETKRGADFLASFLSEKEFP 326

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19 Length = 253

 Score =  176 bits (450), Expect = 4e-56
 Identities = 58/126 (46%), Positives = 82/126 (65%), Gaps = 4/126 (3%)

Query: 12  PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMV 71
           PLR+C+  GG   +  +  ++ GCH++VATPGRL+D ++K  +SL+ C+Y+ LDEADRM+
Sbjct: 128 PLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRML 187

Query: 72  DMGFEEDVRTIFSFFR----GQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASM 127
           DMGFE  +R I           RQTL+FSAT PK+IQ  A   L   I + VGR G+ S 
Sbjct: 188 DMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSD 247

Query: 128 NVVQEV 133
           ++ QE+
Sbjct: 248 SIKQEI 253

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} Length = 242

 Score =  170 bits (433), Expect = 1e-53
 Identities = 46/108 (42%), Positives = 65/108 (60%)

Query: 13  LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
           L++    GG P    +  +++G  + +ATPGRL+D L+    +L    YL LDEADRM+D
Sbjct: 131 LKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLD 190

Query: 73  MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVG 120
           MGFE  +R I    R  RQTL++SAT PK+++  A   L   I IN+G
Sbjct: 191 MGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIG 238

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens} Length = 228

 Score =  156 bits (397), Expect = 2e-48
 Identities = 42/108 (38%), Positives = 61/108 (56%)

Query: 12  PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMV 71
            L++    GG   N  ++ I KG  +++ATPGRL D+     V+L    YL +DEAD+M+
Sbjct: 121 GLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKML 180

Query: 72  DMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINV 119
           DM FE  +R I    R  RQT++ SAT P  ++  A S L  P+ + V
Sbjct: 181 DMEFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV 228

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens} Length = 249

 Score =  146 bits (370), Expect = 4e-44
 Identities = 43/110 (39%), Positives = 66/110 (60%), Gaps = 1/110 (0%)

Query: 11  IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDK-KMVSLDVCRYLCLDEADR 69
           I +++ + +GG+        + K  H+++ATPGRL+D L+  K  +L   +YL +DEADR
Sbjct: 138 IGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADR 197

Query: 70  MVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINV 119
           +++M FE +V  I       R+T LFSATM KK+Q   R+AL  P+   V
Sbjct: 198 ILNMDFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAV 247

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  147 bits (373), Expect = 5e-43
 Identities = 28/191 (14%), Positives = 63/191 (32%), Gaps = 30/191 (15%)

Query: 12  PLRTCLAIGGVPMNQSLDVIKK----GCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEA 67
            ++       +   +     K       H++V +   +    +K  +S     ++ +D+ 
Sbjct: 91  KVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDV 148

Query: 68  DRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVK-------------- 113
           D ++      D   +      +     FS     KI    ++                  
Sbjct: 149 DAVLKASRNIDTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGI 208

Query: 114 -------PITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDV 166
                   +   VGR  + + N+       + + K+V LLE  +     +LIFA+ +++ 
Sbjct: 209 RPLLFRDLLNFTVGRLVSVARNITHVRISSRSKEKLVELLEIFRDG---ILIFAQTEEEG 265

Query: 167 DAIHEYLLLKG 177
             ++EYL    
Sbjct: 266 KELYEYLKRFK 276

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens} Length = 245

 Score =  141 bits (358), Expect = 2e-42
 Identities = 25/120 (20%), Positives = 53/120 (44%), Gaps = 7/120 (5%)

Query: 12  PLRTCLAIGGVP-MNQSLDVIKKGCHMMVATPGRLMDML--DKKMVSLDVCRYLCLDEAD 68
             R  +         +      K   ++V TP RL+ +L  D   + L    +L +DE+D
Sbjct: 126 GFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESD 185

Query: 69  RMVD---MGFEEDVRTIFSFFR-GQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGA 124
           ++ +    GF + + +IF      + +  +FSAT    ++ + +  L   I++++G   +
Sbjct: 186 KLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGARNS 245

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A Length = 207

 Score =  138 bits (350), Expect = 1e-41
 Identities = 41/109 (37%), Positives = 59/109 (54%)

Query: 13  LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
           L+     GG    +  + + +G   +VATPGR +D L + ++ L       LDEAD M+ 
Sbjct: 99  LKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLS 158

Query: 73  MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGR 121
           MGFEE+V  + S     RQTLLFSAT+P   +  A   +  P+ INV +
Sbjct: 159 MGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINVIK 207

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A Length = 400

 Score =  141 bits (358), Expect = 7e-41
 Identities = 45/164 (27%), Positives = 77/164 (46%), Gaps = 3/164 (1%)

Query: 16  CLAI-GGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMG 74
           C+   GG  +   +  + +  H++V TPGR++D+  +K+  L  C    +DEAD+M+   
Sbjct: 120 CMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRD 179

Query: 75  FEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVE 134
           F+  +  I SF     Q+LLFSAT P  ++ F    L KP  IN+         + Q   
Sbjct: 180 FKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLMEELTLK-GITQYYA 238

Query: 135 YVKQEAKIVYLLECLQKTEPP-VLIFAEKKQDVDAIHEYLLLKG 177
           +V++  K+  L     K +    +IF      V+ + + +   G
Sbjct: 239 FVEERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLG 282

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19 Length = 367

 Score =  139 bits (354), Expect = 2e-40
 Identities = 48/162 (29%), Positives = 81/162 (50%), Gaps = 6/162 (3%)

Query: 17  LAI-GGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGF 75
             I GG  +   +  +K   +++V TPGR++D +++  ++L   +Y  LDEAD M++MGF
Sbjct: 106 AKIYGGKAIYPQIKALKNA-NIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGF 164

Query: 76  EEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEY 135
            +DV  I +     ++ LLFSATMP++I N A+  +     I        + N+ Q    
Sbjct: 165 IKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKA----KINANIEQSYVE 220

Query: 136 VKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKG 177
           V +  +   L   L+  E   L+F + K+D   +   L   G
Sbjct: 221 VNENERFEALCRLLKNKEFYGLVFCKTKRDTKELASMLRDIG 262

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C} Length = 579

 Score =  143 bits (361), Expect = 3e-40
 Identities = 42/188 (22%), Positives = 80/188 (42%), Gaps = 20/188 (10%)

Query: 12  PLRTCLAIGGVPMNQSLDVIKK-GCHMMVATPGRLMDMLDKKMV-SLDVCRYLCLDEADR 69
                  +GG     +++ + K   ++++ATPGRL+D+L+K          Y  LDEADR
Sbjct: 127 KYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADR 186

Query: 70  MVDMGFEEDVRTIFSF-------FRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRA 122
           ++++GF +D+ TI               +TLLFSAT+  K+Q  A + + K   + +   
Sbjct: 187 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTV 246

Query: 123 GAASMNVVQEVE--YV------KQEAKIVYLLEC-LQKTEPP--VLIFAEKKQDVDAIHE 171
                   + ++   V            V  ++  +++ +     +IFA   +    +  
Sbjct: 247 DKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCS 306

Query: 172 YLLLKGKP 179
            L  + K 
Sbjct: 307 ILKNEFKK 314

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii} Length = 337

 Score =  138 bits (349), Expect = 5e-40
 Identities = 41/163 (25%), Positives = 81/163 (49%), Gaps = 7/163 (4%)

Query: 12  PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMV 71
             +     GG+P    ++ ++    ++VATPGRL+D+  K ++ L     + +DEAD M 
Sbjct: 84  DTKVAEVYGGMPYKAQINRVR-NADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMF 142

Query: 72  DMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQ 131
           +MGF +D++ I +    ++ T LFSAT+P++I+   +  +     I      A   NV  
Sbjct: 143 EMGFIDDIKIILAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIEACIGLA---NVEH 199

Query: 132 EVEYVKQEAKIVYLLECLQKTEPP-VLIFAEKKQDVDAIHEYL 173
           +  +VK + +    ++ L++ +   V++F   +  V  +    
Sbjct: 200 KFVHVKDDWRS--KVQALRENKDKGVIVFVRTRNRVAKLVRLF 240

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens} Length = 236

 Score =  134 bits (339), Expect = 1e-39
 Identities = 38/110 (34%), Positives = 58/110 (52%), Gaps = 2/110 (1%)

Query: 11  IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDK-KMVSLDVCRYLCLDEADR 69
                 L IGG  +    + I    +++V TPGRL+  +D+         + L LDEADR
Sbjct: 124 HDFSAGLIIGGKDLKHEAERIN-NINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADR 182

Query: 70  MVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINV 119
           ++DMGF + +  +      +RQTLLFSAT  K +++ AR +L  P  + V
Sbjct: 183 ILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWV 232

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* Length = 563

 Score =  140 bits (354), Expect = 2e-39
 Identities = 40/195 (20%), Positives = 81/195 (41%), Gaps = 20/195 (10%)

Query: 12  PLRTCLAIGGVPMNQSLDVIKK-GCHMMVATPGRLMDMLD-KKMVSLDVCRYLCLDEADR 69
                  +GG     +++ + K   ++++ATPGRL+D+L+           Y  LDEADR
Sbjct: 178 KYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADR 237

Query: 70  MVDMGFEEDVRTIFSF-------FRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRA 122
           ++++GF +D+ TI               +TLLFSAT+  K+Q  A + + K   + +   
Sbjct: 238 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTV 297

Query: 123 GAASMNVVQEVE----YVKQEAKIVYLLEC-----LQKTEPP--VLIFAEKKQDVDAIHE 171
                   + ++      ++ A  ++         +++ +     +IFA   +    +  
Sbjct: 298 DKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCS 357

Query: 172 YLLLKGKPFFTLKSL 186
            L  + K    +   
Sbjct: 358 ILKNEFKKDLPILEF 372

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A Length = 410

 Score =  137 bits (347), Expect = 4e-39
 Identities = 46/165 (27%), Positives = 76/165 (46%), Gaps = 3/165 (1%)

Query: 16  CLAI-GGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMG 74
           C A  GG  + + +  +  G H++  TPGR+ DM+ ++ +     + L LDEAD M++ G
Sbjct: 136 CHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKG 195

Query: 75  FEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVE 134
           F+E +  ++ +     Q +L SAT+P +I       +  PI I V R       + Q   
Sbjct: 196 FKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFV 255

Query: 135 YVKQEAKIVYLLECLQKTEPP--VLIFAEKKQDVDAIHEYLLLKG 177
            V++E      L  L  T      +IF   K+ VD + E +    
Sbjct: 256 AVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREAN 300

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19 Length = 206

 Score =  132 bits (334), Expect = 4e-39
 Identities = 35/104 (33%), Positives = 57/104 (54%), Gaps = 1/104 (0%)

Query: 16  CLAI-GGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMG 74
            +A  GG  +   +  +    H+++ATPGR++D++ K +  +D  + + LDEAD+++   
Sbjct: 103 VMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQD 162

Query: 75  FEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITIN 118
           F + +  I       RQ LL+SAT P  +Q F  S L KP  IN
Sbjct: 163 FVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEIN 206

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  131 bits (332), Expect = 8e-39
 Identities = 36/114 (31%), Positives = 62/114 (54%), Gaps = 7/114 (6%)

Query: 6   ISALPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLD 65
           I A  +       IGG    ++L+ +    H+++ TPGR+ D + ++ + +     L +D
Sbjct: 105 IVARCL-------IGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVD 157

Query: 66  EADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINV 119
           EAD M+DMGF  DV  I +      Q L+FSAT+P+K++ F +  +  P  ++V
Sbjct: 158 EADLMLDMGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHV 211

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens} Length = 262

 Score =  128 bits (325), Expect = 3e-37
 Identities = 38/109 (34%), Positives = 63/109 (57%), Gaps = 2/109 (1%)

Query: 11  IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDK-KMVSLDVCRYLCLDEADR 69
                 L +GG   +     +  G +++VATPGRL+D +           + L +DEADR
Sbjct: 153 HVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADR 212

Query: 70  MVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVK-PITI 117
           ++D+GFEE+++ I      +RQT+LFSAT  +K+++ AR +L K P+ +
Sbjct: 213 ILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYV 261

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens} Length = 414

 Score =  130 bits (330), Expect = 1e-36
 Identities = 45/167 (26%), Positives = 80/167 (47%), Gaps = 4/167 (2%)

Query: 15  TCLAI-GGVPMNQSLDVIK-KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
           +C A  GG  +   +  ++ +  H++V TPGR+ DML+++ +S    +   LDEAD M+ 
Sbjct: 138 SCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLS 197

Query: 73  MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQE 132
            GF++ +  IF       Q +L SATMP  +    +  +  PI I V +       + Q 
Sbjct: 198 RGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQF 257

Query: 133 VEYVKQE-AKIVYLLECLQKTEPP-VLIFAEKKQDVDAIHEYLLLKG 177
              V++E  K+  L +  +       +IF   ++ VD + E +  + 
Sbjct: 258 YINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARD 304

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A Length = 391

 Score =  130 bits (328), Expect = 2e-36
 Identities = 46/167 (27%), Positives = 85/167 (50%), Gaps = 5/167 (2%)

Query: 16  CLAI-GGVPMNQSLDVIKKGC-HMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD- 72
                GG+ + +  +V+KK C H++V TPGR++ +   K ++L   ++  LDE D+M++ 
Sbjct: 108 VAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQ 167

Query: 73  MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASM-NVVQ 131
           +    DV+ IF     ++Q ++FSAT+ K+I+   R  +  P+ I V      ++  + Q
Sbjct: 168 LDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQ 227

Query: 132 EVEYVKQEAKIVYLLECLQKTEPP-VLIFAEKKQDVDAIHEYLLLKG 177
               +K   K   L + L   E   V+IF +  Q   A+ + L+ + 
Sbjct: 228 YYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQN 274

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A* Length = 394

 Score =  129 bits (327), Expect = 2e-36
 Identities = 41/168 (24%), Positives = 70/168 (41%), Gaps = 8/168 (4%)

Query: 15  TCLAI-GGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDM 73
              A  GG    +  + ++    ++V TPGR+ D + ++    D  +   LDEAD M+  
Sbjct: 119 KVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSS 177

Query: 74  GFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQ-- 131
           GF+E +  IF+      Q +L SATMP  +       +  P+ I V +       + Q  
Sbjct: 178 GFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFY 237

Query: 132 -EVEYVKQEAKIVYLLECLQKTEPP-VLIFAEKKQDVDAIHEYLLLKG 177
             VE  ++E K   L +          +IF   ++ V+ +   L    
Sbjct: 238 VNVE--EEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDK 283

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A* Length = 237

 Score =  121 bits (307), Expect = 8e-35
 Identities = 37/109 (33%), Positives = 59/109 (54%), Gaps = 2/109 (1%)

Query: 15  TCLA-IGGVPMNQSLDVIK-KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
           TC A IGG  +   +  ++ +  H++V TPGR+ DML+++ +S    +   LDEAD M+ 
Sbjct: 128 TCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLS 187

Query: 73  MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGR 121
            GF++ +  IF       Q +L SATMP  +    +  +  PI I V +
Sbjct: 188 RGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKK 236

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A Length = 224

 Score =  119 bits (300), Expect = 7e-34
 Identities = 32/107 (29%), Positives = 52/107 (48%), Gaps = 2/107 (1%)

Query: 16  CLA-IGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMG 74
             A IGG    +  + ++    ++V TPGR+ D + ++    D  +   LDEAD M+  G
Sbjct: 113 VHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSG 171

Query: 75  FEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGR 121
           F+E +  IF+      Q +L SATMP  +       +  P+ I V +
Sbjct: 172 FKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKK 218

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19 Length = 220

 Score =  117 bits (296), Expect = 2e-33
 Identities = 34/107 (31%), Positives = 62/107 (57%), Gaps = 3/107 (2%)

Query: 16  CLAI-GGVPMNQSLDVIKKGC-HMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD- 72
                GG+ + +  +V+KK C H++V TPGR++ +   K ++L   ++  LDE D+M++ 
Sbjct: 114 VAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQ 173

Query: 73  MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINV 119
           +    DV+ IF     ++Q ++FSAT+ K+I+   R  +  P+ I V
Sbjct: 174 LDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 220

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A* Length = 230

 Score =  118 bits (297), Expect = 2e-33
 Identities = 31/106 (29%), Positives = 55/106 (51%), Gaps = 3/106 (2%)

Query: 16  CLAI-GGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMG 74
           C    GG P++Q    +K  CH+ V +PGR+  +++   ++    R   LDEAD++++ G
Sbjct: 124 CHVFIGGTPLSQDKTRLK-KCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEG 182

Query: 75  -FEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINV 119
            F+E +  I+S     +Q L  SAT P+ + N     +  P  + +
Sbjct: 183 SFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRL 228

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B Length = 412

 Score =  119 bits (301), Expect = 2e-32
 Identities = 38/172 (22%), Positives = 66/172 (38%), Gaps = 13/172 (7%)

Query: 13  LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDK-KMVSLDVCRYLCLDEADRMV 71
           L+   A+ G  + +     K    +++ TPG ++D   K K +     +   LDEAD M+
Sbjct: 125 LKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 181

Query: 72  D-MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVV 130
              G ++    I        Q LLFSAT    +  FA+  +  P  I + R       + 
Sbjct: 182 ATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIK 241

Query: 131 Q-----EVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKG 177
           Q          K +A +  L   +   +   +IF   ++    +   L  +G
Sbjct: 242 QYYVLCSSRDEKFQA-LCNLYGAITIAQ--AMIFCHTRKTASWLAAELSKEG 290

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens} Length = 479

 Score =  119 bits (301), Expect = 4e-32
 Identities = 37/173 (21%), Positives = 66/173 (38%), Gaps = 15/173 (8%)

Query: 13  LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDK-KMVSLDVCRYLCLDEADRMV 71
           L+   A+ G  + +     K    +++ TPG ++D   K K +     +   LDEAD M+
Sbjct: 192 LKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 248

Query: 72  D-MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVV 130
              G ++    I        Q LLFSAT    +  FA+  +  P  I + R       + 
Sbjct: 249 ATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIK 308

Query: 131 Q---EVEYVKQEAK---IVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKG 177
           Q         ++ K   +  L   +   +   +IF   ++    +   L  +G
Sbjct: 309 QYYVLCS--SRDEKFQALCNLYGAITIAQ--AMIFCHTRKTASWLAAELSKEG 357

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A* Length = 395

 Score =  118 bits (297), Expect = 5e-32
 Identities = 34/173 (19%), Positives = 72/173 (41%), Gaps = 13/173 (7%)

Query: 11  IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRM 70
             + + L +     +   +  +    ++V TPG ++D++ +K++ L   +   LDEAD M
Sbjct: 102 TKITSQLIVPD---SFEKN-KQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNM 157

Query: 71  VDM-GFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNV 129
           +D  G  +    +  F     Q +LFSAT    ++ +A+  +    T+ +         +
Sbjct: 158 LDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAI 217

Query: 130 VQ-----EVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKG 177
            Q     + E  K +  +  L   +       +IF   K+  + ++  L  +G
Sbjct: 218 KQLYMDCKNEADKFDV-LTELYGLMTIGS--SIIFVATKKTANVLYGKLKSEG 267

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens} Length = 300

 Score =  114 bits (288), Expect = 2e-31
 Identities = 30/111 (27%), Positives = 48/111 (43%), Gaps = 5/111 (4%)

Query: 13  LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDK-KMVSLDVCRYLCLDEADRMV 71
           L+   A+ G  + +     K    +++ TPG ++D   K K +     +   LDEAD M+
Sbjct: 192 LKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 248

Query: 72  D-MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGR 121
              G ++    I        Q LLFSAT    +  FA+  +  P  I + R
Sbjct: 249 ATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKR 299

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score = 94.2 bits (235), Expect = 1e-24
 Identities = 48/68 (70%), Positives = 55/68 (80%)

Query: 112 VKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHE 171
           +    +     GAAS++V+QEVEYVK+EAK+VYLLECLQKT PPVLIFAEKK DVDAIHE
Sbjct: 13  LGTENLYFQSMGAASLDVIQEVEYVKEEAKMVYLLECLQKTPPPVLIFAEKKADVDAIHE 72

Query: 172 YLLLKGKP 179
           YLLLKG  
Sbjct: 73  YLLLKGVE 80

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens} Length = 185

 Score = 86.5 bits (215), Expect = 9e-22
 Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 2/67 (2%)

Query: 115 ITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPP--VLIFAEKKQDVDAIHEY 172
              N+   G+ S N+ Q+V +V++  K  +LL+ L  T      L+F E K+  D++ ++
Sbjct: 6   HHENLYFQGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDF 65

Query: 173 LLLKGKP 179
           L  +G  
Sbjct: 66  LYHEGYA 72

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 46.4 bits (109), Expect = 3e-06
 Identities = 41/234 (17%), Positives = 70/234 (29%), Gaps = 76/234 (32%)

Query: 12  PLRTCLAIGGVPMNQSLD------VIKK---GCHMMVATPGRLMDMLDKKMVSLDVCRYL 62
           P   CL +        L               C +++ T  R   + D   +S     ++
Sbjct: 242 PYENCLLV--------LLNVQNAKAWNAFNLSCKILLTT--RFKQVTDF--LSAATTTHI 289

Query: 63  CLDEADRMVDMGFEEDVRTIFSFFRGQRQTL-LFSATMPKKIQNFARSAL-VKPITIN-V 119
            LD       M    D            +   L    +  + Q+  R  L   P  ++ +
Sbjct: 290 SLDH----HSMTLTPD------------EVKSLLLKYLDCRPQDLPREVLTTNPRRLSII 333

Query: 120 G---RAGAASMNVVQEVEYVKQEAKIVYLLECLQKTE-----------------PPVLI- 158
               R G A+ +  + V   K    I   L  L+  E                 P +L+ 
Sbjct: 334 AESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLS 393

Query: 159 ---FAEKKQDVDAI----HEYLLLKGKPF-FT-------LKSLKEDQNNQTLEN 197
              F   K DV  +    H+Y L++ +P   T       L+   + +N   L  
Sbjct: 394 LIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHR 447

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19 Length = 494

 Score = 42.9 bits (100), Expect = 3e-05
 Identities = 24/142 (16%), Positives = 48/142 (33%), Gaps = 1/142 (0%)

Query: 9   LPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEAD 68
             +P    +A+ G    +          ++VATP  + + L    +SL+    +  DEA 
Sbjct: 76  FNLPPEKIVALTGEKSPEERSKAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAH 135

Query: 69  RMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMN 128
           R V       +   +         +  +A+ P          +      ++      S +
Sbjct: 136 RAVGNYAYVFIAREYKRQAKNPLVIGLTAS-PGSTPEKIMEVINNLGIEHIEYRSENSPD 194

Query: 129 VVQEVEYVKQEAKIVYLLECLQ 150
           V   V+ ++ E   V L E  +
Sbjct: 195 VRPYVKGIRFEWVRVDLPEIYK 216

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	197
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.97
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.96
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.96
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.95
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.95
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.95
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.95
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.94
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.93
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.93
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.93
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.93
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.91
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.91
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.9
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.89
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.88
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.88
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.87
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.87
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.85
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.85
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.85
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.85
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.84
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.84
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.84
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.84
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.84
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.83
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.82
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.82
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.82
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.82
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.82
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.81
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.81
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.81
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.81
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.81
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.8
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.8
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.8
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.8
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.8
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.79
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.78
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.78
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.78
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.78
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.77
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.76
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.74
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.72
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.71
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.68
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.64
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.58
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.57
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.56
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.56
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.54
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.52
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.5
3h1t_A	590	Type I site-specific restriction-modification syst	99.47
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.44
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.44
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.43
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.38
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.38
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.32
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.3
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.24
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.2
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.19
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.18
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.17
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.17
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.16
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.15
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.12
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.08
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	98.4
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	98.88
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	98.88
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	98.86
3jux_A	822	Protein translocase subunit SECA; protein transloc	98.75
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	98.45
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	97.97
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	96.75
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	95.48
3gk5_A	108	Uncharacterized rhodanese-related protein TVG08686	93.54
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	93.0
1wv9_A	94	Rhodanese homolog TT1651; CDC25, phosphatase, sulf	92.78
3eme_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	92.07
3foj_A	100	Uncharacterized protein; protein SSP1007, structur	91.94
3g5j_A	134	Putative ATP/GTP binding protein; N-terminal domai	91.5
3iwh_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	91.49
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	91.13
2jtq_A	85	Phage shock protein E; solution structure rhodanes	91.06
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	90.75
3hix_A	106	ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q	90.08
3flh_A	124	Uncharacterized protein LP_1913; alpha-beta protei	90.05
2fsx_A	148	RV0390, COG0607: rhodanese-related sulfurtransfera	89.79
2k0z_A	110	Uncharacterized protein HP1203; A/B domain, struct	89.61
1qxn_A	137	SUD, sulfide dehydrogenase; polysulfide-sulfur tra	89.28
3jux_A	822	Protein translocase subunit SECA; protein transloc	88.79
1gmx_A	108	GLPE protein; transferase, rhodanese, sulfurtransf	88.64
1tq1_A	129	AT5G66040, senescence-associated family protein; C	88.38
3nhv_A	144	BH2092 protein; alpha-beta protein, structural gen	88.26
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	87.96
2hhg_A	139	Hypothetical protein RPA3614; MCSG, structural gen	86.57
3d1p_A	139	Putative thiosulfate sulfurtransferase YOR285W; at	86.13
1vee_A	134	Proline-rich protein family; hypothetical protein,	85.81
3ilm_A	141	ALR3790 protein; rhodanese-like, NSR437H, NESG, st	85.28
1urh_A	280	3-mercaptopyruvate sulfurtransferase; rhodanese; 2	83.83
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	83.75
3tg1_B	158	Dual specificity protein phosphatase 10; kinase/rh	83.56
1urh_A	280	3-mercaptopyruvate sulfurtransferase; rhodanese; 2	81.38
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	81.14

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=100.00  E-value=6.6e-32  Score=221.81  Aligned_cols=186  Identities=33%  Similarity=0.572  Sum_probs=174.0

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhc--cC
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF--RG   88 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~--~~   88 (197)
                      .++++..++||.+...+.+.+..+++|+|+||++|.+++.+....+++++++|+||||++++++|...+..++..+  ++
T Consensus       156 ~~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~~~~~l~~~~~lVlDEah~~~~~gf~~~~~~i~~~~~~~~  235 (434)
T 2db3_A          156 SYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRP  235 (434)
T ss_dssp             SSCCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSCCCTTCCEEEEETHHHHTSTTTHHHHHHHHHCTTSCS
T ss_pred             CCcEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHHHHHhCCcccccCCeEEEccHhhhhccCcHHHHHHHHHhcCCCC
Confidence            4789999999999998888888899999999999999999888889999999999999999999999999999885  57


Q ss_pred             CceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecccccHHH
Q psy7789          89 QRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDA  168 (197)
Q Consensus        89 ~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~  168 (197)
                      ..|+++||||+++++...+..++.++..+.+.........+.+.++.+....|...+.+++.....++||||+|++.|+.
T Consensus       236 ~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lVF~~t~~~a~~  315 (434)
T 2db3_A          236 EHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEVNKYAKRSKLIEILSEQADGTIVFVETKRGADF  315 (434)
T ss_dssp             SCEEEEEESCCCHHHHHHHHTTCSSCEEEEESSTTCCCTTEEEEEEECCGGGHHHHHHHHHHHCCTTEEEECSSHHHHHH
T ss_pred             CceEEEEeccCCHHHHHHHHHhccCCEEEEeccccccccccceEEEEeCcHHHHHHHHHHHHhCCCCEEEEEeCcHHHHH
Confidence            88999999999999999999999999999888777777889999999999999999999999887789999999999999


Q ss_pred             HHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         169 IHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       169 l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +++.|++.|+++..+||+|++++|++++
T Consensus       316 l~~~L~~~~~~~~~lhg~~~~~~R~~~l  343 (434)
T 2db3_A          316 LASFLSEKEFPTTSIHGDRLQSQREQAL  343 (434)
T ss_dssp             HHHHHHHTTCCEEEESTTSCHHHHHHHH
T ss_pred             HHHHHHhCCCCEEEEeCCCCHHHHHHHH
Confidence            9999999999999999999999999876

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.97  E-value=4.3e-29  Score=203.25  Aligned_cols=186  Identities=38%  Similarity=0.711  Sum_probs=167.0

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhh--ccC
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSF--FRG   88 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~--~~~   88 (197)
                      .++++..++||.+...+.+.+..+++|+|+||++|...+....+.+++++++|+||||.+.+++|...+..++..  ++.
T Consensus       128 ~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~i~~~~~~~~  207 (417)
T 2i4i_A          128 SRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPP  207 (417)
T ss_dssp             SSCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSBCCTTCCEEEESSHHHHHHTTCHHHHHHHHTSSSCCC
T ss_pred             CCceEEEEECCCCHHHHHHHhhCCCCEEEEChHHHHHHHHcCCcChhhCcEEEEEChhHhhccCcHHHHHHHHHhccCCC
Confidence            478999999999998888888888999999999999999988888999999999999999999999999999875  333


Q ss_pred             --CceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcC--CCCEEEEecccc
Q psy7789          89 --QRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKT--EPPVLIFAEKKQ  164 (197)
Q Consensus        89 --~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~--~~~~lIF~~s~~  164 (197)
                        ..|++++|||+++.+......++.++..+.+.........+.+.+..+...+|...+.++++..  ++++||||++++
T Consensus       208 ~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~lVf~~~~~  287 (417)
T 2i4i_A          208 KGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKK  287 (417)
T ss_dssp             BTTBEEEEEESCCCHHHHHHHHHHCSSCEEEEEC----CCSSEEEEEEECCGGGHHHHHHHHHHTCCTTCEEEEECSSHH
T ss_pred             cCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEeCCCCCCccCceEEEEEeccHhHHHHHHHHHHhcCCCCeEEEEECCHH
Confidence              6799999999999999999999999998888877777788999999999999999999999876  458999999999


Q ss_pred             cHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         165 DVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       165 ~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .++.+++.|++.|+++..+||+|++++|++++
T Consensus       288 ~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~  319 (417)
T 2i4i_A          288 GADSLEDFLYHEGYACTSIHGDRSQRDREEAL  319 (417)
T ss_dssp             HHHHHHHHHHHTTCCEEEECTTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCeeEecCCCCHHHHHHHH
Confidence            99999999999999999999999999999875

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=99.96  E-value=6.6e-29  Score=201.95  Aligned_cols=186  Identities=24%  Similarity=0.408  Sum_probs=168.5

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .++++..++||.....+...+..+++|+|+||++|.+++.+..+.+.+++++|+||||.+.++++...+..+++.+++..
T Consensus       132 ~~~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~i~~~~~~~~  211 (410)
T 2j0s_A          132 MNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT  211 (410)
T ss_dssp             TTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTSTTTHHHHHHHHTTSCTTC
T ss_pred             CCeEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHhCCccHhheeEEEEccHHHHHhhhhHHHHHHHHHhCccCc
Confidence            47899999999999888888888899999999999999998888899999999999999999999999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchh-hHHHHHHHhhcC-CCCEEEEecccccHHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEA-KIVYLLECLQKT-EPPVLIFAEKKQDVDA  168 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~-k~~~l~~~l~~~-~~~~lIF~~s~~~~~~  168 (197)
                      |++++|||+++++.+....++.+|..+.+.........+.+.+..+.... |...+.++++.. .+++||||++++.++.
T Consensus       212 ~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lVf~~~~~~~~~  291 (410)
T 2j0s_A          212 QVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDW  291 (410)
T ss_dssp             EEEEEESCCCHHHHTTGGGTCSSCEEECCCGGGCSCTTEEEEEEEESSTTHHHHHHHHHHHHHTSSEEEEECSSHHHHHH
T ss_pred             eEEEEEcCCCHHHHHHHHHHcCCCEEEEecCccccCCCceEEEEEeCcHHhHHHHHHHHHHhcCCCcEEEEEcCHHHHHH
Confidence            99999999999999888899999988877766667778888888776544 888888888765 3589999999999999


Q ss_pred             HHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         169 IHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       169 l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +++.|.+.|+++..+||+|++++|++++
T Consensus       292 l~~~L~~~~~~~~~~h~~~~~~~r~~~~  319 (410)
T 2j0s_A          292 LTEKMREANFTVSSMHGDMPQKERESIM  319 (410)
T ss_dssp             HHHHHHHTTCCCEEECTTSCHHHHHHHH
T ss_pred             HHHHHHhCCCceEEeeCCCCHHHHHHHH
Confidence            9999999999999999999999999875

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=99.96  E-value=9.4e-28  Score=195.06  Aligned_cols=186  Identities=24%  Similarity=0.400  Sum_probs=165.6

Q ss_pred             CCeeEEEEEcCCChHHhHHHHh-cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCC
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIK-KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~-~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~   89 (197)
                      .++++..++||.+...+...+. ++++|+|+||++|.+.+....+.++++++||+||||.+.++++...+..++..++++
T Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~  214 (414)
T 3eiq_A          135 MGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSN  214 (414)
T ss_dssp             SCCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTSSCSTTCCEEEECSHHHHHHTTTHHHHHHHHTTSCTT
T ss_pred             cCceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccCcEEEEECHHHhhccCcHHHHHHHHHhCCCC
Confidence            3688899999998888877775 679999999999999999888889999999999999999999999999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCc-hhhHHHHHHHhhcCC-CCEEEEecccccHH
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQ-EAKIVYLLECLQKTE-PPVLIFAEKKQDVD  167 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~  167 (197)
                      .|++++|||+++.+......++.++..+...........+.+.+..+.. +.|...+.++++... +++||||++++.++
T Consensus       215 ~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~  294 (414)
T 3eiq_A          215 TQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVD  294 (414)
T ss_dssp             CEEEEECSCCCHHHHHHHTTTCSSCEEECCCCCCCCTTSCCEEEEECSSSTTHHHHHHHHHHSSCCSSCEEECSCHHHHH
T ss_pred             CeEEEEEEecCHHHHHHHHHHcCCCEEEEecCCccCCCCceEEEEEeChHHhHHHHHHHHHHhCCCCcEEEEeCCHHHHH
Confidence            9999999999999999999999999988888777777788888877755 458899999988764 58999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .+++.|.+.|+.+..+||+|++++|++++
T Consensus       295 ~l~~~l~~~~~~~~~~h~~~~~~~r~~~~  323 (414)
T 3eiq_A          295 WLTEKMHARDFTVSAMHGDMDQKERDVIM  323 (414)
T ss_dssp             HHHHHHHTTTCCCEEC---CHHHHHHHHH
T ss_pred             HHHHHHHhcCCeEEEecCCCCHHHHHHHH
Confidence            99999999999999999999999999875

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=99.95  E-value=8.3e-27  Score=188.16  Aligned_cols=185  Identities=25%  Similarity=0.395  Sum_probs=164.7

Q ss_pred             CeeEEEEEcCCChHHhHHHHhc-CCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcC-CCHHHHHHHHhhccCC
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKK-GCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDM-GFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~-~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~-~~~~~i~~i~~~~~~~   89 (197)
                      ++++..++||.+...+...+.. .++|+|+||+++...+.+....+.+++++|+||||.+.++ ++...+..++...++.
T Consensus       105 ~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~vViDEaH~~~~~~~~~~~~~~~~~~~~~~  184 (391)
T 1xti_A          105 NVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHE  184 (391)
T ss_dssp             TCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCSEEEECSHHHHTSSHHHHHHHHHHHHTSCSS
T ss_pred             CeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHcCCccccccCEEEEeCHHHHhhccchHHHHHHHHhhCCCC
Confidence            7999999999998887777754 5899999999999999888888999999999999999885 6788889999999889


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCC-ccCcceeEEEEEcCchhhHHHHHHHhhcCC-CCEEEEecccccHH
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVGRAG-AASMNVVQEVEYVKQEAKIVYLLECLQKTE-PPVLIFAEKKQDVD  167 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~-~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~  167 (197)
                      .|++++|||+++........++.+|..+...... .....+.+.+..+....|...+.++++... +++||||++++.++
T Consensus       185 ~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~lvf~~~~~~~~  264 (391)
T 1xti_A          185 KQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCI  264 (391)
T ss_dssp             SEEEEEESSCCSTHHHHHHHHCSSCEEEECCCCCCCCCTTCEEEEEECCGGGHHHHHHHHHHHSCCSEEEEECSCHHHHH
T ss_pred             ceEEEEEeeCCHHHHHHHHHHcCCCeEEEecCccccCcccceEEEEEcCchhHHHHHHHHHHhcCCCcEEEEeCcHHHHH
Confidence            9999999999999999999999999888776544 344667888888888999999999998664 58999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .+++.|++.|+++..+||+|++++|++++
T Consensus       265 ~l~~~L~~~~~~~~~~~~~~~~~~r~~~~  293 (391)
T 1xti_A          265 ALAQLLVEQNFPAIAIHRGMPQEERLSRY  293 (391)
T ss_dssp             HHHHHHHHTTCCEEEECTTSCHHHHHHHH
T ss_pred             HHHHHHHhCCCcEEEEeCCCCHHHHHHHH
Confidence            99999999999999999999999999875

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=99.95  E-value=2.8e-26  Score=183.27  Aligned_cols=181  Identities=27%  Similarity=0.405  Sum_probs=162.5

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .++++..++||.....+...+. +++|+|+||+++...+......+.+++++|+||||.+.++++...+..++..+++..
T Consensus       101 ~~~~v~~~~~~~~~~~~~~~~~-~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~~~~~~~~~~~~  179 (367)
T 1hv8_A          101 KNLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDK  179 (367)
T ss_dssp             SCCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTTTHHHHHHHHHTSCSSC
T ss_pred             CCceEEEEECCcchHHHHhhcC-CCCEEEecHHHHHHHHHcCCcccccCCEEEEeCchHhhhhchHHHHHHHHHhCCCCc
Confidence            4688999999998887777666 599999999999999988888899999999999999999999999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecccccHHHHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIH  170 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~  170 (197)
                      |++++|||++++.......++.++..+....    ...+.+.+..+...+|...+.++++..+.++||||++++.++.++
T Consensus       180 ~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~lvf~~~~~~~~~l~  255 (367)
T 1hv8_A          180 RILLFSATMPREILNLAKKYMGDYSFIKAKI----NANIEQSYVEVNENERFEALCRLLKNKEFYGLVFCKTKRDTKELA  255 (367)
T ss_dssp             EEEEECSSCCHHHHHHHHHHCCSEEEEECCS----SSSSEEEEEECCGGGHHHHHHHHHCSTTCCEEEECSSHHHHHHHH
T ss_pred             eEEEEeeccCHHHHHHHHHHcCCCeEEEecC----CCCceEEEEEeChHHHHHHHHHHHhcCCCcEEEEECCHHHHHHHH
Confidence            9999999999999999999998877665432    235777888888999999999999987789999999999999999


Q ss_pred             HHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         171 EYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       171 ~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +.|++.|+++..+||+|++++|++++
T Consensus       256 ~~L~~~~~~~~~~~~~~~~~~r~~~~  281 (367)
T 1hv8_A          256 SMLRDIGFKAGAIHGDLSQSQREKVI  281 (367)
T ss_dssp             HHHHHTTCCEEEECSSSCHHHHHHHH
T ss_pred             HHHHhcCCCeEEeeCCCCHHHHHHHH
Confidence            99999999999999999999999875

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=99.95  E-value=9.5e-27  Score=188.56  Aligned_cols=185  Identities=24%  Similarity=0.434  Sum_probs=164.3

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .|+++..++||.....+...+..+++|+|+||+++...+......+.+++++|+||||++.+.++...+..++..+++..
T Consensus       116 ~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~~~~~~~~i~~~~~~~~  195 (400)
T 1s2m_A          116 CGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTH  195 (400)
T ss_dssp             TTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHHHHHHHHHHHTTSCSSC
T ss_pred             cCceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHhCCcccccCCEEEEeCchHhhhhchHHHHHHHHHhCCcCc
Confidence            37899999999988887777778899999999999999988878899999999999999988888889999999998899


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCC-CCEEEEecccccHHHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTE-PPVLIFAEKKQDVDAI  169 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~~l  169 (197)
                      |++++|||+++.+......++.+|..+..... .....+.+.+..+....|...+..+++... +++||||++++.++.+
T Consensus       196 ~~i~lSAT~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lVf~~~~~~~~~l  274 (400)
T 1s2m_A          196 QSLLFSATFPLTVKEFMVKHLHKPYEINLMEE-LTLKGITQYYAFVEERQKLHCLNTLFSKLQINQAIIFCNSTNRVELL  274 (400)
T ss_dssp             EEEEEESCCCHHHHHHHHHHCSSCEEESCCSS-CBCTTEEEEEEECCGGGHHHHHHHHHHHSCCSEEEEECSSHHHHHHH
T ss_pred             eEEEEEecCCHHHHHHHHHHcCCCeEEEeccc-cccCCceeEEEEechhhHHHHHHHHHhhcCCCcEEEEEecHHHHHHH
Confidence            99999999999999999999998877765533 345667888888888899999998888764 5899999999999999


Q ss_pred             HHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         170 HEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       170 ~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      ++.|++.|+.+..+||+|++++|++++
T Consensus       275 ~~~L~~~~~~~~~~~~~~~~~~r~~~~  301 (400)
T 1s2m_A          275 AKKITDLGYSCYYSHARMKQQERNKVF  301 (400)
T ss_dssp             HHHHHHHTCCEEEECTTSCHHHHHHHH
T ss_pred             HHHHHhcCCCeEEecCCCCHHHHHHHH
Confidence            999999999999999999999999875

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=99.95  E-value=3.3e-27  Score=190.57  Aligned_cols=186  Identities=23%  Similarity=0.383  Sum_probs=100.7

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .++++..++||.+...+...+. +++|+|+||+++...+....+.+.+++++|+||||.+.++++...+..++..+++..
T Consensus       116 ~~~~~~~~~g~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~~~~~~~~~vIiDEah~~~~~~~~~~~~~~~~~~~~~~  194 (394)
T 1fuu_A          116 MDIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTT  194 (394)
T ss_dssp             SCCCEEEECSSCCHHHHHHHHH-HCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTC
T ss_pred             CCeeEEEEeCCCchHHHHhhcC-CCCEEEECHHHHHHHHHhCCcchhhCcEEEEEChHHhhCCCcHHHHHHHHHhCCCCc
Confidence            4789999999998877776666 499999999999999988888889999999999999999999999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchh-hHHHHHHHhhcC-CCCEEEEecccccHHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEA-KIVYLLECLQKT-EPPVLIFAEKKQDVDA  168 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~-k~~~l~~~l~~~-~~~~lIF~~s~~~~~~  168 (197)
                      |++++|||+++.+.+....++.+|..+...........+.+.+..+...+ +...+.++++.. .+++||||++++.++.
T Consensus       195 ~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lVf~~~~~~~~~  274 (394)
T 1fuu_A          195 QVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEE  274 (394)
T ss_dssp             EEEEECSSCCHHHHHHHHHHCCSCEEEEECC-------------------------------------------------
T ss_pred             eEEEEEEecCHHHHHHHHHhcCCCeEEEecCccccCCCceEEEEEcCchhhHHHHHHHHHhcCCCCcEEEEECCHHHHHH
Confidence            99999999999999999999999998888777666677777777665544 777777777764 3589999999999999


Q ss_pred             HHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         169 IHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       169 l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      +++.|++.|+++..+||+|++++|+++++
T Consensus       275 l~~~L~~~~~~~~~~~~~~~~~~r~~~~~  303 (394)
T 1fuu_A          275 LTTKLRNDKFTVSAIYSDLPQQERDTIMK  303 (394)
T ss_dssp             -----------------------------
T ss_pred             HHHHHHHcCCeEEEeeCCCCHHHHHHHHH
Confidence            99999999999999999999999998763

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=99.94  E-value=1.1e-25  Score=182.65  Aligned_cols=182  Identities=21%  Similarity=0.291  Sum_probs=158.4

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhc-CCccCCCccEEEeehhhhhhc-CCCHHHHHHHHhhccCC
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDK-KMVSLDVCRYLCLDEADRMVD-MGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~-~~~~l~~l~~vViDEad~l~~-~~~~~~i~~i~~~~~~~   89 (197)
                      ++++....||.......   ..+++|+|+||+++...+.+ +.+.+++++++|+||||.+.+ .++...+..+...++++
T Consensus       124 ~~~~~~~~~~~~~~~~~---~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~~~~~~~~~  200 (412)
T 3fht_A          124 ELKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRN  200 (412)
T ss_dssp             TCCEEEECTTCCCCTTC---CCCCSEEEECHHHHHHHHTTSCSSCGGGCCEEEEETHHHHHSTTTTHHHHHHHHHTSCTT
T ss_pred             cceEEEeecCcchhhhh---cCCCCEEEECchHHHHHHHhcCCcChhhCcEEEEeCHHHHhhcCCcHHHHHHHHhhCCCC
Confidence            67888888887654432   34589999999999999865 567789999999999999987 67888999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCc-hhhHHHHHHHhhcC-CCCEEEEecccccHH
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQ-EAKIVYLLECLQKT-EPPVLIFAEKKQDVD  167 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~~l~~~-~~~~lIF~~s~~~~~  167 (197)
                      .|++++|||+++.+......++.++..+.+.........+.+.+..+.. ..+...+.+++... .+++||||++++.|+
T Consensus       201 ~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~  280 (412)
T 3fht_A          201 CQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTAS  280 (412)
T ss_dssp             CEEEEEESCCCHHHHHHHHHHSSSCEEECCCGGGSSCTTEEEEEEECSSHHHHHHHHHHHHHHHSSSEEEEECSSHHHHH
T ss_pred             ceEEEEEeecCHHHHHHHHHhcCCCeEEeeccccccccCceEEEEEcCChHHHHHHHHHHHhhcCCCCEEEEeCCHHHHH
Confidence            9999999999999999999999999999888777777888888777754 66888888888764 468999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .+++.|.+.|+.+..+||+|++++|++++
T Consensus       281 ~l~~~L~~~~~~~~~~~~~~~~~~r~~~~  309 (412)
T 3fht_A          281 WLAAELSKEGHQVALLSGEMMVEQRAAVI  309 (412)
T ss_dssp             HHHHHHHHTTCCCEEECTTSCHHHHHHHH
T ss_pred             HHHHHHHhCCCeEEEecCCCCHHHHHHHH
Confidence            99999999999999999999999999876

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=99.93  E-value=6.5e-25  Score=176.94  Aligned_cols=182  Identities=21%  Similarity=0.311  Sum_probs=155.4

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhc-CCCHHHHHHHHhhccCC
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD-MGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~-~~~~~~i~~i~~~~~~~   89 (197)
                      .++.+...+|+......    ..+++|+|+||+++...+.+....+.+++++|+||||.+.+ .++...+..+...++++
T Consensus       102 ~~~~~~~~~~~~~~~~~----~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~~~~~~~~~~~~  177 (395)
T 3pey_A          102 TKITSQLIVPDSFEKNK----QINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKD  177 (395)
T ss_dssp             SCCCEEEESTTSSCTTS----CBCCSEEEECHHHHHHHHHTTCBCCTTCCEEEEETHHHHHHSTTHHHHHHHHHHTSCTT
T ss_pred             cCeeEEEEecCchhhhc----cCCCCEEEEcHHHHHHHHHcCCcccccCCEEEEEChhhhcCccccHHHHHHHHHhCCCC
Confidence            35666667766543322    23589999999999999988888899999999999999987 67888999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcC-chhhHHHHHHHhhcCC-CCEEEEecccccHH
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVK-QEAKIVYLLECLQKTE-PPVLIFAEKKQDVD  167 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~-~~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~  167 (197)
                      .|++++|||+++.+......++.++..+...........+.+.+..+. ...+...+..++.... +++||||++++.|+
T Consensus       178 ~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~  257 (395)
T 3pey_A          178 TQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTAN  257 (395)
T ss_dssp             CEEEEEESCCCHHHHHHHHHHSCSCEEECCCGGGCSCTTEEEEEEECSSHHHHHHHHHHHHTTTTSSEEEEECSCHHHHH
T ss_pred             cEEEEEEecCCHHHHHHHHHhCCCCeEEEccccccccccccEEEEEcCchHHHHHHHHHHHHhccCCCEEEEeCCHHHHH
Confidence            999999999999999999999999988888776666777888777774 4667788888877654 68999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .+++.|++.|+++..+||+|++++|++++
T Consensus       258 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~  286 (395)
T 3pey_A          258 VLYGKLKSEGHEVSILHGDLQTQERDRLI  286 (395)
T ss_dssp             HHHHHHHHTTCCCEEECTTSCHHHHHHHH
T ss_pred             HHHHHHHhcCCcEEEeCCCCCHHHHHHHH
Confidence            99999999999999999999999999876

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.93  E-value=3.6e-25  Score=187.70  Aligned_cols=185  Identities=24%  Similarity=0.373  Sum_probs=149.1

Q ss_pred             CeeEEEEEcCCChHHhHHHHh-cCCcEEEeCchHHHHHHhcC-CccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccC-
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIK-KGCHMMVATPGRLMDMLDKK-MVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRG-   88 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~-~~~~Ili~TP~~l~~~l~~~-~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~-   88 (197)
                      .+.+..++||.....+...+. .+++|+|+||++|.+.+.+. ...++.+++||+||||++++++|...+..++..++. 
T Consensus       127 ~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l~~~gf~~~~~~i~~~l~~~  206 (579)
T 3sqw_A          127 KYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEK  206 (579)
T ss_dssp             TSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHHHTSTTTHHHHHHHHHHHHHH
T ss_pred             ceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhccccccccCCEEEEEChHHhhcCCCHHHHHHHHHHhhhh
Confidence            577889999999888887774 47999999999999988764 456899999999999999999999999998877643 


Q ss_pred             ------CceEEEEeecCChhHHHHHHHhcCCCeEEEeCC----CCccCcceeEEEEEcCc-hhhH----HHHHHHhhc--
Q psy7789          89 ------QRQTLLFSATMPKKIQNFARSALVKPITINVGR----AGAASMNVVQEVEYVKQ-EAKI----VYLLECLQK--  151 (197)
Q Consensus        89 ------~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~----~~~~~~~i~~~~~~~~~-~~k~----~~l~~~l~~--  151 (197)
                            ..|++++|||+++.+...+..++.++..+.+..    .......+.+.+..... ..+.    ..+...+..  
T Consensus       207 ~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  286 (579)
T 3sqw_A          207 NSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERD  286 (579)
T ss_dssp             CSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHHTT
T ss_pred             hcccccCceEEEEeccCChHHHHHHHHHcCCCceEEEeecCccccccccccceEEEEecchhhhHHHHHHHHHHHHhhcC
Confidence                  679999999999999999999999887766543    22334556666665543 2222    333344442  


Q ss_pred             CCCCEEEEecccccHHHHHHHHHhC---CCCeEeecCCCChhhhhhhh
Q psy7789         152 TEPPVLIFAEKKQDVDAIHEYLLLK---GKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       152 ~~~~~lIF~~s~~~~~~l~~~L~~~---~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .+.++||||+|++.|+.+++.|++.   |+.+..+||+|++++|++++
T Consensus       287 ~~~~~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~R~~~~  334 (579)
T 3sqw_A          287 SNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLV  334 (579)
T ss_dssp             TCCEEEEECSSHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHH
T ss_pred             CCCcEEEECCcHHHHHHHHHHHHHhhcCCCcEEEecCCCCHHHHHHHH
Confidence            2458999999999999999999987   89999999999999999876

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=99.93  E-value=7.9e-25  Score=184.83  Aligned_cols=185  Identities=24%  Similarity=0.379  Sum_probs=147.7

Q ss_pred             CeeEEEEEcCCChHHhHHHH-hcCCcEEEeCchHHHHHHhcC-CccCCCccEEEeehhhhhhcCCCHHHHHHHHhhcc--
Q psy7789          12 PLRTCLAIGGVPMNQSLDVI-KKGCHMMVATPGRLMDMLDKK-MVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFR--   87 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l-~~~~~Ili~TP~~l~~~l~~~-~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~--   87 (197)
                      ++.+..++||.....+...+ ..+++|+|+||++|.+.+.+. ...++++++||+||||++++++|...+..++..++  
T Consensus       178 ~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l~~~~f~~~~~~i~~~l~~~  257 (563)
T 3i5x_A          178 KYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEK  257 (563)
T ss_dssp             TSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHHHTSTTTHHHHHHHHHHHHHH
T ss_pred             ceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhccccccccceEEEEeCHHHHhccchHHHHHHHHHhhhhc
Confidence            56788899999988887776 457999999999999988764 44678999999999999999999999998887764  


Q ss_pred             -----CCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCC----CccCcceeEEEEEcCc-hhhH----HHHHHHhhc--
Q psy7789          88 -----GQRQTLLFSATMPKKIQNFARSALVKPITINVGRA----GAASMNVVQEVEYVKQ-EAKI----VYLLECLQK--  151 (197)
Q Consensus        88 -----~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~----~~~~~~i~~~~~~~~~-~~k~----~~l~~~l~~--  151 (197)
                           +..|++++|||+++.+......++.++..+.+...    ......+.+.+..... ..+.    ..+...+..  
T Consensus       258 ~~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  337 (563)
T 3i5x_A          258 NSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERD  337 (563)
T ss_dssp             CSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHHTT
T ss_pred             cccCccCceEEEEEccCCHHHHHHHHHhcCCCceEEEeccCCCCccccccCceEEEECchhHhhHHHHHHHHHHHHhhcC
Confidence                 36799999999999999999999998876665322    2334456666665543 2232    333333332  


Q ss_pred             CCCCEEEEecccccHHHHHHHHHhC---CCCeEeecCCCChhhhhhhh
Q psy7789         152 TEPPVLIFAEKKQDVDAIHEYLLLK---GKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       152 ~~~~~lIF~~s~~~~~~l~~~L~~~---~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .+.++||||+|++.|+.+++.|++.   |+++..+||+|++++|++++
T Consensus       338 ~~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R~~~~  385 (563)
T 3i5x_A          338 SNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLV  385 (563)
T ss_dssp             TCCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHH
T ss_pred             CCCcEEEEcCcHHHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHH
Confidence            3458999999999999999999987   89999999999999999876

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=99.93  E-value=7.6e-26  Score=187.71  Aligned_cols=183  Identities=21%  Similarity=0.296  Sum_probs=91.0

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhc-CCccCCCccEEEeehhhhhhc-CCCHHHHHHHHhhccCC
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDK-KMVSLDVCRYLCLDEADRMVD-MGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~-~~~~l~~l~~vViDEad~l~~-~~~~~~i~~i~~~~~~~   89 (197)
                      ++++...+||.......   ..+++|+|+||++|.+++.+ +.+.++++++||+||||.+++ .++...+..+.+.+++.
T Consensus       191 ~~~~~~~~~~~~~~~~~---~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~i~~~~~~~  267 (479)
T 3fmp_B          191 ELKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRN  267 (479)
T ss_dssp             TCCEEEESTTCCCCTTC---CCCCSEEEECHHHHHHHHTTSCCCCGGGCCEEEECCHHHHHTSTTHHHHHHHHHTTSCTT
T ss_pred             CceEEEEeCCccccccc---cCCCCEEEECchHHHHHHHhcCCcCcccCCEEEEECHHHHhhcCCcHHHHHHHHhhCCcc
Confidence            57777777776544332   23579999999999999865 566789999999999999987 57888899999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCc-hhhHHHHHHHhhcCC-CCEEEEecccccHH
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQ-EAKIVYLLECLQKTE-PPVLIFAEKKQDVD  167 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~-~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~  167 (197)
                      .|++++|||++.++......++.++..+.+.........+.+.+..+.. ..+...+..++.... +++||||++++.|+
T Consensus       268 ~~~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvF~~s~~~~~  347 (479)
T 3fmp_B          268 CQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTAS  347 (479)
T ss_dssp             SEEEEEESCCCHHHHHHHHHHSSSEEEEEEC-------------------------------------------------
T ss_pred             ceEEEEeCCCCHHHHHHHHHHcCCCeEEeccccccCcCCceEEEEEeCCHHHHHHHHHHHHhhccCCceEEEeCcHHHHH
Confidence            9999999999999999999999999999998887777888888777764 567888888877653 58999999999999


Q ss_pred             HHHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         168 AIHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       168 ~l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      .+++.|.+.|+.+..+||+|++.+|+++++
T Consensus       348 ~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~  377 (479)
T 3fmp_B          348 WLAAELSKEGHQVALLSGEMMVEQRAAVIE  377 (479)
T ss_dssp             ------------------------------
T ss_pred             HHHHHHHhCCccEEEecCCCCHHHHHHHHH
Confidence            999999999999999999999999998763

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=99.91  E-value=2.2e-23  Score=164.79  Aligned_cols=176  Identities=23%  Similarity=0.406  Sum_probs=147.4

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .++++..++||.+...+...+.+ ++|+|+||++|...+....+.+.+++++|+||||.+.++++...+..++...+...
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~-~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~~~~~~~~~  161 (337)
T 2z0m_A           83 MDTKVAEVYGGMPYKAQINRVRN-ADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRK  161 (337)
T ss_dssp             SCCCEEEECTTSCHHHHHHHHTT-CSEEEECHHHHHHHHHTTSCCGGGCSEEEEESHHHHHHTTCHHHHHHHHHHCTTCS
T ss_pred             cCCcEEEEECCcchHHHHhhcCC-CCEEEECHHHHHHHHHcCCcchhhCcEEEEEChHHhhccccHHHHHHHHhhCCccc
Confidence            46889999999988877776665 99999999999999988888889999999999999999999999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhh-cCCCCEEEEecccccHHHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQ-KTEPPVLIFAEKKQDVDAI  169 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~-~~~~~~lIF~~s~~~~~~l  169 (197)
                      |++++|||+++........++.++..+...   .....+.+.+..+....+..  ...+. ..++++||||++++.++.+
T Consensus       162 ~~~~~SAT~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~lvf~~~~~~~~~l  236 (337)
T 2z0m_A          162 ITGLFSATIPEEIRKVVKDFITNYEEIEAC---IGLANVEHKFVHVKDDWRSK--VQALRENKDKGVIVFVRTRNRVAKL  236 (337)
T ss_dssp             EEEEEESCCCHHHHHHHHHHSCSCEEEECS---GGGGGEEEEEEECSSSSHHH--HHHHHTCCCSSEEEECSCHHHHHHH
T ss_pred             EEEEEeCcCCHHHHHHHHHhcCCceeeecc---cccCCceEEEEEeChHHHHH--HHHHHhCCCCcEEEEEcCHHHHHHH
Confidence            999999999999999999999988776433   33455667666665544322  24444 4456899999999999999


Q ss_pred             HHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         170 HEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       170 ~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      ++.|.    ++..+||+|++++|++++
T Consensus       237 ~~~l~----~~~~~~~~~~~~~r~~~~  259 (337)
T 2z0m_A          237 VRLFD----NAIELRGDLPQSVRNRNI  259 (337)
T ss_dssp             HTTCT----TEEEECTTSCHHHHHHHH
T ss_pred             HHHhh----hhhhhcCCCCHHHHHHHH
Confidence            99887    588999999999999875

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=99.90  E-value=3.9e-23  Score=175.21  Aligned_cols=184  Identities=14%  Similarity=0.125  Sum_probs=137.3

Q ss_pred             CeeEEEEEcCCChHHhHHHH------hcCCcEEEeCchHHHH---HHh--cCCccCCCccEEEeehhhhhhcCC--CHHH
Q psy7789          12 PLRTCLAIGGVPMNQSLDVI------KKGCHMMVATPGRLMD---MLD--KKMVSLDVCRYLCLDEADRMVDMG--FEED   78 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l------~~~~~Ili~TP~~l~~---~l~--~~~~~l~~l~~vViDEad~l~~~~--~~~~   78 (197)
                      |+++..+.|+.+...+...+      .++++|+++||++|..   ++.  .....+.+++++||||||++.+|+  |++.
T Consensus       108 gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~~~~~~~i~~iViDEAH~is~~g~dfr~~  187 (591)
T 2v1x_A          108 GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPD  187 (591)
T ss_dssp             TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHHHHHTTCEEEEEEETGGGGSTTCTTCCGG
T ss_pred             CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHhhhhccCCcEEEEECcccccccccccHHH
Confidence            78899999998766554332      3469999999998852   221  234557899999999999999987  7776


Q ss_pred             HHH--HHhhccCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcC--chhhHHHHHHHhhcC--
Q psy7789          79 VRT--IFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVK--QEAKIVYLLECLQKT--  152 (197)
Q Consensus        79 i~~--i~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~--~~~k~~~l~~~l~~~--  152 (197)
                      +..  .+....++.|++++|||+++.+...+..++..+....+.. ...++++...+....  ...+...+.++++..  
T Consensus       188 ~~~l~~l~~~~~~~~ii~lSAT~~~~v~~~i~~~l~~~~~~~~~~-~~~r~nl~~~v~~~~~~~~~~~~~l~~~l~~~~~  266 (591)
T 2v1x_A          188 YKALGILKRQFPNASLIGLTATATNHVLTDAQKILCIEKCFTFTA-SFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYK  266 (591)
T ss_dssp             GGGGGHHHHHCTTSEEEEEESSCCHHHHHHHHHHTTCCSCEEEEC-CCCCTTEEEEEEECCSSHHHHHHHHHHHHTTTTT
T ss_pred             HHHHHHHHHhCCCCcEEEEecCCCHHHHHHHHHHhCCCCcEEEec-CCCCcccEEEEEeCCCcHHHHHHHHHHHHHHhcc
Confidence            654  3444445789999999999998888777776443222221 122344544444332  245678888888753  


Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +.++||||+|++.|+.+++.|++.|+++..+||+|++++|++++
T Consensus       267 ~~~~IVf~~sr~~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~  310 (591)
T 2v1x_A          267 GQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVH  310 (591)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHH
T ss_pred             CCCeEEEeCcHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHH
Confidence            46899999999999999999999999999999999999999876

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.89  E-value=3.6e-23  Score=168.58  Aligned_cols=167  Identities=20%  Similarity=0.236  Sum_probs=130.2

Q ss_pred             CCeeEEEEEcCCCh---HHhHHHHhcC-CcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhc-----------CCC
Q psy7789          11 IPLRTCLAIGGVPM---NQSLDVIKKG-CHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD-----------MGF   75 (197)
Q Consensus        11 ~~i~~~~~~gg~~~---~~~~~~l~~~-~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~-----------~~~   75 (197)
                      .|+++..++||.+.   ..+.+.+..+ ++|+|+||++|.+.+..  +.+.+++++|+||||++.+           .+|
T Consensus        90 ~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~--~~~~~~~~iViDEaH~~~~~~~~~d~~l~~~~~  167 (414)
T 3oiy_A           90 EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGI  167 (414)
T ss_dssp             SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH--HTTCCCSEEEESCHHHHHHCHHHHHHHHHHTTC
T ss_pred             CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH--hccccccEEEEeChHhhhhccchhhhHHhhcCC
Confidence            58999999999987   5566667655 99999999999988764  6678999999999987654           567


Q ss_pred             HHH-HHHHHhhcc-----------CCceEEEEeec-CChhHH-HHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhh
Q psy7789          76 EED-VRTIFSFFR-----------GQRQTLLFSAT-MPKKIQ-NFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAK  141 (197)
Q Consensus        76 ~~~-i~~i~~~~~-----------~~~q~i~~SAT-~~~~~~-~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k  141 (197)
                      .+. +..++..++           +..|++++||| .+..+. .....++.    +.+.........+.+.+..+   ++
T Consensus       168 ~~~~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~----~~~~~~~~~~~~i~~~~~~~---~~  240 (414)
T 3oiy_A          168 PEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRLVSVARNITHVRISS---RS  240 (414)
T ss_dssp             CHHHHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHHHS----CCSSCCCCCCCSEEEEEESS---CC
T ss_pred             cHHHHHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhHHHHHHHhhc----cCcCccccccccchheeecc---CH
Confidence            777 888888887           88999999999 554443 23333332    22333445556677776655   45


Q ss_pred             HHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCCCeE-eecCC
Q psy7789         142 IVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFF-TLKSL  186 (197)
Q Consensus       142 ~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~-~~h~~  186 (197)
                      ...+.++++..++++||||++++.|+.+++.|++.|+++. .+||+
T Consensus       241 ~~~l~~~l~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~  286 (414)
T 3oiy_A          241 KEKLVELLEIFRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF  286 (414)
T ss_dssp             HHHHHHHHHHHCSSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCH
T ss_pred             HHHHHHHHHHcCCCEEEEECCHHHHHHHHHHHHHcCCceehhhcCc
Confidence            6667777777778999999999999999999999999998 99995

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=99.88  E-value=3.6e-22  Score=167.31  Aligned_cols=180  Identities=14%  Similarity=0.105  Sum_probs=132.6

Q ss_pred             CCeeEEEEEcCCChHHhHH---HH-hcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCC--CHHHHHHH--
Q psy7789          11 IPLRTCLAIGGVPMNQSLD---VI-KKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMG--FEEDVRTI--   82 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~---~l-~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~--~~~~i~~i--   82 (197)
                      .|+++..+.|+.+......   .+ .+.++|+++||++|........+...++++||+||||++.+|+  |++.+..+  
T Consensus        88 ~gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~vViDEaH~i~~~g~~fr~~~~~l~~  167 (523)
T 1oyw_A           88 NGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQ  167 (523)
T ss_dssp             TTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTSSCCCHHHHGGGG
T ss_pred             cCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEEEEeCccccCcCCCccHHHHHHHHH
Confidence            3788888999887655432   22 4569999999999964322233445789999999999999886  66665543  


Q ss_pred             -HhhccCCceEEEEeecCChhHHHHHHHhc--CCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCC-CCEEE
Q psy7789          83 -FSFFRGQRQTLLFSATMPKKIQNFARSAL--VKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTE-PPVLI  158 (197)
Q Consensus        83 -~~~~~~~~q~i~~SAT~~~~~~~~~~~~~--~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~-~~~lI  158 (197)
                       .+.+ ++.+++++|||.++.+.......+  .++..+... .  .++++...  ......+...+.++++... .++||
T Consensus       168 l~~~~-~~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~~~~-~--~r~~l~~~--v~~~~~~~~~l~~~l~~~~~~~~IV  241 (523)
T 1oyw_A          168 LRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPLIQISS-F--DRPNIRYM--LMEKFKPLDQLMRYVQEQRGKSGII  241 (523)
T ss_dssp             HHHHC-TTSCEEEEESCCCHHHHHHHHHHHTCCSCEEEECC-C--CCTTEEEE--EEECSSHHHHHHHHHHHTTTCCEEE
T ss_pred             HHHhC-CCCCEEEEeCCCCHHHHHHHHHHhCCCCCeEEeCC-C--CCCceEEE--EEeCCCHHHHHHHHHHhcCCCcEEE
Confidence             4444 468999999999988766444433  355443322 2  22344332  3344667888888887654 58999


Q ss_pred             EecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         159 FAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       159 F~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      ||+|++.|+.+++.|++.|+++..+||+|++++|++++
T Consensus       242 f~~sr~~~e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~  279 (523)
T 1oyw_A          242 YCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQ  279 (523)
T ss_dssp             ECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHH
T ss_pred             EeCCHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHH
Confidence            99999999999999999999999999999999999876

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.88  E-value=2.8e-22  Score=179.78  Aligned_cols=167  Identities=20%  Similarity=0.235  Sum_probs=133.7

Q ss_pred             CCCeeEEEEEcCCCh---HHhHHHHhcC-CcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhc-----------CC
Q psy7789          10 PIPLRTCLAIGGVPM---NQSLDVIKKG-CHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD-----------MG   74 (197)
Q Consensus        10 ~~~i~~~~~~gg~~~---~~~~~~l~~~-~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~-----------~~   74 (197)
                      +.|+++..++||.+.   ..+.+.+..+ ++|+|+||++|.+++..  +.++++++||+||||++.+           ++
T Consensus       146 ~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~--l~~~~l~~lViDEaH~l~~~~r~~Dr~L~~~g  223 (1104)
T 4ddu_A          146 DEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASRNIDTLLMMVG  223 (1104)
T ss_dssp             CTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH--HHTSCCSEEEESCHHHHTTSSHHHHHHHHTSS
T ss_pred             CCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh--hcccCcCEEEEeCCCccccccccchhhhHhcC
Confidence            468999999999987   6667777766 99999999999888774  6788999999999976554           77


Q ss_pred             CHHH-HHHHHhhcc-----------CCceEEEEeec-CChhHHH-HHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchh
Q psy7789          75 FEED-VRTIFSFFR-----------GQRQTLLFSAT-MPKKIQN-FARSALVKPITINVGRAGAASMNVVQEVEYVKQEA  140 (197)
Q Consensus        75 ~~~~-i~~i~~~~~-----------~~~q~i~~SAT-~~~~~~~-~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~  140 (197)
                      |... +..+++.++           ++.|++++||| .+..+.. .....+.    +.+........++.+.++.+   +
T Consensus       224 f~~~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l~----i~v~~~~~~~~~i~~~~~~~---~  296 (1104)
T 4ddu_A          224 IPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRLVSVARNITHVRISS---R  296 (1104)
T ss_dssp             CCHHHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHTC----CCCCBCCCCCCCEEEEEESC---C
T ss_pred             CCHHHHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhccee----EEeccCCCCcCCceeEEEec---C
Confidence            8887 899999888           88999999999 5544442 2333332    34444455567788877766   4


Q ss_pred             hHHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCCCeE-eecC
Q psy7789         141 KIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFF-TLKS  185 (197)
Q Consensus       141 k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~-~~h~  185 (197)
                      |...+.++++..++++||||++++.|+.+++.|++.|+++. .+||
T Consensus       297 k~~~L~~ll~~~~~~~LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg  342 (1104)
T 4ddu_A          297 SKEKLVELLEIFRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSE  342 (1104)
T ss_dssp             CHHHHHHHHHHHCSSEEEEESSSHHHHHHHHHHHHTTCCEEESSSS
T ss_pred             HHHHHHHHHHhcCCCEEEEECcHHHHHHHHHHHHhCCCCeeeEecC
Confidence            66677777777778999999999999999999999999998 9999

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=99.87  E-value=1.6e-21  Score=148.31  Aligned_cols=111  Identities=41%  Similarity=0.694  Sum_probs=104.8

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCce
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQ   91 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q   91 (197)
                      ++++..++||.+...+...+.++++|+|+||+++.+++.+....+++++++|+||||++++++|...+..+++.++++.|
T Consensus       130 ~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~i~~~~~~~~q  209 (242)
T 3fe2_A          130 RLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQ  209 (242)
T ss_dssp             TCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHHTSCCCTTCCEEEETTHHHHHHTTCHHHHHHHHTTSCSSCE
T ss_pred             CceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCCcccccEEEEeCHHHHhhhCcHHHHHHHHHhCCccce
Confidence            78999999999999998888889999999999999999988888999999999999999999999999999999999999


Q ss_pred             EEEEeecCChhHHHHHHHhcCCCeEEEeCCC
Q psy7789          92 TLLFSATMPKKIQNFARSALVKPITINVGRA  122 (197)
Q Consensus        92 ~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~  122 (197)
                      ++++|||+++++..+++.++++|..+.+...
T Consensus       210 ~~~~SAT~~~~~~~~~~~~l~~~~~i~~~~~  240 (242)
T 3fe2_A          210 TLMWSATWPKEVRQLAEDFLKDYIHINIGAL  240 (242)
T ss_dssp             EEEEESCCCHHHHHHHHHHCSSCEEEEECC-
T ss_pred             EEEEEeecCHHHHHHHHHHCCCCEEEEecCC
Confidence            9999999999999999999999999988754

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=99.87  E-value=6.6e-22  Score=177.47  Aligned_cols=174  Identities=16%  Similarity=0.143  Sum_probs=132.4

Q ss_pred             eEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEE
Q psy7789          14 RTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTL   93 (197)
Q Consensus        14 ~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i   93 (197)
                      ++.+++|+.+..       .+++|+|+||++|.+++.+....++++++|||||||++.+++++..+..++..+++..|++
T Consensus       253 ~VglltGd~~~~-------~~~~IlV~Tpe~L~~~L~~~~~~l~~l~lVVIDEaH~l~d~~rg~~~e~ii~~l~~~~qvl  325 (1108)
T 3l9o_A          253 DVGLMTGDITIN-------PDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYV  325 (1108)
T ss_dssp             SEEEECSSCBCC-------CSCSEEEEEHHHHHHHHHHCSSHHHHEEEEEEETGGGTTSHHHHHHHHHHHHHSCTTSEEE
T ss_pred             CccEEeCccccC-------CCCCEEEeChHHHHHHHHcCccccccCCEEEEhhhhhccccchHHHHHHHHHhcCCCceEE
Confidence            577788887643       3599999999999999998887789999999999999999889999999999999999999


Q ss_pred             EEeecCChh--HHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCc---------------------------------
Q psy7789          94 LFSATMPKK--IQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQ---------------------------------  138 (197)
Q Consensus        94 ~~SAT~~~~--~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~---------------------------------  138 (197)
                      ++|||++..  +..+.......+..+........  .+.++++....                                 
T Consensus       326 ~lSATipn~~e~a~~l~~~~~~~~~vi~~~~rp~--pl~~~~~~~~~~~~~~~vd~~~~~~~~~~~~~~~~l~~~~~~~~  403 (1108)
T 3l9o_A          326 FLSATIPNAMEFAEWICKIHSQPCHIVYTNFRPT--PLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQIGDDP  403 (1108)
T ss_dssp             EEECSCSSCHHHHHHHHHHTCSCEEEEEECCCSS--CEEEEEEETTSSCCEEEEETTTEECHHHHHHHHTTC--------
T ss_pred             EEcCCCCCHHHHHHHHHhhcCCCeEEEecCCCcc--cceEEEeecCCcceeeeeccccchhhhhHHHHHHHHHhhhcccc
Confidence            999999764  44666666667666555433322  23333221110                                 


Q ss_pred             ----------------------hhhHHHHHHHhhcC-CCCEEEEecccccHHHHHHHHHhCCCC----------------
Q psy7789         139 ----------------------EAKIVYLLECLQKT-EPPVLIFAEKKQDVDAIHEYLLLKGKP----------------  179 (197)
Q Consensus       139 ----------------------~~k~~~l~~~l~~~-~~~~lIF~~s~~~~~~l~~~L~~~~~~----------------  179 (197)
                                            ..+...++..+... ..++||||++++.|+.++..|...|+.                
T Consensus       404 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~l~~~~~~~vIVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~  483 (1108)
T 3l9o_A          404 NSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAI  483 (1108)
T ss_dssp             ---------------------CHHHHHHHHHHHHHTTCCCEEEEESCHHHHHHHHHHTCSHHHHCC----CHHHHGGGSC
T ss_pred             cccccccccccccccccccccchhHHHHHHHHHHhcCCCCEEEEeCcHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHH
Confidence                                  22334444454444 459999999999999999998654332                


Q ss_pred             -----------------------eEeecCCCChhhhhhhh
Q psy7789         180 -----------------------FFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       180 -----------------------~~~~h~~~~~~~R~~i~  196 (197)
                                             +..+||+|++.+|+.++
T Consensus       484 ~~l~~~d~~l~~~~~l~~~l~~gV~~~Hg~l~~~~R~~v~  523 (1108)
T 3l9o_A          484 ALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIE  523 (1108)
T ss_dssp             THHHHHTTCCHHHHHHTHHHHHTEEEECSCSCHHHHHHHH
T ss_pred             hhcchhhhhhhhHHHHHHhhhcCeeeecCCCCHHHHHHHH
Confidence                                   78999999999999886

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.85  E-value=1.8e-20  Score=166.86  Aligned_cols=174  Identities=16%  Similarity=0.157  Sum_probs=130.2

Q ss_pred             eEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEE
Q psy7789          14 RTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTL   93 (197)
Q Consensus        14 ~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i   93 (197)
                      ++..++||.+...       +++|+|+||++|.+++.+....++++++||+||||.+.+++++..+..++..+++..|++
T Consensus       155 ~vglltGd~~~~~-------~~~IvV~Tpe~L~~~L~~~~~~l~~l~lVViDEaH~l~d~~rg~~~e~il~~l~~~~~il  227 (1010)
T 2xgj_A          155 DVGLMTGDITINP-------DAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYV  227 (1010)
T ss_dssp             CEEEECSSCEECT-------TCSEEEEEHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHHHHHHHHHSCTTCEEE
T ss_pred             CEEEEeCCCccCC-------CCCEEEEcHHHHHHHHHcCcchhhcCCEEEEechhhhcccchhHHHHHHHHhcCCCCeEE
Confidence            6777888876543       489999999999999988877889999999999999999999999999999999999999


Q ss_pred             EEeecCChhH--HHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcC---------c------------------------
Q psy7789          94 LFSATMPKKI--QNFARSALVKPITINVGRAGAASMNVVQEVEYVK---------Q------------------------  138 (197)
Q Consensus        94 ~~SAT~~~~~--~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~---------~------------------------  138 (197)
                      ++|||++...  ..+.......+..+...+...  ..+.++++...         .                        
T Consensus       228 ~LSATi~n~~e~a~~l~~~~~~~~~vi~~~~rp--~pl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  305 (1010)
T 2xgj_A          228 FLSATIPNAMEFAEWICKIHSQPCHIVYTNFRP--TPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQIGDDP  305 (1010)
T ss_dssp             EEECCCTTHHHHHHHHHHHHTSCEEEEEECCCS--SCEEEEEEETTSSCCEEEECTTCCBCHHHHHHHHHTCC-------
T ss_pred             EEcCCCCCHHHHHHHHHhhcCCCeEEEecCCCc--ccceEEEEecCCcceeeeeccccccchHHHHHHHHHHhhhhcccc
Confidence            9999997642  233333445565554443322  22444433211         0                        


Q ss_pred             ----------------------hhhHHHHHHHhhcCC-CCEEEEecccccHHHHHHHHHhCCCC----------------
Q psy7789         139 ----------------------EAKIVYLLECLQKTE-PPVLIFAEKKQDVDAIHEYLLLKGKP----------------  179 (197)
Q Consensus       139 ----------------------~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~~l~~~L~~~~~~----------------  179 (197)
                                            ......++..+...+ .++||||+|++.|+.++..|...++.                
T Consensus       306 ~~~~~~g~~~~~~k~~~~~~~~~~~l~~l~~~l~~~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~  385 (1010)
T 2xgj_A          306 NSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAI  385 (1010)
T ss_dssp             -----------------------CHHHHHHHHHHHHTCCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccccccccccchHHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHHH
Confidence                                  122334555554443 48999999999999999999875542                


Q ss_pred             -----------------------eEeecCCCChhhhhhhh
Q psy7789         180 -----------------------FFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       180 -----------------------~~~~h~~~~~~~R~~i~  196 (197)
                                             +..+||+|++.+|+.++
T Consensus       386 ~~l~~~d~~l~~~~~l~~~l~~gI~~~Hggl~~~eR~~ve  425 (1010)
T 2xgj_A          386 ALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIE  425 (1010)
T ss_dssp             TTSCGGGTTCHHHHHHHHHHHHTEEEESTTSCHHHHHHHH
T ss_pred             HhcchhhhcchhHHHHHHHHhCCeeEECCCCCHHHHHHHH
Confidence                                   78899999999999886

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=99.85  E-value=1.2e-20  Score=144.20  Aligned_cols=122  Identities=48%  Similarity=0.871  Sum_probs=101.3

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhh--ccC
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSF--FRG   88 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~--~~~   88 (197)
                      .++++..++||.+...+.+.+..+++|+|+||++|.+.+.+..+.+++++++|+||||++++++|...+..++..  .+.
T Consensus       127 ~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~~~  206 (253)
T 1wrb_A          127 TPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPS  206 (253)
T ss_dssp             SSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEEEEETHHHHHHTTCHHHHHHHHHSSCCCC
T ss_pred             CCceEEEEECCCCHHHHHHHhCCCCCEEEECHHHHHHHHHcCCCChhhCCEEEEeCHHHHHhCchHHHHHHHHhhccCCC
Confidence            478999999999988888888888999999999999999988888999999999999999999999999999985  444


Q ss_pred             --CceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEE
Q psy7789          89 --QRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQE  132 (197)
Q Consensus        89 --~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~  132 (197)
                        ..|++++|||+++++..+++.++.+|..+.+.......+++.|.
T Consensus       207 ~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~q~  252 (253)
T 1wrb_A          207 GINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDSIKQE  252 (253)
T ss_dssp             GGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC------------
T ss_pred             CCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEECCCCCCcCCceec
Confidence              67999999999999999999999999999998777777777664

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=99.85  E-value=8.1e-21  Score=142.97  Aligned_cols=110  Identities=38%  Similarity=0.574  Sum_probs=97.6

Q ss_pred             CCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCC
Q psy7789          10 PIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        10 ~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~   89 (197)
                      ..++++..++||.+...+...+.++++|+|+||+++.+++.+....+++++++|+||||++.+++|...+..++..++++
T Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~~  198 (228)
T 3iuy_A          119 YKGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFEPQIRKILLDVRPD  198 (228)
T ss_dssp             CTTCCEEEECC------CHHHHHSCCSEEEECHHHHHHHHHTTCCCCTTCCEEEECCHHHHHHTTCHHHHHHHHHHSCSS
T ss_pred             ccCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCcCcccceEEEEECHHHHhccchHHHHHHHHHhCCcC
Confidence            45899999999999888888888899999999999999999888889999999999999999999999999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEe
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINV  119 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~  119 (197)
                      .|++++|||+++++.+.+..++++|..+.+
T Consensus       199 ~~~l~~SAT~~~~~~~~~~~~l~~p~~i~v  228 (228)
T 3iuy_A          199 RQTVMTSATWPDTVRQLALSYLKDPMIVYV  228 (228)
T ss_dssp             CEEEEEESCCCHHHHHHHHTTCSSCEEEEC
T ss_pred             CeEEEEEeeCCHHHHHHHHHHCCCCEEEeC
Confidence            999999999999999999999999987753

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.85  E-value=3.5e-20  Score=160.53  Aligned_cols=175  Identities=17%  Similarity=0.216  Sum_probs=128.5

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .|+++..++|+.......  + ++++|+|+|||++..++.+....++++++||+||+|.+.+++++..+..++.+++ +.
T Consensus       101 ~g~~v~~~~G~~~~~~~~--~-~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~~~~~l~~i~~~~~-~~  176 (715)
T 2va8_A          101 IGFKVAMTSGDYDTDDAW--L-KNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDPERGPVVESVTIRAK-RR  176 (715)
T ss_dssp             GTCCEEECCSCSSSCCGG--G-GGCSEEEECHHHHHHHHHHCCGGGGGEEEEEECSGGGGGCTTTHHHHHHHHHHHH-TS
T ss_pred             CCCEEEEEeCCCCCchhh--c-CCCCEEEEcHHHHHHHHhCChhHhhccCEEEEechhhcCCcccchHHHHHHHhcc-cC
Confidence            488999999987654431  2 3699999999999999988777789999999999999988889999999988887 89


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEE------------EEEcC--------chhhHHHHHHHhh
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQE------------VEYVK--------QEAKIVYLLECLQ  150 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~------------~~~~~--------~~~k~~~l~~~l~  150 (197)
                      |++++|||+++ ...+...+ ..+ .+......   ..+...            ..+..        ...+...+.+.+.
T Consensus       177 ~ii~lSATl~n-~~~~~~~l-~~~-~~~~~~r~---~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  250 (715)
T 2va8_A          177 NLLALSATISN-YKQIAKWL-GAE-PVATNWRP---VPLIEGVIYPERKKKEYNVIFKDNTTKKVHGDDAIIAYTLDSLS  250 (715)
T ss_dssp             EEEEEESCCTT-HHHHHHHH-TCE-EEECCCCS---SCEEEEEEEECSSTTEEEEEETTSCEEEEESSSHHHHHHHHHHT
T ss_pred             cEEEEcCCCCC-HHHHHHHh-CCC-ccCCCCCC---CCceEEEEecCCcccceeeecCcchhhhcccchHHHHHHHHHHh
Confidence            99999999974 34555444 322 12111111   111111            11111        2344555555554


Q ss_pred             cCCCCEEEEecccccHHHHHHHHHhCC------------------------------------CCeEeecCCCChhhhhh
Q psy7789         151 KTEPPVLIFAEKKQDVDAIHEYLLLKG------------------------------------KPFFTLKSLKEDQNNQT  194 (197)
Q Consensus       151 ~~~~~~lIF~~s~~~~~~l~~~L~~~~------------------------------------~~~~~~h~~~~~~~R~~  194 (197)
                       .++++||||++++.++.++..|.+..                                    ..+..+||+|++++|+.
T Consensus       251 -~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~r~~  329 (715)
T 2va8_A          251 -KNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAYHHAGLSKALRDL  329 (715)
T ss_dssp             -TTCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTEEEECTTSCHHHHHH
T ss_pred             -cCCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCEEEECCCCCHHHHHH
Confidence             45799999999999999999998752                                    24899999999999998


Q ss_pred             hh
Q psy7789         195 LE  196 (197)
Q Consensus       195 i~  196 (197)
                      ++
T Consensus       330 v~  331 (715)
T 2va8_A          330 IE  331 (715)
T ss_dssp             HH
T ss_pred             HH
Confidence            86

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A

Probab=99.84  E-value=2.6e-21  Score=166.63  Aligned_cols=184  Identities=17%  Similarity=0.240  Sum_probs=132.3

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHH-HHHHhcC------CccCCCccEEEeehhhhhh-cCC--------
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRL-MDMLDKK------MVSLDVCRYLCLDEADRMV-DMG--------   74 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l-~~~l~~~------~~~l~~l~~vViDEad~l~-~~~--------   74 (197)
                      .|+++..++||.+...+..  ..+|||+||||++| ++++...      .+.++.++++|+||||.++ +.+        
T Consensus       151 lgl~v~~i~gg~~~~~r~~--~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mLiDea~tplIisg  228 (844)
T 1tf5_A          151 LGLTVGLNLNSMSKDEKRE--AYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISG  228 (844)
T ss_dssp             TTCCEEECCTTSCHHHHHH--HHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEE
T ss_pred             cCCeEEEEeCCCCHHHHHH--hcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhhhhccccchhhcC
Confidence            3899999999988654433  34699999999999 6666432      4568999999999999998 543        


Q ss_pred             -------CHHHHHHHHhhcc---------CCceEE-----------------EEeecCChhHHHH-----HHHhcC-CCe
Q psy7789          75 -------FEEDVRTIFSFFR---------GQRQTL-----------------LFSATMPKKIQNF-----ARSALV-KPI  115 (197)
Q Consensus        75 -------~~~~i~~i~~~~~---------~~~q~i-----------------~~SAT~~~~~~~~-----~~~~~~-~~~  115 (197)
                             |...+..|+..++         +.+|+.                 +||||++.....+     +..++. +..
T Consensus       229 ~~~~~~~~~~~i~~iv~~l~~~~~y~vd~k~rq~~lt~~g~~~~e~~~~i~~Lfsat~~~~~~~i~~al~A~~l~~~d~d  308 (844)
T 1tf5_A          229 QAAKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAMQKDVD  308 (844)
T ss_dssp             EEECCCHHHHHHHHHHTTCCSSSSBCCCSSSCCCCBCHHHHHHHHHHTTCSCTTSGGGHHHHHHHHHHHHHHHTCCBTTT
T ss_pred             CcccchhHHHHHHHHHHhCcccccceeccccceEEecHHHHHHHHHHhCccccCCCccchhHHHHHHHHHHHHHhhcCCc
Confidence                   6788999999997         367887                 8999987433332     222332 211


Q ss_pred             EEE-------e-----------------------------CCCCccCccee-----------------------------
Q psy7789         116 TIN-------V-----------------------------GRAGAASMNVV-----------------------------  130 (197)
Q Consensus       116 ~i~-------~-----------------------------~~~~~~~~~i~-----------------------------  130 (197)
                      .+.       +                             ..+......+.                             
T Consensus       309 Yiv~dg~v~ivDe~tgr~m~grr~sdGLhqaieake~v~I~~e~~t~a~It~q~~fr~y~kl~GmTGTa~te~~e~~~iY  388 (844)
T 1tf5_A          309 YVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMTGTAKTEEEEFRNIY  388 (844)
T ss_dssp             EEEETTEEEEBCTTTCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEEEHHHHHTTSSEEEEEESCCGGGHHHHHHHH
T ss_pred             eEEecCeeEEeecccccccCCCccchhhHHHHhhcccceecccccccceeeHHHHHHHHhhhccCCcccchhHHHHHHHh
Confidence            110       0                             00000000011                             


Q ss_pred             ------------------EEEEEcCchhhHHHHHHHhhc---CCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCCh
Q psy7789         131 ------------------QEVEYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKED  189 (197)
Q Consensus       131 ------------------~~~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~  189 (197)
                                        +.++++...+|...+.+.+..   .+.++||||+|++.++.++..|++.|+++..+||++++
T Consensus       389 ~l~vv~IPtn~p~~r~d~~d~v~~~~~~K~~al~~~i~~~~~~~~pvLVft~s~~~se~Ls~~L~~~gi~~~vLhg~~~~  468 (844)
T 1tf5_A          389 NMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHE  468 (844)
T ss_dssp             CCCEEECCCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHH
T ss_pred             CCceEEecCCCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCccH
Confidence                              124566778899999988864   35689999999999999999999999999999999998


Q ss_pred             hhhhhhh
Q psy7789         190 QNNQTLE  196 (197)
Q Consensus       190 ~~R~~i~  196 (197)
                      .+|+.+.
T Consensus       469 rEr~ii~  475 (844)
T 1tf5_A          469 REAQIIE  475 (844)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHHH
Confidence            8887553

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=99.84  E-value=4.2e-21  Score=166.47  Aligned_cols=177  Identities=16%  Similarity=0.152  Sum_probs=129.9

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .|+++..++|+.......   .++++|+|+||+++..++.+....++++++||+||+|.+.++++...+..++..++++.
T Consensus        94 ~g~~v~~~~G~~~~~~~~---~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~r~~~~~~ll~~l~~~~  170 (720)
T 2zj8_A           94 IGLRVAMATGDYDSKDEW---LGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRDRGATLEVILAHMLGKA  170 (720)
T ss_dssp             GTCCEEEECSCSSCCCGG---GGGCSEEEECHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHHHHHHHHHHBTTB
T ss_pred             cCCEEEEecCCCCccccc---cCCCCEEEECHHHHHHHHHcChhhhhcCCEEEEECCcccCCCcccHHHHHHHHHhhcCC
Confidence            489999999987654431   23699999999999999987776689999999999999998889999999999988789


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEE------EcC-----chhhHHHHHHHhhcCCCCEEEE
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVE------YVK-----QEAKIVYLLECLQKTEPPVLIF  159 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~------~~~-----~~~k~~~l~~~l~~~~~~~lIF  159 (197)
                      |++++|||+++ ...+.. |+..+ .+....   .+..+...+.      +..     ...+...+.+.++. ++++|||
T Consensus       171 ~ii~lSATl~n-~~~~~~-~l~~~-~~~~~~---rp~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~LVF  243 (720)
T 2zj8_A          171 QIIGLSATIGN-PEELAE-WLNAE-LIVSDW---RPVKLRRGVFYQGFVTWEDGSIDRFSSWEELVYDAIRK-KKGALIF  243 (720)
T ss_dssp             EEEEEECCCSC-HHHHHH-HTTEE-EEECCC---CSSEEEEEEEETTEEEETTSCEEECSSTTHHHHHHHHT-TCCEEEE
T ss_pred             eEEEEcCCcCC-HHHHHH-HhCCc-ccCCCC---CCCcceEEEEeCCeeeccccchhhhhHHHHHHHHHHhC-CCCEEEE
Confidence            99999999975 344444 44322 121111   1111222111      111     23445556665553 4799999


Q ss_pred             ecccccHHHHHHHHHhCC---------------------------------CCeEeecCCCChhhhhhhhC
Q psy7789         160 AEKKQDVDAIHEYLLLKG---------------------------------KPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       160 ~~s~~~~~~l~~~L~~~~---------------------------------~~~~~~h~~~~~~~R~~i~~  197 (197)
                      |+|++.|+.++..|.+..                                 ..+..+||+|++++|+.+++
T Consensus       244 ~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~  314 (720)
T 2zj8_A          244 VNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEE  314 (720)
T ss_dssp             CSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECTTSCHHHHHHHHH
T ss_pred             ecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecCCCCHHHHHHHHH
Confidence            999999999999997531                                 24899999999999998863

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=99.84  E-value=6.5e-21  Score=164.84  Aligned_cols=178  Identities=15%  Similarity=0.166  Sum_probs=128.1

Q ss_pred             CCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhc---
Q psy7789          10 PIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF---   86 (197)
Q Consensus        10 ~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~---   86 (197)
                      ..|+++..++|+.......  + ++++|+|+|||++..++.+....++++++||+||+|.+.++++...+..++..+   
T Consensus        93 ~~g~~v~~~~G~~~~~~~~--~-~~~~Iiv~Tpe~l~~~l~~~~~~l~~~~~vIiDE~H~l~~~~r~~~~~~ll~~l~~~  169 (702)
T 2p6r_A           93 KIGLRIGISTGDYESRDEH--L-GDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRM  169 (702)
T ss_dssp             TTTCCEEEECSSCBCCSSC--S-TTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTTTHHHHHHHHHHHHHH
T ss_pred             hcCCEEEEEeCCCCcchhh--c-cCCCEEEECHHHHHHHHHcChhHHhhcCEEEEeeeeecCCCCcccHHHHHHHHHHhc
Confidence            3489999999987654331  1 369999999999999998877678999999999999999988888888877666   


Q ss_pred             cCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEE------EcCchh-------hHHHHHHHhhcCC
Q psy7789          87 RGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVE------YVKQEA-------KIVYLLECLQKTE  153 (197)
Q Consensus        87 ~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~------~~~~~~-------k~~~l~~~l~~~~  153 (197)
                      +++.|++++|||+++ ...+.. ++..+ .+.....   +..+...+.      +.....       +...+.+.++ .+
T Consensus       170 ~~~~~ii~lSATl~n-~~~~~~-~l~~~-~~~~~~r---~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~  242 (702)
T 2p6r_A          170 NKALRVIGLSATAPN-VTEIAE-WLDAD-YYVSDWR---PVPLVEGVLCEGTLELFDGAFSTSRRVKFEELVEECVA-EN  242 (702)
T ss_dssp             CTTCEEEEEECCCTT-HHHHHH-HTTCE-EEECCCC---SSCEEEEEECSSEEEEEETTEEEEEECCHHHHHHHHHH-TT
T ss_pred             CcCceEEEECCCcCC-HHHHHH-HhCCC-cccCCCC---CccceEEEeeCCeeeccCcchhhhhhhhHHHHHHHHHh-cC
Confidence            568999999999985 455554 44432 2222111   111222111      111111       4555555554 45


Q ss_pred             CCEEEEecccccHHHHHHHHHhC------------------------------CCCeEeecCCCChhhhhhhhC
Q psy7789         154 PPVLIFAEKKQDVDAIHEYLLLK------------------------------GKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       154 ~~~lIF~~s~~~~~~l~~~L~~~------------------------------~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      +++||||++++.++.++..|.+.                              +..+..+||+|++++|+.+++
T Consensus       243 ~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~  316 (702)
T 2p6r_A          243 GGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVED  316 (702)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHH
T ss_pred             CCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHHHHHHhcCeEEecCCCCHHHHHHHHH
Confidence            79999999999999999998753                              235889999999999998863

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.84  E-value=1.4e-20  Score=167.52  Aligned_cols=175  Identities=16%  Similarity=0.146  Sum_probs=131.7

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCce
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQ   91 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q   91 (197)
                      |+++..++|+.+...       .++|+|+||++|.+++......++++++|||||||++.+++++..+..++..+++..|
T Consensus       108 ~~~v~~l~G~~~~~~-------~~~IlV~Tpe~L~~~l~~~~~~l~~l~lvViDEaH~l~d~~~g~~~e~ii~~l~~~v~  180 (997)
T 4a4z_A          108 DVNIGLITGDVQINP-------DANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQDRGVVWEEVIIMLPQHVK  180 (997)
T ss_dssp             -CCEEEECSSCEECT-------TSSEEEEEHHHHHHHHHHTCSGGGGEEEEEECCTTCCCTTCTTCCHHHHHHHSCTTCE
T ss_pred             CCeEEEEeCCCccCC-------CCCEEEECHHHHHHHHHhCchhhcCCCEEEEECcccccccchHHHHHHHHHhcccCCC
Confidence            789999999876543       3899999999999999888778899999999999999999999999999999999999


Q ss_pred             EEEEeecCChhHHHHHHHhc---CCCeEEEeCCCCccCcceeEEEE----------------------------------
Q psy7789          92 TLLFSATMPKKIQNFARSAL---VKPITINVGRAGAASMNVVQEVE----------------------------------  134 (197)
Q Consensus        92 ~i~~SAT~~~~~~~~~~~~~---~~~~~i~~~~~~~~~~~i~~~~~----------------------------------  134 (197)
                      ++++|||+++.. ++..++.   ..+..+.......  ..+.++++                                  
T Consensus       181 iIlLSAT~~n~~-ef~~~l~~~~~~~~~vi~~~~r~--~pl~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  257 (997)
T 4a4z_A          181 FILLSATVPNTY-EFANWIGRTKQKNIYVISTPKRP--VPLEINIWAKKELIPVINQNSEFLEANFRKHKEILNGESAKG  257 (997)
T ss_dssp             EEEEECCCTTHH-HHHHHHHHHHTCCEEEEECSSCS--SCEEEEEEETTEEEEEECTTCCBCHHHHHHHHHHHC------
T ss_pred             EEEEcCCCCChH-HHHHHHhcccCCceEEEecCCCC--ccceEEEecCCcchhcccchhhhhHHHHHHHHHHhhcccccc
Confidence            999999997543 4444433   1232222221111  11111111                                  


Q ss_pred             -----------------------------------------------------------EcCchhhHHHHHHHhhcCC-C
Q psy7789         135 -----------------------------------------------------------YVKQEAKIVYLLECLQKTE-P  154 (197)
Q Consensus       135 -----------------------------------------------------------~~~~~~k~~~l~~~l~~~~-~  154 (197)
                                                                                 ......+...+...+...+ .
T Consensus       258 ~~~~~~~~~~~~~~~~~~~~~~~rg~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~l~~~~~~  337 (997)
T 4a4z_A          258 APSKTDNGRGGSTARGGRGGSNTRDGRGGRGNSTRGGANRGGSRGAGAIGSNKRKFFTQDGPSKKTWPEIVNYLRKRELL  337 (997)
T ss_dssp             -----------------------------------------------------------CCCCTTHHHHHHHHHHHTTCC
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhHHHHHHHHHHhCCCC
Confidence                                                                       0112344667777777654 6


Q ss_pred             CEEEEecccccHHHHHHHHHhCCC---------------------------------------CeEeecCCCChhhhhhh
Q psy7789         155 PVLIFAEKKQDVDAIHEYLLLKGK---------------------------------------PFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       155 ~~lIF~~s~~~~~~l~~~L~~~~~---------------------------------------~~~~~h~~~~~~~R~~i  195 (197)
                      ++||||+|++.|+.++..|.+.|+                                       .+..+||+|++.+|+.+
T Consensus       338 ~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gi~~~H~gl~~~~R~~v  417 (997)
T 4a4z_A          338 PMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERGIAVHHGGLLPIVKELI  417 (997)
T ss_dssp             SEEEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHHHTTTEEEECTTSCHHHHHHH
T ss_pred             CEEEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHhhcCeeeecCCCCHHHHHHH
Confidence            999999999999999999987665                                       47899999999999988


Q ss_pred             h
Q psy7789         196 E  196 (197)
Q Consensus       196 ~  196 (197)
                      +
T Consensus       418 ~  418 (997)
T 4a4z_A          418 E  418 (997)
T ss_dssp             H
T ss_pred             H
Confidence            6

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*

Probab=99.84  E-value=7.7e-21  Score=163.48  Aligned_cols=184  Identities=15%  Similarity=0.217  Sum_probs=108.8

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHH-HHHHhcC------CccCCCccEEEeehhhhhh-cC---------
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRL-MDMLDKK------MVSLDVCRYLCLDEADRMV-DM---------   73 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l-~~~l~~~------~~~l~~l~~vViDEad~l~-~~---------   73 (197)
                      .|+++++++||.+...  +.+..++||+||||++| ++++..+      ...+++++++|+||||.++ +.         
T Consensus       142 lgl~v~~i~GG~~~~~--r~~~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~mLiD~a~tpLIiSg  219 (853)
T 2fsf_A          142 LGLTVGINLPGMPAPA--KREAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSILIDEARTPLIISG  219 (853)
T ss_dssp             TTCCEEECCTTCCHHH--HHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHHHTTTTTTCEEEEEE
T ss_pred             cCCeEEEEeCCCCHHH--HHHhcCCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHHHHHhcCcccccccC
Confidence            3899999999988643  33444699999999999 7887654      3567999999999999998 43         


Q ss_pred             ------CCHHHHHHHHhhccC--------------------CceEE------------------------EEeecCChhH
Q psy7789          74 ------GFEEDVRTIFSFFRG--------------------QRQTL------------------------LFSATMPKKI  103 (197)
Q Consensus        74 ------~~~~~i~~i~~~~~~--------------------~~q~i------------------------~~SAT~~~~~  103 (197)
                            ++...+..|+..+++                    .+|+.                        ++|||.++..
T Consensus       220 ~~~~~~~~y~~i~~iv~~L~~~~~~~~~~~~~~~dy~vdek~rqv~lte~g~~~~e~~l~~~~l~~~~~~Lfsat~~~~~  299 (853)
T 2fsf_A          220 PAEDSSEMYKRVNKIIPHLIRQEKEDSETFQGEGHFSVDEKSRQVNLTERGLVLIEELLVKEGIMDEGESLYSPANIMLM  299 (853)
T ss_dssp             C-------------------------------------------------------------------------------
T ss_pred             CCccchhHHHHHHHHHHhchhhhccccccccccccceeccccceEEEcHHHHHHHHHHHHhCCcccccccccCcccchHH
Confidence                  256788888888864                    45654                        8999976422


Q ss_pred             HHH-----HHH------------------------hcC-------------CCeEEEeCCCCccCcceeE----------
Q psy7789         104 QNF-----ARS------------------------ALV-------------KPITINVGRAGAASMNVVQ----------  131 (197)
Q Consensus       104 ~~~-----~~~------------------------~~~-------------~~~~i~~~~~~~~~~~i~~----------  131 (197)
                      ..+     +..                        ++.             .+..+.+..+......+++          
T Consensus       300 ~~i~~al~A~~l~~~d~dYiV~d~~vviVde~tgR~m~grr~sdGLhQaieake~v~I~~e~~tla~It~qnyfr~Y~kl  379 (853)
T 2fsf_A          300 HHVTAALRAHALFTRDVDYIVKDGEVIIVDEHTGRTMQGRRWSDGLHQAVEAKEGVQIQNENQTLASITFQNYFRLYEKL  379 (853)
T ss_dssp             ---------------------------------------------------------CCCCCEEEEEEEHHHHHTTSSEE
T ss_pred             HHHHHHHHHHHHhhcCccceeecCcEEEEecccCcccCCCccchhhhHHHHhcccceecccccccceeehHHHHhhhhhh
Confidence            221     011                        111             0122333333333333332          


Q ss_pred             -------------------------------------EEEEcCchhhHHHHHHHhhc---CCCCEEEEecccccHHHHHH
Q psy7789         132 -------------------------------------EVEYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQDVDAIHE  171 (197)
Q Consensus       132 -------------------------------------~~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~  171 (197)
                                                           .++++...+|...+.+.+..   .+.|+||||+|++.++.++.
T Consensus       380 ~GmTGTa~te~~ef~~iY~l~vv~IPtn~p~~R~d~~d~v~~~~~~K~~al~~~i~~~~~~gqpvLVft~sie~se~Ls~  459 (853)
T 2fsf_A          380 AGMTGTADTEAFEFSSIYKLDTVVVPTNRPMIRKDLPDLVYMTEAEKIQAIIEDIKERTAKGQPVLVGTISIEKSELVSN  459 (853)
T ss_dssp             EEEECTTCCCHHHHHHHHCCEEEECCCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHH
T ss_pred             hcCCCCchhHHHHHHHHhCCcEEEcCCCCCceeecCCcEEEeCHHHHHHHHHHHHHHHhcCCCCEEEEECcHHHHHHHHH
Confidence                                                 24567788899999998854   34589999999999999999


Q ss_pred             HHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         172 YLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       172 ~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .|++.|+++.++||++.+.+|+.+.
T Consensus       460 ~L~~~gi~~~vLnak~~~rEa~iia  484 (853)
T 2fsf_A          460 ELTKAGIKHNVLNAKFHANEAAIVA  484 (853)
T ss_dssp             HHHHTTCCCEECCTTCHHHHHHHHH
T ss_pred             HHHHCCCCEEEecCChhHHHHHHHH
Confidence            9999999999999999888887654

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B*

Probab=99.83  E-value=1.1e-21  Score=175.75  Aligned_cols=164  Identities=16%  Similarity=0.241  Sum_probs=131.0

Q ss_pred             eEEEEEcCCChHHhH---HHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhc----
Q psy7789          14 RTCLAIGGVPMNQSL---DVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF----   86 (197)
Q Consensus        14 ~~~~~~gg~~~~~~~---~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~----   86 (197)
                      ++..++||.+...+.   +.+.+ ++|+|+||++|.+.+.+    ++++++||+||||+++++  +..+..++..+    
T Consensus       133 ~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~----L~~l~~lViDEah~~l~~--~~~~~~i~~~lgf~~  205 (1054)
T 1gku_B          133 LIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRE----LGHFDFIFVDDVDAILKA--SKNVDKLLHLLGFHY  205 (1054)
T ss_dssp             SEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTT----SCCCSEEEESCHHHHHTS--THHHHHHHHHTTEEE
T ss_pred             eEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHH----hccCCEEEEeChhhhhhc--cccHHHHHHHhCcch
Confidence            899999999877643   44455 99999999999998775    679999999999999984  67777777666    


Q ss_pred             -------cCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEE
Q psy7789          87 -------RGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIF  159 (197)
Q Consensus        87 -------~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF  159 (197)
                             +...|++++|||+++. ......++.++..+.+.........+.+.+.   ..+|...+.++++..++++|||
T Consensus       206 ~~~~~~~~~~~q~~l~SAT~t~~-~~~~~~~~~~~~~i~v~~~~~~~~~i~~~~~---~~~k~~~L~~ll~~~~~~~LVF  281 (1054)
T 1gku_B          206 DLKTKSWVGEARGCLMVSTATAK-KGKKAELFRQLLNFDIGSSRITVRNVEDVAV---NDESISTLSSILEKLGTGGIIY  281 (1054)
T ss_dssp             ETTTTEEEECCSSEEEECCCCSC-CCTTHHHHHHHHCCCCSCCEECCCCEEEEEE---SCCCTTTTHHHHTTSCSCEEEE
T ss_pred             hhhhhhcccCCceEEEEecCCCc-hhHHHHHhhcceEEEccCcccCcCCceEEEe---chhHHHHHHHHHhhcCCCEEEE
Confidence                   4578999999999987 5444455544444555545555566777655   4667778888888878899999


Q ss_pred             ecccccHHHHHHHHHhCCCCeEeecCCCCh
Q psy7789         160 AEKKQDVDAIHEYLLLKGKPFFTLKSLKED  189 (197)
Q Consensus       160 ~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~  189 (197)
                      |+|++.|+.+++.|++. +++..+||+|..
T Consensus       282 ~~t~~~a~~l~~~L~~~-~~v~~lhg~~~~  310 (1054)
T 1gku_B          282 ARTGEEAEEIYESLKNK-FRIGIVTATKKG  310 (1054)
T ss_dssp             ESSHHHHHHHHHTTTTS-SCEEECTTSSSH
T ss_pred             EcCHHHHHHHHHHHhhc-cCeeEEeccHHH
Confidence            99999999999999998 999999999953

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=99.82  E-value=1.3e-19  Score=138.33  Aligned_cols=109  Identities=39%  Similarity=0.665  Sum_probs=100.7

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhc-CCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDK-KMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~-~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      ++++..++||.+...+...+.++++|+|+||+++.+.+.+ ..+.+++++++|+||||++.+++|...+..+++.++++.
T Consensus       139 ~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lViDEah~l~~~~~~~~l~~i~~~~~~~~  218 (249)
T 3ber_A          139 GVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDR  218 (249)
T ss_dssp             TCCEEEECTTSCHHHHHHHHHTCCSEEEECHHHHHHHHHHSTTCCCTTCCEEEECSHHHHHHTTCHHHHHHHHHSSCSSS
T ss_pred             CeeEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCcCccccCEEEEcChhhhhccChHHHHHHHHHhCCCCC
Confidence            7899999999998888888888899999999999999875 556789999999999999999999999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeC
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVG  120 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~  120 (197)
                      |++++|||+++++.++++.++++|..+.+.
T Consensus       219 ~~l~~SAT~~~~v~~~~~~~l~~p~~i~v~  248 (249)
T 3ber_A          219 KTFLFSATMTKKVQKLQRAALKNPVKCAVS  248 (249)
T ss_dssp             EEEEEESSCCHHHHHHHHHHCSSCEEEECC
T ss_pred             eEEEEeccCCHHHHHHHHHHCCCCEEEEec
Confidence            999999999999999999999999988764

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=99.82  E-value=1.1e-19  Score=152.57  Aligned_cols=89  Identities=17%  Similarity=0.175  Sum_probs=66.8

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCc-cCCCccEEEeehhhhhhcCCCHHHH-HHHHhh-c--
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMV-SLDVCRYLCLDEADRMVDMGFEEDV-RTIFSF-F--   86 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~-~l~~l~~vViDEad~l~~~~~~~~i-~~i~~~-~--   86 (197)
                      |+++..++||.+...+...+..+++|+|+||++|.+.+..+.+ .+.++++||+||||++.+++....+ ...+.. +  
T Consensus        83 ~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~  162 (556)
T 4a2p_A           83 GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNS  162 (556)
T ss_dssp             TCCEEECCCC-----CHHHHHHHCSEEEECHHHHHHHHHSSSCCCSTTCSEEEEETGGGCSTTSHHHHHHHHHHHHHHCC
T ss_pred             CceEEEEeCCCCcchhHHHhhCCCCEEEECHHHHHHHHHhCcccccccCCEEEEECCcccCCcchHHHHHHHHHHhhhcc
Confidence            7899999999987777777777799999999999999988877 7999999999999999887643333 222222 1  


Q ss_pred             -cCCceEEEEeecCC
Q psy7789          87 -RGQRQTLLFSATMP  100 (197)
Q Consensus        87 -~~~~q~i~~SAT~~  100 (197)
                       ++.+|++++|||.+
T Consensus       163 ~~~~~~~l~lSAT~~  177 (556)
T 4a2p_A          163 ASQLPQILGLTASVG  177 (556)
T ss_dssp             ---CCEEEEEESCCC
T ss_pred             cCCCCeEEEEeCCcc
Confidence             35689999999984

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=99.82  E-value=4.5e-19  Score=145.76  Aligned_cols=89  Identities=17%  Similarity=0.124  Sum_probs=71.8

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCce
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQ   91 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q   91 (197)
                      +.++..++|+.........+. +++|+|+||+++...+....+.+.+++++|+||||.+.+......+...+....+..+
T Consensus        80 ~~~v~~~~g~~~~~~~~~~~~-~~~ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~~~~~~~~~~~~~~~~~~  158 (494)
T 1wp9_A           80 PEKIVALTGEKSPEERSKAWA-RAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPL  158 (494)
T ss_dssp             GGGEEEECSCSCHHHHHHHHH-HCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCSSCC
T ss_pred             hhheEEeeCCcchhhhhhhcc-CCCEEEecHHHHHHHHhcCCcchhhceEEEEECCcccCCCCcHHHHHHHHHhcCCCCe
Confidence            458889999887765544443 5899999999999999888888999999999999999876555555555555667899


Q ss_pred             EEEEeecCCh
Q psy7789          92 TLLFSATMPK  101 (197)
Q Consensus        92 ~i~~SAT~~~  101 (197)
                      ++++|||...
T Consensus       159 ~l~lTaTp~~  168 (494)
T 1wp9_A          159 VIGLTASPGS  168 (494)
T ss_dssp             EEEEESCSCS
T ss_pred             EEEEecCCCC
Confidence            9999999873

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=99.82  E-value=2.2e-19  Score=132.90  Aligned_cols=106  Identities=31%  Similarity=0.559  Sum_probs=98.9

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCce
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQ   91 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q   91 (197)
                      ++++..++||.+...+...+.++++|+|+||+++.+.+.+....+++++++|+||||++.+.++...+..++..++++.|
T Consensus       100 ~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~  179 (206)
T 1vec_A          100 GAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQ  179 (206)
T ss_dssp             SCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTTTHHHHHHHHHHSCTTCE
T ss_pred             CceEEEEeCCccHHHHHHhcCCCCCEEEeCHHHHHHHHHcCCcCcccCCEEEEEChHHhHhhCcHHHHHHHHHhCCccce
Confidence            68899999999988888778888999999999999999988888999999999999999998999999999999998999


Q ss_pred             EEEEeecCChhHHHHHHHhcCCCeEE
Q psy7789          92 TLLFSATMPKKIQNFARSALVKPITI  117 (197)
Q Consensus        92 ~i~~SAT~~~~~~~~~~~~~~~~~~i  117 (197)
                      ++++|||+++++.+.++.++.+|..+
T Consensus       180 ~l~~SAT~~~~~~~~~~~~l~~p~~i  205 (206)
T 1vec_A          180 ILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             EEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             EEEEEeeCCHHHHHHHHHHcCCCeEe
Confidence            99999999999999999999999765

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.82  E-value=2.7e-20  Score=160.63  Aligned_cols=90  Identities=17%  Similarity=0.197  Sum_probs=71.2

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCc-cCCCccEEEeehhhhhhcCC-CHHHHHHHHhh---
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMV-SLDVCRYLCLDEADRMVDMG-FEEDVRTIFSF---   85 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~-~l~~l~~vViDEad~l~~~~-~~~~i~~i~~~---   85 (197)
                      .|+++..++||.+...+...+..+++|+|+||++|...+..+.+ .+.++++||+||||++.+.. +...+...+..   
T Consensus        88 ~~~~v~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~L~~~l~~~~~~~l~~~~~vViDEaH~~~~~~~~~~i~~~~l~~~~~  167 (696)
T 2ykg_A           88 HGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLG  167 (696)
T ss_dssp             TTCCEEEECSSSCSSSCHHHHHHTCSEEEECHHHHHHHHHTTSSCCGGGCSEEEEETGGGCSTTCHHHHHHHHHHHHHHT
T ss_pred             CCceEEEEeCCccccccHHHhccCCCEEEECHHHHHHHHhcCcccccccccEEEEeCCCcccCcccHHHHHHHHHHHhhc
Confidence            48999999999887777777767799999999999999988766 78999999999999998654 22222222222   


Q ss_pred             --ccCCceEEEEeecCC
Q psy7789          86 --FRGQRQTLLFSATMP  100 (197)
Q Consensus        86 --~~~~~q~i~~SAT~~  100 (197)
                        .++.+|++++|||..
T Consensus       168 ~~~~~~~~il~LTATp~  184 (696)
T 2ykg_A          168 GSSGPLPQVIGLTASVG  184 (696)
T ss_dssp             TCCSCCCEEEEEESCCC
T ss_pred             ccCCCCCeEEEEeCccc
Confidence              246789999999986

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=99.81  E-value=2.2e-19  Score=132.98  Aligned_cols=109  Identities=38%  Similarity=0.584  Sum_probs=100.8

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCce
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQ   91 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q   91 (197)
                      ++++..++||.+...+.+.+.++++|+|+||+++...+....+.+++++++|+||||.+.++++...+..++..++++.|
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~i~~~~~~~~~  177 (207)
T 2gxq_A           98 HLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQ  177 (207)
T ss_dssp             TSCEEEECSSSCSHHHHHHHHHCCSEEEECHHHHHHHHHHTSSCCTTCSEEEEESHHHHHHTTCHHHHHHHHHTSCTTSE
T ss_pred             cceEEEEECCCChHHHHHHhhCCCCEEEECHHHHHHHHHcCCcchhhceEEEEEChhHhhccchHHHHHHHHHhCCccCe
Confidence            47889999999888888888788999999999999999888888999999999999999999999999999999999999


Q ss_pred             EEEEeecCChhHHHHHHHhcCCCeEEEeC
Q psy7789          92 TLLFSATMPKKIQNFARSALVKPITINVG  120 (197)
Q Consensus        92 ~i~~SAT~~~~~~~~~~~~~~~~~~i~~~  120 (197)
                      ++++|||+++++.++.+.++++|..+.+.
T Consensus       178 ~i~~SAT~~~~~~~~~~~~~~~p~~i~~~  206 (207)
T 2gxq_A          178 TLLFSATLPSWAKRLAERYMKNPVLINVI  206 (207)
T ss_dssp             EEEECSSCCHHHHHHHHHHCSSCEEEECC
T ss_pred             EEEEEEecCHHHHHHHHHHcCCCeEEEcC
Confidence            99999999999999999999999888653

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=99.81  E-value=1.2e-19  Score=137.50  Aligned_cols=110  Identities=31%  Similarity=0.550  Sum_probs=89.2

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcC-CcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCC
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKG-CHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~-~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~   89 (197)
                      .++++..++||.+...+...+..+ ++|+|+||++|.+++....+.+++++++|+||||++.+++|...+..+++.++..
T Consensus       125 ~~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~~~~~l~~i~~~~~~~  204 (237)
T 3bor_A          125 MGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTS  204 (237)
T ss_dssp             TTCCEEEECC-------------CCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHHTTCHHHHHHHHHHSCTT
T ss_pred             cCceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHhCCcCcccCcEEEECCchHhhccCcHHHHHHHHHhCCCC
Confidence            368889999998887777777555 9999999999999998888889999999999999999999999999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeC
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVG  120 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~  120 (197)
                      .|++++|||+++++.+.++.++++|..+.+.
T Consensus       205 ~~~i~~SAT~~~~~~~~~~~~l~~p~~i~v~  235 (237)
T 3bor_A          205 IQVVLLSATMPTDVLEVTKKFMRDPIRILVK  235 (237)
T ss_dssp             CEEEEECSSCCHHHHHHHHHHCSSCEEEC--
T ss_pred             CeEEEEEEecCHHHHHHHHHHCCCCEEEEec
Confidence            9999999999999999999999999888664

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.81  E-value=4.8e-20  Score=137.94  Aligned_cols=110  Identities=31%  Similarity=0.527  Sum_probs=100.2

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCce
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQ   91 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q   91 (197)
                      ++++..++||.+...+.+.+..+++|+|+||+++.+.+.+..+.+++++++|+||||++.++++...+..+++.+++..|
T Consensus       104 ~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~  183 (219)
T 1q0u_A          104 MIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQ  183 (219)
T ss_dssp             CCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHHHHTTCHHHHHHHHHTSCTTCE
T ss_pred             ceEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHHHHHcCCCCcCcceEEEEcCchHHhhhChHHHHHHHHHhCCcccE
Confidence            68899999998877766666678999999999999999888888899999999999999999999999999999999999


Q ss_pred             EEEEeecCChhHHHHHHHhcCCCeEEEeCC
Q psy7789          92 TLLFSATMPKKIQNFARSALVKPITINVGR  121 (197)
Q Consensus        92 ~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~  121 (197)
                      ++++|||+++++.++++.++++|..+.+..
T Consensus       184 ~l~~SAT~~~~~~~~~~~~~~~p~~~~~~~  213 (219)
T 1q0u_A          184 MLVFSATIPEKLKPFLKKYMENPTFVHVLE  213 (219)
T ss_dssp             EEEEESCCCGGGHHHHHHHCSSCEEEECC-
T ss_pred             EEEEecCCCHHHHHHHHHHcCCCeEEEeec
Confidence            999999999999999999999999887753

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A

Probab=99.81  E-value=3.6e-20  Score=159.78  Aligned_cols=184  Identities=13%  Similarity=0.211  Sum_probs=133.1

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHH-HHHHhcC------CccCCCccEEEeehhhhhhcC----------
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRL-MDMLDKK------MVSLDVCRYLCLDEADRMVDM----------   73 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l-~~~l~~~------~~~l~~l~~vViDEad~l~~~----------   73 (197)
                      .|+++.+++||.+...+.  ...++||++|||++| ++++...      .+.++.++++|+||||.++.+          
T Consensus       179 lGLsv~~i~gg~~~~~r~--~~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmLiDeartPLiiSg  256 (922)
T 1nkt_A          179 LGLQVGVILATMTPDERR--VAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDEARTPLIISG  256 (922)
T ss_dssp             TTCCEEECCTTCCHHHHH--HHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHHTTGGGSCEEEEE
T ss_pred             cCCeEEEEeCCCCHHHHH--HhcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHHHhcCccceeecC
Confidence            489999999998754333  333599999999999 7877643      466889999999999999832          


Q ss_pred             ------CCHHHHHHHHhhcc---------CCceEE-----------------EEeecCChhHHHH-----HHHhcC-C--
Q psy7789          74 ------GFEEDVRTIFSFFR---------GQRQTL-----------------LFSATMPKKIQNF-----ARSALV-K--  113 (197)
Q Consensus        74 ------~~~~~i~~i~~~~~---------~~~q~i-----------------~~SAT~~~~~~~~-----~~~~~~-~--  113 (197)
                            +|...+..|+..++         +..|+.                 ++|||.++....+     +..++. +  
T Consensus       257 ~~~~~~~~y~~i~~iv~~L~~~~dy~vDek~rqv~Lte~G~~~~e~~l~i~~Lfsat~~~l~~~i~~aL~A~~l~~~d~d  336 (922)
T 1nkt_A          257 PADGASNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGIDNLYEAANSPLVSYLNNALKAKELFSRDKD  336 (922)
T ss_dssp             ECCCCHHHHHHHHHHHHHSCBTTTEEEETTTTEEEECHHHHHHHHHHHTCSSTTCSTTCCHHHHHHHHHHHHHHCCBTTT
T ss_pred             CCCcchhHHHHHHHHHHhCcccccceeccCcceEEecHhHHHHHHHHhCCccccCCcchhHHHHHHHHHHHHHHhhcccc
Confidence                  47789999999998         678998                 8999987533332     122222 1  


Q ss_pred             -----CeEEEeC-----------------------------CCCccCccee-----------------------------
Q psy7789         114 -----PITINVG-----------------------------RAGAASMNVV-----------------------------  130 (197)
Q Consensus       114 -----~~~i~~~-----------------------------~~~~~~~~i~-----------------------------  130 (197)
                           ...+.+.                             .+......++                             
T Consensus       337 YiV~dg~vviVDe~TGR~m~grr~sdGLHQaieaKe~V~I~~e~~TlatIt~Qnyfr~Y~kL~GMTGTa~te~~Ef~~iY  416 (922)
T 1nkt_A          337 YIVRDGEVLIVDEFTGRVLIGRRYNEGMHQAIEAKEHVEIKAENQTLATITLQNYFRLYDKLAGMTGTAQTEAAELHEIY  416 (922)
T ss_dssp             EEECSSCEEEBCSSSCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEECHHHHHTTSSEEEEEESCCGGGHHHHHHHH
T ss_pred             eeeecCceEEEecccCcccCCccccchhhHHHhccccccccccccccceeehHHHHHhhhhhhccccCchhHHHHHHHHh
Confidence                 1111111                             1111111111                             


Q ss_pred             ------------------EEEEEcCchhhHHHHHHHhhc---CCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCCh
Q psy7789         131 ------------------QEVEYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKED  189 (197)
Q Consensus       131 ------------------~~~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~  189 (197)
                                        ..++++...+|...+.+.+..   .+.|+||||+|++.++.+++.|++.|+++..+||++.+
T Consensus       417 ~l~vv~IPtn~p~~R~d~~d~v~~t~~~K~~al~~~i~~~~~~gqpvLVft~Sie~sE~Ls~~L~~~Gi~~~vLnak~~~  496 (922)
T 1nkt_A          417 KLGVVSIPTNMPMIREDQSDLIYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHE  496 (922)
T ss_dssp             CCEEEECCCSSCCCCEECCCEEESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHH
T ss_pred             CCCeEEeCCCCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEecCChhH
Confidence                              124566778899999888864   34589999999999999999999999999999999887


Q ss_pred             hhhhhhh
Q psy7789         190 QNNQTLE  196 (197)
Q Consensus       190 ~~R~~i~  196 (197)
                      .+|+.+.
T Consensus       497 rEa~iia  503 (922)
T 1nkt_A          497 QEATIIA  503 (922)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7776553

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.81  E-value=3.7e-19  Score=164.91  Aligned_cols=183  Identities=13%  Similarity=0.138  Sum_probs=125.4

Q ss_pred             CCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCC--ccCCCccEEEeehhhhhhcCCCHHHHHHHHh---
Q psy7789          10 PIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKM--VSLDVCRYLCLDEADRMVDMGFEEDVRTIFS---   84 (197)
Q Consensus        10 ~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~--~~l~~l~~vViDEad~l~~~~~~~~i~~i~~---   84 (197)
                      +.|++|..++||.+...+.   ..+++|+|+|||++..++++..  ..++++++||+||+|.+.+ .++..++.++.   
T Consensus       160 ~~gi~V~~~tGd~~~~~~~---~~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l~d-~RG~~lE~~l~rl~  235 (1724)
T 4f92_B          160 TYGITVAELTGDHQLCKEE---ISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHD-DRGPVLEALVARAI  235 (1724)
T ss_dssp             TTTCCEEECCSSCSSCCTT---GGGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGGGS-TTHHHHHHHHHHHH
T ss_pred             hCCCEEEEEECCCCCCccc---cCCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchhcCC-ccHHHHHHHHHHHH
Confidence            3589999999998755432   2359999999999977776543  2478999999999998865 57777766654   


Q ss_pred             ----hccCCceEEEEeecCChhHHHHHHHhcCCC-eEEEeCCCCccCcceeEEEEEcCchh---hHHH----HHHHhhcC
Q psy7789          85 ----FFRGQRQTLLFSATMPKKIQNFARSALVKP-ITINVGRAGAASMNVVQEVEYVKQEA---KIVY----LLECLQKT  152 (197)
Q Consensus        85 ----~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~-~~i~~~~~~~~~~~i~~~~~~~~~~~---k~~~----l~~~l~~~  152 (197)
                          ..++..|++++|||++ +..++++++..++ ..+...+....+..+.+.++...+..   +...    +.+.+.+.
T Consensus       236 ~~~~~~~~~~riI~LSATl~-N~~dvA~wL~~~~~~~~~~~~~~~RPvpL~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~  314 (1724)
T 4f92_B          236 RNIEMTQEDVRLIGLSATLP-NYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEIVYEKIMEH  314 (1724)
T ss_dssp             HHHHHHTCCCEEEEEECSCT-THHHHHHHTTCCHHHHEEECCGGGCSSCEEEECCEECCCCHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHhCCCCCcEEEEecccC-CHHHHHHHhCCCCCCCeEEECCCCccCccEEEEeccCCcchhhhhHHHHHHHHHHHHHH
Confidence                3467889999999997 4566665544332 22223333334445666555443322   1222    22233332


Q ss_pred             --CCCEEEEecccccHHHHHHHHHhC-------------------------------------CCCeEeecCCCChhhhh
Q psy7789         153 --EPPVLIFAEKKQDVDAIHEYLLLK-------------------------------------GKPFFTLKSLKEDQNNQ  193 (197)
Q Consensus       153 --~~~~lIF~~s~~~~~~l~~~L~~~-------------------------------------~~~~~~~h~~~~~~~R~  193 (197)
                        ++++||||+|++.|+.+|..|.+.                                     ...++++||||++++|+
T Consensus       315 ~~~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HHagL~~~~R~  394 (1724)
T 4f92_B          315 AGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRT  394 (1724)
T ss_dssp             CSSCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEECSSSCTHHHH
T ss_pred             hcCCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEcCCCCHHHHH
Confidence              458999999999999999888531                                     12378999999999999


Q ss_pred             hhhC
Q psy7789         194 TLEN  197 (197)
Q Consensus       194 ~i~~  197 (197)
                      .|++
T Consensus       395 ~vE~  398 (1724)
T 4f92_B          395 LVED  398 (1724)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9873

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.80  E-value=9.6e-19  Score=146.68  Aligned_cols=90  Identities=16%  Similarity=0.185  Sum_probs=71.7

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCc-cCCCccEEEeehhhhhhcCC-CHHHHHHHHhhc---
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMV-SLDVCRYLCLDEADRMVDMG-FEEDVRTIFSFF---   86 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~-~l~~l~~vViDEad~l~~~~-~~~~i~~i~~~~---   86 (197)
                      |+++..++||.+...+...+..+++|+|+||++|...+....+ .+.+++++|+||||++.+.+ +...+...+...   
T Consensus        80 ~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~~  159 (555)
T 3tbk_A           80 GYNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVFTLMIFDECHNTSKNHPYNQIMFRYLDHKLGE  159 (555)
T ss_dssp             TCCEEEECTTTGGGSCHHHHHHHCSEEEECHHHHHHHHHTSSSCCGGGCSEEEETTGGGCSTTCHHHHHHHHHHHHHTSS
T ss_pred             CcEEEEEcCCCcchhhHHHHhcCCCEEEECHHHHHHHHhcCcccccccCCEEEEECccccCCcchHHHHHHHHHHhhhcc
Confidence            7999999999988777777777799999999999999988777 78999999999999998764 233333333322   


Q ss_pred             --cCCceEEEEeecCCh
Q psy7789          87 --RGQRQTLLFSATMPK  101 (197)
Q Consensus        87 --~~~~q~i~~SAT~~~  101 (197)
                        .+.+|++++|||.+.
T Consensus       160 ~~~~~~~~l~lSAT~~~  176 (555)
T 3tbk_A          160 SRDPLPQVVGLTASVGV  176 (555)
T ss_dssp             CCSCCCEEEEEESCCCC
T ss_pred             ccCCCCeEEEEecCccc
Confidence              246799999999853

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=99.80  E-value=2e-19  Score=135.59  Aligned_cols=107  Identities=30%  Similarity=0.558  Sum_probs=97.7

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCC-CHHHHHHHHhhccCCc
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMG-FEEDVRTIFSFFRGQR   90 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~-~~~~i~~i~~~~~~~~   90 (197)
                      ++++..++||.+...+.+.+. +++|+|+||+++.+.+..+.+.+++++++|+||||++++++ |...+..+++.+++..
T Consensus       121 ~~~~~~~~g~~~~~~~~~~~~-~~~Iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~~i~~~~~~~~  199 (230)
T 2oxc_A          121 GLECHVFIGGTPLSQDKTRLK-KCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASK  199 (230)
T ss_dssp             TCCEEEECTTSCHHHHHHHTT-SCSEEEECHHHHHHHHHTTSSCGGGCCEEEESSHHHHHSTTSSHHHHHHHHHHSCSSC
T ss_pred             CceEEEEeCCCCHHHHHHhcc-CCCEEEECHHHHHHHHhcCCcccccCCEEEeCCchHhhcCcchHHHHHHHHHhCCCCC
Confidence            789999999998877766654 69999999999999998888888999999999999999987 9999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEe
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINV  119 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~  119 (197)
                      |++++|||+++++.+.+..++++|..+.+
T Consensus       200 ~~l~lSAT~~~~~~~~~~~~~~~p~~i~~  228 (230)
T 2oxc_A          200 QMLAVSATYPEFLANALTKYMRDPTFVRL  228 (230)
T ss_dssp             EEEEEESCCCHHHHHHHTTTCSSCEEECC
T ss_pred             eEEEEEeccCHHHHHHHHHHcCCCeEEEc
Confidence            99999999999999999999999988765

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=99.80  E-value=2.6e-19  Score=134.18  Aligned_cols=112  Identities=28%  Similarity=0.551  Sum_probs=90.9

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .++++..++||.+...+.+.+.+ ++|+|+||+++...+.+....+++++++|+||||++.++++...+..++..+++..
T Consensus       109 ~~~~~~~~~g~~~~~~~~~~~~~-~~iiv~Tp~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~l~~i~~~~~~~~  187 (224)
T 1qde_A          109 MDIKVHACIGGTSFVEDAEGLRD-AQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTT  187 (224)
T ss_dssp             SCCCEEEECC----------CTT-CSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTC
T ss_pred             cCceEEEEeCCcchHHHHhcCCC-CCEEEECHHHHHHHHHhCCcchhhCcEEEEcChhHHhhhhhHHHHHHHHHhCCccC
Confidence            47899999999887777666655 99999999999999988888899999999999999999999999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCC
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAG  123 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~  123 (197)
                      |++++|||+++++.+.++.++++|..+.+....
T Consensus       188 ~~i~lSAT~~~~~~~~~~~~~~~p~~i~~~~~~  220 (224)
T 1qde_A          188 QVVLLSATMPNDVLEVTTKFMRNPVRILVKKDE  220 (224)
T ss_dssp             EEEEEESSCCHHHHHHHHHHCSSCEEEC-----
T ss_pred             eEEEEEeecCHHHHHHHHHHCCCCEEEEecCCc
Confidence            999999999999999999999999988776443

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=99.80  E-value=5e-19  Score=136.06  Aligned_cols=105  Identities=35%  Similarity=0.576  Sum_probs=95.7

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcC-CccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCC
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKK-MVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~-~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~   89 (197)
                      .++++..++||.....+...+..+++|+|+||+++...+... .+.+++++++|+||||++++++|...+..+++.+++.
T Consensus       153 ~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lViDEah~l~~~~~~~~l~~i~~~~~~~  232 (262)
T 3ly5_A          153 HVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTR  232 (262)
T ss_dssp             CCSCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHCTTCCCTTCCEEEECSHHHHHHTTCHHHHHHHHHHSCSS
T ss_pred             cCceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHccCCcccccCCEEEEcChHHHhhhhHHHHHHHHHHhCCCC
Confidence            478899999999988888888888999999999999988764 4678999999999999999999999999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCe
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPI  115 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~  115 (197)
                      +|++++|||+++++.++++.+++++.
T Consensus       233 ~q~l~~SAT~~~~v~~~~~~~l~~~~  258 (262)
T 3ly5_A          233 RQTMLFSATQTRKVEDLARISLKKEP  258 (262)
T ss_dssp             SEEEEECSSCCHHHHHHHHHHCSSCC
T ss_pred             CeEEEEEecCCHHHHHHHHHHcCCCC
Confidence            99999999999999999999987653

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.80  E-value=7.2e-19  Score=132.92  Aligned_cols=110  Identities=35%  Similarity=0.563  Sum_probs=96.9

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcC-CccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCC
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKK-MVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~-~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~   89 (197)
                      .++++..++||.+...+...+ ++++|+|+||+++.+.+... .+.+++++++|+||||++.+++|...+..++..+++.
T Consensus       124 ~~~~~~~~~g~~~~~~~~~~~-~~~~iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~i~~~~~~~  202 (236)
T 2pl3_A          124 HDFSAGLIIGGKDLKHEAERI-NNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKK  202 (236)
T ss_dssp             SSCCEEEECCC--CHHHHHHH-TTCSEEEECHHHHHHHHHHCSSCCCTTCCEEEETTHHHHHHTTTHHHHHHHHHTSCTT
T ss_pred             CCeeEEEEECCCCHHHHHHhC-CCCCEEEECHHHHHHHHHhcCCcccccccEEEEeChHHHhcCCcHHHHHHHHHhCCCC
Confidence            468999999998877776666 46999999999999988754 5678999999999999999999999999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeCC
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVGR  121 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~  121 (197)
                      .|++++|||+++++.++.+.++++|..+.+.+
T Consensus       203 ~~~l~~SAT~~~~~~~~~~~~~~~p~~i~~~~  234 (236)
T 2pl3_A          203 RQTLLFSATQTKSVKDLARLSLKNPEYVWVHE  234 (236)
T ss_dssp             SEEEEEESSCCHHHHHHHHHSCSSCEEEECCC
T ss_pred             CeEEEEEeeCCHHHHHHHHHhCCCCEEEEeCC
Confidence            99999999999999999999999999887753

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=99.79  E-value=2.9e-19  Score=139.99  Aligned_cols=107  Identities=28%  Similarity=0.457  Sum_probs=95.5

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhc-CCccCCCccEEEeehhhhhhc-CCCHHHHHHHHhhccCC
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDK-KMVSLDVCRYLCLDEADRMVD-MGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~-~~~~l~~l~~vViDEad~l~~-~~~~~~i~~i~~~~~~~   89 (197)
                      ++++..++||.......   ..+++|+||||++|.+++.+ +.++++++++||+||||++++ .+|...+..+++.+++.
T Consensus       191 ~~~~~~~~~~~~~~~~~---~~~~~IlV~TP~~l~~~l~~~~~~~l~~l~~lVlDEad~l~~~~~~~~~~~~i~~~~~~~  267 (300)
T 3fmo_B          191 ELKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRN  267 (300)
T ss_dssp             TCCEEEESTTCCCCTTC---CCCCSEEEECHHHHHHHHTTTCCCCGGGCSEEEETTHHHHHHSTTHHHHHHHHHTTSCTT
T ss_pred             CcEEEEEeCCccHhhhh---cCCCCEEEECHHHHHHHHHhcCCCChhhceEEEEeCHHHHhhccCcHHHHHHHHHhCCCC
Confidence            68899999998755443   45689999999999999965 567889999999999999997 68999999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeCC
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVGR  121 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~  121 (197)
                      +|+++||||+++++..+++.++++|..|.+..
T Consensus       268 ~q~i~~SAT~~~~v~~~a~~~l~~p~~i~~~~  299 (300)
T 3fmo_B          268 CQMLLFSATFEDSVWKFAQKVVPDPNVIKLKR  299 (300)
T ss_dssp             CEEEEEESCCCHHHHHHHHHHSSSCEEEEECC
T ss_pred             CEEEEEeccCCHHHHHHHHHHCCCCeEEEecC
Confidence            99999999999999999999999999998764

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.78  E-value=1.2e-18  Score=161.52  Aligned_cols=182  Identities=9%  Similarity=0.102  Sum_probs=122.8

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhc--CCccCCCccEEEeehhhhhhcCCCHHHHHHHHhh---
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDK--KMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSF---   85 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~--~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~---   85 (197)
                      .|++|..++|+.+.+..  .+ .+++|+|||||++..++++  ....++++++||+||+|.+.+. .+..+..++.+   
T Consensus      1000 ~g~~V~~ltGd~~~~~~--~~-~~~~IiV~TPEkld~llr~~~~~~~l~~v~lvViDE~H~l~d~-rg~~le~il~rl~~ 1075 (1724)
T 4f92_B         1000 LNKKVVLLTGETSTDLK--LL-GKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGE-NGPVLEVICSRMRY 1075 (1724)
T ss_dssp             SCCCEEECCSCHHHHHH--HH-HHCSEEEECHHHHHHHHTTTTTCHHHHSCSEEEECCGGGGGST-THHHHHHHHHHHHH
T ss_pred             cCCEEEEEECCCCcchh--hc-CCCCEEEECHHHHHHHHhCcccccccceeeEEEeechhhcCCC-CCccHHHHHHHHHH
Confidence            48999999998654332  22 3489999999999888765  3344789999999999988764 66666655443   


Q ss_pred             ----ccCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchh---h----HHHHHHHhhc--C
Q psy7789          86 ----FRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEA---K----IVYLLECLQK--T  152 (197)
Q Consensus        86 ----~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~---k----~~~l~~~l~~--~  152 (197)
                          .++..|++++|||++ +..++++++..++..+........+..+..++.......   +    ...+...+..  .
T Consensus      1076 i~~~~~~~~riI~lSATl~-N~~dla~WL~~~~~~~~~~~~~~RPvpL~~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~ 1154 (1724)
T 4f92_B         1076 ISSQIERPIRIVALSSSLS-NAKDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSP 1154 (1724)
T ss_dssp             HHHTTSSCCEEEEEESCBT-THHHHHHHHTCCSTTEEECCGGGCSSCEEEEEEEECCCSHHHHHHTTHHHHHHHHHHHCS
T ss_pred             HHhhcCCCceEEEEeCCCC-CHHHHHHHhCCCCCCeEEeCCCCCCCCeEEEEEeccCCCchhhhhhhcchHHHHHHHhcC
Confidence                456889999999997 456777666554433333223333333444443332221   1    1222233332  3


Q ss_pred             CCCEEEEecccccHHHHHHHHHhC----------------------------------CCCeEeecCCCChhhhhhhhC
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLK----------------------------------GKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~----------------------------------~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      .+++||||+|++.|+.+|..|...                                  ...++.+||+|++++|+.|++
T Consensus      1155 ~~~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHagL~~~~R~~VE~ 1233 (1724)
T 4f92_B         1155 KKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLVEQ 1233 (1724)
T ss_dssp             SSCEEEEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECTTSCHHHHHHHHH
T ss_pred             CCCeeeeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEEECCCCCHHHHHHHHH
Confidence            468999999999999998876321                                  124889999999999999873

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}

Probab=99.78  E-value=2.1e-18  Score=151.01  Aligned_cols=89  Identities=16%  Similarity=0.136  Sum_probs=67.4

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCc-cCCCccEEEeehhhhhhcCCCHHH-HHHHHhhc---
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMV-SLDVCRYLCLDEADRMVDMGFEED-VRTIFSFF---   86 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~-~l~~l~~vViDEad~l~~~~~~~~-i~~i~~~~---   86 (197)
                      |+++..++||.+...+...+..+++|+|+||++|.+.+..+.+ .+.++++||+||||++.+.+.... +...+...   
T Consensus       324 ~~~v~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEaH~~~~~~~~~~i~~~~~~~~~~~  403 (797)
T 4a2q_A          324 GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNS  403 (797)
T ss_dssp             TCCEEEECCC-----CHHHHHHTCSEEEECHHHHHHHHHSSSCCCGGGCSEEEETTGGGCSTTSHHHHHHHHHHHHHHTT
T ss_pred             CceEEEEeCCcchhhhHHHhhCCCCEEEEchHHHHHHHHhccccccccCCEEEEECccccCCCccHHHHHHHHHHHhhcc
Confidence            7999999999988877777777899999999999999988777 789999999999999987643322 22322221   


Q ss_pred             -cCCceEEEEeecCC
Q psy7789          87 -RGQRQTLLFSATMP  100 (197)
Q Consensus        87 -~~~~q~i~~SAT~~  100 (197)
                       .+.+|++++|||.+
T Consensus       404 ~~~~~~~l~lSATp~  418 (797)
T 4a2q_A          404 ASQLPQILGLTASVG  418 (797)
T ss_dssp             CCCCCEEEEEESCCC
T ss_pred             CCCCCeEEEEcCCcc
Confidence             45689999999985

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=99.78  E-value=1.2e-18  Score=130.38  Aligned_cols=107  Identities=30%  Similarity=0.578  Sum_probs=97.2

Q ss_pred             CeeEEEEEcCCChHHhHHHHhc-CCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcC-CCHHHHHHHHhhccCC
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKK-GCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDM-GFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~-~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~-~~~~~i~~i~~~~~~~   89 (197)
                      ++++..++||.+...+.+.+.. .++|+|+||+++...+.+..+.+++++++|+||||+++++ ++...+..+++.++++
T Consensus       111 ~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~~i~~~~~~~  190 (220)
T 1t6n_A          111 NVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHE  190 (220)
T ss_dssp             TCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSSHHHHHHHHHHHHTSCSS
T ss_pred             CceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHhCCCCcccCCEEEEcCHHHHhcccCcHHHHHHHHHhCCCc
Confidence            7999999999998888777754 5899999999999999888888999999999999999874 6888999999999889


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEE
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITIN  118 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~  118 (197)
                      .|++++|||+++++.++++.++++|..+.
T Consensus       191 ~~~i~~SAT~~~~~~~~~~~~~~~p~~i~  219 (220)
T 1t6n_A          191 KQVMMFSATLSKEIRPVCRKFMQDPMEIF  219 (220)
T ss_dssp             SEEEEEESCCCTTTHHHHHTTCSSCEEEE
T ss_pred             CeEEEEEeecCHHHHHHHHHHcCCCeEEe
Confidence            99999999999999999999999998775

>4gl2_A Interferon-induced helicase C domain-containing P; MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerizat helicase, ATPase; HET: ANP; 3.56A {Homo sapiens}

Probab=99.78  E-value=1.7e-19  Score=155.66  Aligned_cols=92  Identities=18%  Similarity=0.190  Sum_probs=65.2

Q ss_pred             CCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHH------hcCCccCCCccEEEeehhhhhhcCC-CHHHHHHH
Q psy7789          10 PIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDML------DKKMVSLDVCRYLCLDEADRMVDMG-FEEDVRTI   82 (197)
Q Consensus        10 ~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l------~~~~~~l~~l~~vViDEad~l~~~~-~~~~i~~i   82 (197)
                      +.++++..++|+.+...+...+.++++|+|+||++|...+      ....+.+.++++||+||||++...+ +...+...
T Consensus        82 ~~~~~v~~~~g~~~~~~~~~~~~~~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~~~~~~~~~~i~~~~  161 (699)
T 4gl2_A           82 KKWYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHY  161 (699)
T ss_dssp             TTTSCEEEEC----CCCCHHHHHHSCSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGGCBTTBSSCSHHHHH
T ss_pred             CcCceEEEEeCCcchhhHHHhhhcCCCEEEECHHHHHHHHhccccccccceecccCcEEEEECccccCccchHHHHHHHH
Confidence            3358999999998877777777778999999999999988      4455778999999999999986533 33333322


Q ss_pred             Hhh----cc---------CCceEEEEeecCCh
Q psy7789          83 FSF----FR---------GQRQTLLFSATMPK  101 (197)
Q Consensus        83 ~~~----~~---------~~~q~i~~SAT~~~  101 (197)
                      +..    ..         +.+|++++|||.+.
T Consensus       162 l~~~~~~~~~~~~~~~~~~~~~il~lTATp~~  193 (699)
T 4gl2_A          162 LMQKLKNNRLKKENKPVIPLPQILGLTASPGV  193 (699)
T ss_dssp             HHHHHHHHHHHC----CCCCCEEEEECSCCCC
T ss_pred             HHhhhcccccccccccCCCCCEEEEecccccc
Confidence            222    11         57899999999985

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=99.77  E-value=8.1e-18  Score=151.77  Aligned_cols=174  Identities=14%  Similarity=0.072  Sum_probs=126.2

Q ss_pred             CCCeeEEEEEcCCChHHhH---HHHhc-CCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhh
Q psy7789          10 PIPLRTCLAIGGVPMNQSL---DVIKK-GCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSF   85 (197)
Q Consensus        10 ~~~i~~~~~~gg~~~~~~~---~~l~~-~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~   85 (197)
                      +.++++..++|+.+..++.   +.+.. .++|+|+||+.+.     +.+.++++++||+||+|++     .......++.
T Consensus       678 ~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~-----~~~~~~~l~lvIiDEaH~~-----g~~~~~~l~~  747 (1151)
T 2eyq_A          678 NWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-----SDVKFKDLGLLIVDEEHRF-----GVRHKERIKA  747 (1151)
T ss_dssp             TTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-----SCCCCSSEEEEEEESGGGS-----CHHHHHHHHH
T ss_pred             cCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHh-----CCccccccceEEEechHhc-----ChHHHHHHHH
Confidence            3478999999887655443   33444 5999999997553     4466899999999999995     3445566777


Q ss_pred             ccCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEeccccc
Q psy7789          86 FRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQD  165 (197)
Q Consensus        86 ~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~  165 (197)
                      ++.+.|++++|||..+.........++++..+...  ......+..++...........+...+. .+++++||||+++.
T Consensus       748 l~~~~~vl~lSATp~p~~l~~~~~~~~~~~~i~~~--~~~r~~i~~~~~~~~~~~i~~~il~~l~-~g~qvlvf~~~v~~  824 (1151)
T 2eyq_A          748 MRANVDILTLTATPIPRTLNMAMSGMRDLSIIATP--PARRLAVKTFVREYDSMVVREAILREIL-RGGQVYYLYNDVEN  824 (1151)
T ss_dssp             HHTTSEEEEEESSCCCHHHHHHHTTTSEEEECCCC--CCBCBCEEEEEEECCHHHHHHHHHHHHT-TTCEEEEECCCSSC
T ss_pred             hcCCCCEEEEcCCCChhhHHHHHhcCCCceEEecC--CCCccccEEEEecCCHHHHHHHHHHHHh-cCCeEEEEECCHHH
Confidence            77889999999999888777766666554443322  2222334554444343333344444333 34689999999999


Q ss_pred             HHHHHHHHHhC--CCCeEeecCCCChhhhhhhh
Q psy7789         166 VDAIHEYLLLK--GKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       166 ~~~l~~~L~~~--~~~~~~~h~~~~~~~R~~i~  196 (197)
                      ++.+++.|++.  ++++..+||+|++++|++++
T Consensus       825 ~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il  857 (1151)
T 2eyq_A          825 IQKAAERLAELVPEARIAIGHGQMRERELERVM  857 (1151)
T ss_dssp             HHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHH
Confidence            99999999987  88999999999999999876

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos}

Probab=99.76  E-value=6.6e-18  Score=149.97  Aligned_cols=89  Identities=16%  Similarity=0.135  Sum_probs=66.5

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCc-cCCCccEEEeehhhhhhcCCC-HHHHHHHHhhc---
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMV-SLDVCRYLCLDEADRMVDMGF-EEDVRTIFSFF---   86 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~-~l~~l~~vViDEad~l~~~~~-~~~i~~i~~~~---   86 (197)
                      ++++..++||.+...+...+..+++|+|+||++|.+.+....+ .+.+++++|+||||++.+.+. ...+..++...   
T Consensus       324 ~~~v~~~~G~~~~~~~~~~~~~~~~IvI~Tp~~L~~~l~~~~~~~l~~~~liViDEaH~~~~~~~~~~i~~~~~~~~~~~  403 (936)
T 4a2w_A          324 GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNS  403 (936)
T ss_dssp             TCCEEEECCC-----CCHHHHHHCSEEEECHHHHHHHHHSSSCCCGGGCSEEEEETGGGCSTTCHHHHHHHHHHHHHHTT
T ss_pred             CceEEEEECCcchhhHHHHhccCCCEEEecHHHHHHHHHcCccccccCCCEEEEECccccCCCccHHHHHHHHHHHhhcc
Confidence            7999999999987777666766799999999999999987776 789999999999999987642 22232333221   


Q ss_pred             -cCCceEEEEeecCC
Q psy7789          87 -RGQRQTLLFSATMP  100 (197)
Q Consensus        87 -~~~~q~i~~SAT~~  100 (197)
                       .+.+|++++|||..
T Consensus       404 ~~~~~~~l~LSATp~  418 (936)
T 4a2w_A          404 ASQLPQILGLTASVG  418 (936)
T ss_dssp             CSCCCEEEEEESCCC
T ss_pred             CCCcCeEEEecCCcc
Confidence             45689999999984

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=99.74  E-value=4.2e-18  Score=144.90  Aligned_cols=154  Identities=16%  Similarity=0.115  Sum_probs=106.0

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCce
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQ   91 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q   91 (197)
                      +.++...+|+..       ...+++|+|+||++|   +.+..+.++++++||+||||++ +.++...+..+++.++...|
T Consensus       282 g~~vg~~vG~~~-------~~~~~~IlV~TPGrL---l~~~~l~l~~l~~lVlDEAH~l-~~~~~~~l~~Il~~l~~~~~  350 (666)
T 3o8b_A          282 GIDPNIRTGVRT-------ITTGAPVTYSTYGKF---LADGGCSGGAYDIIICDECHST-DSTTILGIGTVLDQAETAGA  350 (666)
T ss_dssp             SCCCEEECSSCE-------ECCCCSEEEEEHHHH---HHTTSCCTTSCSEEEETTTTCC-SHHHHHHHHHHHHHTTTTTC
T ss_pred             CCCeeEEECcEe-------ccCCCCEEEECcHHH---HhCCCcccCcccEEEEccchhc-CccHHHHHHHHHHhhhhcCC
Confidence            344555666644       245699999999997   4567788899999999999765 44577888899999987776


Q ss_pred             --EEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecccccHHHH
Q psy7789          92 --TLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAI  169 (197)
Q Consensus        92 --~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l  169 (197)
                        ++++|||+++.+.      ...+....+.....  ..+.    .......      +-....+++||||||++.++.+
T Consensus       351 ~llil~SAT~~~~i~------~~~p~i~~v~~~~~--~~i~----~~~~~~~------l~~~~~~~vLVFv~Tr~~ae~l  412 (666)
T 3o8b_A          351 RLVVLATATPPGSVT------VPHPNIEEVALSNT--GEIP----FYGKAIP------IEAIRGGRHLIFCHSKKKCDEL  412 (666)
T ss_dssp             SEEEEEESSCTTCCC------CCCTTEEEEECBSC--SSEE----ETTEEEC------GGGSSSSEEEEECSCHHHHHHH
T ss_pred             ceEEEECCCCCcccc------cCCcceEEEeeccc--chhH----HHHhhhh------hhhccCCcEEEEeCCHHHHHHH
Confidence              7788999986311      11222211110000  0010    0111101      0112456899999999999999


Q ss_pred             HHHHHhCCCCeEeecCCCChhhhhh
Q psy7789         170 HEYLLLKGKPFFTLKSLKEDQNNQT  194 (197)
Q Consensus       170 ~~~L~~~~~~~~~~h~~~~~~~R~~  194 (197)
                      ++.|++.|+++..+||+|++++|.+
T Consensus       413 a~~L~~~g~~v~~lHG~l~q~er~~  437 (666)
T 3o8b_A          413 AAKLSGLGINAVAYYRGLDVSVIPT  437 (666)
T ss_dssp             HHHHHTTTCCEEEECTTSCGGGSCS
T ss_pred             HHHHHhCCCcEEEecCCCCHHHHHh
Confidence            9999999999999999999998753

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=99.72  E-value=9.7e-18  Score=127.38  Aligned_cols=112  Identities=21%  Similarity=0.427  Sum_probs=89.4

Q ss_pred             CeeEEEEEcCCChHHhH-HHHhcCCcEEEeCchHHHHHHhcC--CccCCCccEEEeehhhhhhc---CCCHHHHHHHHhh
Q psy7789          12 PLRTCLAIGGVPMNQSL-DVIKKGCHMMVATPGRLMDMLDKK--MVSLDVCRYLCLDEADRMVD---MGFEEDVRTIFSF   85 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~-~~l~~~~~Ili~TP~~l~~~l~~~--~~~l~~l~~vViDEad~l~~---~~~~~~i~~i~~~   85 (197)
                      |+++..++||.....+. ....++++|+|+||+++.+++...  .+.+++++++|+||||++++   .+|...+..++..
T Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~~~~i~~~  205 (245)
T 3dkp_A          126 GFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLA  205 (245)
T ss_dssp             CCCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSCSCCCTTCCEEEESSHHHHHHHC--CHHHHHHHHHHH
T ss_pred             CceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCCCcccccCcEEEEeChHHhcccccccHHHHHHHHHHh
Confidence            66777777665433322 222456899999999999999765  56789999999999999987   4688888888877


Q ss_pred             cc-CCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCC
Q psy7789          86 FR-GQRQTLLFSATMPKKIQNFARSALVKPITINVGRAG  123 (197)
Q Consensus        86 ~~-~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~  123 (197)
                      +. +..|++++|||+++++..+++.++++|..+.+...+
T Consensus       206 ~~~~~~~~~~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~  244 (245)
T 3dkp_A          206 CTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGARN  244 (245)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHHHHHHSSSCEEEEECC--
T ss_pred             cCCCCcEEEEEeccCCHHHHHHHHHhCCCCEEEEeCCCC
Confidence            64 578999999999999999999999999999887543

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=99.71  E-value=8.8e-17  Score=140.00  Aligned_cols=156  Identities=13%  Similarity=0.119  Sum_probs=110.7

Q ss_pred             CCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhh-hhcCC-CHHHHHHHHhhccCCceEEEEeecCChhHHHHHHHhc
Q psy7789          34 GCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADR-MVDMG-FEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSAL  111 (197)
Q Consensus        34 ~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~-l~~~~-~~~~i~~i~~~~~~~~q~i~~SAT~~~~~~~~~~~~~  111 (197)
                      +++|+++|||++...+... ..+.++++||+||+|. .++.. ....+..+.... ++.|++++|||++.+  .+ ..++
T Consensus       185 ~~~I~v~T~G~l~r~l~~~-~~l~~~~~lIlDEah~R~ld~d~~~~~l~~l~~~~-~~~~iIl~SAT~~~~--~l-~~~~  259 (773)
T 2xau_A          185 KTILKYMTDGMLLREAMED-HDLSRYSCIILDEAHERTLATDILMGLLKQVVKRR-PDLKIIIMSATLDAE--KF-QRYF  259 (773)
T ss_dssp             TCSEEEEEHHHHHHHHHHS-TTCTTEEEEEECSGGGCCHHHHHHHHHHHHHHHHC-TTCEEEEEESCSCCH--HH-HHHT
T ss_pred             CCCEEEECHHHHHHHHhhC-ccccCCCEEEecCccccccchHHHHHHHHHHHHhC-CCceEEEEeccccHH--HH-HHHh
Confidence            5899999999999887654 3589999999999996 44422 233444544443 578999999999743  33 3455


Q ss_pred             CCCeEEEeCCCCccCcceeEEEEEcCchhhH----HHHHHHhhc-CCCCEEEEecccccHHHHHHHHHh-----------
Q psy7789         112 VKPITINVGRAGAASMNVVQEVEYVKQEAKI----VYLLECLQK-TEPPVLIFAEKKQDVDAIHEYLLL-----------  175 (197)
Q Consensus       112 ~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~----~~l~~~l~~-~~~~~lIF~~s~~~~~~l~~~L~~-----------  175 (197)
                      .++..+.+....   ..+.+++......++.    ..+.++... .++++||||++++.++.+++.|.+           
T Consensus       260 ~~~~vi~v~gr~---~pv~~~~~~~~~~~~~~~~l~~l~~~~~~~~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~  336 (773)
T 2xau_A          260 NDAPLLAVPGRT---YPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGC  336 (773)
T ss_dssp             TSCCEEECCCCC---CCEEEECCSSCCSCHHHHHHHHHHHHHHHSCSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             cCCCcccccCcc---cceEEEEecCCchhHHHHHHHHHHHHHHhcCCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccC
Confidence            555555554332   2355555444444443    333444433 457999999999999999999985           


Q ss_pred             CCCCeEeecCCCChhhhhhhhC
Q psy7789         176 KGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       176 ~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      .++.+..+||+|++++|+++++
T Consensus       337 ~~~~v~~lhg~l~~~eR~~v~~  358 (773)
T 2xau_A          337 GPLSVYPLYGSLPPHQQQRIFE  358 (773)
T ss_dssp             CCEEEEEECTTCCHHHHGGGGS
T ss_pred             CCeEEEEeCCCCCHHHHHHHHh
Confidence            5788999999999999998864

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=99.68  E-value=6.1e-17  Score=140.70  Aligned_cols=171  Identities=12%  Similarity=0.079  Sum_probs=109.4

Q ss_pred             CCeeEEEEEcCCChHHhH---HHHhc-CCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhc
Q psy7789          11 IPLRTCLAIGGVPMNQSL---DVIKK-GCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF   86 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~---~~l~~-~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~   86 (197)
                      .|++++.++||.+..++.   +.+.. .++|+|+||+.+.+     .+.+++++++|+||+|++....     ...+...
T Consensus       444 ~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~~~~~~l~lVVIDEaHr~g~~q-----r~~l~~~  513 (780)
T 1gm5_A          444 FNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-----DVHFKNLGLVIIDEQHRFGVKQ-----REALMNK  513 (780)
T ss_dssp             SSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-----CCCCSCCCEEEEESCCCC----------CCCCSS
T ss_pred             cCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh-----hhhccCCceEEecccchhhHHH-----HHHHHHh
Confidence            479999999998766543   34444 49999999987754     4568899999999999973221     1222333


Q ss_pred             cCCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhh---cCCCCEEEEeccc
Q psy7789          87 RGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQ---KTEPPVLIFAEKK  163 (197)
Q Consensus        87 ~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~---~~~~~~lIF~~s~  163 (197)
                      ...+|++++|||..++.....  +..+.....+.........+...+.   ...+...+.+.+.   ..+.+++|||+++
T Consensus       514 ~~~~~vL~mSATp~p~tl~~~--~~g~~~~s~i~~~p~~r~~i~~~~~---~~~~~~~l~~~i~~~l~~g~qvlVf~~~i  588 (780)
T 1gm5_A          514 GKMVDTLVMSATPIPRSMALA--FYGDLDVTVIDEMPPGRKEVQTMLV---PMDRVNEVYEFVRQEVMRGGQAFIVYPLI  588 (780)
T ss_dssp             SSCCCEEEEESSCCCHHHHHH--HTCCSSCEEECCCCSSCCCCEECCC---CSSTHHHHHHHHHHHTTTSCCBCCBCCCC
T ss_pred             CCCCCEEEEeCCCCHHHHHHH--HhCCcceeeeeccCCCCcceEEEEe---ccchHHHHHHHHHHHHhcCCcEEEEecch
Confidence            457899999999877655433  2333222222221111222333222   2233344444443   2356899999966


Q ss_pred             --------ccHHHHHHHHHh---CCCCeEeecCCCChhhhhhhh
Q psy7789         164 --------QDVDAIHEYLLL---KGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       164 --------~~~~~l~~~L~~---~~~~~~~~h~~~~~~~R~~i~  196 (197)
                              ..++.+++.|++   .++++..+||+|++++|++++
T Consensus       589 e~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~  632 (780)
T 1gm5_A          589 EESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVM  632 (780)
T ss_dssp             --------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHH
T ss_pred             hhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHH
Confidence                    457889999988   478999999999999999876

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.64  E-value=1e-16  Score=133.69  Aligned_cols=174  Identities=10%  Similarity=0.089  Sum_probs=115.1

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCce
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQ   91 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q   91 (197)
                      ++++..++||.+...+   +..+++|+|+||+.+..   .....++++++||+||||++..    ..+..+++.+++..+
T Consensus       185 ~~~v~~~~~~~~~~~~---~~~~~~I~i~T~~~l~~---~~~~~~~~~~liIiDE~H~~~~----~~~~~il~~~~~~~~  254 (510)
T 2oca_A          185 HAMIKKIGGGASKDDK---YKNDAPVVVGTWQTVVK---QPKEWFSQFGMMMNDECHLATG----KSISSIISGLNNCMF  254 (510)
T ss_dssp             GGGEEECGGGCCTTGG---GCTTCSEEEEEHHHHTT---SCGGGGGGEEEEEEETGGGCCH----HHHHHHGGGCTTCCE
T ss_pred             ccceEEEecCCccccc---cccCCcEEEEeHHHHhh---chhhhhhcCCEEEEECCcCCCc----ccHHHHHHhcccCcE
Confidence            5788889998776655   45569999999996543   3345678899999999999854    567788888888899


Q ss_pred             EEEEeecCChhHHHHHH-HhcCCCeEEEeCCCC------ccCcceeEEEEEcC---------------------chhhHH
Q psy7789          92 TLLFSATMPKKIQNFAR-SALVKPITINVGRAG------AASMNVVQEVEYVK---------------------QEAKIV  143 (197)
Q Consensus        92 ~i~~SAT~~~~~~~~~~-~~~~~~~~i~~~~~~------~~~~~i~~~~~~~~---------------------~~~k~~  143 (197)
                      ++++|||.+........ ..+..+.........      ..+..+.......+                     ...+..
T Consensus       255 ~l~lSATp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  334 (510)
T 2oca_A          255 KFGLSGSLRDGKANIMQYVGMFGEIFKPVTTSKLMEDGQVTELKINSIFLRYPDEFTTKLKGKTYQEEIKIITGLSKRNK  334 (510)
T ss_dssp             EEEEESCGGGCSSCHHHHHHHHCSEECCCCCC---------CCEEEEEEEECCHHHHHHHTTCCHHHHHHHHHTCHHHHH
T ss_pred             EEEEEeCCCCCcccHHHhHHhhCCeEEeeCHHHHhhCCcCCCceEEEEeecCChHHhccccccchHHHHHHHhccHHHHH
Confidence            99999999655322111 112233332222211      11111111111111                     122344


Q ss_pred             HHHHHhhcC---CC-CEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         144 YLLECLQKT---EP-PVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       144 ~l~~~l~~~---~~-~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .+.+++...   ++ +++|||+ .+.++.+++.|.+.+.++..+||+|++++|++++
T Consensus       335 ~l~~~l~~~~~~~~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~  390 (510)
T 2oca_A          335 WIAKLAIKLAQKDENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMK  390 (510)
T ss_dssp             HHHHHHHHHHTTTCEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHH
Confidence            455555543   33 4566666 8999999999999988999999999999999875

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=99.58  E-value=9.1e-17  Score=132.00  Aligned_cols=137  Identities=14%  Similarity=0.097  Sum_probs=85.7

Q ss_pred             EEeCchHHHHHHhcCCc--------cCCCccEEEeehhhhhhcCCCHHHHHHHHhhc-cCCceEEEEeecCChhHHHHHH
Q psy7789          38 MVATPGRLMDMLDKKMV--------SLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF-RGQRQTLLFSATMPKKIQNFAR  108 (197)
Q Consensus        38 li~TP~~l~~~l~~~~~--------~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~-~~~~q~i~~SAT~~~~~~~~~~  108 (197)
                      .++||+++.+++..+.+        .+++++++|+||+|++ +.++...+..+.+.. +.++|+++||||+++.+..+..
T Consensus        71 ~v~Tp~~l~~~l~~~~l~~~~~~~~~~~~l~~vViDEah~~-~~~~~~~~~~~~~~~~~~~~~~l~~SAT~~~~~~~~~~  149 (440)
T 1yks_A           71 AHGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFL-DPASIAARGWAAHRARANESATILMTATPPGTSDEFPH  149 (440)
T ss_dssp             CCCCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCC-SHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCC
T ss_pred             eccCCccceeeecccchhHhhhCcccccCccEEEEECcccc-CcchHHHHHHHHHHhccCCceEEEEeCCCCchhhhhhh
Confidence            48888777655443322        3789999999999998 333333333333333 3579999999999876432221


Q ss_pred             HhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCC
Q psy7789         109 SALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKE  188 (197)
Q Consensus       109 ~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~  188 (197)
                      .  ..+              +......+....+ ..+...+.+.++++||||++++.|+.+++.|++.|+++..+||   
T Consensus       150 ~--~~~--------------~~~~~~~~~~~~~-~~~~~~l~~~~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~lhg---  209 (440)
T 1yks_A          150 S--NGE--------------IEDVQTDIPSEPW-NTGHDWILADKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNR---  209 (440)
T ss_dssp             C--SSC--------------EEEEECCCCSSCC-SSSCHHHHHCCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCS---
T ss_pred             c--CCC--------------eeEeeeccChHHH-HHHHHHHHhcCCCEEEEeCCHHHHHHHHHHHHHcCCCEEEecc---
Confidence            1  011              1111111121111 1122334445679999999999999999999999999999999   


Q ss_pred             hhhhhhhh
Q psy7789         189 DQNNQTLE  196 (197)
Q Consensus       189 ~~~R~~i~  196 (197)
                       ++|++++
T Consensus       210 -~~R~~~~  216 (440)
T 1yks_A          210 -KTFEREY  216 (440)
T ss_dssp             -SSCC---
T ss_pred             -hhHHHHH
Confidence             3565554

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=99.57  E-value=9.4e-16  Score=130.58  Aligned_cols=137  Identities=14%  Similarity=0.105  Sum_probs=92.2

Q ss_pred             EEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhcc-CCceEEEEeecCChhHHHHHHHhcCCCe
Q psy7789          37 MMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFR-GQRQTLLFSATMPKKIQNFARSALVKPI  115 (197)
Q Consensus        37 Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~-~~~q~i~~SAT~~~~~~~~~~~~~~~~~  115 (197)
                      +.++|.+.+...+... ..+++++++|+||||++ +.++...+..+.+.++ ++.|+++||||++..+..+..   .++.
T Consensus       257 i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~~~~~~~~~i~~~l~~~~~q~il~SAT~~~~~~~~~~---~~~~  331 (618)
T 2whx_A          257 VDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DPCSVAARGYISTRVEMGEAAAIFMTATPPGSTDPFPQ---SNSP  331 (618)
T ss_dssp             EEEEEHHHHHHHHHHC-SSCCCCSEEEEESTTCC-SHHHHHHHHHHHHHHHHTSCEEEEECSSCTTCCCSSCC---CSSC
T ss_pred             EEEEChHHHHHHHhcc-ccccCCeEEEEECCCCC-CccHHHHHHHHHHHhcccCccEEEEECCCchhhhhhhc---cCCc
Confidence            3344444444433322 23789999999999998 5457777888877775 689999999999876443221   2333


Q ss_pred             EEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhh
Q psy7789         116 TINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       116 ~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i  195 (197)
                      .+.+....             +. .+...+...+.+..+++||||+|++.|+.+++.|++.|+++..+||+    +|+++
T Consensus       332 ~~~v~~~~-------------~~-~~~~~ll~~l~~~~~~~LVF~~s~~~a~~l~~~L~~~g~~v~~lhg~----~R~~~  393 (618)
T 2whx_A          332 IEDIEREI-------------PE-RSWNTGFDWITDYQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRK----TFDTE  393 (618)
T ss_dssp             EEEEECCC-------------CS-SCCSSSCHHHHHCCSCEEEECSSHHHHHHHHHHHHHTTCCEEEECTT----THHHH
T ss_pred             eeeecccC-------------CH-HHHHHHHHHHHhCCCCEEEEECChhHHHHHHHHHHHcCCcEEEEChH----HHHHH
Confidence            33332211             00 11122333444456799999999999999999999999999999985    55554


Q ss_pred             h
Q psy7789         196 E  196 (197)
Q Consensus       196 ~  196 (197)
                      +
T Consensus       394 l  394 (618)
T 2whx_A          394 Y  394 (618)
T ss_dssp             T
T ss_pred             H
Confidence            4

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.56  E-value=7e-15  Score=120.45  Aligned_cols=134  Identities=16%  Similarity=0.134  Sum_probs=88.2

Q ss_pred             CCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhc-cCCceEEEEeecCChhHHHHHHHhcC
Q psy7789          34 GCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF-RGQRQTLLFSATMPKKIQNFARSALV  112 (197)
Q Consensus        34 ~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~-~~~~q~i~~SAT~~~~~~~~~~~~~~  112 (197)
                      +.-+.+.|.+.+.+.+.. ...+++++++|+||+|++ +.++......+.... +.++|++++|||+++.+..+...  +
T Consensus        70 ~~~~~~~~~~~l~~~l~~-~~~~~~l~~vViDEaH~~-~~~~~~~~~~l~~~~~~~~~~~l~~SAT~~~~~~~~~~~--~  145 (431)
T 2v6i_A           70 NEIVDFMCHSTFTMKLLQ-GVRVPNYNLYIMDEAHFL-DPASVAARGYIETRVSMGDAGAIFMTATPPGTTEAFPPS--N  145 (431)
T ss_dssp             CCSEEEEEHHHHHHHHHH-TCCCCCCSEEEEESTTCC-SHHHHHHHHHHHHHHHTTSCEEEEEESSCTTCCCSSCCC--S
T ss_pred             CceEEEEchHHHHHHHhc-CccccCCCEEEEeCCccC-CccHHHHHHHHHHHhhCCCCcEEEEeCCCCcchhhhcCC--C
Confidence            355667788888776655 455899999999999997 322333333333332 46899999999998642211100  1


Q ss_pred             CCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCC
Q psy7789         113 KPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSL  186 (197)
Q Consensus       113 ~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~  186 (197)
                      .|              +.......+ ..+...+.+.+.+.++++||||++++.|+.+++.|++.|+++..+||+
T Consensus       146 ~~--------------i~~~~~~~~-~~~~~~~~~~l~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg~  204 (431)
T 2v6i_A          146 SP--------------IIDEETRIP-DKAWNSGYEWITEFDGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNRK  204 (431)
T ss_dssp             SC--------------CEEEECCCC-SSCCSSCCHHHHSCSSCEEEECSSHHHHHHHHHHHHHTTCCEEEESTT
T ss_pred             Cc--------------eeeccccCC-HHHHHHHHHHHHcCCCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCc
Confidence            11              111000011 112233344555667799999999999999999999999999999997

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=99.56  E-value=4.7e-15  Score=122.14  Aligned_cols=138  Identities=13%  Similarity=0.060  Sum_probs=93.0

Q ss_pred             CCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHh-hccCCceEEEEeecCChhHHHHHHHhcC
Q psy7789          34 GCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFS-FFRGQRQTLLFSATMPKKIQNFARSALV  112 (197)
Q Consensus        34 ~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~-~~~~~~q~i~~SAT~~~~~~~~~~~~~~  112 (197)
                      +..|.++||+.+.+.+... ..+++++++|+||||++ +.++...+..+.. ..+++.|+++||||+++....   .+..
T Consensus        87 ~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~---~~~~  161 (451)
T 2jlq_A           87 REIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DPCSVAARGYISTRVEMGEAAAIFMTATPPGSTDP---FPQS  161 (451)
T ss_dssp             SCCEEEEEHHHHHHHHHHC-SCCCCCSEEEEETTTCC-SHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCS---SCCC
T ss_pred             CceEEEEChHHHHHHhhCc-ccccCCCEEEEeCCccC-CcchHHHHHHHHHhhcCCCceEEEEccCCCccchh---hhcC
Confidence            3578899999998877644 45789999999999987 3223333333322 234589999999999865433   2233


Q ss_pred             CCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChh
Q psy7789         113 KPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQ  190 (197)
Q Consensus       113 ~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~  190 (197)
                      ++..+.+.....  ..            ....+.+.+....+++||||+|++.|+.+++.|++.|+++..+||++.++
T Consensus       162 ~~~~~~~~~~~p--~~------------~~~~~~~~l~~~~~~~lVF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~  225 (451)
T 2jlq_A          162 NSPIEDIEREIP--ER------------SWNTGFDWITDYQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTFDT  225 (451)
T ss_dssp             SSCEEEEECCCC--SS------------CCSSSCHHHHHCCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECTTTHHH
T ss_pred             CCceEecCccCC--ch------------hhHHHHHHHHhCCCCEEEEcCCHHHHHHHHHHHHHcCCeEEECCHHHHHH
Confidence            443333321110  00            00112334445567999999999999999999999999999999987643

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.54  E-value=2.1e-14  Score=123.07  Aligned_cols=160  Identities=10%  Similarity=0.006  Sum_probs=110.4

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhcc-CCc
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFR-GQR   90 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~-~~~   90 (197)
                      |+++..++||.......  -....+++++|++.+.        ....++++|+||||++.+.+++..+..++..++ ...
T Consensus       203 g~~v~lltG~~~~iv~T--pGr~~~il~~T~e~~~--------l~~~v~lvVIDEaH~l~d~~~g~~~~~~l~~l~~~~i  272 (677)
T 3rc3_A          203 GVPCDLVTGEERVTVQP--NGKQASHVSCTVEMCS--------VTTPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEV  272 (677)
T ss_dssp             TCCEEEECSSCEECCST--TCCCCSEEEEEGGGCC--------SSSCEEEEEECSGGGGGCTTTHHHHHHHHHHCCEEEE
T ss_pred             CCcEEEEECCeeEEecC--CCcccceeEecHhHhh--------hcccCCEEEEecceecCCccchHHHHHHHHccCccce
Confidence            78888999986651100  0112678888875443        246779999999999999899999999988887 678


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecccccHHHHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIH  170 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~  170 (197)
                      |++++|||. +.+....... .....+...... .+  ..   + ..  ..    +..+....+..+|||+|++.++.++
T Consensus       273 ~il~~SAT~-~~i~~l~~~~-~~~~~v~~~~r~-~~--l~---~-~~--~~----l~~l~~~~~g~iIf~~s~~~ie~la  337 (677)
T 3rc3_A          273 HLCGEPAAI-DLVMELMYTT-GEEVEVRDYKRL-TP--IS---V-LD--HA----LESLDNLRPGDCIVCFSKNDIYSVS  337 (677)
T ss_dssp             EEEECGGGH-HHHHHHHHHH-TCCEEEEECCCS-SC--EE---E-CS--SC----CCSGGGCCTTEEEECSSHHHHHHHH
T ss_pred             EEEeccchH-HHHHHHHHhc-CCceEEEEeeec-ch--HH---H-HH--HH----HHHHHhcCCCCEEEEcCHHHHHHHH
Confidence            999999995 3344444443 333333221111 00  00   0 00  00    0122333456799999999999999


Q ss_pred             HHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         171 EYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       171 ~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +.|.+.|+.+..+||+|++++|++++
T Consensus       338 ~~L~~~g~~v~~lHG~L~~~~R~~~~  363 (677)
T 3rc3_A          338 RQIEIRGLESAVIYGSLPPGTKLAQA  363 (677)
T ss_dssp             HHHHHTTCCCEEECTTSCHHHHHHHH
T ss_pred             HHHHhcCCCeeeeeccCCHHHHHHHH
Confidence            99999999999999999999999875

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=99.52  E-value=1.4e-15  Score=125.68  Aligned_cols=163  Identities=17%  Similarity=0.092  Sum_probs=108.3

Q ss_pred             Cee-EEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          12 PLR-TCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        12 ~i~-~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      |++ +..++|+...         .++|+|+||+.+...+..   ..++++++|+||||.+.+.++..    +.+.+ +..
T Consensus       157 ~~~~v~~~~g~~~~---------~~~Ivv~T~~~l~~~~~~---~~~~~~liIvDEaH~~~~~~~~~----~~~~~-~~~  219 (472)
T 2fwr_A          157 GEEYVGEFSGRIKE---------LKPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPAESYVQ----IAQMS-IAP  219 (472)
T ss_dssp             CGGGEEEBSSSCBC---------CCSEEEEEHHHHHHTHHH---HTTTCSEEEEETGGGTTSTTTHH----HHHTC-CCS
T ss_pred             CCcceEEECCCcCC---------cCCEEEEEcHHHHHHHHH---hcCCCCEEEEECCcCCCChHHHH----HHHhc-CCC
Confidence            677 7778777643         489999999998876642   12568999999999998877764    44455 468


Q ss_pred             eEEEEeecCCh-------------------hHHHHHHHhcCCCeE--EEeCCCCc------------------------c
Q psy7789          91 QTLLFSATMPK-------------------KIQNFARSALVKPIT--INVGRAGA------------------------A  125 (197)
Q Consensus        91 q~i~~SAT~~~-------------------~~~~~~~~~~~~~~~--i~~~~~~~------------------------~  125 (197)
                      +++++|||...                   ...+....++.++..  +.+.....                        .
T Consensus       220 ~~l~lSATp~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  299 (472)
T 2fwr_A          220 FRLGLTATFEREDGRHEILKEVVGGKVFELFPDSLAGKHLAKYTIKRIFVPLAEDERVEYEKREKVYKQFLRARGITLRR  299 (472)
T ss_dssp             EEEEEESCCCCTTSGGGSHHHHTCCEEEECCHHHHTSCCCCSEEECCEEECCCHHHHHHTTTTTHHHHSCSSSCCCTTTC
T ss_pred             eEEEEecCccCCCCHHHHHHHHhCCeEeecCHHHHhcCcCCCeEEEEEEcCCCHHHHHHHHHHHHHHHHHHHhcCccccc
Confidence            89999999862                   223332223333222  11110000                        0


Q ss_pred             CcceeEE---------------------EEEcCchhhHHHHHHHhhcC-CCCEEEEecccccHHHHHHHHHhCCCCeEee
Q psy7789         126 SMNVVQE---------------------VEYVKQEAKIVYLLECLQKT-EPPVLIFAEKKQDVDAIHEYLLLKGKPFFTL  183 (197)
Q Consensus       126 ~~~i~~~---------------------~~~~~~~~k~~~l~~~l~~~-~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~  183 (197)
                      .....+.                     ...+....|...+.++++.. +.++||||++.+.++.+++.|.     +..+
T Consensus       300 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~k~lvF~~~~~~~~~l~~~l~-----~~~~  374 (472)
T 2fwr_A          300 AEDFNKIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKDKIIIFTRHNELVYRISKVFL-----IPAI  374 (472)
T ss_dssp             CSSSTTTTTTTCCSSSSSTTTHHHHHHHHHHHSCSHHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHTT-----CCBC
T ss_pred             hhhHHHHHHHhccCHHHHHHHHHHHHHHHHhhcChHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHHHhC-----ccee
Confidence            0000000                     00123456778888888775 4689999999999999999884     6689


Q ss_pred             cCCCChhhhhhhh
Q psy7789         184 KSLKEDQNNQTLE  196 (197)
Q Consensus       184 h~~~~~~~R~~i~  196 (197)
                      ||++++++|++++
T Consensus       375 ~g~~~~~~R~~~~  387 (472)
T 2fwr_A          375 THRTSREEREEIL  387 (472)
T ss_dssp             CSSSCSHHHHTHH
T ss_pred             eCCCCHHHHHHHH
Confidence            9999999999875

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.50  E-value=2.5e-15  Score=128.92  Aligned_cols=120  Identities=17%  Similarity=0.154  Sum_probs=77.1

Q ss_pred             cCCCccEEEeehhhhhhcCCCHHHHHHHHhhcc-CCceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEE
Q psy7789          55 SLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFR-GQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEV  133 (197)
Q Consensus        55 ~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~-~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~  133 (197)
                      .++++++||+||||++ +..+...+..+....+ ...|+++||||+++.+..+...  +.+              +....
T Consensus       329 ~l~~l~lvViDEaH~~-~~~~~~~~~~l~~~~~~~~~~vl~~SAT~~~~i~~~~~~--~~~--------------i~~v~  391 (673)
T 2wv9_A          329 RVPNYNLFVMDEAHFT-DPASIAARGYIATRVEAGEAAAIFMTATPPGTSDPFPDT--NSP--------------VHDVS  391 (673)
T ss_dssp             CCCCCSEEEEESTTCC-CHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCCC--SSC--------------EEEEE
T ss_pred             ccccceEEEEeCCccc-CccHHHHHHHHHHhccccCCcEEEEcCCCChhhhhhccc--CCc--------------eEEEe
Confidence            5789999999999998 2212233333434443 6789999999998663321110  111              11111


Q ss_pred             EEcCchhhHHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         134 EYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       134 ~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      ...... +...++..+.+..+++||||++++.|+.+++.|++.|+++..+||+    +|++++
T Consensus       392 ~~~~~~-~~~~~l~~l~~~~~~~lVF~~s~~~~e~la~~L~~~g~~v~~lHg~----eR~~v~  449 (673)
T 2wv9_A          392 SEIPDR-AWSSGFEWITDYAGKTVWFVASVKMSNEIAQCLQRAGKRVIQLNRK----SYDTEY  449 (673)
T ss_dssp             CCCCSS-CCSSCCHHHHSCCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECSS----SHHHHG
T ss_pred             eecCHH-HHHHHHHHHHhCCCCEEEEECCHHHHHHHHHHHHhCCCeEEEeChH----HHHHHH
Confidence            111111 1112233444566799999999999999999999999999999994    666654

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.47  E-value=5.8e-14  Score=119.14  Aligned_cols=161  Identities=15%  Similarity=0.118  Sum_probs=87.2

Q ss_pred             cCCcEEEeCchHHHHHHhc----CCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEeecCChhHHHHHH
Q psy7789          33 KGCHMMVATPGRLMDMLDK----KMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFAR  108 (197)
Q Consensus        33 ~~~~Ili~TP~~l~~~l~~----~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SAT~~~~~~~~~~  108 (197)
                      .+++|+|+||++|......    ..+...++++||+||||++...+ ...+..+++.++ ..+++++|||..........
T Consensus       273 ~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~~-~~~~~~il~~~~-~~~~l~lTATP~~~~~~~~~  350 (590)
T 3h1t_A          273 KSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARD-NSNWREILEYFE-PAFQIGMTATPLREDNRDTY  350 (590)
T ss_dssp             SSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC----------CHHHHHHST-TSEEEEEESSCSCTTTHHHH
T ss_pred             CCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccccc-hHHHHHHHHhCC-cceEEEeccccccccchhHH
Confidence            4589999999999987642    34456789999999999986532 345667777775 57899999997643222222


Q ss_pred             HhcCCCe------------------EEEeCCCCcc-------------CcceeEEEEEcCc-------hhhHH----HHH
Q psy7789         109 SALVKPI------------------TINVGRAGAA-------------SMNVVQEVEYVKQ-------EAKIV----YLL  146 (197)
Q Consensus       109 ~~~~~~~------------------~i~~~~~~~~-------------~~~i~~~~~~~~~-------~~k~~----~l~  146 (197)
                      .++.++.                  ...+......             ...+....+....       ..+..    .+.
T Consensus       351 ~~f~~~~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~i~~~l~  430 (590)
T 3h1t_A          351 RYFGNPIYTYSLRQGIDDGFLAPYRVHRVISEVDAAGWRPSKGDVDRFGREIPDGEYQTKDFERVIALKARTDAFAKHLT  430 (590)
T ss_dssp             HHSCSCSEEECHHHHHHHTSSCCEEEEEEEETTCC-----------------------CCSHHHHHHHHHTHHHHHHHHH
T ss_pred             HHcCCceEecCHHHHhhCCccCCcEEEEeeeeeeccccccccccccccccccccccCCHHHhhhHhcChHHHHHHHHHHH
Confidence            3333221                  1111100000             0000000000000       11222    233


Q ss_pred             HHhhcC--CCCEEEEecccccHHHHHHHHHhCCC--------CeEeecCCCChhhhhhhh
Q psy7789         147 ECLQKT--EPPVLIFAEKKQDVDAIHEYLLLKGK--------PFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       147 ~~l~~~--~~~~lIF~~s~~~~~~l~~~L~~~~~--------~~~~~h~~~~~~~R~~i~  196 (197)
                      +.++..  .+++||||++++.|+.+++.|.+.+.        .+..+||++++ +|++++
T Consensus       431 ~~l~~~~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~~-~r~~~l  489 (590)
T 3h1t_A          431 DFMKRTDRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEGK-IGKGHL  489 (590)
T ss_dssp             HHHHHHCTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTHH-HHHHHH
T ss_pred             HHHHhcCCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCChH-HHHHHH
Confidence            334432  36899999999999999999987543        37789999875 576654

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.44  E-value=2e-13  Score=99.93  Aligned_cols=89  Identities=55%  Similarity=0.796  Sum_probs=67.1

Q ss_pred             HHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCC
Q psy7789         108 RSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLK  187 (197)
Q Consensus       108 ~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~  187 (197)
                      ..++.+|..+.+......+.++.|.++.+.+++|...|.+++...++++||||+++..++.+++.|+..|+++..+||+|
T Consensus         9 ~~~~~~p~~i~v~~~~~~~~~i~q~~~~~~~~~K~~~L~~~l~~~~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~   88 (191)
T 2p6n_A            9 SGVDLGTENLYFQSMGAASLDVIQEVEYVKEEAKMVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGK   88 (191)
T ss_dssp             -------------------CCSEEEEEECCGGGHHHHHHHHHTTSCSCEEEECSCHHHHHHHHHHHHHHTCCEEEECTTS
T ss_pred             ccccCCCEEEEECCCCCCCcCceEEEEEcChHHHHHHHHHHHHhCCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCC
Confidence            46788999999887777888999999999999999999999998888999999999999999999999999999999999


Q ss_pred             Chhhhhhhh
Q psy7789         188 EDQNNQTLE  196 (197)
Q Consensus       188 ~~~~R~~i~  196 (197)
                      ++++|++++
T Consensus        89 ~~~~R~~~l   97 (191)
T 2p6n_A           89 DQEERTKAI   97 (191)
T ss_dssp             CHHHHHHHH
T ss_pred             CHHHHHHHH
Confidence            999999875

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B*

Probab=99.44  E-value=1.4e-13  Score=118.14  Aligned_cols=142  Identities=17%  Similarity=0.168  Sum_probs=90.4

Q ss_pred             eCchHHHHHHhcCCccCCCccEEEeehhhhhhcC--CCHHH----HHHHHh------------------hccCCceEEEE
Q psy7789          40 ATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDM--GFEED----VRTIFS------------------FFRGQRQTLLF   95 (197)
Q Consensus        40 ~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~--~~~~~----i~~i~~------------------~~~~~~q~i~~   95 (197)
                      +||++|++++.+..       ++|+||+|++++.  ++...    ......                  ..+...|++++
T Consensus       320 ~tpg~LlDyl~~~~-------llVlDEa~~~l~~~~~~~~~~~~~~~~l~~~G~~lp~~l~~~~l~~~e~~~~~~q~i~~  392 (661)
T 2d7d_A          320 STPYTLLDYFPDDF-------MIVVDESHVTIPQVRGMFNGDQARKQVLVDHGFRLPSALDNRPLRFEEFEKHMHNIVYV  392 (661)
T ss_dssp             CCCBCGGGGSCSSC-------EEEEETHHHHHHHHHHHHHHHHHHHHHHHHTTSSCGGGGGSCCCCHHHHHHTCSEEEEE
T ss_pred             CCccHHHHHcccCc-------EEEEecHHHHHHHHHHHHHHHHHHHHHHHHccccchhhhhcccccHHHHhccCCCEEEE
Confidence            89999999975433       8999999997631  11111    111111                  11246799999


Q ss_pred             eecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhc---CCCCEEEEecccccHHHHHHH
Q psy7789          96 SATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQDVDAIHEY  172 (197)
Q Consensus        96 SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~~  172 (197)
                      |||.++.....    ........+.......+.    +...+...+...++..+..   .+.++||||+|++.|+.+++.
T Consensus       393 SAT~~~~~~~~----~~~~~~~~~r~~~l~~p~----i~v~~~~~~~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~~  464 (661)
T 2d7d_A          393 SATPGPYEIEH----TDEMVEQIIRPTGLLDPL----IDVRPIEGQIDDLIGEIQARIERNERVLVTTLTKKMSEDLTDY  464 (661)
T ss_dssp             CSSCCHHHHHH----CSSCEEECCCTTCCCCCE----EEEECSTTHHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHH
T ss_pred             ecCCChhHHHh----hhCeeeeeecccCCCCCe----EEEecccchHHHHHHHHHHHHhcCCeEEEEECCHHHHHHHHHH
Confidence            99997654222    122222212211111111    1112333455555555543   346899999999999999999


Q ss_pred             HHhCCCCeEeecCCCChhhhhhhh
Q psy7789         173 LLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       173 L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      |++.|+++..+||+|++.+|.+++
T Consensus       465 L~~~gi~~~~lh~~~~~~~R~~~l  488 (661)
T 2d7d_A          465 LKEIGIKVNYLHSEIKTLERIEII  488 (661)
T ss_dssp             HHHTTCCEEEECTTCCHHHHHHHH
T ss_pred             HHhcCCCeEEEeCCCCHHHHHHHH
Confidence            999999999999999999999875

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A

Probab=99.43  E-value=3.7e-14  Score=117.06  Aligned_cols=128  Identities=17%  Similarity=0.136  Sum_probs=79.7

Q ss_pred             cEEEeCchHHHHHHhcCCccCCCccEEEeehhhhh-----hcCCCHHHHHHHHhhccCCceEEEEeecCChhHHHHHHHh
Q psy7789          36 HMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRM-----VDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSA  110 (197)
Q Consensus        36 ~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l-----~~~~~~~~i~~i~~~~~~~~q~i~~SAT~~~~~~~~~~~~  110 (197)
                      -+.++|.+.+...+... ..++++++||+||||.+     +..++.....     .+++.|+++||||+++.+..+... 
T Consensus        91 ~i~~~~~~~l~~~l~~~-~~l~~~~~iViDEaH~~~~~~~~~~~~~~~~~-----~~~~~~~il~SAT~~~~~~~~~~~-  163 (459)
T 2z83_A           91 IVDVMCHATLTHRLMSP-NRVPNYNLFVMDEAHFTDPASIAARGYIATKV-----ELGEAAAIFMTATPPGTTDPFPDS-  163 (459)
T ss_dssp             SEEEEEHHHHHHHHHSC-C-CCCCSEEEESSTTCCSHHHHHHHHHHHHHH-----HTTSCEEEEECSSCTTCCCSSCCC-
T ss_pred             EEEEEchHHHHHHhhcc-ccccCCcEEEEECCccCCchhhHHHHHHHHHh-----ccCCccEEEEEcCCCcchhhhccC-
Confidence            34556666555544432 35789999999999984     2222222111     136889999999998654322111 


Q ss_pred             cCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCC
Q psy7789         111 LVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSL  186 (197)
Q Consensus       111 ~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~  186 (197)
                       ..|+.....              ..+ ..+...+.+.+....+++||||+|++.|+.+++.|++.|+++..+||+
T Consensus       164 -~~pi~~~~~--------------~~~-~~~~~~~~~~l~~~~~~~LVF~~s~~~~~~l~~~L~~~g~~v~~lh~~  223 (459)
T 2z83_A          164 -NAPIHDLQD--------------EIP-DRAWSSGYEWITEYAGKTVWFVASVKMGNEIAMCLQRAGKKVIQLNRK  223 (459)
T ss_dssp             -SSCEEEEEC--------------CCC-SSCCSSCCHHHHHCCSCEEEECSCHHHHHHHHHHHHHTTCCEEEESTT
T ss_pred             -CCCeEEecc--------------cCC-cchhHHHHHHHHhcCCCEEEEeCChHHHHHHHHHHHhcCCcEEecCHH
Confidence             223222111              001 111111233445557899999999999999999999999999999995

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*

Probab=99.38  E-value=1.2e-12  Score=112.42  Aligned_cols=140  Identities=19%  Similarity=0.175  Sum_probs=89.4

Q ss_pred             eCchHHHHHHhcCCccCCCccEEEeehhhhhhcC--CCHHH----HHHHHh------------------hccCCceEEEE
Q psy7789          40 ATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDM--GFEED----VRTIFS------------------FFRGQRQTLLF   95 (197)
Q Consensus        40 ~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~--~~~~~----i~~i~~------------------~~~~~~q~i~~   95 (197)
                      +||++|++++.+.       .+||+||+|++.+.  ++...    ......                  ..+...|++++
T Consensus       314 ~tp~~LlDyl~~~-------~llVlDEah~~~~~~~~~~~~~~~~~~~l~~~G~~lp~~l~~~~l~~~e~~~~~~q~i~~  386 (664)
T 1c4o_A          314 EPPYTLLDYFPED-------FLVFLDESHVTVPQLQGMYRGDYARKKTLVDYGFRLPSALDNRPLRFEEFLERVSQVVFV  386 (664)
T ss_dssp             SCCCCGGGGSCTT-------CEEEEETHHHHHHHHHHHHHHHHHHHHHHHHTTSSCGGGGGSSCCCHHHHHHTCSEEEEE
T ss_pred             CCchHHHHHHhhc-------cEEEEecccccHHHHHHHHHHHHHHHHHHHHccccchhhhhcCcccHHHHHhhcCCEEEE
Confidence            8999999987533       28999999997631  01111    111111                  11246799999


Q ss_pred             eecCChhHHHHHHHhcCCCeEEEeC--CCCccCcceeEEEEEcCchhhHHHHHHHhhc---CCCCEEEEecccccHHHHH
Q psy7789          96 SATMPKKIQNFARSALVKPITINVG--RAGAASMNVVQEVEYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQDVDAIH  170 (197)
Q Consensus        96 SAT~~~~~~~~~~~~~~~~~~i~~~--~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~  170 (197)
                      |||.++.....    ..  ..+...  ......+.    +...+...+...++..+..   .+.++||||+|++.++.++
T Consensus       387 SAT~~~~~~~~----~~--~~~~~~~r~~~l~~p~----i~v~~~~~~~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~  456 (664)
T 1c4o_A          387 SATPGPFELAH----SG--RVVEQIIRPTGLLDPL----VRVKPTENQILDLMEGIRERAARGERTLVTVLTVRMAEELT  456 (664)
T ss_dssp             ESSCCHHHHHH----CS--EEEEECSCTTCCCCCE----EEEECSTTHHHHHHHHHHHHHHTTCEEEEECSSHHHHHHHH
T ss_pred             ecCCCHHHHHh----hh--CeeeeeeccCCCCCCe----EEEecccchHHHHHHHHHHHHhcCCEEEEEECCHHHHHHHH
Confidence            99998653221    11  112221  11111111    1112333455555555543   3568999999999999999


Q ss_pred             HHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         171 EYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       171 ~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +.|.+.|+++..+||+|++.+|.+++
T Consensus       457 ~~L~~~gi~~~~lh~~~~~~~R~~~~  482 (664)
T 1c4o_A          457 SFLVEHGIRARYLHHELDAFKRQALI  482 (664)
T ss_dssp             HHHHHTTCCEEEECTTCCHHHHHHHH
T ss_pred             HHHHhcCCCceeecCCCCHHHHHHHH
Confidence            99999999999999999999999875

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=99.38  E-value=3e-12  Score=106.45  Aligned_cols=57  Identities=11%  Similarity=0.115  Sum_probs=47.7

Q ss_pred             hhHHHHHHHhhc---CCCCEEEEecccccHHHHHHHHHhC-CCCeEeecCCCChhhhhhhh
Q psy7789         140 AKIVYLLECLQK---TEPPVLIFAEKKQDVDAIHEYLLLK-GKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       140 ~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~~L~~~-~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .|...+.+++.+   .+.++||||++...++.+++.|... |+++..+||+|++++|++++
T Consensus       325 ~K~~~l~~~l~~~~~~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~  385 (500)
T 1z63_A          325 GKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDII  385 (500)
T ss_dssp             HHHHHHHHHHHHHHTTTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHccCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHH
Confidence            355555666654   3569999999999999999999986 99999999999999999875

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=99.32  E-value=1.7e-12  Score=97.89  Aligned_cols=76  Identities=20%  Similarity=0.312  Sum_probs=58.8

Q ss_pred             cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhh-hcCCCH-HHHHHHHhhccCCceEEEEeecCChhHHHHHHHh
Q psy7789          33 KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRM-VDMGFE-EDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSA  110 (197)
Q Consensus        33 ~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l-~~~~~~-~~i~~i~~~~~~~~q~i~~SAT~~~~~~~~~~~~  110 (197)
                      .+++|+|+||+++.+.+..   .+++++++|+||||.+ ++.++. ..++.++... ++.|++++|||++.+.  +.+.+
T Consensus       154 ~~~~Ivv~Tpg~l~~~l~~---~l~~~~~lVlDEah~~~~~~~~~~~~l~~i~~~~-~~~~~il~SAT~~~~~--~~~~~  227 (235)
T 3llm_A          154 PHASIMFCTVGVLLRKLEA---GIRGISHVIVDEIHERDINTDFLLVVLRDVVQAY-PEVRIVLMSATIDTSM--FCEYF  227 (235)
T ss_dssp             SSSEEEEEEHHHHHHHHHH---CCTTCCEEEECCTTSCCHHHHHHHHHHHHHHHHC-TTSEEEEEECSSCCHH--HHHHT
T ss_pred             CCCeEEEECHHHHHHHHHh---hhcCCcEEEEECCccCCcchHHHHHHHHHHHhhC-CCCeEEEEecCCCHHH--HHHHc
Confidence            3488999999999999875   4899999999999985 555555 4566666665 4789999999999776  44444


Q ss_pred             cCCC
Q psy7789         111 LVKP  114 (197)
Q Consensus       111 ~~~~  114 (197)
                      ..+|
T Consensus       228 ~~~p  231 (235)
T 3llm_A          228 FNCP  231 (235)
T ss_dssp             TSCC
T ss_pred             CCCC
Confidence            4444

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=99.30  E-value=2.1e-12  Score=95.56  Aligned_cols=88  Identities=18%  Similarity=0.166  Sum_probs=57.9

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCC------ccCCCccEEEeehhhhhhcCCCHHHH-HHHH
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKM------VSLDVCRYLCLDEADRMVDMGFEEDV-RTIF   83 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~------~~l~~l~~vViDEad~l~~~~~~~~i-~~i~   83 (197)
                      .++++..++|+.....+...+..+++|+|+||+++...+....      ..+.+++++|+||||++.+.++...+ ..++
T Consensus       109 ~~~~v~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~~~~~~  188 (216)
T 3b6e_A          109 KWYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYL  188 (216)
T ss_dssp             TTSCEEECCC---CCCCHHHHHHHCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC-------CHHHHHHHHH
T ss_pred             cCceEEEEeCCcccchhHHhhccCCCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchhhccCCcHHHHHHHHH
Confidence            3688888999887666665565679999999999999887643      56789999999999999876655544 3332


Q ss_pred             hhc-------------cCCceEEEEeec
Q psy7789          84 SFF-------------RGQRQTLLFSAT   98 (197)
Q Consensus        84 ~~~-------------~~~~q~i~~SAT   98 (197)
                      ...             .+.++++++|||
T Consensus       189 ~~~~~~~~~~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          189 MQKLKNNRLKKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             HHHHHHHHHHHTTCCCCCCCEEEEEECC
T ss_pred             HHhcccccccccccCCCCcceEEEeecC
Confidence            221             157899999998

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}

Probab=99.24  E-value=8.8e-12  Score=111.17  Aligned_cols=59  Identities=12%  Similarity=0.131  Sum_probs=52.4

Q ss_pred             chhhHHHHHHHhhcC-CCCEEEEecccccHHHHHHHHHh-CCCCeEeecCCCChhhhhhhh
Q psy7789         138 QEAKIVYLLECLQKT-EPPVLIFAEKKQDVDAIHEYLLL-KGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       138 ~~~k~~~l~~~l~~~-~~~~lIF~~s~~~~~~l~~~L~~-~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      ...|...+.++++.. +.++||||+++..++.+++.|.+ .|+++..+||+|++++|++++
T Consensus       487 ~~~K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~~~~~~R~~~l  547 (968)
T 3dmq_A          487 FDPRVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDRAA  547 (968)
T ss_dssp             TSHHHHHHHHHHHHTSSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTTSCTTHHHHHH
T ss_pred             ccHHHHHHHHHHHhCCCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHH
Confidence            345888899999865 46999999999999999999995 599999999999999999876

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=99.20  E-value=5e-11  Score=84.88  Aligned_cols=73  Identities=19%  Similarity=0.245  Sum_probs=66.2

Q ss_pred             ccCcceeEEEEEcCchhhHHHHHHHhhcCC-CCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         124 AASMNVVQEVEYVKQEAKIVYLLECLQKTE-PPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       124 ~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      ..+.++.|.++.++.++|...|.++++..+ +++||||++++.++.+++.|.+.|+++..+||+|++++|++++
T Consensus         5 ~~~~~i~~~~~~~~~~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~   78 (163)
T 2hjv_A            5 LTTRNIEHAVIQVREENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVM   78 (163)
T ss_dssp             -CCCCEEEEEEECCGGGHHHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHH
T ss_pred             cCcccceEEEEECChHHHHHHHHHHHHhcCCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHH
Confidence            455679999999999999999999998654 5899999999999999999999999999999999999999875

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19

Probab=99.19  E-value=6.2e-11  Score=85.17  Aligned_cols=71  Identities=18%  Similarity=0.151  Sum_probs=64.6

Q ss_pred             CcceeEEEEEcCchhhHHHHHHHhhcCC-CCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         126 SMNVVQEVEYVKQEAKIVYLLECLQKTE-PPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       126 ~~~i~~~~~~~~~~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +..+.|+++.+..++|...|.++++... +++||||+++..++.+++.|...|+++..+||+|++++|++++
T Consensus         3 ~~~i~q~~~~~~~~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~   74 (172)
T 1t5i_A            3 LHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRY   74 (172)
T ss_dssp             --CCEEEEEECCGGGHHHHHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHH
T ss_pred             cCCeEEEEEECChHHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHH
Confidence            4678999999999999999999998764 5899999999999999999999999999999999999999875

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens}

Probab=99.18  E-value=5.5e-11  Score=86.50  Aligned_cols=76  Identities=24%  Similarity=0.443  Sum_probs=59.2

Q ss_pred             CCCccCcceeEEEEEcCchhhHHHHHHHhhcC--CCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         121 RAGAASMNVVQEVEYVKQEAKIVYLLECLQKT--EPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       121 ~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~--~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .....++++.|.++.++..+|...|.++++..  ++++||||++++.++.+++.|+..|+++..+||+|++++|++++
T Consensus        12 ~~~~~~~~i~q~~~~v~~~~K~~~L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~   89 (185)
T 2jgn_A           12 FQGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEAL   89 (185)
T ss_dssp             ----CCTTEEEEEEECCGGGHHHHHHHHHHHC-CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHH
T ss_pred             ccCCCCCCceEEEEEeCcHHHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHH
Confidence            34456788999999999999999999999876  46899999999999999999999999999999999999998875

>2w00_A HSDR, R.ECOR124I; ATP-binding, DNA-binding, restriction system, helicase, HYDR R.ECOR124I, nucleotide-binding; HET: ATP; 2.6A {Escherichia coli} PDB: 2y3t_A* 2w74_B*

Probab=99.17  E-value=1e-10  Score=104.49  Aligned_cols=78  Identities=14%  Similarity=0.127  Sum_probs=57.7

Q ss_pred             cCCChHHhHHHHh-cCCcEEEeCchHHHHHHhcCC--ccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEe
Q psy7789          20 GGVPMNQSLDVIK-KGCHMMVATPGRLMDMLDKKM--VSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFS   96 (197)
Q Consensus        20 gg~~~~~~~~~l~-~~~~Ili~TP~~l~~~l~~~~--~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~S   96 (197)
                      |+.+.....+.+. .+++|+|+||+++...+....  ..++...+||+||||++..   ......+.+.+| ++++++||
T Consensus       360 ~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~~~~~~lvIiDEAHrs~~---~~~~~~I~~~~p-~a~~lgfT  435 (1038)
T 2w00_A          360 GSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQF---GEAQKNLKKKFK-RYYQFGFT  435 (1038)
T ss_dssp             SSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGGGGSCEEEEEESCCTTHH---HHHHHHHHHHCS-SEEEEEEE
T ss_pred             cccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccchhccccccEEEEEccchhcc---hHHHHHHHHhCC-cccEEEEe
Confidence            4445555556664 469999999999999876432  2456788999999999753   344567777775 58999999


Q ss_pred             ecCCh
Q psy7789          97 ATMPK  101 (197)
Q Consensus        97 AT~~~  101 (197)
                      ||...
T Consensus       436 ATP~~  440 (1038)
T 2w00_A          436 GTPIF  440 (1038)
T ss_dssp             SSCCC
T ss_pred             CCccc
Confidence            99753

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}

Probab=99.17  E-value=9.4e-11  Score=84.37  Aligned_cols=72  Identities=11%  Similarity=0.113  Sum_probs=65.4

Q ss_pred             cCcceeEEEEEcCchh-hHHHHHHHhhcCC-CCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         125 ASMNVVQEVEYVKQEA-KIVYLLECLQKTE-PPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       125 ~~~~i~~~~~~~~~~~-k~~~l~~~l~~~~-~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .+.++.|+++.++..+ |...|.++++..+ +++||||++++.|+.+++.|...|+++..+||+|++++|++++
T Consensus         4 ~~~~i~q~~~~~~~~~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~   77 (175)
T 2rb4_A            4 TLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASII   77 (175)
T ss_dssp             CBCCEEEEEEECSSHHHHHHHHHHHHTTSCCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHH
T ss_pred             ccCCceEEEEEcCChHhHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHH
Confidence            4578999999998765 9999999998764 5899999999999999999999999999999999999999875

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.16  E-value=2.4e-09  Score=93.14  Aligned_cols=82  Identities=13%  Similarity=0.156  Sum_probs=57.3

Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcC---CCCEEEEecccccHH
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKT---EPPVLIFAEKKQDVD  167 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~---~~~~lIF~~s~~~~~  167 (197)
                      .+.+||.|...+..++.+.|.-+  .+.++........-..-.++....+|...+.+-+.+.   +.|+||+|.|++.++
T Consensus       380 kLsGMTGTA~tE~~Ef~~iY~l~--Vv~IPTn~p~~R~D~~d~vy~t~~~K~~AIv~eI~~~~~~GqPVLVgT~SIe~SE  457 (997)
T 2ipc_A          380 KRAGMTGTAKTEEKEFQEIYGMD--VVVVPTNRPVIRKDFPDVVYRTEKGKFYAVVEEIAEKYERGQPVLVGTISIEKSE  457 (997)
T ss_dssp             EEEEEESSCGGGHHHHHHHHCCC--EEECCCSSCCCCEEEEEEEESSHHHHHHHHHHHHHHHHHHTCCEEEECSSHHHHH
T ss_pred             HheecCCCchHHHHHHHHHhCCC--EEEcCCCCCcccccCCCeEEcCHHHHHHHHHHHHHHHHHCCCCEEEEeCCHHHHH
Confidence            45678888877777777777555  3444433222222223345677888988888777643   568999999999999


Q ss_pred             HHHHHHH
Q psy7789         168 AIHEYLL  174 (197)
Q Consensus       168 ~l~~~L~  174 (197)
                      .+++.|+
T Consensus       458 ~LS~~L~  464 (997)
T 2ipc_A          458 RLSQMLK  464 (997)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            9999999

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.15  E-value=4.4e-10  Score=98.54  Aligned_cols=56  Identities=27%  Similarity=0.370  Sum_probs=48.3

Q ss_pred             hHHHHHHHhhc---CCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         141 KIVYLLECLQK---TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       141 k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      |...+.+++..   .+.++||||+....++.+...|...|+++..+||+++.++|++++
T Consensus       557 K~~~L~~lL~~~~~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i  615 (800)
T 3mwy_W          557 KMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISI  615 (800)
T ss_dssp             HHHHHHHHHHHHTTTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHH
Confidence            55556666654   356999999999999999999999999999999999999999875

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=99.12  E-value=1.7e-10  Score=82.18  Aligned_cols=70  Identities=17%  Similarity=0.146  Sum_probs=62.5

Q ss_pred             cceeEEEEEcCchh-hHHHHHHHhhcC-CCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         127 MNVVQEVEYVKQEA-KIVYLLECLQKT-EPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       127 ~~i~~~~~~~~~~~-k~~~l~~~l~~~-~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .++.|+++.+.+++ |...|.++++.. .+++||||++++.++.+++.|++.|+.+..+||+|++++|++++
T Consensus         2 ~~i~~~~~~~~~~~~K~~~l~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~   73 (165)
T 1fuk_A            2 EGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIM   73 (165)
T ss_dssp             --CEEEEEEEESGGGHHHHHHHHHHHTTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHH
T ss_pred             CCcEEEEEECCcchhHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHH
Confidence            46888999888777 999999999875 46899999999999999999999999999999999999999875

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19

Probab=99.08  E-value=1.5e-09  Score=93.03  Aligned_cols=44  Identities=9%  Similarity=0.117  Sum_probs=41.5

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +.++||||+....++.+...|...|+++..+||+|++++|+++.
T Consensus       416 ~~k~lIFs~~~~~~~~l~~~l~~~g~~~~~l~G~~~~~~R~~~i  459 (644)
T 1z3i_X          416 SDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIV  459 (644)
T ss_dssp             CCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHH
T ss_pred             CCEEEEEEccHHHHHHHHHHHHHCCCCEEEEeCCCCHHHHHHHH
Confidence            56899999999999999999999999999999999999999875

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli}

Probab=98.40  E-value=1.9e-10  Score=82.44  Aligned_cols=71  Identities=17%  Similarity=0.189  Sum_probs=63.5

Q ss_pred             cceeEEEEEcCc-hhhHHHHHHHhhcCC-CCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         127 MNVVQEVEYVKQ-EAKIVYLLECLQKTE-PPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       127 ~~i~~~~~~~~~-~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      +++.|.++.++. +.|...|.++++..+ +++||||++++.++.+++.|+..|+.+..+||+|++++|+++++
T Consensus         2 ~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~   74 (170)
T 2yjt_D            2 KKIHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIK   74 (170)
Confidence            457788888887 889999999998754 58999999999999999999999999999999999999998753

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=98.88  E-value=1.1e-09  Score=84.58  Aligned_cols=81  Identities=12%  Similarity=0.058  Sum_probs=61.2

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCce
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQ   91 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q   91 (197)
                      ++++..++||.....   ....+++|+|+||+++...   ....+++++++|+||||++.    ...+..++..+++..+
T Consensus       185 ~~~~~~~~~~~~~~~---~~~~~~~I~v~T~~~l~~~---~~~~~~~~~~vIiDEaH~~~----~~~~~~il~~~~~~~~  254 (282)
T 1rif_A          185 HAMIKKIGGGASKDD---KYKNDAPVVVGTWQTVVKQ---PKEWFSQFGMMMNDECHLAT----GKSISSIISGLNNCMF  254 (282)
T ss_dssp             GGGEEECSTTCSSTT---CCCTTCSEEEECHHHHTTS---CGGGGGGEEEEEEETGGGCC----HHHHHHHTTTCTTCCE
T ss_pred             cceEEEEeCCCcchh---hhccCCcEEEEchHHHHhh---HHHHHhhCCEEEEECCccCC----cccHHHHHHHhhcCCe
Confidence            466777777765433   1124589999999876443   23456789999999999985    3577888888888999


Q ss_pred             EEEEeecCChh
Q psy7789          92 TLLFSATMPKK  102 (197)
Q Consensus        92 ~i~~SAT~~~~  102 (197)
                      ++++|||.+..
T Consensus       255 ~l~lSATp~~~  265 (282)
T 1rif_A          255 KFGLSGSLRDG  265 (282)
T ss_dssp             EEEECSSCCTT
T ss_pred             EEEEeCCCCCc
Confidence            99999999754

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=98.88  E-value=3.5e-09  Score=82.54  Aligned_cols=68  Identities=16%  Similarity=0.202  Sum_probs=62.9

Q ss_pred             eeEEEEEcCchhhHHHHHHHhhcC-CCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         129 VVQEVEYVKQEAKIVYLLECLQKT-EPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       129 i~~~~~~~~~~~k~~~l~~~l~~~-~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +.++++.+...+|...|.++++.. ++++||||++++.++.+++.|.+.|+.+..+||+|++++|++++
T Consensus         3 v~~~~i~~~~~~K~~~L~~ll~~~~~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~   71 (300)
T 3i32_A            3 YEEEAVPAPVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVM   71 (300)
T ss_dssp             SEEEEEECCSSSHHHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHH
T ss_pred             eEEEEEECCHHHHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHH
Confidence            678888999999999999999864 56999999999999999999999999999999999999999875

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A

Probab=98.86  E-value=3.4e-09  Score=78.60  Aligned_cols=68  Identities=16%  Similarity=0.195  Sum_probs=61.6

Q ss_pred             eeEEEEEcCchhhHHHHHHHhhcC-CCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         129 VVQEVEYVKQEAKIVYLLECLQKT-EPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       129 i~~~~~~~~~~~k~~~l~~~l~~~-~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +.+..+.+....|...|.++++.. ++++||||++++.++.+++.|.+.|+++..+||+|++++|++++
T Consensus         6 ~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~   74 (212)
T 3eaq_A            6 YEEEAVPAPVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVL   74 (212)
T ss_dssp             BCCEEEECCTTSHHHHHHHHHHHHCCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHH
T ss_pred             eeeeEEeCCHHHHHHHHHHHHHhCCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHH
Confidence            456677788899999999999865 46999999999999999999999999999999999999999875

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=98.75  E-value=5e-08  Score=83.54  Aligned_cols=103  Identities=14%  Similarity=0.200  Sum_probs=79.7

Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeE-EEEEcCchhhHHHHHHHhhc---CCCCEEEEeccccc
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQ-EVEYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQD  165 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~-~~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~  165 (197)
                      .++.+||+|+..+..++.+.|..+  .+.++. ......+.+ ..++....+|...+.+.+..   .+.|+||||+|++.
T Consensus       410 ~kL~GMTGTa~te~~Ef~~iY~l~--vv~IPt-nkp~~R~d~~d~vy~t~~eK~~al~~~I~~~~~~gqpVLVFt~S~e~  486 (822)
T 3jux_A          410 EKLAGMTGTAKTEESEFVQVYGME--VVVIPT-HKPMIRKDHDDLVFRTQKEKYEKIVEEIEKRYKKGQPVLVGTTSIEK  486 (822)
T ss_dssp             SEEEEEESSCGGGHHHHHHHSCCC--EEECCC-SSCCCCEECCCEEESSHHHHHHHHHHHHHHHHHHTCCEEEEESSHHH
T ss_pred             hHHeEECCCCchHHHHHHHHhCCe--EEEECC-CCCcceeecCcEEEecHHHHHHHHHHHHHHHhhCCCCEEEEECCHHH
Confidence            368899999998888888777544  444443 332233333 35678889999999998875   35689999999999


Q ss_pred             HHHHHHHHHhCCCCeEeecCCCChhhhhhh
Q psy7789         166 VDAIHEYLLLKGKPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       166 ~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i  195 (197)
                      ++.++..|++.|+++..+||+..+.+|..+
T Consensus       487 sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii  516 (822)
T 3jux_A          487 SELLSSMLKKKGIPHQVLNAKYHEKEAEIV  516 (822)
T ss_dssp             HHHHHHHHHTTTCCCEEECSCHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCEEEeeCCchHHHHHHH
Confidence            999999999999999999999766666543

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=98.45  E-value=1.7e-07  Score=70.59  Aligned_cols=73  Identities=15%  Similarity=0.017  Sum_probs=52.5

Q ss_pred             Cee-EEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          12 PLR-TCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        12 ~i~-~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      |++ +..+.|+...         ..+|+|+||+.+......   ..+++++||+||||.+.+..+.    .++..++ ..
T Consensus       157 ~~~~v~~~~g~~~~---------~~~i~v~T~~~l~~~~~~---~~~~~~llIiDEaH~l~~~~~~----~i~~~~~-~~  219 (237)
T 2fz4_A          157 GEEYVGEFSGRIKE---------LKPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPAESYV----QIAQMSI-AP  219 (237)
T ss_dssp             CGGGEEEESSSCBC---------CCSEEEEEHHHHHHTHHH---HTTTCSEEEEECSSCCCTTTHH----HHHHTCC-CS
T ss_pred             CCCeEEEEeCCCCC---------cCCEEEEeHHHHHhhHHH---hcccCCEEEEECCccCCChHHH----HHHHhcc-CC
Confidence            566 6666665432         479999999998766542   1256899999999999776544    4555554 67


Q ss_pred             eEEEEeecCCh
Q psy7789          91 QTLLFSATMPK  101 (197)
Q Consensus        91 q~i~~SAT~~~  101 (197)
                      +++++|||...
T Consensus       220 ~~l~LSATp~r  230 (237)
T 2fz4_A          220 FRLGLTATFER  230 (237)
T ss_dssp             EEEEEEESCC-
T ss_pred             EEEEEecCCCC
Confidence            89999999863

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=97.97  E-value=8.4e-06  Score=62.51  Aligned_cols=61  Identities=11%  Similarity=0.154  Sum_probs=53.7

Q ss_pred             cCchhhHHHHHHHhhcC---CCCEEEEecccccHHHHHHHHHhC-CCCeEeecCCCChhhhhhhh
Q psy7789         136 VKQEAKIVYLLECLQKT---EPPVLIFAEKKQDVDAIHEYLLLK-GKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       136 ~~~~~k~~~l~~~l~~~---~~~~lIF~~s~~~~~~l~~~L~~~-~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .....|+..|.+++...   +.++||||++...++.+...|.+. |+++..+||++++++|+++.
T Consensus        92 ~~~s~K~~~L~~ll~~~~~~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i  156 (271)
T 1z5z_A           92 VRRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDII  156 (271)
T ss_dssp             STTCHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHH
T ss_pred             cccCHHHHHHHHHHHHHHhCCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHH
Confidence            45567999998888753   569999999999999999999985 99999999999999998875

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=96.75  E-value=0.0014  Score=55.16  Aligned_cols=42  Identities=10%  Similarity=0.025  Sum_probs=32.4

Q ss_pred             HhcCCcEEEeCchHHHHHHhcCCccC-CCccEEEeehhhhhhc
Q psy7789          31 IKKGCHMMVATPGRLMDMLDKKMVSL-DVCRYLCLDEADRMVD   72 (197)
Q Consensus        31 l~~~~~Ili~TP~~l~~~l~~~~~~l-~~l~~vViDEad~l~~   72 (197)
                      ...++||||+|+..|++...+..+.+ .....+||||||.+.+
T Consensus       145 ~~~~adIVV~~~~~l~~~~~~~~~~~~~~~~~vIiDEAHnl~d  187 (551)
T 3crv_A          145 SLYKADVIALTYPYFFIDRYREFIDIDLREYMIVIDEAHNLDK  187 (551)
T ss_dssp             HGGGCSEEEEETHHHHCHHHHTTSCCCSTTEEEEETTGGGGGG
T ss_pred             hhhcCCEEEeCchHhcCHHHHHhcCCCcCCeEEEEecccchHH
Confidence            34569999999999998754443333 4677999999999876

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=95.48  E-value=0.0044  Score=51.90  Aligned_cols=42  Identities=17%  Similarity=0.216  Sum_probs=30.2

Q ss_pred             HHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCC
Q psy7789         143 VYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLK  187 (197)
Q Consensus       143 ~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~  187 (197)
                      ..+.++++..++.+|||++|....+.+++.+..  .. ...+|..
T Consensus       374 ~~l~~~~~~~~g~~lvff~S~~~~~~v~~~l~~--~~-~~~q~~~  415 (540)
T 2vl7_A          374 ILLKRIYENSSKSVLVFFPSYEMLESVRIHLSG--IP-VIEENKK  415 (540)
T ss_dssp             HHHHHHHHTCSSEEEEEESCHHHHHHHHTTCTT--SC-EEESTTT
T ss_pred             HHHHHHHHhCCCCEEEEeCCHHHHHHHHHHhcc--Cc-eEecCCC
Confidence            445555566667899999999999999998865  23 3445543

>3gk5_A Uncharacterized rhodanese-related protein TVG0868615; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Thermoplasma volcanium GSS1}

Probab=93.54  E-value=0.15  Score=32.78  Aligned_cols=37  Identities=11%  Similarity=0.068  Sum_probs=33.3

Q ss_pred             CCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChh
Q psy7789         154 PPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQ  190 (197)
Q Consensus       154 ~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~  190 (197)
                      .++++||.+-.++...+..|++.|+++..+.||+..=
T Consensus        56 ~~ivvyC~~G~rs~~aa~~L~~~G~~v~~l~GG~~~W   92 (108)
T 3gk5_A           56 KKYAVICAHGNRSAAAVEFLSQLGLNIVDVEGGIQSW   92 (108)
T ss_dssp             SCEEEECSSSHHHHHHHHHHHTTTCCEEEETTHHHHH
T ss_pred             CeEEEEcCCCcHHHHHHHHHHHcCCCEEEEcCcHHHH
Confidence            5799999999999999999999999999999987653

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=93.00  E-value=0.15  Score=43.46  Aligned_cols=100  Identities=10%  Similarity=0.086  Sum_probs=54.8

Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeCCCCccCcceeEEEEE--cC------chh----hHHHHHHHhhcCCCCEE
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEY--VK------QEA----KIVYLLECLQKTEPPVL  157 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~--~~------~~~----k~~~l~~~l~~~~~~~l  157 (197)
                      ..+|++|||+++ ...+...+.-+...+.....- ..++.. .++.  .+      ++.    -...+.++++..++.++
T Consensus       376 ~~~il~SaTL~p-~~~~~~~lGl~~~~~~~~spf-~~~~~~-~~~~~~~~~~~~~r~~~~~~~~~~~i~~l~~~~~g~~l  452 (620)
T 4a15_A          376 SKTIHMSGTLDP-FDFYSDITGFEIPFKKIGEIF-PPENRY-IAYYDGVSSKYDTLDEKELDRMATVIEDIILKVKKNTI  452 (620)
T ss_dssp             SEEEEEESSCCS-HHHHHHHHCCCCCEEECCCCS-CGGGEE-EEEECCC-------CHHHHHHHHHHHHHHHHHHCSCEE
T ss_pred             CeEEEEccCCCc-HHHHHHHhCCCceeeecCCCC-CHHHeE-EEEeCCCCCcCCCCCHHHHHHHHHHHHHHHHhCCCCEE
Confidence            457899999986 555555554443333332211 112211 1111  11      111    12344555555678899


Q ss_pred             EEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhh
Q psy7789         158 IFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTL  195 (197)
Q Consensus       158 IF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i  195 (197)
                      ||++|....+.+++.++..+  .. ...+++..+|.++
T Consensus       453 vlF~Sy~~l~~v~~~l~~~~--~~-~~q~~~~~~~~~l  487 (620)
T 4a15_A          453 VYFPSYSLMDRVENRVSFEH--MK-EYRGIDQKELYSM  487 (620)
T ss_dssp             EEESCHHHHHHHTSSCCSCC--EE-CCTTCCSHHHHHH
T ss_pred             EEeCCHHHHHHHHHHHHhcc--hh-ccCCCChhHHHHH
Confidence            99999999999998887222  22 4445555566554

>1wv9_A Rhodanese homolog TT1651; CDC25, phosphatase, sulfurtransferase, structural genomics, NPPSFA; 2.00A {Thermus thermophilus}

Probab=92.78  E-value=0.1  Score=32.56  Aligned_cols=36  Identities=22%  Similarity=0.242  Sum_probs=32.5

Q ss_pred             CCEEEEecccccHHHHHHHHHhCCCCeEeecCCCCh
Q psy7789         154 PPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKED  189 (197)
Q Consensus       154 ~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~  189 (197)
                      .++++||.+-.++...+..|+..|+++..+.||+..
T Consensus        54 ~~ivvyC~~g~rs~~a~~~L~~~G~~v~~l~GG~~~   89 (94)
T 1wv9_A           54 RPLLLVCEKGLLSQVAALYLEAEGYEAMSLEGGLQA   89 (94)
T ss_dssp             SCEEEECSSSHHHHHHHHHHHHHTCCEEEETTGGGC
T ss_pred             CCEEEEcCCCChHHHHHHHHHHcCCcEEEEcccHHH
Confidence            679999999989999999999999998889999864

>3foj_A Uncharacterized protein; protein SSP1007, structural genomics, PSI-2, protein structure initiative; 1.60A {Staphylococcus saprophyticus subsp}

Probab=91.94  E-value=0.11  Score=32.80  Aligned_cols=36  Identities=11%  Similarity=0.161  Sum_probs=32.5

Q ss_pred             CCEEEEecccccHHHHHHHHHhCCCCeEeecCCCCh
Q psy7789         154 PPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKED  189 (197)
Q Consensus       154 ~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~  189 (197)
                      .++++||.+-.++...+..|+..|+++..+.||+..
T Consensus        57 ~~ivvyC~~g~rs~~a~~~L~~~G~~v~~l~GG~~~   92 (100)
T 3foj_A           57 ETYYIICKAGGRSAQVVQYLEQNGVNAVNVEGGMDE   92 (100)
T ss_dssp             SEEEEECSSSHHHHHHHHHHHTTTCEEEEETTHHHH
T ss_pred             CcEEEEcCCCchHHHHHHHHHHCCCCEEEecccHHH
Confidence            579999999999999999999999999999998764

>3g5j_A Putative ATP/GTP binding protein; N-terminal domain of ATP/GTP binding protein, PSI, MCSG, STR genomics, protein structure initiative; HET: PGE; 1.76A {Clostridium difficile}

Probab=91.50  E-value=0.26  Score=32.56  Aligned_cols=39  Identities=15%  Similarity=0.192  Sum_probs=33.6

Q ss_pred             CCEEEEe-cccccHHHHHHHHHhCCCCeEeecCCCChhhh
Q psy7789         154 PPVLIFA-EKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNN  192 (197)
Q Consensus       154 ~~~lIF~-~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R  192 (197)
                      .++++|| .+-.++...+..|+..|+++..+.||+..=.+
T Consensus        90 ~~ivvyC~~~G~rs~~a~~~L~~~G~~v~~l~GG~~~W~~  129 (134)
T 3g5j_A           90 DNIVIYCARGGMRSGSIVNLLSSLGVNVYQLEGGYKAYRN  129 (134)
T ss_dssp             SEEEEECSSSSHHHHHHHHHHHHTTCCCEEETTHHHHHHH
T ss_pred             CeEEEEECCCChHHHHHHHHHHHcCCceEEEeCcHHHHHH
Confidence            6799999 58888999999999999999999999876443

>3iwh_A Rhodanese-like domain protein; alpha-beta-alpha sandwich, structural genomics, C structural genomics of infectious diseases, csgid; 2.00A {Staphylococcus aureus subsp} PDB: 3mzz_A

Probab=91.49  E-value=0.14  Score=32.78  Aligned_cols=36  Identities=14%  Similarity=0.074  Sum_probs=31.8

Q ss_pred             CCEEEEecccccHHHHHHHHHhCCCCeEeecCCCCh
Q psy7789         154 PPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKED  189 (197)
Q Consensus       154 ~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~  189 (197)
                      .++++||.+-.++...+..|++.|+++..+.||+..
T Consensus        57 ~~ivv~C~~G~rS~~aa~~L~~~G~~~~~l~GG~~~   92 (103)
T 3iwh_A           57 EIYYIVCAGGVRSAKVVEYLEANGIDAVNVEGGMHA   92 (103)
T ss_dssp             SEEEEECSSSSHHHHHHHHHHTTTCEEEEETTHHHH
T ss_pred             CeEEEECCCCHHHHHHHHHHHHcCCCEEEecChHHH
Confidence            479999999999999999999999998888888753

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=91.13  E-value=2.1  Score=35.77  Aligned_cols=101  Identities=13%  Similarity=0.125  Sum_probs=54.2

Q ss_pred             hccCC-ceEEEEeecCChhHHHHHHHhcCC-CeEE---EeCCCCccCcceeEEEEEc----Cc------hh----hHHHH
Q psy7789          85 FFRGQ-RQTLLFSATMPKKIQNFARSALVK-PITI---NVGRAGAASMNVVQEVEYV----KQ------EA----KIVYL  145 (197)
Q Consensus        85 ~~~~~-~q~i~~SAT~~~~~~~~~~~~~~~-~~~i---~~~~~~~~~~~i~~~~~~~----~~------~~----k~~~l  145 (197)
                      .+... ..+|++|||+++ ...+...+.-+ +...   ...-. +.-  ..+..+++    +.      +.    -...+
T Consensus       310 ~~~~~~~svIltSaTL~~-~~~~~~~lGl~~~~~~~~~~~~~~-spf--~~~~~l~v~~~~~~~~~~r~~~~~~~l~~~i  385 (551)
T 3crv_A          310 LLNDNELSIILMSGTLPP-REYMEKVWGIKRNMLYLDVEREIQ-KRV--SGSYECYIGVDVTSKYDMRSDNMWKRYADYL  385 (551)
T ss_dssp             GGGCTTCEEEEEESSCCC-HHHHHHTSCCCSCEEEEEHHHHTT-SCC--SCEEEEEEECSCCCCTTTCCHHHHHHHHHHH
T ss_pred             HHhccCceEEEEeeCCCc-HHHHHHHhCCCCccccccceeecC-CcC--CCceEEEEeCCCCCccccCCHHHHHHHHHHH
Confidence            34445 789999999987 55555555544 2221   00001 111  12222222    11      11    12344


Q ss_pred             HHHhhcCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhh
Q psy7789         146 LECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNN  192 (197)
Q Consensus       146 ~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R  192 (197)
                      .++++..++.++||++|....+.+++   ..+.++..=..+++.+++
T Consensus       386 ~~l~~~~~g~~lvlF~Sy~~l~~v~~---~~~~~v~~q~~~~~~~~~  429 (551)
T 3crv_A          386 LKIYFQAKANVLVVFPSYEIMDRVMS---RISLPKYVESEDSSVEDL  429 (551)
T ss_dssp             HHHHHHCSSEEEEEESCHHHHHHHHT---TCCSSEEECCSSCCHHHH
T ss_pred             HHHHHhCCCCEEEEecCHHHHHHHHH---hcCCcEEEcCCCCCHHHH
Confidence            44555567789999999999999987   335444433335554443

>2jtq_A Phage shock protein E; solution structure rhodanese, stress response, transferase; NMR {Escherichia coli} PDB: 2jtr_A 2jts_A

Probab=91.06  E-value=0.65  Score=28.09  Aligned_cols=37  Identities=14%  Similarity=0.087  Sum_probs=30.5

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCCC-eEeecCCCChh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGKP-FFTLKSLKEDQ  190 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~~-~~~~h~~~~~~  190 (197)
                      ..++++||.+-.++...+..|++.|++ +..+ |++..-
T Consensus        41 ~~~ivv~C~~g~rs~~aa~~L~~~G~~~v~~l-GG~~~w   78 (85)
T 2jtq_A           41 NDTVKVYCNAGRQSGQAKEILSEMGYTHVENA-GGLKDI   78 (85)
T ss_dssp             TSEEEEEESSSHHHHHHHHHHHHTTCSSEEEE-EETTTC
T ss_pred             CCcEEEEcCCCchHHHHHHHHHHcCCCCEEec-cCHHHH
Confidence            457999999988999999999999985 6666 887653

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=90.75  E-value=0.031  Score=46.81  Aligned_cols=39  Identities=18%  Similarity=0.100  Sum_probs=29.3

Q ss_pred             cCCcEEEeCchHHHHHHhcCCc-------cCCCccEEEeehhhhhh
Q psy7789          33 KGCHMMVATPGRLMDMLDKKMV-------SLDVCRYLCLDEADRMV   71 (197)
Q Consensus        33 ~~~~Ili~TP~~l~~~l~~~~~-------~l~~l~~vViDEad~l~   71 (197)
                      .++||+|+|+..|++....+.+       .+.....+||||||.+.
T Consensus       143 ~~adiVV~n~~~l~~~~~~~~~~~~~~~~~~~~~~~vIiDEAHnl~  188 (540)
T 2vl7_A          143 KDKDVIAMTYPYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNLL  188 (540)
T ss_dssp             GGCSEEEEETHHHHSHHHHHHHSCSSTTSCCGGGEEEEETTGGGGG
T ss_pred             hcCCEEEEChHHhcCHHHHHhhCcccccccCcCCCEEEEEccccHH
Confidence            3589999999999975543222       23567899999999983

>3hix_A ALR3790 protein; rhodanese, rhodanese_3, Q8YQN0, Q8YQN0_anAsp, NSR437I, NESG, structural genomics, PSI-2, protein structure initiative; 1.92A {Anabaena SP} PDB: 3k9r_A

Probab=90.08  E-value=0.26  Score=31.50  Aligned_cols=38  Identities=11%  Similarity=0.074  Sum_probs=32.6

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCCC-eEeecCCCChh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGKP-FFTLKSLKEDQ  190 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~~-~~~~h~~~~~~  190 (197)
                      ..++++||.+-.++...+..|+..|++ +..+.||+..=
T Consensus        52 ~~~ivvyc~~g~rs~~a~~~L~~~G~~~v~~l~GG~~~W   90 (106)
T 3hix_A           52 SRDIYVYGAGDEQTSQAVNLLRSAGFEHVSELKGGLAAW   90 (106)
T ss_dssp             TSCEEEECSSHHHHHHHHHHHHHTTCSCEEECTTHHHHH
T ss_pred             CCeEEEEECCCChHHHHHHHHHHcCCcCEEEecCCHHHH
Confidence            357999999988899999999999994 88899987653

>3flh_A Uncharacterized protein LP_1913; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.00A {Lactobacillus plantarum} PDB: 3fnj_A 3i3u_A

Probab=90.05  E-value=0.37  Score=31.69  Aligned_cols=36  Identities=14%  Similarity=0.080  Sum_probs=31.6

Q ss_pred             CCEEEEeccccc--HHHHHHHHHhCCCCeEeecCCCCh
Q psy7789         154 PPVLIFAEKKQD--VDAIHEYLLLKGKPFFTLKSLKED  189 (197)
Q Consensus       154 ~~~lIF~~s~~~--~~~l~~~L~~~~~~~~~~h~~~~~  189 (197)
                      .++++||.+-.+  +...+..|+..|+++..+.||+..
T Consensus        72 ~~ivvyC~~g~r~~s~~a~~~L~~~G~~v~~l~GG~~~  109 (124)
T 3flh_A           72 KTYVVYDWTGGTTLGKTALLVLLSAGFEAYELAGALEG  109 (124)
T ss_dssp             SEEEEECSSSSCSHHHHHHHHHHHHTCEEEEETTHHHH
T ss_pred             CeEEEEeCCCCchHHHHHHHHHHHcCCeEEEeCCcHHH
Confidence            479999998877  899999999999999999998764

>2fsx_A RV0390, COG0607: rhodanese-related sulfurtransferase; RV0390 BR SAD DATA with FBAR, structural genomics, PSI; 1.80A {Mycobacterium tuberculosis}

Probab=89.79  E-value=0.51  Score=32.04  Aligned_cols=36  Identities=19%  Similarity=0.207  Sum_probs=31.6

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCC-CeEeecCCCC
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGK-PFFTLKSLKE  188 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~-~~~~~h~~~~  188 (197)
                      ..++++||.+-.++...+..|+..|+ ++..+.|++.
T Consensus        80 ~~~ivvyC~~G~rS~~aa~~L~~~G~~~v~~l~GG~~  116 (148)
T 2fsx_A           80 ERPVIFLCRSGNRSIGAAEVATEAGITPAYNVLDGFE  116 (148)
T ss_dssp             -CCEEEECSSSSTHHHHHHHHHHTTCCSEEEETTTTT
T ss_pred             CCEEEEEcCCChhHHHHHHHHHHcCCcceEEEcCChh
Confidence            35799999998889999999999999 5999999984

>2k0z_A Uncharacterized protein HP1203; A/B domain, structural genomics, unknown function, PSI-2, PR structure initiative; NMR {Helicobacter pylori}

Probab=89.61  E-value=1.2  Score=28.46  Aligned_cols=39  Identities=13%  Similarity=0.054  Sum_probs=32.8

Q ss_pred             CCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChh
Q psy7789         152 TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQ  190 (197)
Q Consensus       152 ~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~  190 (197)
                      ...++++||.+-.++...+..|+..|++...+.||+..=
T Consensus        55 ~~~~ivvyC~~G~rs~~aa~~L~~~G~~~~~l~GG~~~W   93 (110)
T 2k0z_A           55 KDKKVLLHCRAGRRALDAAKSMHELGYTPYYLEGNVYDF   93 (110)
T ss_dssp             SSSCEEEECSSSHHHHHHHHHHHHTTCCCEEEESCGGGT
T ss_pred             CCCEEEEEeCCCchHHHHHHHHHHCCCCEEEecCCHHHH
Confidence            345899999999999999999999999667888987653

>1qxn_A SUD, sulfide dehydrogenase; polysulfide-sulfur transferase, homodimer; NMR {Wolinella succinogenes} SCOP: c.46.1.3

Probab=89.28  E-value=0.36  Score=32.44  Aligned_cols=38  Identities=16%  Similarity=0.209  Sum_probs=33.1

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCC-CeEeecCCCChh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGK-PFFTLKSLKEDQ  190 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~-~~~~~h~~~~~~  190 (197)
                      ..++++||.+-.++...+..|+..|+ ++..+.||+..=
T Consensus        82 ~~~ivvyC~~G~rS~~aa~~L~~~G~~~v~~l~GG~~~W  120 (137)
T 1qxn_A           82 EKPVVVFCKTAARAALAGKTLREYGFKTIYNSEGGMDKW  120 (137)
T ss_dssp             TSCEEEECCSSSCHHHHHHHHHHHTCSCEEEESSCHHHH
T ss_pred             CCeEEEEcCCCcHHHHHHHHHHHcCCcceEEEcCcHHHH
Confidence            35899999999999999999999999 599999997653

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=88.79  E-value=0.68  Score=40.34  Aligned_cols=37  Identities=24%  Similarity=0.301  Sum_probs=27.2

Q ss_pred             CcEEEeCchHHH-HHHhcC------CccCCCccEEEeehhhhhh
Q psy7789          35 CHMMVATPGRLM-DMLDKK------MVSLDVCRYLCLDEADRMV   71 (197)
Q Consensus        35 ~~Ili~TP~~l~-~~l~~~------~~~l~~l~~vViDEad~l~   71 (197)
                      +||..+|..-+- ++++.+      ..-.+.+.+.||||+|.++
T Consensus       215 ~DItYgTn~EfgFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiL  258 (822)
T 3jux_A          215 CDVTYGTNNEFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVL  258 (822)
T ss_dssp             SSEEEEEHHHHHHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHH
T ss_pred             CCCEEccCcchhhHhHHhhccCCHHHhccCCCCeEEEeccccee
Confidence            899999987765 444422      1224778899999999886

>1gmx_A GLPE protein; transferase, rhodanese, sulfurtransferase, glycerol metabolism; 1.1A {Escherichia coli} SCOP: c.46.1.3 PDB: 1gn0_A

Probab=88.64  E-value=0.34  Score=30.96  Aligned_cols=37  Identities=19%  Similarity=0.400  Sum_probs=32.3

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCC-CeEeecCCCCh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGK-PFFTLKSLKED  189 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~-~~~~~h~~~~~  189 (197)
                      ..++++||.+-.++...+..|+..|+ ++..+.||+..
T Consensus        58 ~~~ivvyc~~g~rs~~a~~~L~~~G~~~v~~l~GG~~~   95 (108)
T 1gmx_A           58 DTPVMVMCYHGNSSKGAAQYLLQQGYDVVYSIDGGFEA   95 (108)
T ss_dssp             TSCEEEECSSSSHHHHHHHHHHHHTCSSEEEETTHHHH
T ss_pred             CCCEEEEcCCCchHHHHHHHHHHcCCceEEEecCCHHH
Confidence            35899999998899999999999999 48889998764

>1tq1_A AT5G66040, senescence-associated family protein; CESG, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana} SCOP: c.46.1.3

Probab=88.38  E-value=0.36  Score=32.03  Aligned_cols=37  Identities=8%  Similarity=-0.052  Sum_probs=32.5

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCCC-eEeecCCCCh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGKP-FFTLKSLKED  189 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~~-~~~~h~~~~~  189 (197)
                      ..++++||.+-.++...+..|+..|++ +..+.||+..
T Consensus        82 ~~~ivvyC~~G~rs~~aa~~L~~~G~~~v~~l~GG~~~  119 (129)
T 1tq1_A           82 SDNIIVGCQSGGRSIKATTDLLHAGFTGVKDIVGGYSA  119 (129)
T ss_dssp             TSSEEEEESSCSHHHHHHHHHHHHHCCSEEEEECCHHH
T ss_pred             CCeEEEECCCCcHHHHHHHHHHHcCCCCeEEeCCcHHH
Confidence            358999999989999999999999994 8899999865

>3nhv_A BH2092 protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 2.50A {Bacillus halodurans} PDB: 3o3w_A

Probab=88.26  E-value=0.33  Score=32.94  Aligned_cols=37  Identities=8%  Similarity=-0.093  Sum_probs=32.1

Q ss_pred             CCEEEEeccc--ccHHHHHHHHHhCCCCeEeecCCCChh
Q psy7789         154 PPVLIFAEKK--QDVDAIHEYLLLKGKPFFTLKSLKEDQ  190 (197)
Q Consensus       154 ~~~lIF~~s~--~~~~~l~~~L~~~~~~~~~~h~~~~~~  190 (197)
                      .++++||.+-  .++...+..|+..|+++..+.||+..=
T Consensus        73 ~~ivvyC~~g~~~rs~~aa~~L~~~G~~v~~l~GG~~~W  111 (144)
T 3nhv_A           73 KVIITYCWGPACNGATKAAAKFAQLGFRVKELIGGIEYW  111 (144)
T ss_dssp             SEEEEECSCTTCCHHHHHHHHHHHTTCEEEEEESHHHHH
T ss_pred             CeEEEEECCCCccHHHHHHHHHHHCCCeEEEeCCcHHHH
Confidence            4799999987  689999999999999999999987643

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=87.96  E-value=0.59  Score=39.67  Aligned_cols=37  Identities=14%  Similarity=0.222  Sum_probs=30.8

Q ss_pred             CccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEeec
Q psy7789          58 VCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSAT   98 (197)
Q Consensus        58 ~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SAT   98 (197)
                      .++++|||||+.+ +   .+.+..+++.++...|++++.-.
T Consensus       262 ~~d~lIIDEAsml-~---~~~~~~Ll~~l~~~~~liLvGD~  298 (608)
T 1w36_D          262 HLDVLVVDEASMI-D---LPMMSRLIDALPDHARVIFLGDR  298 (608)
T ss_dssp             SCSEEEECSGGGC-B---HHHHHHHHHTCCTTCEEEEEECT
T ss_pred             CCCEEEEechhhC-C---HHHHHHHHHhCCCCCEEEEEcch
Confidence            6789999999955 3   56778889999999999998765

>2hhg_A Hypothetical protein RPA3614; MCSG, structural genomics, rohopseudom palustris, PSI-2, protein structure initiative; 1.20A {Rhodopseudomonas palustris}

Probab=86.57  E-value=0.4  Score=32.07  Aligned_cols=37  Identities=3%  Similarity=-0.088  Sum_probs=32.2

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCCC-eEeecCCCCh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGKP-FFTLKSLKED  189 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~~-~~~~h~~~~~  189 (197)
                      ..++++||.+-.++...+..|+..|++ +..+.||+..
T Consensus        86 ~~~ivvyC~~G~rs~~a~~~L~~~G~~~v~~l~GG~~~  123 (139)
T 2hhg_A           86 DKKFVFYCAGGLRSALAAKTAQDMGLKPVAHIEGGFGA  123 (139)
T ss_dssp             SSEEEEECSSSHHHHHHHHHHHHHTCCSEEEETTHHHH
T ss_pred             CCeEEEECCCChHHHHHHHHHHHcCCCCeEEecCCHHH
Confidence            457999999988999999999999995 9999998754

>3d1p_A Putative thiosulfate sulfurtransferase YOR285W; atomic structure, atomic resolution structure, PSI, MCSG; HET: MSE; 0.98A {Saccharomyces cerevisiae}

Probab=86.13  E-value=0.54  Score=31.46  Aligned_cols=36  Identities=6%  Similarity=0.021  Sum_probs=31.7

Q ss_pred             CCEEEEecccccHHHHHHHHHhCCC-CeEeecCCCCh
Q psy7789         154 PPVLIFAEKKQDVDAIHEYLLLKGK-PFFTLKSLKED  189 (197)
Q Consensus       154 ~~~lIF~~s~~~~~~l~~~L~~~~~-~~~~~h~~~~~  189 (197)
                      .++++||.+-.++...+..|++.|+ ++..+.||+..
T Consensus        92 ~~ivvyC~~G~rs~~aa~~L~~~G~~~v~~l~GG~~~  128 (139)
T 3d1p_A           92 KELIFYCASGKRGGEAQKVASSHGYSNTSLYPGSMND  128 (139)
T ss_dssp             SEEEEECSSSHHHHHHHHHHHTTTCCSEEECTTHHHH
T ss_pred             CeEEEECCCCchHHHHHHHHHHcCCCCeEEeCCcHHH
Confidence            4799999999999999999999999 48889998764

>1vee_A Proline-rich protein family; hypothetical protein, structural genomics, rhodanese domain, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} PDB: 2dcq_A

Probab=85.81  E-value=0.74  Score=30.64  Aligned_cols=36  Identities=17%  Similarity=0.292  Sum_probs=31.6

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCCC-eEeecCCCC
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGKP-FFTLKSLKE  188 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~~-~~~~h~~~~  188 (197)
                      ..++++||.+=.++...+..|++.|+. +..+.|++.
T Consensus        74 ~~~ivv~C~sG~RS~~aa~~L~~~G~~~v~~l~GG~~  110 (134)
T 1vee_A           74 NTTLYILDKFDGNSELVAELVALNGFKSAYAIKDGAE  110 (134)
T ss_dssp             GCEEEEECSSSTTHHHHHHHHHHHTCSEEEECTTTTT
T ss_pred             CCEEEEEeCCCCcHHHHHHHHHHcCCcceEEecCCcc
Confidence            357999999988999999999999994 888999984

>3ilm_A ALR3790 protein; rhodanese-like, NSR437H, NESG, structural genomics, protein structure initiative, northeast structural genomics consortium; 2.26A {Nostoc SP} PDB: 2kl3_A

Probab=85.28  E-value=0.59  Score=31.56  Aligned_cols=36  Identities=11%  Similarity=0.101  Sum_probs=31.2

Q ss_pred             CCEEEEecccccHHHHHHHHHhCCCC-eEeecCCCCh
Q psy7789         154 PPVLIFAEKKQDVDAIHEYLLLKGKP-FFTLKSLKED  189 (197)
Q Consensus       154 ~~~lIF~~s~~~~~~l~~~L~~~~~~-~~~~h~~~~~  189 (197)
                      .++++||.+-.++...+..|+..|+. +..+.||+..
T Consensus        57 ~~ivvyC~~g~rs~~aa~~L~~~G~~~v~~l~GG~~~   93 (141)
T 3ilm_A           57 RDIYVYGAGDEQTSQAVNLLRSAGFEHVSELKGGLAA   93 (141)
T ss_dssp             SEEEEECSSHHHHHHHHHHHHHTTCCSEEECTTHHHH
T ss_pred             CeEEEEECCChHHHHHHHHHHHcCCCCEEEecCHHHH
Confidence            47999999988999999999999994 8888888754

>1urh_A 3-mercaptopyruvate sulfurtransferase; rhodanese; 2.8A {Escherichia coli} SCOP: c.46.1.2 c.46.1.2

Probab=83.83  E-value=2.7  Score=31.54  Aligned_cols=38  Identities=5%  Similarity=-0.015  Sum_probs=33.0

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCC-CeEeecCCCChh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGK-PFFTLKSLKEDQ  190 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~-~~~~~h~~~~~~  190 (197)
                      .+++++||.+-.++...+..|+..|+ ++..+.|++..=
T Consensus       230 ~~~ivv~C~~G~rs~~a~~~L~~~G~~~v~~~~GG~~~W  268 (280)
T 1urh_A          230 DKPIIVSCGSGVTAAVVLLALATLDVPNVKLYDGAWSEW  268 (280)
T ss_dssp             SSCEEEECCSSSTHHHHHHHHHHTTCSSCEEECCSCCC-
T ss_pred             CCCEEEECChHHHHHHHHHHHHHcCCCCceeeCChHHHH
Confidence            35799999999999999999999999 599999998754

>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain, chromatin regulator, coiled coil, nucleus, repressor, transcription; 2.20A {Saccharomyces cerevisiae} PDB: 3hgq_A

Probab=83.75  E-value=1.5  Score=34.23  Aligned_cols=54  Identities=13%  Similarity=0.130  Sum_probs=42.2

Q ss_pred             CchhhHHHHHHHhh---cCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChh
Q psy7789         137 KQEAKIVYLLECLQ---KTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQ  190 (197)
Q Consensus       137 ~~~~k~~~l~~~l~---~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~  190 (197)
                      ....|+..|.+++.   +.+.+++||++..+.-+-+-.++...|++...+.|.....
T Consensus       106 ~~SGKf~~L~~LL~~l~~~~~kVLIfsq~t~~LDilE~~l~~~~~~y~RlDG~~~~~  162 (328)
T 3hgt_A          106 ENSGKFSVLRDLINLVQEYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKS  162 (328)
T ss_dssp             HTCHHHHHHHHHHHHHTTSCEEEEEEECSTHHHHHHHHHHTTSSCEEEESSSCCC--
T ss_pred             HcCccHHHHHHHHHHHHhCCCEEEEEECChhHHHHHHHHHhcCCCceEeCCCCchhh
Confidence            34567766666654   4556899999999999999999999999999999885443

>3tg1_B Dual specificity protein phosphatase 10; kinase/rhodanese-like domain, docking interaction, transfera hydrolase complex; 2.71A {Homo sapiens}

Probab=83.56  E-value=0.89  Score=31.20  Aligned_cols=37  Identities=19%  Similarity=0.289  Sum_probs=31.0

Q ss_pred             CCCEEEEecccc---------cHHHHHHHHHhCCCCeEeecCCCCh
Q psy7789         153 EPPVLIFAEKKQ---------DVDAIHEYLLLKGKPFFTLKSLKED  189 (197)
Q Consensus       153 ~~~~lIF~~s~~---------~~~~l~~~L~~~~~~~~~~h~~~~~  189 (197)
                      ..++++||.+-.         .+..++..|...|+++..+.||+..
T Consensus        93 ~~~IVvyc~~g~~~~~~~~~~~s~~a~~~L~~~G~~v~~L~GG~~~  138 (158)
T 3tg1_B           93 SKEIIVYDENTNEPSRVMPSQPLHIVLESLKREGKEPLVLKGGLSS  138 (158)
T ss_dssp             TSCEEEECSCCSCTTSCCSSSHHHHHHHHHHTTTCCEEEETTHHHH
T ss_pred             CCeEEEEECCCCcccccCcchHHHHHHHHHHhCCCcEEEeCCcHHH
Confidence            458999998873         5888899999999999999998754

>1urh_A 3-mercaptopyruvate sulfurtransferase; rhodanese; 2.8A {Escherichia coli} SCOP: c.46.1.2 c.46.1.2

Probab=81.38  E-value=2  Score=32.34  Aligned_cols=51  Identities=10%  Similarity=0.008  Sum_probs=36.9

Q ss_pred             hhhHHHHHHHhh-cCCCCEEEEeccccc-HHHHHHHHHhCCC-CeEeecCCCCh
Q psy7789         139 EAKIVYLLECLQ-KTEPPVLIFAEKKQD-VDAIHEYLLLKGK-PFFTLKSLKED  189 (197)
Q Consensus       139 ~~k~~~l~~~l~-~~~~~~lIF~~s~~~-~~~l~~~L~~~~~-~~~~~h~~~~~  189 (197)
                      .+.+...+..+. ....+++|||.+-.. +..++..|+..|+ ++..+.||+..
T Consensus        71 ~~~~~~~~~~~gi~~~~~ivvyc~~g~~~a~~a~~~L~~~G~~~v~~l~GG~~~  124 (280)
T 1urh_A           71 PETFAVAMRELGVNQDKHLIVYDEGNLFSAPRAWWMLRTFGVEKVSILGGGLAG  124 (280)
T ss_dssp             HHHHHHHHHHTTCCTTSEEEEECSSSCSSHHHHHHHHHHTTCSCEEEETTHHHH
T ss_pred             HHHHHHHHHHcCCCCCCeEEEECCCCCccHHHHHHHHHHcCCCCEEEecCCHHH
Confidence            344544444442 234579999988666 8899999999999 69999998754

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=81.14  E-value=5.3  Score=32.27  Aligned_cols=85  Identities=16%  Similarity=0.294  Sum_probs=45.7

Q ss_pred             eeEEEEEcCCC--hHHhHHHHh-----c--CCcEEEeCchHHHHHH----hcCCc-----cCC-CccEEEeehhhhhhcC
Q psy7789          13 LRTCLAIGGVP--MNQSLDVIK-----K--GCHMMVATPGRLMDML----DKKMV-----SLD-VCRYLCLDEADRMVDM   73 (197)
Q Consensus        13 i~~~~~~gg~~--~~~~~~~l~-----~--~~~Ili~TP~~l~~~l----~~~~~-----~l~-~l~~vViDEad~l~~~   73 (197)
                      .+..+++|+..  ...-...+.     .  +..++..+...+..-+    .....     .+. ..+.+++||+|.+...
T Consensus       130 ~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vL~IDEi~~l~~~  209 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKFLNDLVDSMKEGKLNEFREKYRKKVDILLIDDVQFLIGK  209 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEHHHHHHHHHHHHHTTCHHHHHHHHTTTCSEEEEECGGGGSSC
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHHHHHHHHHHHcccHHHHHHHhcCCCCEEEEeCcccccCC
Confidence            56778888643  333333332     1  5667766665554322    21111     124 6789999999999763


Q ss_pred             -CCHHHHHHHHhhcc-CCceEEEEee
Q psy7789          74 -GFEEDVRTIFSFFR-GQRQTLLFSA   97 (197)
Q Consensus        74 -~~~~~i~~i~~~~~-~~~q~i~~SA   97 (197)
                       .....+..++..+. ...++++.|.
T Consensus       210 ~~~q~~l~~~l~~l~~~~~~iIitt~  235 (440)
T 2z4s_A          210 TGVQTELFHTFNELHDSGKQIVICSD  235 (440)
T ss_dssp             HHHHHHHHHHHHHHHTTTCEEEEEES
T ss_pred             hHHHHHHHHHHHHHHHCCCeEEEEEC
Confidence             23344444444433 3455555443

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	197
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	2e-33
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	2e-25
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	4e-25
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	6e-25
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	2e-24
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	3e-23
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	1e-21
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	4e-20
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	2e-15
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	1e-13
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	8e-10
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	1e-09
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	1e-08
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	2e-05
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	0.002

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 208

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score =  116 bits (291), Expect = 2e-33
 Identities = 36/108 (33%), Positives = 61/108 (56%), Gaps = 1/108 (0%)

Query: 12  PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMV 71
            L+     GG  +   +  +K   +++V TPGR++D +++  ++L   +Y  LDEAD M+
Sbjct: 100 NLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEML 158

Query: 72  DMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINV 119
           +MGF +DV  I +     ++ LLFSATMP++I N A+  +     I  
Sbjct: 159 NMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKA 206

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 222

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 96.1 bits (238), Expect = 2e-25
 Identities = 33/109 (30%), Positives = 58/109 (53%)

Query: 13  LRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
           ++    IGG  + + +  +  G H++  TPGR+ DM+ ++ +     + L LDEAD M++
Sbjct: 114 VQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLN 173

Query: 73  MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGR 121
            GF+E +  ++ +     Q +L SAT+P +I       +  PI I V R
Sbjct: 174 KGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKR 222

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 212

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 95.3 bits (236), Expect = 4e-25
 Identities = 28/87 (32%), Positives = 44/87 (50%)

Query: 33  KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQT 92
           +   ++V TPGR+ D + ++    D  +   LDEAD M+  GF+E +  IF+      Q 
Sbjct: 126 RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQV 185

Query: 93  LLFSATMPKKIQNFARSALVKPITINV 119
           +L SATMP  +       +  P+ I V
Sbjct: 186 VLLSATMPNDVLEVTTKFMRNPVRILV 212

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]} Length = 218

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 94.9 bits (235), Expect = 6e-25
 Identities = 31/89 (34%), Positives = 49/89 (55%)

Query: 33  KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQT 92
           +  H++V TPGR+ DML+++ +S    +   LDEAD M+  GF++ +  IF       Q 
Sbjct: 130 EAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQV 189

Query: 93  LLFSATMPKKIQNFARSALVKPITINVGR 121
           +L SATMP  +    +  +  PI I V +
Sbjct: 190 VLLSATMPSDVLEVTKKFMRDPIRILVKK 218

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 93.4 bits (231), Expect = 2e-24
 Identities = 33/108 (30%), Positives = 63/108 (58%), Gaps = 2/108 (1%)

Query: 14  RTCLAIGGVPMNQSLDVIKK-GCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD 72
           +  +  GG+ + +  +V+KK   H++V TPGR++ +   K ++L   ++  LDE D+M++
Sbjct: 100 KVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLE 159

Query: 73  -MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINV 119
            +    DV+ IF     ++Q ++FSAT+ K+I+   R  +  P+ I V
Sbjct: 160 QLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 207

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]} Length = 238

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

 Score = 91.1 bits (225), Expect = 3e-23
 Identities = 53/114 (46%), Positives = 73/114 (64%), Gaps = 4/114 (3%)

Query: 11  IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRM 70
            PLR+C+  GG   +  +  ++ GCH++VATPGRL+D ++K  +SL+ C+Y+ LDEADRM
Sbjct: 125 TPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRM 184

Query: 71  VDMGFEEDVRTIFSFFR----GQRQTLLFSATMPKKIQNFARSALVKPITINVG 120
           +DMGFE  +R I           RQTL+FSAT PK+IQ  A   L   I + VG
Sbjct: 185 LDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVG 238

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 85.8 bits (211), Expect = 1e-21
 Identities = 34/99 (34%), Positives = 55/99 (55%)

Query: 20  GGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDV 79
           GG  +   +  +    H+++ATPGR++D++ K +  +D  + + LDEAD+++   F + +
Sbjct: 108 GGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIM 167

Query: 80  RTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITIN 118
             I       RQ LL+SAT P  +Q F  S L KP  IN
Sbjct: 168 EDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEIN 206

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 81.6 bits (200), Expect = 4e-20
 Identities = 35/111 (31%), Positives = 57/111 (51%)

Query: 10  PIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADR 69
              +   +  GG  +   +  + +  H++V TPGR++D+  +K+  L  C    +DEAD+
Sbjct: 95  HCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADK 154

Query: 70  MVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVG 120
           M+   F+  +  I SF     Q+LLFSAT P  ++ F    L KP  IN+ 
Sbjct: 155 MLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLM 205

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]} Length = 209

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 69.7 bits (169), Expect = 2e-15
 Identities = 34/101 (33%), Positives = 59/101 (58%)

Query: 19  IGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEED 78
           IGG    ++L+ +    H+++ TPGR+ D + ++ + +     L +DEAD M+DMGF  D
Sbjct: 108 IGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITD 167

Query: 79  VRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINV 119
           V  I +      Q L+FSAT+P+K++ F +  +  P  ++V
Sbjct: 168 VDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHV 208

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 65.3 bits (158), Expect = 1e-13
 Identities = 14/129 (10%), Positives = 37/129 (28%), Gaps = 14/129 (10%)

Query: 5   FISALPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCL 64
           +     +     +      + +                      L K    L    ++ +
Sbjct: 109 YAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYRELGHFDFIFV 168

Query: 65  DEADRMVD-----------MGFEEDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVK 113
           D+ D ++            +GF  D++T       +   ++ +AT  K  +      L  
Sbjct: 169 DDVDAILKASKNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFRQL-- 226

Query: 114 PITINVGRA 122
            +  ++G +
Sbjct: 227 -LNFDIGSS 234

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 53.9 bits (128), Expect = 8e-10
 Identities = 12/88 (13%), Positives = 26/88 (29%), Gaps = 4/88 (4%)

Query: 21  GVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMG--FEED 78
              +            ++   P RLM     + ++      L +DEA  +   G  F  +
Sbjct: 102 EQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPE 161

Query: 79  VRTIFSFFR--GQRQTLLFSATMPKKIQ 104
              +    +       +  +AT     +
Sbjct: 162 YAALGQLRQRFPTLPFMALTATADDTTR 189

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]} Length = 305

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

 Score = 54.2 bits (129), Expect = 1e-09
 Identities = 19/160 (11%), Positives = 38/160 (23%), Gaps = 17/160 (10%)

Query: 20  GGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDV 79
                  ++     G  ++         M     + +     + +DEA            
Sbjct: 62  PIRYQTPAIRAEHTGREIVDLMCHATFTMRLLSPIRVPNYNLIIMDEAHFTDPASIAARG 121

Query: 80  RTIFSFFRGQRQTLLFSATMPKKIQNFARSALVKPITINVGRAGAASMNVVQEVEYVKQE 139
                   G+   +  +AT P     F +S                    + + E    E
Sbjct: 122 YISTRVEMGEAAGIFMTATPPGSRDPFPQSNA-----------------PIMDEEREIPE 164

Query: 140 AKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKP 179
                  E +   +   + F    +  + I   L   GK 
Sbjct: 165 RSWNSGHEWVTDFKGKTVWFVPSIKAGNDIAACLRKNGKK 204

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 202

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 50.7 bits (120), Expect = 1e-08
 Identities = 12/77 (15%), Positives = 27/77 (35%), Gaps = 4/77 (5%)

Query: 35  CHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFR---GQRQ 91
           C ++V T  +   ++  +   +     L +DE   +        +  + +  R      +
Sbjct: 115 CDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALR 174

Query: 92  TLLFSATMPKKIQNFAR 108
            +  SAT P  +   A 
Sbjct: 175 VIGLSATAP-NVTEIAE 190

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 41.7 bits (96), Expect = 2e-05
 Identities = 13/76 (17%), Positives = 26/76 (34%)

Query: 33  KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQT 92
               ++VATP  + + L    +SL+    +  DEA R V       +   +         
Sbjct: 100 ARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLV 159

Query: 93  LLFSATMPKKIQNFAR 108
           +  +A+     +    
Sbjct: 160 IGLTASPGSTPEKIME 175

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 248

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score = 35.5 bits (81), Expect = 0.002
 Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 130 VQEVEYVKQEA-KIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYL 173
           V+ VE V      I  L   L+K     +I+A   ++ + I+E L
Sbjct: 1   VRNVEDVAVNDESISTLSSILEKLGTGGIIYARTGEEAEEIYESL 45

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	197
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.92
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.91
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.91
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.9
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.88
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.88
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.87
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.87
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.86
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.56
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.38
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.37
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.34
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.24
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.24
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.22
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.21
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.2
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.12
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.01
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	98.97
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	98.95
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	98.75
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	98.65
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	98.63
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	98.57
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.38
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	98.25
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	98.21
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	98.14
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	97.94
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	97.7
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	97.65
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	97.61
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	97.51
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	97.51
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	97.45
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	97.41
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	97.09
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	96.97
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	96.23
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	95.81
d1yt8a4	130	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	95.75
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	95.71
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	95.68
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	94.97
d1yt8a2	101	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	94.91
d1yt8a1	136	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	94.65
d1qxna_	137	Polysulfide-sulfur transferase (sulfide dehydrogen	92.6
d2eyqa2	117	Transcription-repair coupling factor, TRCF {Escher	92.45
d1tq1a_	119	Thiosulfate sulfurtransferase/Senescence-associate	92.15
d1gmxa_	108	Sulfurtransferase GlpE {Escherichia coli [TaxId: 5	91.96
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	91.87
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	90.94
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	90.24
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	88.96
d1urha2	120	3-mercaptopyruvate sulfurtransferase {Escherichia	88.18
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	87.84
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	86.18
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	84.21
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	82.75
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	82.45

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.92  E-value=5.8e-25  Score=163.26  Aligned_cols=111  Identities=29%  Similarity=0.576  Sum_probs=105.5

Q ss_pred             CCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCC
Q psy7789          10 PIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        10 ~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~   89 (197)
                      +.++++..++||.+...+...+..++||+|+||+++.+++.++.+++++++++|+||||.+++.+|.+.+..|++.+|++
T Consensus       111 ~~~i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~f~~~i~~I~~~l~~~  190 (222)
T d2j0sa1         111 YMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPA  190 (222)
T ss_dssp             TTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTSTTTHHHHHHHHTTSCTT
T ss_pred             ccceeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccccccccccceeeeecchhHhhhcCcHHHHHHHHHhCCCC
Confidence            35799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeC
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVG  120 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~  120 (197)
                      +|+++||||+++++.++++.++++|+.|.+.
T Consensus       191 ~Q~ilfSAT~~~~v~~l~~~~l~~Pv~I~V~  221 (222)
T d2j0sa1         191 TQVVLISATLPHEILEMTNKFMTDPIRILVK  221 (222)
T ss_dssp             CEEEEEESCCCHHHHTTGGGTCSSCEEECCC
T ss_pred             CEEEEEEEeCCHHHHHHHHHHCCCCEEEEEe
Confidence            9999999999999999999999999988664

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.91  E-value=1.6e-24  Score=159.42  Aligned_cols=111  Identities=32%  Similarity=0.589  Sum_probs=105.4

Q ss_pred             CCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCC
Q psy7789          10 PIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        10 ~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~   89 (197)
                      ..++++...+|+.....+...+..++||+|+||++|.++++.+.+++++++++|+||||.+++.+|.+.+..|++.++++
T Consensus        95 ~~~~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~lV~DEaD~l~~~~f~~~v~~I~~~l~~~  174 (206)
T d1s2ma1          95 HCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPT  174 (206)
T ss_dssp             TTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHHHHHHHHHHHTTSCSS
T ss_pred             ccCeeEEeecCccchhhHHHHhcccceEEEECCcccccccccceeecccceEEEeechhhhhhhhhHHHHHHHHHhCCCC
Confidence            45899999999999999999899999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeC
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVG  120 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~  120 (197)
                      +|+++||||+++++.++++.++++|..|.+.
T Consensus       175 ~Q~il~SATl~~~v~~~~~~~l~~P~~I~~~  205 (206)
T d1s2ma1         175 HQSLLFSATFPLTVKEFMVKHLHKPYEINLM  205 (206)
T ss_dssp             CEEEEEESCCCHHHHHHHHHHCSSCEEESCC
T ss_pred             CEEEEEEEeCCHHHHHHHHHHCCCCEEEEee
Confidence            9999999999999999999999999888664

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=6.1e-24  Score=156.25  Aligned_cols=107  Identities=31%  Similarity=0.540  Sum_probs=101.9

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .++.+....||.....+...+..++||+|+||+++.+++..+..++++++++|+||||.+++.+|.+.+..|++.+++++
T Consensus        99 ~~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~f~~~i~~I~~~~~~~~  178 (206)
T d1veca_          99 GGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNR  178 (206)
T ss_dssp             SSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTTTHHHHHHHHHHSCTTC
T ss_pred             cCcccccccCCccHHHHHHHHHhccCeEEeCCccccccccchhccccccceEEEeccccccccchHHHHHHHHHhCCCCC
Confidence            46888889999999999888999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEE
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITI  117 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i  117 (197)
                      |+++||||+++++.++++.++++|..|
T Consensus       179 Q~~l~SAT~~~~v~~l~~~~l~~P~~I  205 (206)
T d1veca_         179 QILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             EEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             EEEEEEecCCHHHHHHHHHHCCCCEEE
Confidence            999999999999999999999999876

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.90  E-value=3e-23  Score=152.77  Aligned_cols=108  Identities=33%  Similarity=0.595  Sum_probs=100.9

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .++++..++|+.+...+.+.+. ++||+||||++|.++++++.+++++++++|+||||.+++.++.+.+..|++.+++++
T Consensus        99 ~~~~v~~~~g~~~~~~~~~~l~-~~~IlV~TP~~l~~~l~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~I~~~~~~~~  177 (208)
T d1hv8a1          99 KNLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDK  177 (208)
T ss_dssp             SCCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTTTHHHHHHHHHTSCSSC
T ss_pred             CCeEEEEeeCCCChHHHHHhcC-CCCEEEEChHHHHHHHHcCCCCcccCcEEEEEChHHhhcCCChHHHHHHHHhCCCCC
Confidence            4688999999999888887775 599999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEEe
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITINV  119 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~~  119 (197)
                      |++++|||+++++.++++.++++|..|.+
T Consensus       178 Q~i~~SAT~~~~v~~~~~~~l~~~~~I~~  206 (208)
T d1hv8a1         178 RILLFSATMPREILNLAKKYMGDYSFIKA  206 (208)
T ss_dssp             EEEEECSSCCHHHHHHHHHHCCSEEEEEC
T ss_pred             eEEEEEccCCHHHHHHHHHHCCCCeEEEE
Confidence            99999999999999999999999988865

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=7.1e-23  Score=150.57  Aligned_cols=108  Identities=30%  Similarity=0.576  Sum_probs=99.6

Q ss_pred             CeeEEEEEcCCChHHhHHHH-hcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcC-CCHHHHHHHHhhccCC
Q psy7789          12 PLRTCLAIGGVPMNQSLDVI-KKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDM-GFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l-~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~-~~~~~i~~i~~~~~~~   89 (197)
                      .++++.++||.+...+...+ ..+|||+|+||+++.+++.++.+++++++++|+||||.+++. +|.+.+..|++.++++
T Consensus        98 ~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~~~~l~~l~~lVlDEaD~ll~~~~~~~~i~~I~~~~~~~  177 (207)
T d1t6na_          98 NVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHE  177 (207)
T ss_dssp             TCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSSHHHHHHHHHHHHTSCSS
T ss_pred             CceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccCCceeccccceeehhhhhhhhhcCCcHHHHHHHHHhCCCC
Confidence            57889999999988888776 567999999999999999999999999999999999999985 7999999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEe
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINV  119 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~  119 (197)
                      +|+++||||+++++.++++.++++|..|.+
T Consensus       178 ~Q~il~SAT~~~~v~~l~~~~l~~P~~I~V  207 (207)
T d1t6na_         178 KQVMMFSATLSKEIRPVCRKFMQDPMEIFV  207 (207)
T ss_dssp             SEEEEEESCCCTTTHHHHHTTCSSCEEEEC
T ss_pred             CEEEEEeeeCCHHHHHHHHHHCCCCEEEeC
Confidence            999999999999999999999999988753

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.88  E-value=9.8e-23  Score=150.30  Aligned_cols=107  Identities=28%  Similarity=0.563  Sum_probs=91.3

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .++++..+.|+.+...+...++ ++||+|+||+++..++..+.+++++++++|+||||.+++.+|.+.+..|++.+++++
T Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~-~~~IvI~TP~~l~~~~~~~~~~l~~l~~lVlDEad~lld~~f~~~v~~I~~~~~~~~  183 (212)
T d1qdea_         105 MDIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTT  183 (212)
T ss_dssp             SCCCEEEECC----------CT-TCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTCHHHHHHHHHHSCTTC
T ss_pred             cccceeeEeeccchhHHHHHhc-CCcEEEECCCccccccccCceecCcceEEeehhhhhhcccchHHHHHHHHHhCCCCC
Confidence            4688888899888877776655 599999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEeecCChhHHHHHHHhcCCCeEEE
Q psy7789          91 QTLLFSATMPKKIQNFARSALVKPITIN  118 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~~~~~~~~~~~i~  118 (197)
                      |+++||||+++++.++++.++++|+.|.
T Consensus       184 Q~vl~SAT~~~~v~~l~~~~l~~Pv~i~  211 (212)
T d1qdea_         184 QVVLLSATMPNDVLEVTTKFMRNPVRIL  211 (212)
T ss_dssp             EEEEEESSCCHHHHHHHHHHCSSCEEEC
T ss_pred             eEEEEEeeCCHHHHHHHHHHCCCCEEEe
Confidence            9999999999999999999999998874

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=1.3e-22  Score=150.24  Aligned_cols=110  Identities=31%  Similarity=0.564  Sum_probs=97.7

Q ss_pred             CCeeEEEEEcCCChHHhHHHH-hcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCC
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVI-KKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQ   89 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l-~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~   89 (197)
                      .++++..+.||.....+.... .+++||+|+||+++.+++.++...+++++++|+||||.+++.+|.+.+..|++.++++
T Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~~~l~~lVlDEaD~ll~~~f~~~~~~Il~~~~~~  186 (218)
T d2g9na1         107 MGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSN  186 (218)
T ss_dssp             TTCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHHTTCHHHHHHHHHHSCTT
T ss_pred             cceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhcCCcccccceEEEeeecchhhcCchHHHHHHHHHhCCCC
Confidence            467888888887666555443 4579999999999999999998999999999999999999999999999999999999


Q ss_pred             ceEEEEeecCChhHHHHHHHhcCCCeEEEeC
Q psy7789          90 RQTLLFSATMPKKIQNFARSALVKPITINVG  120 (197)
Q Consensus        90 ~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~  120 (197)
                      +|++++|||+++++.++++.++++|+.|.+.
T Consensus       187 ~Q~il~SAT~~~~v~~~~~~~l~~pv~i~v~  217 (218)
T d2g9na1         187 TQVVLLSATMPSDVLEVTKKFMRDPIRILVK  217 (218)
T ss_dssp             CEEEEEESCCCHHHHHHHHHHCSSCEEEECC
T ss_pred             CeEEEEEecCCHHHHHHHHHHCCCCEEEEEe
Confidence            9999999999999999999999999998875

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=99.87  E-value=8.7e-22  Score=147.59  Aligned_cols=111  Identities=48%  Similarity=0.868  Sum_probs=101.9

Q ss_pred             CCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhcc--
Q psy7789          10 PIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFR--   87 (197)
Q Consensus        10 ~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~--   87 (197)
                      +.++++..++|+.....+.+....++||+|+||++|.+++..+.+.+++++++|+||||.+++.+|.+++..|++.+.  
T Consensus       124 ~~~~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~~~~~l~~v~~lViDEaD~ll~~~f~~~i~~Il~~~~~~  203 (238)
T d1wrba1         124 NTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMP  203 (238)
T ss_dssp             TSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEEEEETHHHHHHTTCHHHHHHHHHSSCCC
T ss_pred             CCCcEEEEEeccchhhHHHhhcccCCceeecCHHHHHhHHccCceeccccceeeeehhhhhhhhccHHHHHHHHHHhcCC
Confidence            357999999999998888888888999999999999999999999999999999999999999999999999998764  


Q ss_pred             --CCceEEEEeecCChhHHHHHHHhcCCCeEEEeC
Q psy7789          88 --GQRQTLLFSATMPKKIQNFARSALVKPITINVG  120 (197)
Q Consensus        88 --~~~q~i~~SAT~~~~~~~~~~~~~~~~~~i~~~  120 (197)
                        .++|+++||||+++++..+++.++++|+.+.++
T Consensus       204 ~~~~~Q~il~SAT~~~~v~~l~~~~~~~p~~i~vg  238 (238)
T d1wrba1         204 SGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVG  238 (238)
T ss_dssp             CGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC
T ss_pred             CCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEEeC
Confidence              367999999999999999999999999888663

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.86  E-value=3.5e-22  Score=146.97  Aligned_cols=108  Identities=31%  Similarity=0.549  Sum_probs=98.4

Q ss_pred             CeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCce
Q psy7789          12 PLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQ   91 (197)
Q Consensus        12 ~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q   91 (197)
                      ...+..+.|+.+...+......+|+|+|+||+++..++.+....+++++++|+||||.+++++|.+.+..|++.++++.|
T Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~~~~~~~~~l~~lViDEad~ll~~~f~~~v~~I~~~~~~~~Q  180 (209)
T d1q0ua_         101 MIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQ  180 (209)
T ss_dssp             CCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHHHHTTCHHHHHHHHHTSCTTCE
T ss_pred             cccccccccchhhHHHHHHhccCceEEEecCchhhhhhhhhccccccceEEEEeecccccccccHHHHHHHHHHCCCCCE
Confidence            46666777777777776667788999999999999999988889999999999999999999999999999999999999


Q ss_pred             EEEEeecCChhHHHHHHHhcCCCeEEEe
Q psy7789          92 TLLFSATMPKKIQNFARSALVKPITINV  119 (197)
Q Consensus        92 ~i~~SAT~~~~~~~~~~~~~~~~~~i~~  119 (197)
                      ++++|||+++++.++++.++++|..|.+
T Consensus       181 ~il~SATl~~~v~~l~~~~l~~p~~i~V  208 (209)
T d1q0ua_         181 MLVFSATIPEKLKPFLKKYMENPTFVHV  208 (209)
T ss_dssp             EEEEESCCCGGGHHHHHHHCSSCEEEEC
T ss_pred             EEEEEccCCHHHHHHHHHHCCCCEEEEe
Confidence            9999999999999999999999988865

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=99.56  E-value=3.7e-15  Score=114.40  Aligned_cols=144  Identities=14%  Similarity=0.087  Sum_probs=95.1

Q ss_pred             cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhc--cCCceEEEEeecCChhHHHHHHHh
Q psy7789          33 KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF--RGQRQTLLFSATMPKKIQNFARSA  110 (197)
Q Consensus        33 ~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~--~~~~q~i~~SAT~~~~~~~~~~~~  110 (197)
                      ....++++||+.+...... ...+.+++++|+||+|++..+++  ....++..+  ....|++++|||.+......   .
T Consensus        76 ~~~~i~~~t~~~l~~~~~~-~~~~~~~~~vViDE~H~~~~~~~--~~~~~l~~~~~~~~~~~v~~SAT~~~~~~~~---~  149 (305)
T d2bmfa2          76 GREIVDLMCHATFTMRLLS-PIRVPNYNLIIMDEAHFTDPASI--AARGYISTRVEMGEAAGIFMTATPPGSRDPF---P  149 (305)
T ss_dssp             CCCSEEEEEHHHHHHHHTS-SSCCCCCSEEEEESTTCCSHHHH--HHHHHHHHHHHHTSCEEEEECSSCTTCCCSS---C
T ss_pred             CccccccCCcHHHHHHHhc-CccccceeEEEeeeeeecchhhH--HHHHHHHHhhccccceEEEeecCCCcceeee---c
Confidence            4578999999988877653 44578999999999999866532  122222222  35779999999986432110   0


Q ss_pred             cCCCeEEEeCCCCccCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChh
Q psy7789         111 LVKPITINVGRAGAASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQ  190 (197)
Q Consensus       111 ~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~  190 (197)
                      ...             ..+...........+... ...+.+.+++++|||++++.++.+++.|++.|+++..+||+++++
T Consensus       150 ~~~-------------~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~l~~~~~~~  215 (305)
T d2bmfa2         150 QSN-------------APIMDEEREIPERSWNSG-HEWVTDFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDS  215 (305)
T ss_dssp             CCS-------------SCEEEEECCCCCSCCSSC-CHHHHSSCSCEEEECSCHHHHHHHHHHHHHHTCCCEECCTTCHHH
T ss_pred             ccC-------------CcceEEEEeccHHHHHHH-HHHHHhhCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeCCcChHH
Confidence            000             111111111111111111 123345567999999999999999999999999999999999999


Q ss_pred             hhhhhh
Q psy7789         191 NNQTLE  196 (197)
Q Consensus       191 ~R~~i~  196 (197)
                      +|..+.
T Consensus       216 ~~~~~~  221 (305)
T d2bmfa2         216 EYIKTR  221 (305)
T ss_dssp             HGGGGG
T ss_pred             HHhhhh
Confidence            887764

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.38  E-value=7.3e-13  Score=92.08  Aligned_cols=70  Identities=17%  Similarity=0.142  Sum_probs=66.7

Q ss_pred             cceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         127 MNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       127 ~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      .++.|.|+.+.+++|++.|.++++..+.++||||+|+++|+.+++.|++.|+.+..+||++++.+|.+++
T Consensus         2 ~nI~~~~i~v~~~~K~~~L~~ll~~~~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~   71 (155)
T d1hv8a2           2 ANIEQSYVEVNENERFEALCRLLKNKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVI   71 (155)
T ss_dssp             SSSEEEEEECCGGGHHHHHHHHHCSTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHH
T ss_pred             CCeEEEEEEeChHHHHHHHHHHHccCCCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhh
Confidence            5789999999999999999999998888999999999999999999999999999999999999998875

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=7.8e-13  Score=93.13  Aligned_cols=69  Identities=19%  Similarity=0.172  Sum_probs=64.5

Q ss_pred             ceeEEEEEcCchhhHHHHHHHhhcCC-CCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         128 NVVQEVEYVKQEAKIVYLLECLQKTE-PPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       128 ~i~~~~~~~~~~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +++|+|+.+.+++|.+.|.++++... .++||||++++.++.+++.|.+.|+++..+||+|++++|.+++
T Consensus         1 ~l~q~~v~~~~~~K~~~L~~ll~~~~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l   70 (168)
T d1t5ia_           1 GLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRY   70 (168)
T ss_dssp             CCEEEEEECCGGGHHHHHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHH
T ss_pred             CcEEEEEEeChHHHHHHHHHHHHhCCCCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhh
Confidence            47899999999999999999998765 5899999999999999999999999999999999999999875

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.34  E-value=1.2e-12  Score=92.46  Aligned_cols=72  Identities=14%  Similarity=0.206  Sum_probs=67.2

Q ss_pred             cCcceeEEEEEcCchhhHHHHHHHhhcCC-CCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         125 ASMNVVQEVEYVKQEAKIVYLLECLQKTE-PPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       125 ~~~~i~~~~~~~~~~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +++++.|+++.+.+++|...|.++++..+ .++||||+|++.|+.++..|+..|+++..+||+|++++|++++
T Consensus         3 tl~~i~q~yi~v~~~~K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~   75 (171)
T d1s2ma2           3 TLKGITQYYAFVEERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVF   75 (171)
T ss_dssp             BCTTEEEEEEECCGGGHHHHHHHHHHHSCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHH
T ss_pred             CccceEEEEEEcCHHHHHHHHHHHHHhCCCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhh
Confidence            46789999999999999999999999875 5899999999999999999999999999999999999999875

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.24  E-value=7e-12  Score=88.14  Aligned_cols=73  Identities=15%  Similarity=0.128  Sum_probs=65.8

Q ss_pred             ccCcceeEEEEEcCch-hhHHHHHHHhhcCC-CCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         124 AASMNVVQEVEYVKQE-AKIVYLLECLQKTE-PPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       124 ~~~~~i~~~~~~~~~~-~k~~~l~~~l~~~~-~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      ..+++++|+++.++++ +|...|.++++..+ .++||||++++.|+.+++.|+..|+++..+||+|++++|.+++
T Consensus         3 ~tl~~i~q~~v~v~~~~~K~~~L~~ll~~~~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~   77 (168)
T d2j0sa2           3 LTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIM   77 (168)
T ss_dssp             CSCTTEEEEEEEESSTTHHHHHHHHHHHHHTSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHH
T ss_pred             CCCCCcEEEEEEecChHHHHHHHHHHHHhCCCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHH
Confidence            4568899999999764 59999999998764 5899999999999999999999999999999999999998775

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.24  E-value=1.1e-11  Score=86.69  Aligned_cols=68  Identities=18%  Similarity=0.157  Sum_probs=61.3

Q ss_pred             eeEEEEEcCc-hhhHHHHHHHhhcCC-CCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         129 VVQEVEYVKQ-EAKIVYLLECLQKTE-PPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       129 i~~~~~~~~~-~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      |.|+|+.|.+ +.|.+.|.++++..+ .++||||+|+..++.+++.|...|+++..+||+|++++|++++
T Consensus         1 I~q~~~~v~~~e~K~~~L~~ll~~~~~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l   70 (162)
T d1fuka_           1 IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIM   70 (162)
T ss_dssp             CEEEEEEEESGGGHHHHHHHHHHHTTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHH
T ss_pred             CEEEEEEeCCcHHHHHHHHHHHHhCCCCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHH
Confidence            5788888864 569999999998764 5899999999999999999999999999999999999999875

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=99.22  E-value=7.7e-11  Score=84.65  Aligned_cols=95  Identities=16%  Similarity=0.124  Sum_probs=72.0

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQR   90 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~   90 (197)
                      .+.++....++.........+.. ++++++||+++...+....+.+++++++|+||||.+........+...+......+
T Consensus        79 ~~~~v~~~~~~~~~~~~~~~~~~-~~i~i~t~~~~~~~~~~~~~~~~~~~~vIiDE~H~~~~~~~~~~~~~~~~~~~~~~  157 (200)
T d1wp9a1          79 PPEKIVALTGEKSPEERSKAWAR-AKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNP  157 (200)
T ss_dssp             CGGGEEEECSCSCHHHHHHHHHH-CSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCSSC
T ss_pred             cccceeeeecccchhHHHHhhhc-ccccccccchhHHHHhhhhhhccccceEEEEehhhhhcchhHHHHHHHHHhcCCCC
Confidence            36778777777776655555544 79999999999999988888899999999999999877654444444444445678


Q ss_pred             eEEEEeecCChhHHHH
Q psy7789          91 QTLLFSATMPKKIQNF  106 (197)
Q Consensus        91 q~i~~SAT~~~~~~~~  106 (197)
                      +++++|||........
T Consensus       158 ~~l~~SATp~~~~~~~  173 (200)
T d1wp9a1         158 LVIGLTASPGSTPEKI  173 (200)
T ss_dssp             CEEEEESCSCSSHHHH
T ss_pred             cEEEEEecCCCcHHHH
Confidence            9999999975444443

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.20  E-value=3.2e-11  Score=87.06  Aligned_cols=101  Identities=16%  Similarity=0.205  Sum_probs=74.1

Q ss_pred             CCCCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHH---hh
Q psy7789           9 LPIPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIF---SF   85 (197)
Q Consensus         9 ~~~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~---~~   85 (197)
                      .+...++...+|+......   ....++|+++||..+..++.+....+..++++|+||+|.+.++.+...+..++   +.
T Consensus        92 ~~~~~~v~~~~~~~~~~~~---~~~~~~ii~~~~~~~~~~~~~~~~~~~~~~~ii~DE~h~~~~~~r~~~~~~~l~~i~~  168 (202)
T d2p6ra3          92 EKIGLRIGISTGDYESRDE---HLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRR  168 (202)
T ss_dssp             TTTTCCEEEECSSCBCCSS---CSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTTTHHHHHHHHHHHHH
T ss_pred             hhccccceeeccCcccccc---cccccceeeeccHHHHHHHhccchhhhhhhhccccHHHHhcccccchHHHHHHHHHHh
Confidence            3445667677776543322   12358999999999999998888888999999999999998877666555444   44


Q ss_pred             ccCCceEEEEeecCChhHHHHHHHhcCCC
Q psy7789          86 FRGQRQTLLFSATMPKKIQNFARSALVKP  114 (197)
Q Consensus        86 ~~~~~q~i~~SAT~~~~~~~~~~~~~~~~  114 (197)
                      .+++.|++++|||+++ ..++. .|+..+
T Consensus       169 ~~~~~~~l~lSATl~n-~~~~~-~~l~~~  195 (202)
T d2p6ra3         169 MNKALRVIGLSATAPN-VTEIA-EWLDAD  195 (202)
T ss_dssp             HCTTCEEEEEECCCTT-HHHHH-HHTTCE
T ss_pred             cCCCCcEEEEcCCCCc-HHHHH-HHcCCC
Confidence            4678899999999975 45555 555443

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=99.12  E-value=3e-11  Score=87.42  Aligned_cols=84  Identities=18%  Similarity=0.152  Sum_probs=62.4

Q ss_pred             HhcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCC--HH---HHHHHHhhccCCceEEEEeecCChhHHH
Q psy7789          31 IKKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGF--EE---DVRTIFSFFRGQRQTLLFSATMPKKIQN  105 (197)
Q Consensus        31 l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~--~~---~i~~i~~~~~~~~q~i~~SAT~~~~~~~  105 (197)
                      .....+|+++||+++............+++++|+||||++.++++  ..   .+..+...+ ++.|++++|||+++.+.+
T Consensus       112 ~~~~~~i~~~t~~~~~~~~~~~~~~~~~v~~lviDEaH~~~~~~~~~~~~~~~~~~l~~~~-~~~~ii~lSATl~~~v~~  190 (206)
T d1oywa2         112 RTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQ  190 (206)
T ss_dssp             HHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTSSCCCHHHHGGGGHHHHC-TTSCEEEEESCCCHHHHH
T ss_pred             hcCCceEEEEechhhhchhhcccchhheeeeeeeeeeeeeeccccchHHHHHHHHHHHHhC-CCCceEEEEeCCCHHHHH
Confidence            345699999999988766555556678899999999999988753  22   223444444 478999999999998865


Q ss_pred             -HHHHh-cCCCe
Q psy7789         106 -FARSA-LVKPI  115 (197)
Q Consensus       106 -~~~~~-~~~~~  115 (197)
                       +++.+ +.+|.
T Consensus       191 di~~~L~l~~p~  202 (206)
T d1oywa2         191 DIVRLLGLNDPL  202 (206)
T ss_dssp             HHHHHHTCCSCE
T ss_pred             HHHHHcCCCCCc
Confidence             55554 67884

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.01  E-value=1.6e-11  Score=90.93  Aligned_cols=85  Identities=13%  Similarity=0.223  Sum_probs=56.4

Q ss_pred             EEEEEcCCChHHhHHHHh--cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhh-------
Q psy7789          15 TCLAIGGVPMNQSLDVIK--KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSF-------   85 (197)
Q Consensus        15 ~~~~~gg~~~~~~~~~l~--~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~-------   85 (197)
                      +....++.....+.+.+.  .+++|+|+||++|...    ...+++++++|+||+|.+++.+..  +..++..       
T Consensus       121 ~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~----~~~~~~~~~vVvDE~d~~l~~~~~--~~~~~~~~g~~~~~  194 (237)
T d1gkub1         121 IGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKH----YRELGHFDFIFVDDVDAILKASKN--VDKLLHLLGFHYDL  194 (237)
T ss_dssp             EEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHC----STTSCCCSEEEESCHHHHHTSTHH--HHHHHHHTTEEEET
T ss_pred             EeeeecccchhhhhhhhccccccceeccChHHHHHh----hhhcCCCCEEEEEChhhhhhcccc--hhHHHHhcCChHHH
Confidence            444455555555555544  3589999999887653    335688999999999999876422  2222221       


Q ss_pred             ------ccCCceEEEEeecCChhHHH
Q psy7789          86 ------FRGQRQTLLFSATMPKKIQN  105 (197)
Q Consensus        86 ------~~~~~q~i~~SAT~~~~~~~  105 (197)
                            .+...|++++|||+++....
T Consensus       195 ~~~~~~~~~~~~~i~~SAT~~~~~~~  220 (237)
T d1gkub1         195 KTKSWVGEARGCLMVSTATAKKGKKA  220 (237)
T ss_dssp             TTTEEEECCSSEEEECCCCSCCCTTH
T ss_pred             HHHHhhCCCCCeEEEEeCCCCcccHH
Confidence                  23467999999999865443

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=98.97  E-value=6.2e-10  Score=80.06  Aligned_cols=69  Identities=13%  Similarity=0.157  Sum_probs=59.2

Q ss_pred             CcceeEEEEEcCchhhHHHHHHHhhcCC-CCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         126 SMNVVQEVEYVKQEAKIVYLLECLQKTE-PPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       126 ~~~i~~~~~~~~~~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      ++++...  .+...+|++.|+++++... .++||||+|++.|+.++..|+..|+.+..+||+|++++|++++
T Consensus         4 RpNi~y~--v~~~~~k~~~L~~~l~~~~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~   73 (200)
T d1oywa3           4 RPNIRYM--LMEKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQ   73 (200)
T ss_dssp             CTTEEEE--EEECSSHHHHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHH
T ss_pred             CCCcEEE--EEcCCcHHHHHHHHHHhcCCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHH
Confidence            4556433  3456779999999998764 5899999999999999999999999999999999999999875

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=98.95  E-value=4.9e-10  Score=78.46  Aligned_cols=59  Identities=17%  Similarity=0.195  Sum_probs=49.3

Q ss_pred             hhhHHHHHHHhhc---CCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         139 EAKIVYLLECLQK---TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       139 ~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      +...+.|++.+++   .+.++||||+|++.|+.+++.|++.|+++..+||+|++++|+++++
T Consensus        14 ~~qv~dll~~i~~~~~~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~   75 (174)
T d1c4oa2          14 ENQILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIR   75 (174)
T ss_dssp             TTHHHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHhcCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHH
Confidence            3344555555543   3568999999999999999999999999999999999999999863

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=98.75  E-value=5.6e-09  Score=73.72  Aligned_cols=58  Identities=16%  Similarity=0.166  Sum_probs=48.8

Q ss_pred             hhhHHHHHHHhhc---CCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         139 EAKIVYLLECLQK---TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       139 ~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      ..+.+.++..+.+   .+.++||||+++..++.++..|++.|+++..+||+|++++|++++
T Consensus        14 ~~qvd~ll~~i~~~~~~~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l   74 (181)
T d1t5la2          14 KGQIDDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEII   74 (181)
T ss_dssp             TTHHHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHhcCCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHH
Confidence            3444555555543   356899999999999999999999999999999999999999886

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=98.65  E-value=1.9e-09  Score=72.81  Aligned_cols=43  Identities=19%  Similarity=0.108  Sum_probs=39.9

Q ss_pred             CCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhh
Q psy7789         152 TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQT  194 (197)
Q Consensus       152 ~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~  194 (197)
                      ..+++||||+|++.|+.+++.|++.|+++..+||+|++++|++
T Consensus        34 ~~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~~~~~~   76 (138)
T d1jr6a_          34 KGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPT   76 (138)
T ss_dssp             TTSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCSCCCTT
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchhhhhhh
Confidence            3568999999999999999999999999999999999998865

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=98.63  E-value=9.8e-08  Score=69.69  Aligned_cols=88  Identities=18%  Similarity=0.222  Sum_probs=64.2

Q ss_pred             CCeeEEEEEcCCChHHhHHHH----hcCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVI----KKGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF   86 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l----~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~   86 (197)
                      .|+++.+++|+.+..++.+.+    ++.++|+|||     +.+-...+.++++.++|+||-|.+   ++.  -+..++..
T Consensus       131 ~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGt-----hs~l~~~~~f~~LgLiIiDEeH~f---g~k--Q~~~l~~~  200 (233)
T d2eyqa3         131 WPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGT-----HKLLQSDVKFKDLGLLIVDEEHRF---GVR--HKERIKAM  200 (233)
T ss_dssp             TTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEEC-----THHHHSCCCCSSEEEEEEESGGGS---CHH--HHHHHHHH
T ss_pred             CCCEEEeccCcccchhHHHHHHHHhCCCCCEEEee-----hhhhccCCccccccceeeechhhh---hhH--HHHHHHhh
Confidence            689999999998866655433    3458999999     444445667899999999999985   222  22334444


Q ss_pred             cCCceEEEEeecCChhHHHHHH
Q psy7789          87 RGQRQTLLFSATMPKKIQNFAR  108 (197)
Q Consensus        87 ~~~~q~i~~SAT~~~~~~~~~~  108 (197)
                      ..++.++++|||-.++....+.
T Consensus       201 ~~~~~~l~~SATPiprtl~~~~  222 (233)
T d2eyqa3         201 RANVDILTLTATPIPRTLNMAM  222 (233)
T ss_dssp             HTTSEEEEEESSCCCHHHHHHH
T ss_pred             CCCCCEEEEecchhHHHHHHHH
Confidence            5688999999998877666553

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=98.57  E-value=3.6e-08  Score=73.35  Aligned_cols=87  Identities=18%  Similarity=0.169  Sum_probs=59.3

Q ss_pred             CCeeEEEEEcCCChHHhHHHH---h-cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVI---K-KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF   86 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l---~-~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~   86 (197)
                      .|+++..++|+.+..+..+.+   . +.++|+|||-     .+-...+.++++.++||||-|.+.-.     -+..+.+-
T Consensus       159 ~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGTh-----sl~~~~~~f~~LglviiDEqH~fgv~-----Qr~~l~~~  228 (264)
T d1gm5a3         159 FNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTH-----ALIQEDVHFKNLGLVIIDEQHRFGVK-----QREALMNK  228 (264)
T ss_dssp             SSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECT-----THHHHCCCCSCCCEEEEESCCCC----------CCCCSS
T ss_pred             ccccceeeccccchHHHHHHHHHHHCCCCCEEEeeh-----HHhcCCCCccccceeeeccccccchh-----hHHHHHHh
Confidence            489999999998865554443   3 4599999994     33334556789999999999997322     12222333


Q ss_pred             cCCceEEEEeecCChhHHHHH
Q psy7789          87 RGQRQTLLFSATMPKKIQNFA  107 (197)
Q Consensus        87 ~~~~q~i~~SAT~~~~~~~~~  107 (197)
                      ..+++++++|||-.++.....
T Consensus       229 ~~~~~~l~~SATPiprtl~~~  249 (264)
T d1gm5a3         229 GKMVDTLVMSATPIPRSMALA  249 (264)
T ss_dssp             SSCCCEEEEESSCCCHHHHHH
T ss_pred             CcCCCEEEEECCCCHHHHHHH
Confidence            457889999999766655444

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=98.38  E-value=1.7e-07  Score=62.33  Aligned_cols=64  Identities=14%  Similarity=0.055  Sum_probs=40.3

Q ss_pred             CcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCH-HHHHHHHhhccCCceEEEEeecCC
Q psy7789          35 CHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFE-EDVRTIFSFFRGQRQTLLFSATMP  100 (197)
Q Consensus        35 ~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~-~~i~~i~~~~~~~~q~i~~SAT~~  100 (197)
                      ..+.+.|...+..... ....+.+++++|+||||.+...++. ..+...+.. .++.+++++|||.|
T Consensus        76 ~~~~~~~~~~l~~~~~-~~~~~~~~~lvIiDEaH~~~~~~~~~~~~~~~~~~-~~~~~~l~lTATPp  140 (140)
T d1yksa1          76 EVIDAMCHATLTYRML-EPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRAR-ANESATILMTATPP  140 (140)
T ss_dssp             CCEEEEEHHHHHHHHT-SSSCCCCCSEEEETTTTCCSHHHHHHHHHHHHHHH-TTSCEEEEECSSCT
T ss_pred             cchhhhhHHHHHHHHh-ccccccceeEEEEccccccChhhHHHHHHHHHHhh-CCCCCEEEEEcCCC
Confidence            4566666666555433 3445789999999999987433211 112222222 35789999999975

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=98.25  E-value=3.4e-07  Score=68.47  Aligned_cols=41  Identities=17%  Similarity=0.092  Sum_probs=38.7

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQ  193 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~  193 (197)
                      ++++||||||++.|+++++.|++.|+++..+||+|+++.|.
T Consensus        36 ggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~   76 (299)
T d1a1va2          36 GGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIP   76 (299)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSC
T ss_pred             CCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHH
Confidence            56899999999999999999999999999999999999874

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.21  E-value=1.2e-07  Score=70.09  Aligned_cols=53  Identities=19%  Similarity=0.149  Sum_probs=48.0

Q ss_pred             chhhHHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         138 QEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       138 ~~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +++|+..|..+++..++++||||+|++.|+.++++|++.      +||+|++++|.+++
T Consensus        10 ~~~~~~~l~~~l~~~~~~~iif~~~~~~~~~l~~~l~~~------~hg~~~~~~R~~~~   62 (248)
T d1gkub2          10 NDESISTLSSILEKLGTGGIIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDY   62 (248)
T ss_dssp             SCCCTTTTHHHHTTSCSCEEEEESSHHHHHHHHHTTTTS------SCEEECTTSSSHHH
T ss_pred             CchHHHHHHHHHHHhCCCEEEEECCHHHHHHHHHHHHHh------ccCCCCHHHHHHHH
Confidence            577889999999988889999999999999999999863      89999999998876

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.14  E-value=4.6e-07  Score=64.74  Aligned_cols=54  Identities=15%  Similarity=0.162  Sum_probs=41.3

Q ss_pred             HHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCC------------------------------CCeEeecCCCChhhh
Q psy7789         143 VYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKG------------------------------KPFFTLKSLKEDQNN  192 (197)
Q Consensus       143 ~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~------------------------------~~~~~~h~~~~~~~R  192 (197)
                      +.+.+.+++ ++++||||+|++.|+.+|..|.+..                              ..++++||+|++++|
T Consensus        31 ~l~~~~i~~-~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~~~r  109 (201)
T d2p6ra4          31 ELVEECVAE-NGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQR  109 (201)
T ss_dssp             HHHHHHHHT-TCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHH
T ss_pred             HHHHHHHHc-CCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhhhhH
Confidence            334444554 4799999999999999998876420                              127899999999999


Q ss_pred             hhhhC
Q psy7789         193 QTLEN  197 (197)
Q Consensus       193 ~~i~~  197 (197)
                      +.|++
T Consensus       110 ~~ie~  114 (201)
T d2p6ra4         110 RVVED  114 (201)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            98873

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=97.94  E-value=5.7e-06  Score=61.97  Aligned_cols=62  Identities=11%  Similarity=0.063  Sum_probs=46.1

Q ss_pred             CCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEeecCChh
Q psy7789          34 GCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMPKK  102 (197)
Q Consensus        34 ~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SAT~~~~  102 (197)
                      ..+++|+|++++...   ....++++++||+||||++-    ...+..++..+.+....+++|||++..
T Consensus       204 ~~~i~i~t~qs~~~~---~~~~~~~f~~VIvDEaH~~~----a~~~~~il~~~~~~~~rlGlTaT~~~~  265 (282)
T d1rifa_         204 DAPVVVGTWQTVVKQ---PKEWFSQFGMMMNDECHLAT----GKSISSIISGLNNCMFKFGLSGSLRDG  265 (282)
T ss_dssp             TCSEEEECHHHHTTS---CGGGGGGEEEEEEETGGGCC----HHHHHHHTTTCTTCCEEEEECSSCCTT
T ss_pred             cceEEEEeeehhhhh---cccccCCCCEEEEECCCCCC----chhHHHHHHhccCCCeEEEEEeecCCC
Confidence            368999999776543   23346789999999999973    556778887776555678999998543

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=97.70  E-value=1.6e-05  Score=59.79  Aligned_cols=46  Identities=15%  Similarity=0.216  Sum_probs=37.0

Q ss_pred             cCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         151 KTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       151 ~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      +..++++|||++...++.+++.|++.|.++..+||.++.++++++.
T Consensus        34 ~~~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~~~~   79 (299)
T d1yksa2          34 ADKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYPTIK   79 (299)
T ss_dssp             HCCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC-------
T ss_pred             hcCCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHhhhh
Confidence            3568999999999999999999999999999999999999987653

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.65  E-value=2e-05  Score=56.08  Aligned_cols=58  Identities=17%  Similarity=0.021  Sum_probs=40.0

Q ss_pred             CcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEeecCC
Q psy7789          35 CHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMP  100 (197)
Q Consensus        35 ~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SAT~~  100 (197)
                      .+|+|+|.+.+......   ..+++++||+||||++....    +..+++.+ +....+++|||+.
T Consensus       149 ~~i~i~t~~~~~~~~~~---~~~~~~lvIiDEaH~~~a~~----~~~i~~~~-~~~~~lgLTATl~  206 (206)
T d2fz4a1         149 KPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPAES----YVQIAQMS-IAPFRLGLTATFE  206 (206)
T ss_dssp             CSEEEEEHHHHHHTHHH---HTTTCSEEEEECSSCCCTTT----HHHHHHTC-CCSEEEEEEESCC
T ss_pred             cccccceehhhhhhhHh---hCCcCCEEEEECCeeCCcHH----HHHHHhcc-CCCcEEEEecCCC
Confidence            56888888776654331   23578899999999985433    34555555 3456789999974

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=97.61  E-value=2.3e-05  Score=51.80  Aligned_cols=60  Identities=18%  Similarity=0.139  Sum_probs=38.0

Q ss_pred             CcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhcc--CCceEEEEeec
Q psy7789          35 CHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFR--GQRQTLLFSAT   98 (197)
Q Consensus        35 ~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~--~~~q~i~~SAT   98 (197)
                      ..++++|.+.+...   ....+++++++|+||+|.+-.. ....+..+++.+.  ...+++++|||
T Consensus        74 ~~~~~~~~~~~~~~---~~~~~~~~~~vIiDE~H~~~~~-~~~~~~~~l~~~~~~~~~~~l~~TAT  135 (136)
T d1a1va1          74 SPITYSTYGKFLAD---GGCSGGAYDIIICDECHSTDAT-SILGIGTVLDQAETAGARLVVLATAT  135 (136)
T ss_dssp             CSEEEEEHHHHHHT---TGGGGCCCSEEEEETTTCCSHH-HHHHHHHHHHHTTTTTCSEEEEEESS
T ss_pred             cceEEEeeeeeccc---cchhhhcCCEEEEecccccCHH-HHHHHHHHHHHHHHCCCCcEEEEeCC
Confidence            45666666554433   2335688999999999987332 2223445555443  35578888998

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.51  E-value=1.5e-05  Score=56.41  Aligned_cols=55  Identities=16%  Similarity=0.244  Sum_probs=45.9

Q ss_pred             chhhHHHHHHHhhcCC-CCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhhC
Q psy7789         138 QEAKIVYLLECLQKTE-PPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       138 ~~~k~~~l~~~l~~~~-~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      ...|...+.++++... .++||||++...++.+++.|     .+..+||++++++|+++++
T Consensus        77 ~~~K~~~l~~ll~~~~~~k~lvf~~~~~~~~~l~~~l-----~~~~i~g~~~~~~R~~~l~  132 (200)
T d2fwra1          77 SKNKIRKLREILERHRKDKIIIFTRHNELVYRISKVF-----LIPAITHRTSREEREEILE  132 (200)
T ss_dssp             CSHHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHT-----TCCBCCSSSCSHHHHTHHH
T ss_pred             cHHHHHHHHHHHHhCCCCcEEEEeCcHHHHHHHHhhc-----CcceeeCCCCHHHHHHHHH
Confidence            3468899999998774 58999999999999998876     3456899999999998763

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=97.51  E-value=6.4e-05  Score=56.00  Aligned_cols=58  Identities=12%  Similarity=0.192  Sum_probs=44.0

Q ss_pred             hhhHHHHHHHhhc-----CCCCEEEEecccccHHHHHHHHHhCCCCeEeecC--------CCChhhhhhhh
Q psy7789         139 EAKIVYLLECLQK-----TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKS--------LKEDQNNQTLE  196 (197)
Q Consensus       139 ~~k~~~l~~~l~~-----~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~--------~~~~~~R~~i~  196 (197)
                      ..|+..+.+++.+     .+.++||||+++..++.+++.|.+.|+++..+||        +|++.+|.+++
T Consensus       142 ~pK~~~l~~~l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~  212 (286)
T d1wp9a2         142 HPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLIL  212 (286)
T ss_dssp             CHHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHH
Confidence            3577777776642     3468999999999999999999999999998877        45666666554

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=97.45  E-value=0.00024  Score=50.29  Aligned_cols=46  Identities=9%  Similarity=0.018  Sum_probs=41.7

Q ss_pred             CCCCEEEEecccccHHHHHHHHHhC--CCCeEeecCCCChhhhhhhhC
Q psy7789         152 TEPPVLIFAEKKQDVDAIHEYLLLK--GKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       152 ~~~~~lIF~~s~~~~~~l~~~L~~~--~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      .++|+.+.||..+..+.+++.+++.  ++++..+||.|++++++++++
T Consensus        30 rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~   77 (211)
T d2eyqa5          30 RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMN   77 (211)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHH
T ss_pred             cCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHH
Confidence            3579999999999999999999886  789999999999999999873

>d1z5za1 c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=97.41  E-value=8.9e-05  Score=53.95  Aligned_cols=59  Identities=10%  Similarity=0.121  Sum_probs=50.2

Q ss_pred             chhhHHHHHHHhhc---CCCCEEEEecccccHHHHHHHHHhC-CCCeEeecCCCChhhhhhhh
Q psy7789         138 QEAKIVYLLECLQK---TEPPVLIFAEKKQDVDAIHEYLLLK-GKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       138 ~~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~~L~~~-~~~~~~~h~~~~~~~R~~i~  196 (197)
                      ...|+..+.+++.+   .+.++||||+.....+.+...+.+. |.++..+||++++++|+++.
T Consensus        67 ~S~K~~~l~~~l~~~~~~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i  129 (244)
T d1z5za1          67 RSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDII  129 (244)
T ss_dssp             TCHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHH
T ss_pred             hhhHHHHHHHHHHhhcccccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhh
Confidence            34688888888864   4569999999999999999988755 88999999999999998764

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=97.09  E-value=0.00066  Score=46.48  Aligned_cols=60  Identities=25%  Similarity=0.295  Sum_probs=50.6

Q ss_pred             EEcCchhhHHHHHHHhhc---CCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhh
Q psy7789         134 EYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQ  193 (197)
Q Consensus       134 ~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~  193 (197)
                      ++...++|...+.+.++.   .+.|+||+|.|++.++.++..|++.|++...+++....++-+
T Consensus        12 vf~T~~eK~~AIi~eV~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~   74 (175)
T d1tf5a4          12 IYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQ   74 (175)
T ss_dssp             EESSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHH
T ss_pred             EEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHH
Confidence            556788899888888865   356999999999999999999999999999999887655544

>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=96.97  E-value=0.00046  Score=52.79  Aligned_cols=58  Identities=14%  Similarity=0.137  Sum_probs=50.2

Q ss_pred             hhhHHHHHHHhhc----CCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCChhhhhhhh
Q psy7789         139 EAKIVYLLECLQK----TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKEDQNNQTLE  196 (197)
Q Consensus       139 ~~k~~~l~~~l~~----~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~~~R~~i~  196 (197)
                      ..|+..|.+++..    .+.|+|||++.....+.+...|...|+++..++|+++.++|.++.
T Consensus       100 S~Kl~~L~~ll~~~~~~~g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i  161 (346)
T d1z3ix1         100 SGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIV  161 (346)
T ss_dssp             SHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhcCCceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHHHHHH
Confidence            4577777777753    346999999999999999999999999999999999999998764

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=96.23  E-value=0.0046  Score=45.79  Aligned_cols=60  Identities=10%  Similarity=0.153  Sum_probs=38.7

Q ss_pred             CcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEeecC
Q psy7789          35 CHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATM   99 (197)
Q Consensus        35 ~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SAT~   99 (197)
                      .+++|+|.+.+.....  .+.-.+.+++|+||+|.+-+.+ .... ..+..+ +....+++|||.
T Consensus       171 ~~v~i~sy~~~~~~~~--~l~~~~~~~vI~DEaH~ikn~~-s~~~-~a~~~l-~~~~rllLTGTP  230 (298)
T d1z3ix2         171 TPILIISYETFRLHAE--VLHKGKVGLVICDEGHRLKNSD-NQTY-LALNSM-NAQRRVLISGTP  230 (298)
T ss_dssp             CCEEEEEHHHHHHHTT--TTTTSCCCEEEETTGGGCCTTC-HHHH-HHHHHH-CCSEEEEECSSC
T ss_pred             ceEEEEeecccccchh--cccccceeeeeccccccccccc-chhh-hhhhcc-ccceeeeecchH
Confidence            5799999877665432  2223456799999999996543 2222 223333 456678999996

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=95.81  E-value=0.0011  Score=46.85  Aligned_cols=59  Identities=10%  Similarity=0.102  Sum_probs=38.2

Q ss_pred             hhhHHHHHHHhhc---CCCCEEEEecccccHH--------HHHHHHHhC---CCCeEeecCCCChhhhhhhhC
Q psy7789         139 EAKIVYLLECLQK---TEPPVLIFAEKKQDVD--------AIHEYLLLK---GKPFFTLKSLKEDQNNQTLEN  197 (197)
Q Consensus       139 ~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~--------~l~~~L~~~---~~~~~~~h~~~~~~~R~~i~~  197 (197)
                      .++.+.+.+.+++   .++|+.+.||.++..+        +.++.|.+.   ++++..+||+|++++|+++++
T Consensus        12 ~~~~~~v~~~I~~el~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~   84 (206)
T d1gm5a4          12 MDRVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVML   84 (206)
T ss_dssp             SSTHHHHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHH
T ss_pred             cccHHHHHHHHHHHHHcCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHH
Confidence            3455666666654   3468988898765444        444555443   678999999999999999873

>d1yt8a4 c.46.1.2 (A:243-372) Thiosulfate sulfurtransferase PA2603 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Thiosulfate sulfurtransferase PA2603
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=95.75  E-value=0.0039  Score=40.40  Aligned_cols=39  Identities=13%  Similarity=0.167  Sum_probs=34.4

Q ss_pred             cCCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCCh
Q psy7789         151 KTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKED  189 (197)
Q Consensus       151 ~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~  189 (197)
                      ...+++++||++-.++...+..|++.|+++..+.||+..
T Consensus        78 ~~~~~ivl~C~~G~rS~~aa~~L~~~G~~v~~l~GG~~a  116 (130)
T d1yt8a4          78 VRGARLVLVDDDGVRANMSASWLAQMGWQVAVLDGLSEA  116 (130)
T ss_dssp             SBTCEEEEECSSSSHHHHHHHHHHHTTCEEEEECSCCGG
T ss_pred             CccceEEeecCCCccHHHHHHHHHHcCCCeEEEcCchHH
Confidence            344689999999999999999999999999999998764

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=95.71  E-value=0.01  Score=43.12  Aligned_cols=98  Identities=13%  Similarity=0.221  Sum_probs=66.1

Q ss_pred             CCeeEEEEEcCCChHHhHHHHhcCCcEEEeCchHHH-HHHhcC------CccCCCccEEEeehhhhhh-cCCCH------
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIKKGCHMMVATPGRLM-DMLDKK------MVSLDVCRYLCLDEADRMV-DMGFE------   76 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~~~~~Ili~TP~~l~-~~l~~~------~~~l~~l~~vViDEad~l~-~~~~~------   76 (197)
                      .|++|..+..+.+.++..+...  +||+.+|...+- ++++..      ..-.+.+.+.|+||+|.++ +...-      
T Consensus       148 lGlsvg~~~~~~~~~~r~~~Y~--~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDsiliDeartpliisg  225 (273)
T d1tf5a3         148 LGLTVGLNLNSMSKDEKREAYA--ADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISG  225 (273)
T ss_dssp             TTCCEEECCTTSCHHHHHHHHH--SSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEE
T ss_pred             cCCCccccccccCHHHHHHHhh--CCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchhhhhhccCCceEecc
Confidence            3788888888877666555554  899999998775 555432      2225778999999999886 32110      


Q ss_pred             -------HHHHHHHhhccCCceEEEEeecCChhHHHHHHHhcCC
Q psy7789          77 -------EDVRTIFSFFRGQRQTLLFSATMPKKIQNFARSALVK  113 (197)
Q Consensus        77 -------~~i~~i~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~  113 (197)
                             -.++..++.+   .++..++.|...+..++.+.|.-+
T Consensus       226 ~~~~~a~it~q~~f~~y---~~l~gmtgta~~~~~e~~~iy~l~  266 (273)
T d1tf5a3         226 QSMTLATITFQNYFRMY---EKLAGMTGTAKTEEEEFRNIYNMQ  266 (273)
T ss_dssp             EEEEEEEEEHHHHHTTS---SEEEEEESCCGGGHHHHHHHHCCC
T ss_pred             CccchhhhhHHHHHHHH---HHHhCCccccHHHHHHHHhccCCc
Confidence                   0134444443   477888999887777777777533

>d1nkta4 c.37.1.19 (A:397-615) Translocation ATPase SecA, nucleotide-binding domains {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.97  E-value=0.035  Score=38.70  Aligned_cols=57  Identities=18%  Similarity=0.257  Sum_probs=48.8

Q ss_pred             EEEcCchhhHHHHHHHhhc---CCCCEEEEecccccHHHHHHHHHhCCCCeEeecCCCCh
Q psy7789         133 VEYVKQEAKIVYLLECLQK---TEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKSLKED  189 (197)
Q Consensus       133 ~~~~~~~~k~~~l~~~l~~---~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~~~~~  189 (197)
                      .++....+|...+.+-+..   .+.|+||.+.|++.++.++..|++.|++..++++.-..
T Consensus        11 ~Vy~T~~~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~he   70 (219)
T d1nkta4          11 LIYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHE   70 (219)
T ss_dssp             EEESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHH
T ss_pred             eEEcCHHHHHHHHHHHHHHHHhcCCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhHH
Confidence            4567788899888888764   35699999999999999999999999999999997443

>d1yt8a2 c.46.1.2 (A:6-106) Thiosulfate sulfurtransferase PA2603 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Thiosulfate sulfurtransferase PA2603
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=94.91  E-value=0.032  Score=33.92  Aligned_cols=76  Identities=8%  Similarity=0.051  Sum_probs=48.6

Q ss_pred             CCeEEEeCCCCc-cCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCC-CeEeecCCCCh
Q psy7789         113 KPITINVGRAGA-ASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGK-PFFTLKSLKED  189 (197)
Q Consensus       113 ~~~~i~~~~~~~-~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~-~~~~~h~~~~~  189 (197)
                      +...+++.+... ....+... +.++.......+..+......+++++|++-.++...+..|.+.|+ ++..+.|++..
T Consensus        18 ~~~liDvR~~~e~~~ghIpgA-i~~~~~~~~~~~~~~~~~~~~~vv~~~~~g~~s~~~~~~l~~~G~~nV~~l~GG~~~   95 (101)
T d1yt8a2          18 ELALLDVREEDPFAQAHPLFA-ANLPLSRLELEIHARVPRRDTPITVYDDGEGLAPVAAQRLHDLGYSDVALLDGGLSG   95 (101)
T ss_dssp             CBEEEECSCHHHHTTSBCTTC-EECCGGGHHHHHHHHSCCTTSCEEEECSSSSHHHHHHHHHHHTTCSSEEEETTHHHH
T ss_pred             CeEEEECCCHHHHHhccCCCc-ccccccchhhhhhhcccccCceeeeccchhhhHHHHHHHHHHcCCCcEEEeCChHHH
Confidence            446777764331 11122211 223444444444444444556899999999999999999999998 58888998764

>d1yt8a1 c.46.1.2 (A:107-242) Thiosulfate sulfurtransferase PA2603 {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: Thiosulfate sulfurtransferase PA2603
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=94.65  E-value=0.019  Score=37.34  Aligned_cols=75  Identities=13%  Similarity=0.122  Sum_probs=47.0

Q ss_pred             CCeEEEeCCCCc-cCcceeEEEEEcCchhhHHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCC--CeEeecCCCC
Q psy7789         113 KPITINVGRAGA-ASMNVVQEVEYVKQEAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGK--PFFTLKSLKE  188 (197)
Q Consensus       113 ~~~~i~~~~~~~-~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~--~~~~~h~~~~  188 (197)
                      +...+++.+... ....+.. -+.++...-...+.++......++++||.+-.++...+..|+..|+  ++..+.||+.
T Consensus        40 ~~~liDvR~~~e~~~ghIpG-Ai~ip~~~l~~~~~~l~~~~~~~iV~~C~~g~rs~~aa~~L~~~G~~~~V~~L~GG~~  117 (136)
T d1yt8a1          40 EAVILDARRFDEYQTMSIPG-GISVPGAELVLRVAELAPDPRTRVIVNCAGRTRSIIGTQSLLNAGIPNPVAALRNGTI  117 (136)
T ss_dssp             SEEEEECSCHHHHHHSBCTT-CEECCGGGHHHHHHHHCCSTTSEEEEECSSSHHHHHHHHHHHHTTCSSCEEEETTHHH
T ss_pred             CcEEEEcCChhhccceecCC-chhhhhhHHHHHhhcccccccceEEEEcCCCCchHHHHHHHHHcCCCceEEEeCCcHH
Confidence            456777765431 1111111 1223433333334444444455799999999999999999999998  3888999864

>d1qxna_ c.46.1.3 (A:) Polysulfide-sulfur transferase (sulfide dehydrogenase, Sud) {Wolinella succinogenes [TaxId: 844]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Polysulfide-sulfur transferase (sulfide dehydrogenase, Sud)
species: Wolinella succinogenes [TaxId: 844]

Probab=92.60  E-value=0.13  Score=33.14  Aligned_cols=37  Identities=16%  Similarity=0.239  Sum_probs=32.5

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCC-CeEeecCCCCh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGK-PFFTLKSLKED  189 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~-~~~~~h~~~~~  189 (197)
                      ..++++||.+-.++...+..|++.|+ ++..+.||+..
T Consensus        82 ~~~ivvyC~~G~rs~~aa~~L~~~G~~nV~~l~GG~~~  119 (137)
T d1qxna_          82 EKPVVVFCKTAARAALAGKTLREYGFKTIYNSEGGMDK  119 (137)
T ss_dssp             TSCEEEECCSSSCHHHHHHHHHHHTCSCEEEESSCHHH
T ss_pred             ccceeeeecccchHHHHHHHHHHcCCCcEEEecCHHHH
Confidence            45799999999999999999999999 68889998753

>d2eyqa2 c.37.1.19 (A:349-465) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=92.45  E-value=0.061  Score=33.82  Aligned_cols=47  Identities=19%  Similarity=0.148  Sum_probs=38.9

Q ss_pred             hhhHHHHHHHhhcCCCCEEEEecccccHHHHHHHHHhCCCCeEeecC
Q psy7789         139 EAKIVYLLECLQKTEPPVLIFAEKKQDVDAIHEYLLLKGKPFFTLKS  185 (197)
Q Consensus       139 ~~k~~~l~~~l~~~~~~~lIF~~s~~~~~~l~~~L~~~~~~~~~~h~  185 (197)
                      .+-+..|..++++...++|+.|.|....+.+.+.|++.|+++..+.+
T Consensus        20 ~~p~~~L~~~i~~~~~~Vli~a~s~g~~erl~e~L~~~~i~~~~~~~   66 (117)
T d2eyqa2          20 KAPLDALRKFLETFDGPVVFSVESEGRREALGELLARIKIAPQRIMR   66 (117)
T ss_dssp             SSTTHHHHHHHTTCCSCCCEEESSHHHHHHHHHHHGGGTCCCEECSS
T ss_pred             hcHHHHHHHHHHhCCCeEEEEECCccHHHHHHHHHHHcCCCceEecC
Confidence            34567788888887779999999999999999999999887655543

>d1tq1a_ c.46.1.3 (A:) Thiosulfate sulfurtransferase/Senescence-associated protein {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Thiosulfate sulfurtransferase/Senescence-associated protein
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=92.15  E-value=0.052  Score=34.13  Aligned_cols=36  Identities=8%  Similarity=-0.071  Sum_probs=32.4

Q ss_pred             CCEEEEecccccHHHHHHHHHhCCC-CeEeecCCCCh
Q psy7789         154 PPVLIFAEKKQDVDAIHEYLLLKGK-PFFTLKSLKED  189 (197)
Q Consensus       154 ~~~lIF~~s~~~~~~l~~~L~~~~~-~~~~~h~~~~~  189 (197)
                      .++++||++-.++...+..|.+.|+ ++..+.||+..
T Consensus        73 ~~iv~~C~~G~rs~~a~~~L~~~G~~nv~~l~GG~~~  109 (119)
T d1tq1a_          73 DNIIVGCQSGGRSIKATTDLLHAGFTGVKDIVGGYSA  109 (119)
T ss_dssp             SSEEEEESSCSHHHHHHHHHHHHHCCSEEEEECCHHH
T ss_pred             cEEEEEcCCcCcHHHHHHHHHhcccCCeEEecChHHH
Confidence            5799999999999999999999998 69999999864

>d1gmxa_ c.46.1.3 (A:) Sulfurtransferase GlpE {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Single-domain sulfurtransferase
domain: Sulfurtransferase GlpE
species: Escherichia coli [TaxId: 562]

Probab=91.96  E-value=0.1  Score=32.05  Aligned_cols=38  Identities=18%  Similarity=0.366  Sum_probs=33.1

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCC-CeEeecCCCChh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGK-PFFTLKSLKEDQ  190 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~-~~~~~h~~~~~~  190 (197)
                      ..++++||.+-.++...+..|.+.|+ ++..+.||+..=
T Consensus        58 ~~~ivv~c~~g~rs~~~a~~L~~~G~~~v~~l~GG~~~W   96 (108)
T d1gmxa_          58 DTPVMVMCYHGNSSKGAAQYLLQQGYDVVYSIDGGFEAW   96 (108)
T ss_dssp             TSCEEEECSSSSHHHHHHHHHHHHTCSSEEEETTHHHHH
T ss_pred             cCcccccCCCChHHHHHHHHHHHcCCCCEEEEcChHHHH
Confidence            35799999999999999999999999 588899987653

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=91.87  E-value=0.069  Score=37.49  Aligned_cols=60  Identities=12%  Similarity=0.184  Sum_probs=37.9

Q ss_pred             CcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEeecCC
Q psy7789          35 CHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMP  100 (197)
Q Consensus        35 ~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SAT~~  100 (197)
                      .+|+++|.+.+...-.   +.--..+++|+||+|.+-...... ... ...+. ....+++|+|.-
T Consensus       104 ~~vvi~~~~~~~~~~~---l~~~~~~~vI~DEah~~k~~~s~~-~~~-~~~l~-a~~r~~LTgTPi  163 (230)
T d1z63a1         104 YDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKNPQTKI-FKA-VKELK-SKYRIALTGTPI  163 (230)
T ss_dssp             SSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSCTTSHH-HHH-HHTSC-EEEEEEECSSCS
T ss_pred             cCEEEeeHHHHHhHHH---HhcccceEEEEEhhhcccccchhh-hhh-hhhhc-cceEEEEecchH
Confidence            6899999877654321   222356789999999997653322 222 33342 445788999963

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=90.94  E-value=0.15  Score=35.50  Aligned_cols=67  Identities=10%  Similarity=0.192  Sum_probs=48.7

Q ss_pred             CCeeEEEEEcCCChHHhHHHHh----cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhc
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIK----KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFF   86 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~----~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~   86 (197)
                      .++++.+++|..+.++..+.+.    +..+|+|||.     .++ .-++..+...+||..||++    -..++..+..+.
T Consensus        56 p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Tt-----vIE-vGiDvpnA~~iiI~~a~rf----GLaQLhQLRGRV  125 (211)
T d2eyqa5          56 PEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT-----IIE-TGIDIPTANTIIIERADHF----GLAQLHQLRGRV  125 (211)
T ss_dssp             TTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS-----TTG-GGSCCTTEEEEEETTTTSS----CHHHHHHHHTTC
T ss_pred             CceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEeh-----hhh-hccCCCCCcEEEEecchhc----ccccccccccee
Confidence            3789999999987665554443    4599999994     444 5567889999999999997    234555665555


Q ss_pred             c
Q psy7789          87 R   87 (197)
Q Consensus        87 ~   87 (197)
                      .
T Consensus       126 G  126 (211)
T d2eyqa5         126 G  126 (211)
T ss_dssp             C
T ss_pred             e
Confidence            3

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=90.24  E-value=0.22  Score=34.11  Aligned_cols=65  Identities=9%  Similarity=0.107  Sum_probs=42.0

Q ss_pred             CCcEEEeCchH-------HHHHH---hcCCccCCCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEeecCC
Q psy7789          34 GCHMMVATPGR-------LMDML---DKKMVSLDVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSATMP  100 (197)
Q Consensus        34 ~~~Ili~TP~~-------l~~~l---~~~~~~l~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SAT~~  100 (197)
                      .||++.-.|+.       +.++.   .... ..+..+.+|+||||.|-.. ....+.+++.--|++..+++++....
T Consensus        46 h~D~~~i~~~~~~I~Id~IR~i~~~~~~~~-~~~~~KviIId~ad~l~~~-aqNaLLK~LEEPp~~t~fiLit~~~~  120 (198)
T d2gnoa2          46 ASDVLEIDPEGENIGIDDIRTIKDFLNYSP-ELYTRKYVIVHDCERMTQQ-AANAFLKALEEPPEYAVIVLNTRRWH  120 (198)
T ss_dssp             TTTEEEECCSSSCBCHHHHHHHHHHHTSCC-SSSSSEEEEETTGGGBCHH-HHHHTHHHHHSCCTTEEEEEEESCGG
T ss_pred             CCCEEEEeCCcCCCCHHHHHHHHHHHhhCc-ccCCCEEEEEeCccccchh-hhhHHHHHHhCCCCCceeeeccCChh
Confidence            48999988852       23322   2222 2477889999999999543 34455566666666777777765543

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=88.96  E-value=0.25  Score=34.28  Aligned_cols=92  Identities=14%  Similarity=0.175  Sum_probs=52.6

Q ss_pred             CCCCeeEEEEEcCCC--hHHhHHH-----HhcCCcEEEeCchHHHHHHhc----CC-----ccCCCccEEEeehhhhhhc
Q psy7789           9 LPIPLRTCLAIGGVP--MNQSLDV-----IKKGCHMMVATPGRLMDMLDK----KM-----VSLDVCRYLCLDEADRMVD   72 (197)
Q Consensus         9 ~~~~i~~~~~~gg~~--~~~~~~~-----l~~~~~Ili~TP~~l~~~l~~----~~-----~~l~~l~~vViDEad~l~~   72 (197)
                      .+...++..++|...  ...-...     ...+..++..+...+...+..    +.     -.+...+++++|++|.+..
T Consensus        32 ~~~~~n~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dll~iDDi~~i~~  111 (213)
T d1l8qa2          32 LGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSG  111 (213)
T ss_dssp             TTTSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHHHHHHHHHHHHTCHHHHHHHHHTCSEEEEECGGGGTT
T ss_pred             cCCCCCcEEEECCCCCcHHHHHHHHHHHhccCccceEEechHHHHHHHHHHHHccchhhHHHHHhhccchhhhhhhhhcC
Confidence            344456678888754  3333322     234677777776666554321    11     1256789999999999975


Q ss_pred             CC-CHHHHHHHHhhccC-CceEEEEeecCCh
Q psy7789          73 MG-FEEDVRTIFSFFRG-QRQTLLFSATMPK  101 (197)
Q Consensus        73 ~~-~~~~i~~i~~~~~~-~~q~i~~SAT~~~  101 (197)
                      .. ....+-.++..+.. ..++++ |+..++
T Consensus       112 ~~~~~~~lf~lin~~~~~~~~iii-ts~~~p  141 (213)
T d1l8qa2         112 KERTQIEFFHIFNTLYLLEKQIIL-ASDRHP  141 (213)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCEEEE-EESSCG
T ss_pred             chHHHHHHHHHHHHHhhccceEEE-ecCCcc
Confidence            42 34445556655543 455555 555443

>d1urha2 c.46.1.2 (A:149-268) 3-mercaptopyruvate sulfurtransferase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Rhodanese/Cell cycle control phosphatase
superfamily: Rhodanese/Cell cycle control phosphatase
family: Multidomain sulfurtransferase (rhodanese)
domain: 3-mercaptopyruvate sulfurtransferase
species: Escherichia coli [TaxId: 562]

Probab=88.18  E-value=0.54  Score=28.91  Aligned_cols=37  Identities=5%  Similarity=0.009  Sum_probs=31.8

Q ss_pred             CCCEEEEecccccHHHHHHHHHhCCC-CeEeecCCCCh
Q psy7789         153 EPPVLIFAEKKQDVDAIHEYLLLKGK-PFFTLKSLKED  189 (197)
Q Consensus       153 ~~~~lIF~~s~~~~~~l~~~L~~~~~-~~~~~h~~~~~  189 (197)
                      ..++++||++=.++-..+..|+..|+ ++..+.|+++.
T Consensus        82 ~~~ii~yC~sG~~A~~~~~~L~~lG~~~v~~y~Gs~~e  119 (120)
T d1urha2          82 DKPIIVSCGSGVTAAVVLLALATLDVPNVKLYDGAWSE  119 (120)
T ss_dssp             SSCEEEECCSSSTHHHHHHHHHHTTCSSCEEECCSCCC
T ss_pred             cCceEEEccchhHHHHHHHHHHHcCCCCceEcCCChhh
Confidence            35799999998889999999999998 58888998863

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=87.84  E-value=2.6  Score=27.98  Aligned_cols=89  Identities=12%  Similarity=0.134  Sum_probs=55.9

Q ss_pred             CCeeEEEEEcCCChHHhHHHHh----cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhcC-CCHHHHHHHHhh
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIK----KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVDM-GFEEDVRTIFSF   85 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~----~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~~-~~~~~i~~i~~~   85 (197)
                      .|+++..++|+.+..+..+.+.    +..+|||+|.     ++. .-++..++++||+=.++..... .....++.+-+.
T Consensus        54 ~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~-----v~~-~GiDip~V~~Vi~~~~~~~~~~~~~~~~iq~~GR~  127 (174)
T d1c4oa2          54 HGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGIN-----LLR-EGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRA  127 (174)
T ss_dssp             TTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESC-----CCC-TTCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGG
T ss_pred             cCCceEEEecccchHHHHHHHHHHHCCCeEEEEeee-----eee-eeccCCCCcEEEEeccccccccchhHHHHHHhhhh
Confidence            3899999999998666654443    4599999993     443 5668899999998777654321 123344444433


Q ss_pred             ccC-CceEEEEeecCChhHHH
Q psy7789          86 FRG-QRQTLLFSATMPKKIQN  105 (197)
Q Consensus        86 ~~~-~~q~i~~SAT~~~~~~~  105 (197)
                      ... ....+++....+..+..
T Consensus       128 gR~~~g~~~~~~~~~~~~~~~  148 (174)
T d1c4oa2         128 ARNARGEVWLYADRVSEAMQR  148 (174)
T ss_dssp             TTSTTCEEEEECSSCCHHHHH
T ss_pred             hhcCCCeeEEeecCCCHHHHH
Confidence            332 33555555555544443

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=86.18  E-value=0.64  Score=31.24  Aligned_cols=71  Identities=11%  Similarity=0.131  Sum_probs=48.7

Q ss_pred             CCeeEEEEEcCCChHHhHHHHh----cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhhc-CCCHHHHHHHHhh
Q psy7789          11 IPLRTCLAIGGVPMNQSLDVIK----KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMVD-MGFEEDVRTIFSF   85 (197)
Q Consensus        11 ~~i~~~~~~gg~~~~~~~~~l~----~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~~-~~~~~~i~~i~~~   85 (197)
                      .|+++..++|+.+..++.+.+.    +..+|||||.     .+. .-++..++++||.-+++.... .++...+..+-+.
T Consensus        54 ~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTd-----v~~-rGiDip~v~~VI~~d~p~~~~~~s~~~yi~R~GRa  127 (181)
T d1t5la2          54 AGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN-----LLR-EGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRA  127 (181)
T ss_dssp             TTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESC-----CCS-SSCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGG
T ss_pred             CCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehh-----HHH-ccCCCCCCCEEEEecCCcccccccHHHHHHHHHhh
Confidence            4899999999998776665543    4699999993     443 566889999999888875321 1234445555444


Q ss_pred             cc
Q psy7789          86 FR   87 (197)
Q Consensus        86 ~~   87 (197)
                      -.
T Consensus       128 gR  129 (181)
T d1t5la2         128 AR  129 (181)
T ss_dssp             TT
T ss_pred             cc
Confidence            33

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=84.21  E-value=1.1  Score=29.37  Aligned_cols=52  Identities=19%  Similarity=0.270  Sum_probs=42.3

Q ss_pred             CCCccEEEeehhhhhhcCCC--HHHHHHHHhhccCCceEEEEeecCChhHHHHH
Q psy7789          56 LDVCRYLCLDEADRMVDMGF--EEDVRTIFSFFRGQRQTLLFSATMPKKIQNFA  107 (197)
Q Consensus        56 l~~l~~vViDEad~l~~~~~--~~~i~~i~~~~~~~~q~i~~SAT~~~~~~~~~  107 (197)
                      -...++||+||+-..++.++  .+.+..+++.-|...-+|+..-..|+++.+.+
T Consensus        92 ~~~~dllILDEi~~Ai~~gli~~~~v~~ll~~rp~~~evVlTGr~~p~~L~e~A  145 (157)
T d1g5ta_          92 DPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILDLA  145 (157)
T ss_dssp             CTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHHHC
T ss_pred             cCccCEEeHHHHHHHHHcCCCCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhc
Confidence            36689999999998888774  56788888888888888888888888876654

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=82.75  E-value=0.12  Score=35.83  Aligned_cols=59  Identities=10%  Similarity=0.208  Sum_probs=41.3

Q ss_pred             ccCCCCeeEEEEEcCCChHHhHHH---Hh-cCCcEEEeCchHHHHHHhcCCccCCCccEEEeehhhhhh
Q psy7789           7 SALPIPLRTCLAIGGVPMNQSLDV---IK-KGCHMMVATPGRLMDMLDKKMVSLDVCRYLCLDEADRMV   71 (197)
Q Consensus         7 ~~~~~~i~~~~~~gg~~~~~~~~~---l~-~~~~Ili~TP~~l~~~l~~~~~~l~~l~~vViDEad~l~   71 (197)
                      +....++++.+++|+.+.++..+.   +. +..+|+|||.     .+. .-++..+..++|+..++.+.
T Consensus        59 ~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLVaTt-----ViE-~GIDip~a~~iii~~a~~fg  121 (206)
T d1gm5a4          59 KEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTT-----VIE-VGIDVPRANVMVIENPERFG  121 (206)
T ss_dssp             GSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSS-----CCC-SCSCCTTCCEEEBCSCSSSC
T ss_pred             HhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEEEEeh-----hhh-ccccccCCcEEEEEccCCcc
Confidence            334457899999999875554444   43 3599999993     443 55678999999999999873

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=82.45  E-value=0.51  Score=32.95  Aligned_cols=40  Identities=10%  Similarity=-0.001  Sum_probs=24.9

Q ss_pred             CCccEEEeehhhhhhcCCCHHHHHHHHhhccCCceEEEEee
Q psy7789          57 DVCRYLCLDEADRMVDMGFEEDVRTIFSFFRGQRQTLLFSA   97 (197)
Q Consensus        57 ~~l~~vViDEad~l~~~~~~~~i~~i~~~~~~~~q~i~~SA   97 (197)
                      ...+.+|+||+|.+... ....+..++...+++..+++.+.
T Consensus       114 ~~~kviiIde~d~l~~~-~q~~Llk~lE~~~~~~~~il~tn  153 (239)
T d1njfa_         114 GRFKVYLIDEVHMLSRH-SFNALLKTLEEPPEHVKFLLATT  153 (239)
T ss_dssp             SSSEEEEEETGGGSCHH-HHHHHHHHHHSCCTTEEEEEEES
T ss_pred             CCCEEEEEECcccCCHH-HHHHHHHHHhcCCCCeEEEEEcC
Confidence            45679999999998432 33445555555455555555543