Psyllid ID: psy1548

---

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-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------45
Protein Sequence
VEESRSSQEKLSCGSGNVFLFFRAFIRFSSSFPHSKMADNDDLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR
Secondary Structure (PSIPRED)
cccccHHHHHHcccccEEEEEEEEEEEEcccccccccccccccccccccccccccccccHHHHHHHHHHHcccEEEEccccccccccHHHHHHHHHccccEEEEcccccccccccccEEEEEcccccccccHHcccccccccccccccccEEEEEEcccccccHHHHHHHHHHcccccccEEEEEEcccHHHHHHHHHHHHHHHccccccEEEEEEccccHHHHHHHHHHccccEEEcccHHHHHHHcccccccccccEEEEEcccccccccccHHHHHHHHHHccccccEEEEEccccHHHHHHHHHHcccccEEEEcccccccccccEEEEEEcccccHHHHHHHHHccccccEEEEEEccHHHHHHHHHHHHHccccEEcccccccHHHHHHHHHHHHcccccccEEEEccHHccccccccccccEEEEcccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccHHHHccccccccccHHHHHHHHHHcccccccccHHccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccEEEcccccccccccHHHccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEccccHHHHHHHHHHHHHHcccccccccEEEEcccHHHHHHHHHHHHHHHHHccccEEEEEEccccHHHHHHHHHHccccEEEEcHHHHHHHHcccccccccccEEEEccHHHHHHHcccHHHHHHHHHHccHHHcEEEEEccccHHHHHHHHHHHcccEEEEEcccccccccccEEEEEEEccHHHHHHHHHHHHHcccccEEEEEcccHHHHHHHHHHHHccccHHHHcccccHHHHHHHHHHHHcccccccEEEEHHHHHHHHHccccccEEEEEEcccccccHcEEEccc
Coil and Loop (DISEMBL)
veesrssqeklscgsgnVFLFFRAFIRfsssfphskmadnddlldyedeenteQIVADGAGDALAKQKEVKGAYVSIHSsgfrdfllkPEILRAIVDCWRILVATNlfgrgmdierVNIVfnydmpedsdtYLHRVARAGRFGTKAVLGMDILCqaksgmgkTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVgvffgglpiqkdeeylkthnpqivvgtpGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIfrssphtkQVMMFSATLSKEIRPVckkfmhdpmevyvddeaKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTllseqnfpavsihrgMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDrfdvsiselpdeidlstyiegr
Flexible Loop (DISEMBL)
veesrssqeklscgsgNVFLFFRAFIRFSSSFPHSKMADNDDLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATnlfgrgmdieRVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKThnpqivvgtpgRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEifrssphtkqVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALStllseqnfpavsIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDrfdvsiselpdeidlstyiegr
Low Complexity Region (SEG)
VEESRSSQEKLSCGSGNVflffrafirfsssfPHSKMAdnddlldyedeenteQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVklkeneknkklfellDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR
Disordered region (IsUnstruct)
************CGSGNVFLFFRAFIRFSS*********************************LAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFR****TKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISE**************
Disordered Region (DISOPRED)
*************GSGNVFLFFRAFIRFSSSFPHSKMADNDDLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFR**LL*PEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR
Disordered Region (DISEMBL)
************CGSGNVFLFFRAFIRFSSSFPHSKMADNDDLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR
Disordered Region (DISPRO)
***********SCGSGNVFLFFRAFIRFSSSFPHSKMADNDDLLDYEDEEN******DGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEG*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
VEESRSSQEKLSCGSGNVFLFFRAFIRFSSSFPHSKMADNDDLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	448	2.2.26 [Sep-21-2011]
Q27268	424	ATP-dependent RNA helicas	yes	N/A	0.841	0.889	0.681	1e-163
Q5RE47	428	Spliceosome RNA helicase	yes	N/A	0.839	0.878	0.642	1e-158
Q29024	428	Spliceosome RNA helicase	yes	N/A	0.839	0.878	0.642	1e-158
P60024	428	Spliceosome RNA helicase	yes	N/A	0.839	0.878	0.642	1e-158
Q5TM17	428	Spliceosome RNA helicase	yes	N/A	0.839	0.878	0.642	1e-158
Q13838	428	Spliceosome RNA helicase	yes	N/A	0.839	0.878	0.642	1e-158
Q63413	428	Spliceosome RNA helicase	yes	N/A	0.839	0.878	0.642	1e-158
Q9Z1N5	428	Spliceosome RNA helicase	yes	N/A	0.839	0.878	0.642	1e-158
Q5WR10	428	Spliceosome RNA helicase	yes	N/A	0.839	0.878	0.633	1e-157
Q3T147	428	Spliceosome RNA helicase	yes	N/A	0.839	0.878	0.640	1e-157

>sp|Q27268|DX39B_DROME ATP-dependent RNA helicase WM6 OS=Drosophila melanogaster GN=Hel25E PE=1 SV=1

 Score =  576 bits (1484), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 313/459 (68%), Positives = 338/459 (73%), Gaps = 82/459 (17%)

Query: 37  MADNDDLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIV 96
           MADNDDLLDYEDEE TE    +      A +K+VKG YVSIHSSGFRDFLLKPEILRAIV
Sbjct: 1   MADNDDLLDYEDEEQTETTAVENQE---APKKDVKGTYVSIHSSGFRDFLLKPEILRAIV 57

Query: 97  DCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQA 156
           DC                E  + V +  +P+                  AVLGMDILCQA
Sbjct: 58  DCG--------------FEHPSEVQHECIPQ------------------AVLGMDILCQA 85

Query: 157 KSGMGKTAVFVLATLQQLETTDSNV-YVLVMCHTRELAFQISKEYERFSKYMSNIKVGVF 215
           KSGMGKTAVFVLATLQQLE +D+N  +VLVMCHTRELAFQISKEYERFSKYM  +KV VF
Sbjct: 86  KSGMGKTAVFVLATLQQLEPSDNNTCHVLVMCHTRELAFQISKEYERFSKYMPTVKVAVF 145

Query: 216 FGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMR 275
           FGG+ IQKDEE LK+  P IVVGTPGRILAL+RNKKLNL LLKHF+LDECDKMLEQL+MR
Sbjct: 146 FGGMAIQKDEETLKSGTPHIVVGTPGRILALIRNKKLNLKLLKHFVLDECDKMLEQLDMR 205

Query: 276 RDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVK 335
           RDVQEIFRS+PH KQVMMFSATLSK+IRPVCKKFM DPMEVYVDDEAKLTLHGLQQHYV 
Sbjct: 206 RDVQEIFRSTPHGKQVMMFSATLSKDIRPVCKKFMQDPMEVYVDDEAKLTLHGLQQHYVN 265

Query: 336 LKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLK 395
           LKENEKNKKLFELLDVLEFNQVVIFVKSV RC+ALS LL+EQNFPA+ IHRGMTQEERL 
Sbjct: 266 LKENEKNKKLFELLDVLEFNQVVIFVKSVQRCVALSQLLTEQNFPAIGIHRGMTQEERLN 325

Query: 396 KYQEFKDFH----------------------------------------------KGLAI 409
           +YQ+FKDF                                               KGLAI
Sbjct: 326 RYQQFKDFQKRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAI 385

Query: 410 TFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR 448
           TF SDENDAKILN VQDRFDV+ISELP+EIDLSTYIEGR
Sbjct: 386 TFVSDENDAKILNEVQDRFDVNISELPEEIDLSTYIEGR 424

Required for mRNA export out of the nucleus. Probable RNA helicase that may regulate entry into mitosis by down-regulating the expression of other genes whose activity may be rate-limiting for entry into mitosis during embryogenesis. Binds to salivary gland chromosomes and modifies position effect variegation. Promotes an open chromatin structure that favors transcription during development by regulating the spread of heterochromatin.
Drosophila melanogaster (taxid: 7227)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q5RE47|DX39B_PONAB Spliceosome RNA helicase DDX39B OS=Pongo abelii GN=DDX39B PE=2 SV=1

 Score =  556 bits (1434), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 295/459 (64%), Positives = 331/459 (72%), Gaps = 83/459 (18%)

Query: 37  MADND---DLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILR 93
           MA+ND   +LLDYED+E       DGA +A AK K+VKG+YVSIHSSGFRDFLLKPE+LR
Sbjct: 1   MAENDVDNELLDYEDDEVETAAGGDGA-EAPAK-KDVKGSYVSIHSSGFRDFLLKPELLR 58

Query: 94  AIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDIL 153
           AIVDC         F    +++   I                         +A+LGMD+L
Sbjct: 59  AIVDCG--------FEHPSEVQHECI------------------------PQAILGMDVL 86

Query: 154 CQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG 213
           CQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQISKEYERFSKYM N+KV 
Sbjct: 87  CQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVA 146

Query: 214 VFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLE 273
           VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK LNL  +KHFILDECDKMLEQL+
Sbjct: 147 VFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLD 206

Query: 274 MRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHY 333
           MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++VDDE KLTLHGLQQ+Y
Sbjct: 207 MRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYY 266

Query: 334 VKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEER 393
           VKLK+NEKN+KLF+LLDVLEFNQVVIFVKSV RCIAL+ LL EQNFPA++IHRGM QEER
Sbjct: 267 VKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEER 326

Query: 394 LKKYQEFKDFH----------------------------------------------KGL 407
           L +YQ+FKDF                                               KGL
Sbjct: 327 LSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGL 386

Query: 408 AITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIE 446
           AITF SDENDAKILN+VQDRF+V+ISELPDEID+S+YIE
Sbjct: 387 AITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIE 425

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q29024|DX39B_PIG Spliceosome RNA helicase DDX39B OS=Sus scrofa GN=DDX39B PE=2 SV=2

 Score =  556 bits (1434), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 295/459 (64%), Positives = 331/459 (72%), Gaps = 83/459 (18%)

Query: 37  MADND---DLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILR 93
           MA+ND   +LLDYED+E       DGA +A AK K+VKG+YVSIHSSGFRDFLLKPE+LR
Sbjct: 1   MAENDVDNELLDYEDDEVETAAGGDGA-EAPAK-KDVKGSYVSIHSSGFRDFLLKPELLR 58

Query: 94  AIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDIL 153
           AIVDC         F    +++   I                         +A+LGMD+L
Sbjct: 59  AIVDCG--------FEHPSEVQHECI------------------------PQAILGMDVL 86

Query: 154 CQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG 213
           CQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQISKEYERFSKYM N+KV 
Sbjct: 87  CQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVA 146

Query: 214 VFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLE 273
           VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK LNL  +KHFILDECDKMLEQL+
Sbjct: 147 VFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLD 206

Query: 274 MRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHY 333
           MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++VDDE KLTLHGLQQ+Y
Sbjct: 207 MRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYY 266

Query: 334 VKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEER 393
           VKLK+NEKN+KLF+LLDVLEFNQVVIFVKSV RCIAL+ LL EQNFPA++IHRGM QEER
Sbjct: 267 VKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEER 326

Query: 394 LKKYQEFKDFH----------------------------------------------KGL 407
           L +YQ+FKDF                                               KGL
Sbjct: 327 LSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGL 386

Query: 408 AITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIE 446
           AITF SDENDAKILN+VQDRF+V+ISELPDEID+S+YIE
Sbjct: 387 AITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIE 425

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Sus scrofa (taxid: 9823)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P60024|DX39B_PANTR Spliceosome RNA helicase DDX39B OS=Pan troglodytes GN=DDX39B PE=3 SV=1

 Score =  556 bits (1434), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 295/459 (64%), Positives = 331/459 (72%), Gaps = 83/459 (18%)

Query: 37  MADND---DLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILR 93
           MA+ND   +LLDYED+E       DGA +A AK K+VKG+YVSIHSSGFRDFLLKPE+LR
Sbjct: 1   MAENDVDNELLDYEDDEVETAAGGDGA-EAPAK-KDVKGSYVSIHSSGFRDFLLKPELLR 58

Query: 94  AIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDIL 153
           AIVDC         F    +++   I                         +A+LGMD+L
Sbjct: 59  AIVDCG--------FEHPSEVQHECI------------------------PQAILGMDVL 86

Query: 154 CQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG 213
           CQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQISKEYERFSKYM N+KV 
Sbjct: 87  CQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVA 146

Query: 214 VFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLE 273
           VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK LNL  +KHFILDECDKMLEQL+
Sbjct: 147 VFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLD 206

Query: 274 MRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHY 333
           MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++VDDE KLTLHGLQQ+Y
Sbjct: 207 MRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYY 266

Query: 334 VKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEER 393
           VKLK+NEKN+KLF+LLDVLEFNQVVIFVKSV RCIAL+ LL EQNFPA++IHRGM QEER
Sbjct: 267 VKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEER 326

Query: 394 LKKYQEFKDFH----------------------------------------------KGL 407
           L +YQ+FKDF                                               KGL
Sbjct: 327 LSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGL 386

Query: 408 AITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIE 446
           AITF SDENDAKILN+VQDRF+V+ISELPDEID+S+YIE
Sbjct: 387 AITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIE 425

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Pan troglodytes (taxid: 9598)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5TM17|DX39B_MACMU Spliceosome RNA helicase DDX39B OS=Macaca mulatta GN=DDX39B PE=3 SV=1

 Score =  556 bits (1434), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 295/459 (64%), Positives = 331/459 (72%), Gaps = 83/459 (18%)

Query: 37  MADND---DLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILR 93
           MA+ND   +LLDYED+E       DGA +A AK K+VKG+YVSIHSSGFRDFLLKPE+LR
Sbjct: 1   MAENDVDNELLDYEDDEVETAAGGDGA-EAPAK-KDVKGSYVSIHSSGFRDFLLKPELLR 58

Query: 94  AIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDIL 153
           AIVDC         F    +++   I                         +A+LGMD+L
Sbjct: 59  AIVDCG--------FEHPSEVQHECI------------------------PQAILGMDVL 86

Query: 154 CQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG 213
           CQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQISKEYERFSKYM N+KV 
Sbjct: 87  CQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVA 146

Query: 214 VFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLE 273
           VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK LNL  +KHFILDECDKMLEQL+
Sbjct: 147 VFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLD 206

Query: 274 MRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHY 333
           MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++VDDE KLTLHGLQQ+Y
Sbjct: 207 MRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYY 266

Query: 334 VKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEER 393
           VKLK+NEKN+KLF+LLDVLEFNQVVIFVKSV RCIAL+ LL EQNFPA++IHRGM QEER
Sbjct: 267 VKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEER 326

Query: 394 LKKYQEFKDFH----------------------------------------------KGL 407
           L +YQ+FKDF                                               KGL
Sbjct: 327 LSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGL 386

Query: 408 AITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIE 446
           AITF SDENDAKILN+VQDRF+V+ISELPDEID+S+YIE
Sbjct: 387 AITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIE 425

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Macaca mulatta (taxid: 9544)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q13838|DX39B_HUMAN Spliceosome RNA helicase DDX39B OS=Homo sapiens GN=DDX39B PE=1 SV=1

 Score =  556 bits (1434), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 295/459 (64%), Positives = 331/459 (72%), Gaps = 83/459 (18%)

Query: 37  MADND---DLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILR 93
           MA+ND   +LLDYED+E       DGA +A AK K+VKG+YVSIHSSGFRDFLLKPE+LR
Sbjct: 1   MAENDVDNELLDYEDDEVETAAGGDGA-EAPAK-KDVKGSYVSIHSSGFRDFLLKPELLR 58

Query: 94  AIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDIL 153
           AIVDC         F    +++   I                         +A+LGMD+L
Sbjct: 59  AIVDCG--------FEHPSEVQHECI------------------------PQAILGMDVL 86

Query: 154 CQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG 213
           CQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQISKEYERFSKYM N+KV 
Sbjct: 87  CQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVA 146

Query: 214 VFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLE 273
           VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK LNL  +KHFILDECDKMLEQL+
Sbjct: 147 VFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLD 206

Query: 274 MRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHY 333
           MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++VDDE KLTLHGLQQ+Y
Sbjct: 207 MRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYY 266

Query: 334 VKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEER 393
           VKLK+NEKN+KLF+LLDVLEFNQVVIFVKSV RCIAL+ LL EQNFPA++IHRGM QEER
Sbjct: 267 VKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEER 326

Query: 394 LKKYQEFKDFH----------------------------------------------KGL 407
           L +YQ+FKDF                                               KGL
Sbjct: 327 LSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGL 386

Query: 408 AITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIE 446
           AITF SDENDAKILN+VQDRF+V+ISELPDEID+S+YIE
Sbjct: 387 AITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIE 425

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. Can unwind 5' or 3' overhangs or blunt end RNA duplexes in vitro. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q63413|DX39B_RAT Spliceosome RNA helicase Ddx39b OS=Rattus norvegicus GN=Ddx39b PE=1 SV=3

 Score =  556 bits (1434), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 295/459 (64%), Positives = 331/459 (72%), Gaps = 83/459 (18%)

Query: 37  MADND---DLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILR 93
           MA+ND   +LLDYED+E      ADG  +A AK K+VKG+YVSIHSSGFRDFLLKPE+LR
Sbjct: 1   MAENDVDNELLDYEDDEVETAAGADGT-EAPAK-KDVKGSYVSIHSSGFRDFLLKPELLR 58

Query: 94  AIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDIL 153
           AIVDC         F    +++   I                         +A+LGMD+L
Sbjct: 59  AIVDCG--------FEHPSEVQHECI------------------------PQAILGMDVL 86

Query: 154 CQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG 213
           CQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQISKEYERFSKYM N+KV 
Sbjct: 87  CQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVA 146

Query: 214 VFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLE 273
           VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK LNL  +KHFILDECDKMLEQL+
Sbjct: 147 VFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLD 206

Query: 274 MRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHY 333
           MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++VDDE KLTLHGLQQ+Y
Sbjct: 207 MRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYY 266

Query: 334 VKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEER 393
           VKLK+NEKN+KLF+LLDVLEFNQVVIFVKSV RCIAL+ LL EQNFPA++IHRGM QEER
Sbjct: 267 VKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEER 326

Query: 394 LKKYQEFKDFH----------------------------------------------KGL 407
           L +YQ+FKDF                                               KGL
Sbjct: 327 LSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGL 386

Query: 408 AITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIE 446
           AITF SDENDAKILN+VQDRF+V+ISELPDEID+S+YIE
Sbjct: 387 AITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIE 425

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9Z1N5|DX39B_MOUSE Spliceosome RNA helicase Ddx39b OS=Mus musculus GN=Ddx39b PE=1 SV=1

 Score =  556 bits (1434), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 295/459 (64%), Positives = 331/459 (72%), Gaps = 83/459 (18%)

Query: 37  MADND---DLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILR 93
           MA+ND   +LLDYED+E      ADG  +A AK K+VKG+YVSIHSSGFRDFLLKPE+LR
Sbjct: 1   MAENDVDNELLDYEDDEVETAAGADGT-EAPAK-KDVKGSYVSIHSSGFRDFLLKPELLR 58

Query: 94  AIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDIL 153
           AIVDC         F    +++   I                         +A+LGMD+L
Sbjct: 59  AIVDCG--------FEHPSEVQHECI------------------------PQAILGMDVL 86

Query: 154 CQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG 213
           CQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQISKEYERFSKYM N+KV 
Sbjct: 87  CQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVA 146

Query: 214 VFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLE 273
           VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK LNL  +KHFILDECDKMLEQL+
Sbjct: 147 VFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLD 206

Query: 274 MRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHY 333
           MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++VDDE KLTLHGLQQ+Y
Sbjct: 207 MRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYY 266

Query: 334 VKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEER 393
           VKLK+NEKN+KLF+LLDVLEFNQVVIFVKSV RCIAL+ LL EQNFPA++IHRGM QEER
Sbjct: 267 VKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEER 326

Query: 394 LKKYQEFKDFH----------------------------------------------KGL 407
           L +YQ+FKDF                                               KGL
Sbjct: 327 LSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGL 386

Query: 408 AITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIE 446
           AITF SDENDAKILN+VQDRF+V+ISELPDEID+S+YIE
Sbjct: 387 AITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIE 425

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5WR10|DX39B_CANFA Spliceosome RNA helicase DDX39B OS=Canis familiaris GN=DDX39B PE=3 SV=1

 Score =  555 bits (1431), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 291/459 (63%), Positives = 329/459 (71%), Gaps = 83/459 (18%)

Query: 37  MADND---DLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILR 93
           MA+ND   +LLDYE++E   +  A G G     +K+VKG+YVSIHSSGFRDFLLKPE+LR
Sbjct: 1   MAENDVDNELLDYEEDEV--ETAAGGDGSEAPAKKDVKGSYVSIHSSGFRDFLLKPELLR 58

Query: 94  AIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDIL 153
           AIVDC         F    +++   I                         +A+LGMD+L
Sbjct: 59  AIVDCG--------FEHPSEVQHECI------------------------PQAILGMDVL 86

Query: 154 CQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG 213
           CQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQISKEYERFSKYM N+KV 
Sbjct: 87  CQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVA 146

Query: 214 VFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLE 273
           VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK LNL  +KHFILDECDKMLEQL+
Sbjct: 147 VFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLD 206

Query: 274 MRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHY 333
           MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++VDDE KLTLHGLQQ+Y
Sbjct: 207 MRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYY 266

Query: 334 VKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEER 393
           VKLK+NEKN+KLF+LLDVLEFNQVVIFVKSV RCIAL+ LL EQNFPA++IHRGM QEER
Sbjct: 267 VKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEER 326

Query: 394 LKKYQEFKDFH----------------------------------------------KGL 407
           L +YQ+FKDF                                               KGL
Sbjct: 327 LSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGL 386

Query: 408 AITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIE 446
           AITF SDENDAKILN+VQDRF+V+ISELPDEID+S+YIE
Sbjct: 387 AITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIE 425

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Canis familiaris (taxid: 9615)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q3T147|DX39B_BOVIN Spliceosome RNA helicase DDX39B OS=Bos taurus GN=DDX39B PE=2 SV=1

 Score =  554 bits (1428), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 294/459 (64%), Positives = 331/459 (72%), Gaps = 83/459 (18%)

Query: 37  MADND---DLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILR 93
           MA+ND   +LLDYED+E       DGA +A AK K+VKG+YVSIHSSGFRDFLLKPE+LR
Sbjct: 1   MAENDVDNELLDYEDDEVETAAGGDGA-EAPAK-KDVKGSYVSIHSSGFRDFLLKPELLR 58

Query: 94  AIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDIL 153
           AIVDC         F    +++   I                         +A+LGMD+L
Sbjct: 59  AIVDCG--------FEHPSEVQHECI------------------------PQAILGMDVL 86

Query: 154 CQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG 213
           CQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQISKEYERFSKYM ++KV 
Sbjct: 87  CQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPSVKVA 146

Query: 214 VFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLE 273
           VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK LNL  +KHFILDECDKMLEQL+
Sbjct: 147 VFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLD 206

Query: 274 MRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHY 333
           MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++VDDE KLTLHGLQQ+Y
Sbjct: 207 MRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYY 266

Query: 334 VKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEER 393
           VKLK+NEKN+KLF+LLDVLEFNQVVIFVKSV RCIAL+ LL EQNFPA++IHRGM QEER
Sbjct: 267 VKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEER 326

Query: 394 LKKYQEFKDFH----------------------------------------------KGL 407
           L +YQ+FKDF                                               KGL
Sbjct: 327 LSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGL 386

Query: 408 AITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIE 446
           AITF SDENDAKILN+VQDRF+V+ISELPDEID+S+YIE
Sbjct: 387 AITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIE 425

Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. The ATPase and helicase activities are not influenced by U2AF2 and ALYREF/THOC4.

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	448
194856731	424	GG24297 [Drosophila erecta] gi|195473856	0.841	0.889	0.679	1e-167
321453633	425	hypothetical protein DAPPUDRAFT_219465 [	0.845	0.891	0.670	1e-166
194759123	424	GF14747 [Drosophila ananassae] gi|190615	0.841	0.889	0.679	1e-166
198476804	424	GA20225 [Drosophila pseudoobscura pseudo	0.841	0.889	0.679	1e-166
195118098	424	GI21901 [Drosophila mojavensis] gi|19538	0.841	0.889	0.673	1e-165
307178480	425	Spliceosome RNA helicase Bat1 [Camponotu	0.845	0.891	0.696	1e-165
195434048	424	GK14902 [Drosophila willistoni] gi|19416	0.841	0.889	0.671	1e-165
195034694	424	GH11448 [Drosophila grimshawi] gi|193904	0.841	0.889	0.673	1e-164
156550340	425	PREDICTED: ATP-dependent RNA helicase WM	0.845	0.891	0.687	1e-164
66532824	424	PREDICTED: ATP-dependent RNA helicase WM	0.843	0.891	0.696	1e-163

>gi|194856731|ref|XP_001968815.1| GG24297 [Drosophila erecta] gi|195473856|ref|XP_002089208.1| Hel25E [Drosophila yakuba] gi|190660682|gb|EDV57874.1| GG24297 [Drosophila erecta] gi|194175309|gb|EDW88920.1| Hel25E [Drosophila yakuba]

 Score =  592 bits (1527), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 312/459 (67%), Positives = 337/459 (73%), Gaps = 82/459 (17%)

Query: 37  MADNDDLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIV 96
           MADNDDLLDYEDEE TE    +      A +K+VKG YVSIHSSGFRDFLLKPEILRAIV
Sbjct: 1   MADNDDLLDYEDEEQTETTAVENQE---APKKDVKGTYVSIHSSGFRDFLLKPEILRAIV 57

Query: 97  DCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQA 156
           DC                E  + V +  +P+                  AVLGMDILCQA
Sbjct: 58  DCG--------------FEHPSEVQHECIPQ------------------AVLGMDILCQA 85

Query: 157 KSGMGKTAVFVLATLQQLETTDSNV-YVLVMCHTRELAFQISKEYERFSKYMSNIKVGVF 215
           KSGMGKTAVFVLATLQQLE +D+N  +VLVMCHTRELAFQISKEYERFSKYM  +KV VF
Sbjct: 86  KSGMGKTAVFVLATLQQLEPSDNNTCHVLVMCHTRELAFQISKEYERFSKYMPTVKVAVF 145

Query: 216 FGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMR 275
           FGG+ IQKDEE LK+  P IVVGTPGRILAL+RNKKLNL  LKHF+LDECDKMLEQL+MR
Sbjct: 146 FGGMAIQKDEETLKSGTPHIVVGTPGRILALIRNKKLNLKHLKHFVLDECDKMLEQLDMR 205

Query: 276 RDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVK 335
           RDVQEIFRS+PH KQVMMFSATLSK+IRPVCKKFM DPMEVYVDDEAKLTLHGLQQHYV 
Sbjct: 206 RDVQEIFRSTPHGKQVMMFSATLSKDIRPVCKKFMQDPMEVYVDDEAKLTLHGLQQHYVN 265

Query: 336 LKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLK 395
           LKENEKNKKLFELLDVLEFNQVVIFVKSV RC+ALS LL+EQNFPA+ IHRGMTQEERL 
Sbjct: 266 LKENEKNKKLFELLDVLEFNQVVIFVKSVQRCVALSQLLTEQNFPAIGIHRGMTQEERLN 325

Query: 396 KYQEFKDFH----------------------------------------------KGLAI 409
           +YQ+FKDF                                               KGLAI
Sbjct: 326 RYQQFKDFQKRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAI 385

Query: 410 TFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR 448
           TF SDENDAKILN VQDRFDV+ISELP+EIDLSTYIEGR
Sbjct: 386 TFVSDENDAKILNEVQDRFDVNISELPEEIDLSTYIEGR 424

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321453633|gb|EFX64849.1| hypothetical protein DAPPUDRAFT_219465 [Daphnia pulex]

 Score =  592 bits (1526), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 307/458 (67%), Positives = 341/458 (74%), Gaps = 79/458 (17%)

Query: 37  MADNDDLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIV 96
           MADN+DLLDYEDEE TEQ+  +GAGDA AK KEVKG YVSIHSSGFRDFLLKPEILRAIV
Sbjct: 1   MADNEDLLDYEDEEATEQVAVEGAGDAPAK-KEVKGTYVSIHSSGFRDFLLKPEILRAIV 59

Query: 97  DCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQA 156
           DC                E  + V +  +P+                  AVLGMD+LCQA
Sbjct: 60  DCG--------------FEHPSEVQHECIPQ------------------AVLGMDVLCQA 87

Query: 157 KSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFF 216
           KSGMGKTAVFVLATLQQLE  ++ V VLV+CHTRELAFQISKEYERFSKYM+ IKVGVFF
Sbjct: 88  KSGMGKTAVFVLATLQQLEMVENQVSVLVLCHTRELAFQISKEYERFSKYMTTIKVGVFF 147

Query: 217 GGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRR 276
           GGL I KDE+ LK++ P IVVGTPGRILALVR+KKLNL  LKHF+LDECDKMLE L+MRR
Sbjct: 148 GGLNIAKDEQTLKSNCPHIVVGTPGRILALVRSKKLNLRTLKHFVLDECDKMLEALDMRR 207

Query: 277 DVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKL 336
           DVQEIFR++PH KQVMMFSATLSKEIRPVCKKFM DPMEVYVDDE+KLTLHGLQQHYVKL
Sbjct: 208 DVQEIFRNTPHEKQVMMFSATLSKEIRPVCKKFMQDPMEVYVDDESKLTLHGLQQHYVKL 267

Query: 337 KENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKK 396
           K+NEKN+KLFELLDVLEFNQVVIFVKS+ RC+AL  LL EQNFPA++IHR MTQEERL +
Sbjct: 268 KDNEKNRKLFELLDVLEFNQVVIFVKSIQRCMALCQLLGEQNFPAIAIHRSMTQEERLSR 327

Query: 397 YQEFKDFH----------------------------------------------KGLAIT 410
           YQ+FKDF                                               KGL IT
Sbjct: 328 YQQFKDFKKRILVATDLFGRGMDIERVNIVFNYDMPENSDSYLHRVARAGRFGTKGLGIT 387

Query: 411 FASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR 448
           F SDENDAK+LN+VQ+RFDVSI+ LPDEIDLS+YIEGR
Sbjct: 388 FVSDENDAKVLNDVQERFDVSITPLPDEIDLSSYIEGR 425

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194759123|ref|XP_001961799.1| GF14747 [Drosophila ananassae] gi|190615496|gb|EDV31020.1| GF14747 [Drosophila ananassae]

 Score =  591 bits (1523), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 312/459 (67%), Positives = 336/459 (73%), Gaps = 82/459 (17%)

Query: 37  MADNDDLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIV 96
           MADNDDLLDYEDEE TE    +      A +K+VKG YVSIHSSGFRDFLLKPEILRAIV
Sbjct: 1   MADNDDLLDYEDEEQTETTAVENQE---APKKDVKGTYVSIHSSGFRDFLLKPEILRAIV 57

Query: 97  DCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQA 156
           DC                E  + V +  +P+                  AVLGMDILCQA
Sbjct: 58  DCG--------------FEHPSEVQHECIPQ------------------AVLGMDILCQA 85

Query: 157 KSGMGKTAVFVLATLQQLETTDSNV-YVLVMCHTRELAFQISKEYERFSKYMSNIKVGVF 215
           KSGMGKTAVFVLATLQQLE +D+N  +VLVMCHTRELAFQISKEYERFSKYM  +KV VF
Sbjct: 86  KSGMGKTAVFVLATLQQLEPSDNNTCHVLVMCHTRELAFQISKEYERFSKYMPTVKVAVF 145

Query: 216 FGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMR 275
           FGGL I KDEE LK+  P IVVGTPGRILAL+RNKKLNL  LKHF+LDECDKMLEQL+MR
Sbjct: 146 FGGLAITKDEETLKSGTPHIVVGTPGRILALIRNKKLNLKHLKHFVLDECDKMLEQLDMR 205

Query: 276 RDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVK 335
           RDVQEIFRS+PH KQVMMFSATLSK+IRPVCKKFM DPMEVYVDDEAKLTLHGLQQHYV 
Sbjct: 206 RDVQEIFRSTPHGKQVMMFSATLSKDIRPVCKKFMQDPMEVYVDDEAKLTLHGLQQHYVN 265

Query: 336 LKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLK 395
           LKENEKNKKLFELLDVLEFNQVVIFVKSV RC+ALS LL+EQNFPA+ IHRGMTQEERL 
Sbjct: 266 LKENEKNKKLFELLDVLEFNQVVIFVKSVQRCVALSQLLTEQNFPAIGIHRGMTQEERLN 325

Query: 396 KYQEFKDFH----------------------------------------------KGLAI 409
           +YQ+FKDF                                               KGLAI
Sbjct: 326 RYQQFKDFQKRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAI 385

Query: 410 TFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR 448
           TF SDENDAKILN VQDRFDV+ISELP+EIDLSTYIEGR
Sbjct: 386 TFVSDENDAKILNEVQDRFDVNISELPEEIDLSTYIEGR 424

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198476804|ref|XP_001357483.2| GA20225 [Drosophila pseudoobscura pseudoobscura] gi|198137859|gb|EAL34553.2| GA20225 [Drosophila pseudoobscura pseudoobscura]

 Score =  591 bits (1523), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 312/459 (67%), Positives = 336/459 (73%), Gaps = 82/459 (17%)

Query: 37  MADNDDLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIV 96
           MADNDDLLDYEDEE TE    +      A +K+VKG YVSIHSSGFRDFLLKPEILRAIV
Sbjct: 1   MADNDDLLDYEDEEQTETTAVENQE---APKKDVKGTYVSIHSSGFRDFLLKPEILRAIV 57

Query: 97  DCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQA 156
           DC                E  + V +  +P+                  AVLGMDILCQA
Sbjct: 58  DCG--------------FEHPSEVQHECIPQ------------------AVLGMDILCQA 85

Query: 157 KSGMGKTAVFVLATLQQLETTDSNV-YVLVMCHTRELAFQISKEYERFSKYMSNIKVGVF 215
           KSGMGKTAVFVLATLQQLE  D+N  +VLVMCHTRELAFQISKEYERFSKYM  +KV VF
Sbjct: 86  KSGMGKTAVFVLATLQQLEPADNNTCHVLVMCHTRELAFQISKEYERFSKYMPTVKVAVF 145

Query: 216 FGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMR 275
           FGGL IQKDEE LK+  P IVVGTPGRILAL+RNKKLNL  LKHF+LDECDKMLEQL+MR
Sbjct: 146 FGGLAIQKDEETLKSGTPHIVVGTPGRILALIRNKKLNLKHLKHFVLDECDKMLEQLDMR 205

Query: 276 RDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVK 335
           RDVQEIFRSSPH KQVMMFSATLSK+IRPVCKKFM DPMEVYVDDEAKLTLHGLQQHYV 
Sbjct: 206 RDVQEIFRSSPHGKQVMMFSATLSKDIRPVCKKFMQDPMEVYVDDEAKLTLHGLQQHYVN 265

Query: 336 LKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLK 395
           LKENEKNKKLFELLDVLEFNQVVIFVKSV RC+AL+ LL+EQNFPA+ IHRGMTQEERL 
Sbjct: 266 LKENEKNKKLFELLDVLEFNQVVIFVKSVQRCVALAMLLTEQNFPAIGIHRGMTQEERLN 325

Query: 396 KYQEFKDFH----------------------------------------------KGLAI 409
           +YQ+FKDF                                               KGLAI
Sbjct: 326 RYQQFKDFQKRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAI 385

Query: 410 TFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR 448
           TF SD+NDAKILN VQDRFDV+ISELP+EIDLSTYIEGR
Sbjct: 386 TFVSDDNDAKILNEVQDRFDVNISELPEEIDLSTYIEGR 424

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195118098|ref|XP_002003577.1| GI21901 [Drosophila mojavensis] gi|195388486|ref|XP_002052911.1| GJ17817 [Drosophila virilis] gi|193914152|gb|EDW13019.1| GI21901 [Drosophila mojavensis] gi|194149368|gb|EDW65066.1| GJ17817 [Drosophila virilis]

 Score =  588 bits (1515), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 309/459 (67%), Positives = 333/459 (72%), Gaps = 82/459 (17%)

Query: 37  MADNDDLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIV 96
           MADNDDLLDYEDEE  E    +      A +K+VKG YVSIHSSGFRDFLLKPEILRAIV
Sbjct: 1   MADNDDLLDYEDEEQNETTAVENQE---APKKDVKGTYVSIHSSGFRDFLLKPEILRAIV 57

Query: 97  DCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQA 156
           DC         F    +++   I                         +AVLGMDILCQA
Sbjct: 58  DCG--------FEHPSEVQHECI------------------------PQAVLGMDILCQA 85

Query: 157 KSGMGKTAVFVLATLQQLETTDSNV-YVLVMCHTRELAFQISKEYERFSKYMSNIKVGVF 215
           KSGMGKTAVFVLATLQQLE +D+N  +VLVMCHTRELAFQISKEYERFSKYM  +KV VF
Sbjct: 86  KSGMGKTAVFVLATLQQLEPSDNNTCHVLVMCHTRELAFQISKEYERFSKYMPTVKVAVF 145

Query: 216 FGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMR 275
           FGGL IQKDEE LK   P IVVGTPGRILAL+RNKKLNL  LKHF+LDECDKMLEQL+MR
Sbjct: 146 FGGLAIQKDEETLKNGTPHIVVGTPGRILALIRNKKLNLKHLKHFVLDECDKMLEQLDMR 205

Query: 276 RDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVK 335
           RDVQEIFRS+PH KQVMMFSATLSKEIRPVCKKFM DPMEVYVDDEAKLTLHGLQQHYV 
Sbjct: 206 RDVQEIFRSTPHGKQVMMFSATLSKEIRPVCKKFMQDPMEVYVDDEAKLTLHGLQQHYVN 265

Query: 336 LKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLK 395
           LKENEKNKKLFELLDVLEFNQVVIFVKSV RC+AL+ LL+EQNFPA+ IHRGM Q+ERL 
Sbjct: 266 LKENEKNKKLFELLDVLEFNQVVIFVKSVQRCVALAQLLTEQNFPAIGIHRGMNQDERLN 325

Query: 396 KYQEFKDFH----------------------------------------------KGLAI 409
           +YQ+FKDF                                               KGLAI
Sbjct: 326 RYQQFKDFQKRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAI 385

Query: 410 TFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR 448
           TF SDENDAKILN VQDRFDV+ISELP+EIDLSTYIEGR
Sbjct: 386 TFVSDENDAKILNEVQDRFDVNISELPEEIDLSTYIEGR 424

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307178480|gb|EFN67169.1| Spliceosome RNA helicase Bat1 [Camponotus floridanus]

 Score =  587 bits (1514), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 319/458 (69%), Positives = 346/458 (75%), Gaps = 79/458 (17%)

Query: 37  MADNDDLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIV 96
           MADNDDLLDYEDEE TEQ+V DG+GD  AK KEVKG YVSIHSSGFRDFLLKPEILRAIV
Sbjct: 1   MADNDDLLDYEDEEQTEQVV-DGSGDVPAKNKEVKGTYVSIHSSGFRDFLLKPEILRAIV 59

Query: 97  DCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQA 156
           DC         F    +++   I                         +AVLGMDILCQA
Sbjct: 60  DCG--------FEHPSEVQHECI------------------------PQAVLGMDILCQA 87

Query: 157 KSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFF 216
           KSGMGKTAVFVLATLQQLE T++ VYVLVMCHTRELAFQISKEYERFSKYM ++KVGVFF
Sbjct: 88  KSGMGKTAVFVLATLQQLELTENQVYVLVMCHTRELAFQISKEYERFSKYMPHVKVGVFF 147

Query: 217 GGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRR 276
           GGLPIQKDEE LKT  P IVVGTPGRILALVR KKLNL  LKHFILDECDKMLE L+MRR
Sbjct: 148 GGLPIQKDEEVLKTVCPHIVVGTPGRILALVRTKKLNLKHLKHFILDECDKMLELLDMRR 207

Query: 277 DVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKL 336
           DVQEIFRS+PH+KQVMMFSATLSKEIRPVCKKFM DPMEVYVDDEAKLTL+GLQQHYVKL
Sbjct: 208 DVQEIFRSTPHSKQVMMFSATLSKEIRPVCKKFMQDPMEVYVDDEAKLTLNGLQQHYVKL 267

Query: 337 KENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKK 396
           KENEKNKKLFELLDVLEFNQVVIFVKSV RC+AL+ LL+EQNFPA+ IHRGMTQEERL +
Sbjct: 268 KENEKNKKLFELLDVLEFNQVVIFVKSVQRCMALAQLLTEQNFPAIGIHRGMTQEERLSR 327

Query: 397 YQEFKDFH----------------------------------------------KGLAIT 410
           YQ+FKDF                                               KGLAIT
Sbjct: 328 YQQFKDFQKRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAIT 387

Query: 411 FASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR 448
             SDE+DAKILN+VQ+RFDV+I+ELPDEIDL++YIEGR
Sbjct: 388 LVSDESDAKILNDVQERFDVNITELPDEIDLASYIEGR 425

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195434048|ref|XP_002065015.1| GK14902 [Drosophila willistoni] gi|194161100|gb|EDW76001.1| GK14902 [Drosophila willistoni]

 Score =  586 bits (1510), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 308/459 (67%), Positives = 336/459 (73%), Gaps = 82/459 (17%)

Query: 37  MADNDDLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIV 96
           MADNDDLLDYEDEE TE    +      A +K+VKG YVSIHSSGFRDFLLKPEILRAIV
Sbjct: 1   MADNDDLLDYEDEEQTETTAVENRE---APKKDVKGTYVSIHSSGFRDFLLKPEILRAIV 57

Query: 97  DCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQA 156
           DC                E  + V +  +P+                  AVLGMDILCQA
Sbjct: 58  DCG--------------FEHPSEVQHECIPQ------------------AVLGMDILCQA 85

Query: 157 KSGMGKTAVFVLATLQQLETTDSNV-YVLVMCHTRELAFQISKEYERFSKYMSNIKVGVF 215
           KSGMGKTAVFVLATLQQLE +D+N  +VLVMCHTRELAFQISKEYERFSKYM  +KV VF
Sbjct: 86  KSGMGKTAVFVLATLQQLEPSDNNTCHVLVMCHTRELAFQISKEYERFSKYMPTVKVAVF 145

Query: 216 FGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMR 275
           FGGL IQKDEE LK+  P IVVGTPGRILAL+RNKKLNL  LKHF+LDECDKMLEQL+MR
Sbjct: 146 FGGLAIQKDEETLKSGTPHIVVGTPGRILALIRNKKLNLKHLKHFVLDECDKMLEQLDMR 205

Query: 276 RDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVK 335
           RDVQEIFRS+PH KQVMMFSATLSK+IRPVCKKFM DPMEVYVDDEAKLTLHGLQQHY  
Sbjct: 206 RDVQEIFRSTPHGKQVMMFSATLSKDIRPVCKKFMQDPMEVYVDDEAKLTLHGLQQHYNN 265

Query: 336 LKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLK 395
           LKENEKNKKLFELLDVLEFNQVVIFVKSV RC+AL+ LL+EQNFPA+ IHRGM+QEERL 
Sbjct: 266 LKENEKNKKLFELLDVLEFNQVVIFVKSVQRCVALAQLLTEQNFPAIGIHRGMSQEERLN 325

Query: 396 KYQEFKDFH----------------------------------------------KGLAI 409
           +YQ+FKDF                                               KGLAI
Sbjct: 326 RYQQFKDFQKRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAI 385

Query: 410 TFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR 448
           TF SDENDAKILN VQDRFDV+I+ELP+EIDLS+YIEGR
Sbjct: 386 TFVSDENDAKILNEVQDRFDVNITELPEEIDLSSYIEGR 424

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195034694|ref|XP_001988957.1| GH11448 [Drosophila grimshawi] gi|193904957|gb|EDW03824.1| GH11448 [Drosophila grimshawi]

 Score =  585 bits (1507), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 309/459 (67%), Positives = 332/459 (72%), Gaps = 82/459 (17%)

Query: 37  MADNDDLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIV 96
           MADNDDLLDYEDEE  E    +      A +K+VKG YVSIHSSGFRDFLLKPEILRAIV
Sbjct: 1   MADNDDLLDYEDEEQNETTAVESQE---APKKDVKGTYVSIHSSGFRDFLLKPEILRAIV 57

Query: 97  DCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQA 156
           DC                E  + V +  +P+                  AVLGMDILCQA
Sbjct: 58  DCG--------------FEHPSEVQHECIPQ------------------AVLGMDILCQA 85

Query: 157 KSGMGKTAVFVLATLQQLETTDSNV-YVLVMCHTRELAFQISKEYERFSKYMSNIKVGVF 215
           KSGMGKTAVFVLATLQQLE  D+N  +VLVMCHTRELAFQISKEYERFSKYM  +KV VF
Sbjct: 86  KSGMGKTAVFVLATLQQLEPADNNTCHVLVMCHTRELAFQISKEYERFSKYMPTVKVAVF 145

Query: 216 FGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMR 275
           FGGL IQKDEE LK   P IVVGTPGRILAL+RNKKLNL  LKHF+LDECDKMLEQL+MR
Sbjct: 146 FGGLAIQKDEETLKNGTPHIVVGTPGRILALIRNKKLNLKHLKHFVLDECDKMLEQLDMR 205

Query: 276 RDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVK 335
           RDVQEIFRS+PH KQVMMFSATLSKEIRPVCKKFM DPMEVYVDDEAKLTLHGLQQHYV 
Sbjct: 206 RDVQEIFRSTPHGKQVMMFSATLSKEIRPVCKKFMQDPMEVYVDDEAKLTLHGLQQHYVN 265

Query: 336 LKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLK 395
           LKENEKNKKLFELLDVLEFNQVVIFVKSV RC AL+ LL+EQNFPA+ IHRGM Q++RL 
Sbjct: 266 LKENEKNKKLFELLDVLEFNQVVIFVKSVQRCTALAQLLTEQNFPAIGIHRGMNQDDRLN 325

Query: 396 KYQEFKDFH----------------------------------------------KGLAI 409
           +YQ+FKDF                                               KGLAI
Sbjct: 326 RYQQFKDFQKRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAI 385

Query: 410 TFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR 448
           TF SDENDAKILN VQDRFDV+ISELP+EIDLSTYIEGR
Sbjct: 386 TFVSDENDAKILNEVQDRFDVNISELPEEIDLSTYIEGR 424

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156550340|ref|XP_001606535.1| PREDICTED: ATP-dependent RNA helicase WM6-like [Nasonia vitripennis]

 Score =  583 bits (1502), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 315/458 (68%), Positives = 346/458 (75%), Gaps = 79/458 (17%)

Query: 37  MADNDDLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIV 96
           MADNDDLLDYEDEE TEQIV +G G+    +KEVKG YVSIHSSGFRDFLLKPEILRAIV
Sbjct: 1   MADNDDLLDYEDEEQTEQIV-EGNGEVAPAKKEVKGTYVSIHSSGFRDFLLKPEILRAIV 59

Query: 97  DCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQA 156
           DC                E  + V +  +P+                  AVLGMDILCQA
Sbjct: 60  DCG--------------FEHPSEVQHECIPQ------------------AVLGMDILCQA 87

Query: 157 KSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFF 216
           KSGMGKTAVFVLATLQQLE+T+++VYVLVMCHTRELAFQISKEYERFSKYM N+KV VFF
Sbjct: 88  KSGMGKTAVFVLATLQQLESTENHVYVLVMCHTRELAFQISKEYERFSKYMQNVKVSVFF 147

Query: 217 GGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRR 276
           GGLPIQKDEE LK   P IVVGTPGRILAL+++KKLNL  LKHF+LDECDKMLEQL+MR+
Sbjct: 148 GGLPIQKDEEVLKNTCPHIVVGTPGRILALIKSKKLNLKHLKHFVLDECDKMLEQLDMRK 207

Query: 277 DVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKL 336
           DVQEIFRS+PH KQVMMFSATLSKEIRPVCKKFM DPMEVYVDDEAKLTLHGLQQHY+KL
Sbjct: 208 DVQEIFRSTPHGKQVMMFSATLSKEIRPVCKKFMQDPMEVYVDDEAKLTLHGLQQHYIKL 267

Query: 337 KENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKK 396
           KENEKNKKLFELLDVLEFNQVVIFVKSV RC+AL+ LL+EQNFPA+ IHRGMTQEERL K
Sbjct: 268 KENEKNKKLFELLDVLEFNQVVIFVKSVQRCMALAQLLTEQNFPAIGIHRGMTQEERLTK 327

Query: 397 YQEFKDFH----------------------------------------------KGLAIT 410
           YQ FKDF                                               KGLAIT
Sbjct: 328 YQSFKDFQKRILVATNLFGRGMDIERVNIVFNYDMPENSDTYLHRVARAGRFGTKGLAIT 387

Query: 411 FASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR 448
           F SDE+DAKILN+VQ+RFDV+I+ELPDEIDL++YIEGR
Sbjct: 388 FISDESDAKILNDVQERFDVNITELPDEIDLASYIEGR 425

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66532824|ref|XP_624894.1| PREDICTED: ATP-dependent RNA helicase WM6-like [Apis mellifera] gi|380028013|ref|XP_003697706.1| PREDICTED: ATP-dependent RNA helicase WM6-like [Apis florea]

 Score =  581 bits (1497), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 319/458 (69%), Positives = 345/458 (75%), Gaps = 80/458 (17%)

Query: 37  MADNDDLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIV 96
           MADNDDLLDYEDEE TEQ+V DG+ D  AK KEVKG YVSIHSSGFRDFLLKPEILRAI+
Sbjct: 1   MADNDDLLDYEDEEQTEQLV-DGSRDTPAK-KEVKGTYVSIHSSGFRDFLLKPEILRAII 58

Query: 97  DCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQA 156
           DC                E  + V +  +P+                  AVLGMDILCQA
Sbjct: 59  DCG--------------FEHPSEVQHECIPQ------------------AVLGMDILCQA 86

Query: 157 KSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFF 216
           KSGMGKTAVFVLATLQQLE T++ VYVLVMCHTRELAFQISKEYERFSKYM ++KVGVFF
Sbjct: 87  KSGMGKTAVFVLATLQQLELTENQVYVLVMCHTRELAFQISKEYERFSKYMPHVKVGVFF 146

Query: 217 GGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRR 276
           GGLPIQKDEE LK   P IVVGTPGRILALVRNKKLNL  LKHFILDECDKMLE L+MRR
Sbjct: 147 GGLPIQKDEEVLKNTCPHIVVGTPGRILALVRNKKLNLKHLKHFILDECDKMLELLDMRR 206

Query: 277 DVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKL 336
           DVQEIFRS+PH KQVMMFSATLSKEIRPVCKKFM DPMEVYVDDEAKLTLHGLQQHYVKL
Sbjct: 207 DVQEIFRSTPHGKQVMMFSATLSKEIRPVCKKFMQDPMEVYVDDEAKLTLHGLQQHYVKL 266

Query: 337 KENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKK 396
           KENEKNKKLFELLDVLEFNQVVIFVKSV RC+AL+ LL+EQNFPA+ IHRGMTQEERL +
Sbjct: 267 KENEKNKKLFELLDVLEFNQVVIFVKSVQRCMALAQLLTEQNFPAIGIHRGMTQEERLSR 326

Query: 397 YQEFKDFH----------------------------------------------KGLAIT 410
           YQ+FKDF                                               KGLAIT
Sbjct: 327 YQQFKDFQKRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAIT 386

Query: 411 FASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR 448
             SDE+DAKILN+VQ+RFDV+I+ELPDEIDL++YIEGR
Sbjct: 387 LVSDESDAKILNDVQERFDVNITELPDEIDLASYIEGR 424

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

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	448
FB|FBgn0014189	424	Hel25E "Helicase at 25E" [Dros	0.591	0.625	0.793	2.1e-143
UNIPROTKB|Q5WR10	428	DDX39B "Spliceosome RNA helica	0.591	0.619	0.754	9.2e-137
UNIPROTKB|Q13838	428	DDX39B "Spliceosome RNA helica	0.591	0.619	0.754	1.2e-136
UNIPROTKB|Q29024	428	DDX39B "Spliceosome RNA helica	0.591	0.619	0.754	1.2e-136
MGI|MGI:99240	428	Ddx39b "DEAD (Asp-Glu-Ala-Asp)	0.591	0.619	0.754	1.2e-136
RGD|70923	428	Ddx39b "DEAD (Asp-Glu-Ala-Asp)	0.591	0.619	0.754	1.2e-136
UNIPROTKB|Q3T147	428	DDX39B "Spliceosome RNA helica	0.591	0.619	0.750	3.9e-136
UNIPROTKB|Q5ZHZ0	428	DDX39B "Spliceosome RNA helica	0.591	0.619	0.747	5e-136
UNIPROTKB|E2QY95	427	DDX39A "Uncharacterized protei	0.591	0.620	0.735	6.4e-134
UNIPROTKB|F1SCH3	475	DDX39A "Uncharacterized protei	0.591	0.557	0.735	6.4e-134

FB|FBgn0014189 Hel25E "Helicase at 25E" [Drosophila melanogaster (taxid:7227)]

 Score = 1081 (385.6 bits), Expect = 2.1e-143, Sum P(3) = 2.1e-143
 Identities = 211/266 (79%), Positives = 230/266 (86%)

Query:   145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNV-YVLVMCHTRELAFQISKEYERF 203
             +AVLGMDILCQAKSGMGKTAVFVLATLQQLE +D+N  +VLVMCHTRELAFQISKEYERF
Sbjct:    74 QAVLGMDILCQAKSGMGKTAVFVLATLQQLEPSDNNTCHVLVMCHTRELAFQISKEYERF 133

Query:   204 SKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILD 263
             SKYM  +KV VFFGG+ IQKDEE LK+  P IVVGTPGRILAL+RNKKLNL LLKHF+LD
Sbjct:   134 SKYMPTVKVAVFFGGMAIQKDEETLKSGTPHIVVGTPGRILALIRNKKLNLKLLKHFVLD 193

Query:   264 ECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAK 323
             ECDKMLEQL+MRRDVQEIFRS+PH KQVMMFSATLSK+IRPVCKKFM DPMEVYVDDEAK
Sbjct:   194 ECDKMLEQLDMRRDVQEIFRSTPHGKQVMMFSATLSKDIRPVCKKFMQDPMEVYVDDEAK 253

Query:   324 LTLHGLQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVS 383
             LTLHGLQQHYV               DVLEFNQVVIFVKSV RC+ALS LL+EQNFPA+ 
Sbjct:   254 LTLHGLQQHYVNLKENEKNKKLFELLDVLEFNQVVIFVKSVQRCVALSQLLTEQNFPAIG 313

Query:   384 IHRGMTQEERLKKYQEFKDFHKGLAI 409
             IHRGMTQEERL +YQ+FKDF K + +
Sbjct:   314 IHRGMTQEERLNRYQQFKDFQKRILV 339

GO:0005634 "nucleus" evidence=IC;NAS;IDA

GO:0006338 "chromatin remodeling" evidence=IMP

GO:0005700 "polytene chromosome" evidence=IDA

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

GO:0003724 "RNA helicase activity" evidence=ISS

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

GO:0005681 "spliceosomal complex" evidence=ISS

GO:0006406 "mRNA export from nucleus" evidence=IMP

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=IMP

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0005875 "microtubule associated complex" evidence=IDA

UNIPROTKB|Q5WR10 DDX39B "Spliceosome RNA helicase DDX39B" [Canis lupus familiaris (taxid:9615)]

 Score = 1028 (366.9 bits), Expect = 9.2e-137, Sum P(3) = 9.2e-137
 Identities = 200/265 (75%), Positives = 221/265 (83%)

Query:   145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS 204
             +A+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQISKEYERFS
Sbjct:    78 QAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFS 137

Query:   205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDE 264
             KYM N+KV VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK LNL  +KHFILDE
Sbjct:   138 KYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDE 197

Query:   265 CDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKL 324
             CDKMLEQL+MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++VDDE KL
Sbjct:   198 CDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKL 257

Query:   325 TLHGLQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSI 384
             TLHGLQQ+YV               DVLEFNQVVIFVKSV RCIAL+ LL EQNFPA++I
Sbjct:   258 TLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAI 317

Query:   385 HRGMTQEERLKKYQEFKDFHKGLAI 409
             HRGM QEERL +YQ+FKDF + + +
Sbjct:   318 HRGMPQEERLSRYQQFKDFQRRILV 342

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IEA

GO:0043008 "ATP-dependent protein binding" evidence=IEA

GO:0030621 "U4 snRNA binding" evidence=IEA

GO:0017070 "U6 snRNA binding" evidence=IEA

GO:0010501 "RNA secondary structure unwinding" evidence=IEA

GO:0005688 "U6 snRNP" evidence=IEA

GO:0005687 "U4 snRNP" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

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

GO:0000346 "transcription export complex" evidence=IEA

GO:0000245 "spliceosomal complex assembly" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|Q13838 DDX39B "Spliceosome RNA helicase DDX39B" [Homo sapiens (taxid:9606)]

 Score = 1028 (366.9 bits), Expect = 1.2e-136, Sum P(3) = 1.2e-136
 Identities = 200/265 (75%), Positives = 221/265 (83%)

Query:   145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS 204
             +A+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQISKEYERFS
Sbjct:    78 QAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFS 137

Query:   205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDE 264
             KYM N+KV VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK LNL  +KHFILDE
Sbjct:   138 KYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDE 197

Query:   265 CDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKL 324
             CDKMLEQL+MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++VDDE KL
Sbjct:   198 CDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKL 257

Query:   325 TLHGLQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSI 384
             TLHGLQQ+YV               DVLEFNQVVIFVKSV RCIAL+ LL EQNFPA++I
Sbjct:   258 TLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAI 317

Query:   385 HRGMTQEERLKKYQEFKDFHKGLAI 409
             HRGM QEERL +YQ+FKDF + + +
Sbjct:   318 HRGMPQEERLSRYQQFKDFQRRILV 342

GO:0005524 "ATP binding" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0006406 "mRNA export from nucleus" evidence=IGI;IDA

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

GO:0000346 "transcription export complex" evidence=IDA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IDA

GO:0008186 "RNA-dependent ATPase activity" evidence=IDA

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

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0008380 "RNA splicing" evidence=IDA

GO:0000245 "spliceosomal complex assembly" evidence=IDA

GO:0005681 "spliceosomal complex" evidence=IDA

GO:0043008 "ATP-dependent protein binding" evidence=IDA

GO:0005687 "U4 snRNP" evidence=IDA

GO:0005688 "U6 snRNP" evidence=IDA

GO:0030621 "U4 snRNA binding" evidence=IDA

GO:0017070 "U6 snRNA binding" evidence=IDA

GO:0010501 "RNA secondary structure unwinding" evidence=IDA

UNIPROTKB|Q29024 DDX39B "Spliceosome RNA helicase DDX39B" [Sus scrofa (taxid:9823)]

 Score = 1028 (366.9 bits), Expect = 1.2e-136, Sum P(3) = 1.2e-136
 Identities = 200/265 (75%), Positives = 221/265 (83%)

Query:   145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS 204
             +A+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQISKEYERFS
Sbjct:    78 QAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFS 137

Query:   205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDE 264
             KYM N+KV VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK LNL  +KHFILDE
Sbjct:   138 KYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDE 197

Query:   265 CDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKL 324
             CDKMLEQL+MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++VDDE KL
Sbjct:   198 CDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKL 257

Query:   325 TLHGLQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSI 384
             TLHGLQQ+YV               DVLEFNQVVIFVKSV RCIAL+ LL EQNFPA++I
Sbjct:   258 TLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAI 317

Query:   385 HRGMTQEERLKKYQEFKDFHKGLAI 409
             HRGM QEERL +YQ+FKDF + + +
Sbjct:   318 HRGMPQEERLSRYQQFKDFQRRILV 342

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IEA

GO:0043008 "ATP-dependent protein binding" evidence=IEA

GO:0030621 "U4 snRNA binding" evidence=IEA

GO:0017070 "U6 snRNA binding" evidence=IEA

GO:0010501 "RNA secondary structure unwinding" evidence=IEA

GO:0005688 "U6 snRNP" evidence=IEA

GO:0005687 "U4 snRNP" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

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

GO:0000346 "transcription export complex" evidence=IEA

GO:0000245 "spliceosomal complex assembly" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

MGI|MGI:99240 Ddx39b "DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B" [Mus musculus (taxid:10090)]

 Score = 1028 (366.9 bits), Expect = 1.2e-136, Sum P(3) = 1.2e-136
 Identities = 200/265 (75%), Positives = 221/265 (83%)

Query:   145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS 204
             +A+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQISKEYERFS
Sbjct:    78 QAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFS 137

Query:   205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDE 264
             KYM N+KV VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK LNL  +KHFILDE
Sbjct:   138 KYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDE 197

Query:   265 CDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKL 324
             CDKMLEQL+MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++VDDE KL
Sbjct:   198 CDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKL 257

Query:   325 TLHGLQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSI 384
             TLHGLQQ+YV               DVLEFNQVVIFVKSV RCIAL+ LL EQNFPA++I
Sbjct:   258 TLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAI 317

Query:   385 HRGMTQEERLKKYQEFKDFHKGLAI 409
             HRGM QEERL +YQ+FKDF + + +
Sbjct:   318 HRGMPQEERLSRYQQFKDFQRRILV 342

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000245 "spliceosomal complex assembly" evidence=ISO

GO:0000346 "transcription export complex" evidence=ISO

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005681 "spliceosomal complex" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006406 "mRNA export from nucleus" evidence=ISO

GO:0006810 "transport" evidence=IEA

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

GO:0008186 "RNA-dependent ATPase activity" evidence=ISO

GO:0008380 "RNA splicing" evidence=ISO

GO:0010501 "RNA secondary structure unwinding" evidence=ISO

GO:0016787 "hydrolase activity" evidence=IEA

GO:0017070 "U6 snRNA binding" evidence=ISO

GO:0030621 "U4 snRNA binding" evidence=ISO

GO:0043008 "ATP-dependent protein binding" evidence=ISO

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=ISO

GO:0051028 "mRNA transport" evidence=IEA

RGD|70923 Ddx39b "DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B" [Rattus norvegicus (taxid:10116)]

 Score = 1028 (366.9 bits), Expect = 1.2e-136, Sum P(3) = 1.2e-136
 Identities = 200/265 (75%), Positives = 221/265 (83%)

Query:   145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS 204
             +A+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQISKEYERFS
Sbjct:    78 QAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFS 137

Query:   205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDE 264
             KYM N+KV VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK LNL  +KHFILDE
Sbjct:   138 KYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDE 197

Query:   265 CDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKL 324
             CDKMLEQL+MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++VDDE KL
Sbjct:   198 CDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKL 257

Query:   325 TLHGLQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSI 384
             TLHGLQQ+YV               DVLEFNQVVIFVKSV RCIAL+ LL EQNFPA++I
Sbjct:   258 TLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAI 317

Query:   385 HRGMTQEERLKKYQEFKDFHKGLAI 409
             HRGM QEERL +YQ+FKDF + + +
Sbjct:   318 HRGMPQEERLSRYQQFKDFQRRILV 342

GO:0000245 "spliceosomal complex assembly" evidence=IEA;ISO

GO:0000346 "transcription export complex" evidence=IEA;ISO

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004004 "ATP-dependent RNA helicase activity" evidence=IEA;ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005681 "spliceosomal complex" evidence=IEA;ISO

GO:0005687 "U4 snRNP" evidence=IEA;ISO

GO:0005688 "U6 snRNP" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0006406 "mRNA export from nucleus" evidence=ISO

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

GO:0008186 "RNA-dependent ATPase activity" evidence=ISO

GO:0008380 "RNA splicing" evidence=ISO

GO:0010501 "RNA secondary structure unwinding" evidence=IEA;ISO

GO:0016607 "nuclear speck" evidence=IEA

GO:0017070 "U6 snRNA binding" evidence=IEA;ISO

GO:0030621 "U4 snRNA binding" evidence=IEA;ISO

GO:0043008 "ATP-dependent protein binding" evidence=IEA;ISO

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IEA;ISO

UNIPROTKB|Q3T147 DDX39B "Spliceosome RNA helicase DDX39B" [Bos taurus (taxid:9913)]

 Score = 1023 (365.2 bits), Expect = 3.9e-136, Sum P(3) = 3.9e-136
 Identities = 199/265 (75%), Positives = 221/265 (83%)

Query:   145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS 204
             +A+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQISKEYERFS
Sbjct:    78 QAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFS 137

Query:   205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDE 264
             KYM ++KV VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK LNL  +KHFILDE
Sbjct:   138 KYMPSVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDE 197

Query:   265 CDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKL 324
             CDKMLEQL+MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++VDDE KL
Sbjct:   198 CDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKL 257

Query:   325 TLHGLQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSI 384
             TLHGLQQ+YV               DVLEFNQVVIFVKSV RCIAL+ LL EQNFPA++I
Sbjct:   258 TLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAI 317

Query:   385 HRGMTQEERLKKYQEFKDFHKGLAI 409
             HRGM QEERL +YQ+FKDF + + +
Sbjct:   318 HRGMPQEERLSRYQQFKDFQRRILV 342

GO:0006406 "mRNA export from nucleus" evidence=ISS

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

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0046784 "intronless viral mRNA export from host nucleus" evidence=IEA

GO:0043008 "ATP-dependent protein binding" evidence=IEA

GO:0030621 "U4 snRNA binding" evidence=IEA

GO:0017070 "U6 snRNA binding" evidence=IEA

GO:0010501 "RNA secondary structure unwinding" evidence=IEA

GO:0005688 "U6 snRNP" evidence=IEA

GO:0005687 "U4 snRNP" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

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

GO:0000346 "transcription export complex" evidence=IEA

GO:0000245 "spliceosomal complex assembly" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|Q5ZHZ0 DDX39B "Spliceosome RNA helicase DDX39B" [Gallus gallus (taxid:9031)]

 Score = 1022 (364.8 bits), Expect = 5.0e-136, Sum P(3) = 5.0e-136
 Identities = 198/265 (74%), Positives = 221/265 (83%)

Query:   145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS 204
             +A+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQISKEYERFS
Sbjct:    78 QAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFS 137

Query:   205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDE 264
             KYM ++KV VFFGGL ++KDEE LK + P IVVGTPGRILAL RNK LNL  +KHFILDE
Sbjct:   138 KYMPSVKVAVFFGGLAVKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDE 197

Query:   265 CDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKL 324
             CDKMLEQL+MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++VDDE KL
Sbjct:   198 CDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKL 257

Query:   325 TLHGLQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSI 384
             TLHGLQQ+YV               DVLEFNQVVIFVKSV RCIAL+ LL EQNFPA++I
Sbjct:   258 TLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAI 317

Query:   385 HRGMTQEERLKKYQEFKDFHKGLAI 409
             HRGM QEERL +YQ+FKDF + + +
Sbjct:   318 HRGMPQEERLSRYQQFKDFQRRILV 342

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

UNIPROTKB|E2QY95 DDX39A "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 1015 (362.4 bits), Expect = 6.4e-134, Sum P(3) = 6.4e-134
 Identities = 195/265 (73%), Positives = 222/265 (83%)

Query:   145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS 204
             +A+LGMD+LCQAKSGMGKTAVFVLATLQQ+E  +  V VLVMCHTRELAFQISKEYERFS
Sbjct:    77 QAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVNGQVTVLVMCHTRELAFQISKEYERFS 136

Query:   205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDE 264
             KYM ++KV VFFGGL I+KDEE LK + P +VVGTPGRILALVRN+ LNL  +KHF+LDE
Sbjct:   137 KYMPSVKVSVFFGGLSIKKDEEVLKKNCPHVVVGTPGRILALVRNRSLNLKNVKHFVLDE 196

Query:   265 CDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKL 324
             CDKMLEQL+MRRDVQEIFR +PH KQ MMFSATLSKEIRPVC+KFM DPMEV+VDDE KL
Sbjct:   197 CDKMLEQLDMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEVFVDDETKL 256

Query:   325 TLHGLQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSI 384
             TLHGLQQ+YV               DVLEFNQVVIFVKSV RC+AL+ LL EQNFPA++I
Sbjct:   257 TLHGLQQYYVKLKDSEKNRKLFDLLDVLEFNQVVIFVKSVQRCMALAQLLVEQNFPAIAI 316

Query:   385 HRGMTQEERLKKYQEFKDFHKGLAI 409
             HRGM QEERL +YQ+FKDF + + +
Sbjct:   317 HRGMAQEERLSRYQQFKDFQRRILV 341

GO:0006406 "mRNA export from nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1SCH3 DDX39A "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 1015 (362.4 bits), Expect = 6.4e-134, Sum P(3) = 6.4e-134
 Identities = 195/265 (73%), Positives = 222/265 (83%)

Query:   145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS 204
             +A+LGMD+LCQAKSGMGKTAVFVLATLQQ+E  +  V VLVMCHTRELAFQISKEYERFS
Sbjct:   125 QAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVNGQVTVLVMCHTRELAFQISKEYERFS 184

Query:   205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDE 264
             KYM ++KV VFFGGL I+KDEE LK + P +VVGTPGRILALVRN+ LNL  +KHF+LDE
Sbjct:   185 KYMPSVKVSVFFGGLSIKKDEEVLKKNCPHVVVGTPGRILALVRNRSLNLKNVKHFVLDE 244

Query:   265 CDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKL 324
             CDKMLEQL+MRRDVQEIFR +PH KQ MMFSATLSKEIRPVC+KFM DPMEV+VDDE KL
Sbjct:   245 CDKMLEQLDMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEVFVDDETKL 304

Query:   325 TLHGLQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSI 384
             TLHGLQQ+YV               DVLEFNQVVIFVKSV RC+AL+ LL EQNFPA++I
Sbjct:   305 TLHGLQQYYVKLKDSEKNRKLFDLLDVLEFNQVVIFVKSVQRCMALAQLLVEQNFPAIAI 364

Query:   385 HRGMTQEERLKKYQEFKDFHKGLAI 409
             HRGM QEERL +YQ+FKDF + + +
Sbjct:   365 HRGMAQEERLSRYQQFKDFQRRILV 389

GO:0006406 "mRNA export from nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5RE47	DX39B_PONAB	3, ., 6, ., 4, ., 1, 3	0.6427	0.8392	0.8785	yes	N/A
Q5WR10	DX39B_CANFA	3, ., 6, ., 4, ., 1, 3	0.6339	0.8392	0.8785	yes	N/A
Q5ZHZ0	DX39B_CHICK	3, ., 6, ., 4, ., 1, 3	0.6296	0.8392	0.8785	yes	N/A
O13792	SUB2_SCHPO	3, ., 6, ., 4, ., 1, 3	0.5032	0.8325	0.8594	yes	N/A
Q18212	DX39B_CAEEL	3, ., 6, ., 4, ., 1, 3	0.5698	0.8348	0.88	yes	N/A
Q6CH90	SUB2_YARLI	3, ., 6, ., 4, ., 1, 3	0.4666	0.8325	0.8458	yes	N/A
Q2U6P7	SUB2_ASPOR	3, ., 6, ., 4, ., 1, 3	0.4851	0.8415	0.8548	yes	N/A
O00148	DX39A_HUMAN	3, ., 6, ., 4, ., 1, 3	0.5991	0.8370	0.8782	no	N/A
Q9Z1N5	DX39B_MOUSE	3, ., 6, ., 4, ., 1, 3	0.6427	0.8392	0.8785	yes	N/A
Q4WCW2	SUB2_ASPFU	3, ., 6, ., 4, ., 1, 3	0.4843	0.8415	0.8415	yes	N/A
Q759L6	SUB2_ASHGO	3, ., 6, ., 4, ., 1, 3	0.4610	0.8325	0.8515	yes	N/A
Q5ASK8	SUB2_EMENI	3, ., 6, ., 4, ., 1, 3	0.4672	0.8236	0.8502	yes	N/A
P0CQ96	SUB2_CRYNJ	3, ., 6, ., 4, ., 1, 3	0.5	0.8281	0.8393	yes	N/A
Q63413	DX39B_RAT	3, ., 6, ., 4, ., 1, 3	0.6427	0.8392	0.8785	yes	N/A
Q9LFN6	RH56_ARATH	3, ., 6, ., 4, ., 1, 3	0.5402	0.7678	0.8056	yes	N/A
Q6FL17	SUB2_CANGA	3, ., 6, ., 4, ., 1, 3	0.4730	0.8325	0.8496	yes	N/A
A3LST5	SUB2_PICST	3, ., 6, ., 4, ., 1, 3	0.4868	0.8303	0.8591	yes	N/A
Q5TM17	DX39B_MACMU	3, ., 6, ., 4, ., 1, 3	0.6427	0.8392	0.8785	yes	N/A
Q5U216	DX39A_RAT	3, ., 6, ., 4, ., 1, 3	0.6056	0.8370	0.8782	no	N/A
Q29024	DX39B_PIG	3, ., 6, ., 4, ., 1, 3	0.6427	0.8392	0.8785	yes	N/A
Q6BME5	SUB2_DEBHA	3, ., 6, ., 4, ., 1, 3	0.4782	0.8303	0.8551	yes	N/A
Q0JM17	RH56_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.5410	0.8281	0.8587	no	N/A
Q56XG6	RH15_ARATH	3, ., 6, ., 4, ., 1, 3	0.5402	0.7678	0.8056	yes	N/A
Q3T147	DX39B_BOVIN	3, ., 6, ., 4, ., 1, 3	0.6405	0.8392	0.8785	yes	N/A
Q27268	DX39B_DROME	3, ., 6, ., 4, ., 1, 3	0.6819	0.8415	0.8891	yes	N/A
A2R0B5	SUB2_ASPNC	3, ., 6, ., 4, ., 1, 3	0.4904	0.8415	0.8568	yes	N/A
Q5JK84	RH15_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.5410	0.8281	0.8587	no	N/A
P60024	DX39B_PANTR	3, ., 6, ., 4, ., 1, 3	0.6427	0.8392	0.8785	yes	N/A
Q8VDW0	DX39A_MOUSE	3, ., 6, ., 4, ., 1, 3	0.6013	0.8370	0.8782	no	N/A
Q13838	DX39B_HUMAN	3, ., 6, ., 4, ., 1, 3	0.6427	0.8392	0.8785	yes	N/A
Q6CM95	SUB2_KLULA	3, ., 6, ., 4, ., 1, 3	0.4642	0.8325	0.8535	yes	N/A
Q07478	SUB2_YEAST	3, ., 6, ., 4, ., 1, 3	0.4702	0.8325	0.8363	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4.13	0.991
3rd Layer	3.6.4	0.976

---

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	448
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	9e-77
cd00268	203	cd00268, DEADc, DEAD-box helicases	4e-66
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	2e-49
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	1e-43
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	6e-41
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	1e-38
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	8e-37
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	3e-33
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	4e-30
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	2e-27
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	5e-26
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	6e-26
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	2e-23
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	2e-20
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	8e-20
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	1e-14
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	4e-14
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	2e-13
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	4e-13
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	2e-12
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-11
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	1e-10
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	9e-10
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	1e-09
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	3e-09
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	6e-09
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	1e-08
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	2e-08
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	2e-07
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	3e-06
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	2e-05
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	9e-05
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	2e-04
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	6e-04
COG1205	851	COG1205, COG1205, Distinct helicase family with a	0.001

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

 Score =  247 bits (633), Expect = 9e-77
 Identities = 96/270 (35%), Positives = 168/270 (62%), Gaps = 8/270 (2%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYV--LVMCHTRELAFQISKEYERFSKY 206
           G D+L QA++G GKTA F+L  LQ++  +    YV  L++  TRELA QI++E  +  K 
Sbjct: 66  GRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKN 125

Query: 207 MSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECD 266
           +  ++V V +GG+ I+K  E LK     IVV TPGR+L L++  KL+LS ++  +LDE D
Sbjct: 126 LGGLRVAVVYGGVSIRKQIEALKR-GVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEAD 184

Query: 267 KMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEA-KLT 325
           +ML+ +    D+++I ++ P  +Q ++FSAT+  +IR + +++++DP+E+ V  E  + T
Sbjct: 185 RMLD-MGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERT 243

Query: 326 LHGLQQHYVKLK-ENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSI 384
           L  ++Q Y++++ E EK + L +LL   +  +V++FV++      L+  L ++ F   ++
Sbjct: 244 LKKIKQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAAL 303

Query: 385 HRGMTQEERLKKYQEFKDFHKGLAITFASD 414
           H  + QEER +  ++FKD    L +  A+D
Sbjct: 304 HGDLPQEERDRALEKFKD--GELRVLVATD 331

Length = 513

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

 Score =  210 bits (536), Expect = 4e-66
 Identities = 66/170 (38%), Positives = 106/170 (62%), Gaps = 5/170 (2%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSN--VYVLVMCHTRELAFQISKEYERFSKY 206
           G D++ QA++G GKTA F++  L++L+ +        L++  TRELA QI++   +  K+
Sbjct: 36  GRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQIAEVARKLGKH 95

Query: 207 MSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECD 266
             N+KV V +GG  I K    LK   P IVV TPGR+L L+   KL+LS +K+ +LDE D
Sbjct: 96  T-NLKVVVIYGGTSIDKQIRKLK-RGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEAD 153

Query: 267 KMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEV 316
           +ML+       ++EI +  P  +Q ++FSAT+ KE+R + +KF+ +P+ +
Sbjct: 154 RMLDM-GFEDQIREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRI 202

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

 Score =  174 bits (444), Expect = 2e-49
 Identities = 88/247 (35%), Positives = 140/247 (56%), Gaps = 8/247 (3%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D++ QAK+G GKTA F L  LQ+L+     V  LV+C TRELA Q++KE  R ++++ 
Sbjct: 41  GKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELADQVAKEIRRLARFIP 100

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
           NIKV    GG+P+    + L+ H   I+VGTPGRIL  +R   L+L  L   +LDE D+M
Sbjct: 101 NIKVLTLCGGVPMGPQIDSLE-HGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRM 159

Query: 269 LEQLEM--RRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTL 326
              L+M  +  +  I R +P  +Q ++FSAT  + I  + ++F  DP+EV V+    L  
Sbjct: 160 ---LDMGFQDAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTHDLP- 215

Query: 327 HGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHR 386
             ++Q + ++  +E+   L  LL   +    V+F  +   C  ++  L+ Q F A+++H 
Sbjct: 216 -AIEQRFYEVSPDERLPALQRLLLHHQPESCVVFCNTKKECQEVADALNAQGFSALALHG 274

Query: 387 GMTQEER 393
            + Q +R
Sbjct: 275 DLEQRDR 281

Length = 460

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

 Score =  150 bits (381), Expect = 1e-43
 Identities = 58/156 (37%), Positives = 87/156 (55%), Gaps = 3/156 (1%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D+L QA +G GKT  F+L  LQ L         LV+  TRELA QI +E ++  K + 
Sbjct: 14  GKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQIYEELKKLFKIL- 72

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLS-LLKHFILDECDK 267
            ++V +  GG  +++    LK     I+VGTPGR+L L+R  KL L   LK  +LDE  +
Sbjct: 73  GLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLKNLKLLVLDEAHR 132

Query: 268 MLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIR 303
           +L+      D++EI    P  +Q+++ SATL + + 
Sbjct: 133 LLDM-GFGDDLEEILSRLPPDRQILLLSATLPRNLE 167

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|185609 PTZ00424, PTZ00424, helicase 45; Provisional

 Score =  150 bits (380), Expect = 6e-41
 Identities = 91/261 (34%), Positives = 142/261 (54%), Gaps = 6/261 (2%)

Query: 143 GTKAVL-GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYE 201
           G K +L G D + QA+SG GKTA FV+A LQ ++   +    L++  TRELA QI K   
Sbjct: 58  GIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTRELAQQIQKVVL 117

Query: 202 RFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFI 261
               Y+  ++     GG  ++ D   LK     +VVGTPGR+  ++  + L +  LK FI
Sbjct: 118 ALGDYL-KVRCHACVGGTVVRDDINKLKA-GVHMVVGTPGRVYDMIDKRHLRVDDLKLFI 175

Query: 262 LDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDE 321
           LDE D+ML +   +  + ++F+  P   QV +FSAT+  EI  +  KFM DP  + V  +
Sbjct: 176 LDEADEMLSR-GFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKD 234

Query: 322 AKLTLHGLQQHYVKL-KENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFP 380
            +LTL G++Q YV + KE  K   L +L + L   Q +I+  +  +   L+  + E++F 
Sbjct: 235 -ELTLEGIRQFYVAVEKEEWKFDTLCDLYETLTITQAIIYCNTRRKVDYLTKKMHERDFT 293

Query: 381 AVSIHRGMTQEERLKKYQEFK 401
              +H  M Q++R    +EF+
Sbjct: 294 VSCMHGDMDQKDRDLIMREFR 314

Length = 401

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

 Score =  138 bits (349), Expect = 1e-38
 Identities = 55/183 (30%), Positives = 98/183 (53%), Gaps = 6/183 (3%)

Query: 150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN 209
            D++  A +G GKT   +L  L+ L+       VLV+  TRELA Q ++E ++    +  
Sbjct: 25  RDVILAAPTGSGKTLAALLPALEALKR-GKGGRVLVLVPTRELAEQWAEELKKLGPSLGL 83

Query: 210 IKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKML 269
             VG++ GG   ++    L++    I+V TPGR+L L+ N KL+LS +   ILDE  ++L
Sbjct: 84  KVVGLY-GGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLL 142

Query: 270 EQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGL 329
           +       ++++ +  P   Q+++ SAT  +EI  + + F++DP+ + V       L  +
Sbjct: 143 DG-GFGDQLEKLLKLLPKNVQLLLLSATPPEEIENLLELFLNDPVFIDVGF---TPLEPI 198

Query: 330 QQH 332
           +Q 
Sbjct: 199 EQF 201

Length = 201

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

 Score =  142 bits (359), Expect = 8e-37
 Identities = 88/268 (32%), Positives = 140/268 (52%), Gaps = 9/268 (3%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D+L  A++G GKTA F L  L  L+       +LV+  TRELA Q+++    FSK+M 
Sbjct: 43  GRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELAVQVAEAMTDFSKHMR 102

Query: 209 NIKVGVFFGGLPIQKDEEYLKT--HNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECD 266
            + V   +GG   Q+ +  L+     PQIVVGTPGR+L  ++   L+LS L   +LDE D
Sbjct: 103 GVNVVALYGG---QRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEAD 159

Query: 267 KMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTL 326
           +ML ++    DV+ I    P   Q  +FSAT+ + IR + ++FM +P EV +      T 
Sbjct: 160 EML-RMGFIEDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVT-TR 217

Query: 327 HGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHR 386
             + Q Y  +    KN+ L   L+  +F+  +IFV++    + ++  L    + + +++ 
Sbjct: 218 PDISQSYWTVWGMRKNEALVRFLEAEDFDAAIIFVRTKNATLEVAEALERNGYNSAALNG 277

Query: 387 GMTQEERLKKYQEFKDFHKGLAITFASD 414
            M Q  R +  +  KD    L I  A+D
Sbjct: 278 DMNQALREQTLERLKDGR--LDILIATD 303

Length = 629

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

 Score =  122 bits (307), Expect = 3e-33
 Identities = 55/149 (36%), Positives = 77/149 (51%), Gaps = 5/149 (3%)

Query: 150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN 209
            D+L  A +G GKT   +L  L+ L++      VLV+  TRELA Q+++  +        
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSLK-GGQVLVLAPTRELANQVAERLKELFGE--G 57

Query: 210 IKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKML 269
           IKVG   GG  I K +E L +    IVVGTPGR+L  +   KL+L  L   ILDE  ++L
Sbjct: 58  IKVGYLIGGTSI-KQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLL 116

Query: 270 EQLEMRRDVQEIFRSSPHTKQVMMFSATL 298
            Q        +I    P  +QV++ SAT 
Sbjct: 117 NQ-GFGLLGLKILLKLPKDRQVLLLSATP 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|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional

 Score =  121 bits (304), Expect = 4e-30
 Identities = 87/281 (30%), Positives = 142/281 (50%), Gaps = 45/281 (16%)

Query: 146 AVL-GMDILCQAKSGMGKTAVFVLATLQQLETTDSN------VYVLVMCHTRELAFQISK 198
           AVL G D++  A++G GKTA F L  LQ L T   +      V  L++  TRELA QI +
Sbjct: 34  AVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTRELAAQIGE 93

Query: 199 EYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQ---------IVVGTPGRILALVRN 249
               +SKY+ NI+  V FGG+ I          NPQ         ++V TPGR+L L   
Sbjct: 94  NVRDYSKYL-NIRSLVVFGGVSI----------NPQMMKLRGGVDVLVATPGRLLDLEHQ 142

Query: 250 KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKF 309
             + L  ++  +LDE D+ML+ +    D++ +    P  +Q ++FSAT S +I+ + +K 
Sbjct: 143 NAVKLDQVEILVLDEADRMLD-MGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKL 201

Query: 310 MHDPMEVYV----DDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVL----EFNQVVIFV 361
           +H+P+E+ V        ++T H    H+V     +K +K  ELL  +     + QV++F 
Sbjct: 202 LHNPLEIEVARRNTASEQVTQH---VHFV-----DKKRKR-ELLSQMIGKGNWQQVLVFT 252

Query: 362 KSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKD 402
           ++      L+  L++    + +IH   +Q  R +   +FK 
Sbjct: 253 RTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKS 293

Length = 456

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

 Score =  113 bits (285), Expect = 2e-27
 Identities = 83/332 (25%), Positives = 155/332 (46%), Gaps = 44/332 (13%)

Query: 80  SGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARA 139
           + F DF L PE++ AI D                     + F Y  P  +    + +A  
Sbjct: 87  TRFHDFNLAPELMHAIHD---------------------LGFPYCTPIQAQVLGYTLA-- 123

Query: 140 GRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTD-------SNVYVLVMCHTREL 192
                    G D + +A++G GKTA F+++ + QL  T             L++  TREL
Sbjct: 124 ---------GHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTREL 174

Query: 193 AFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKL 252
             QI+K+    +KY + + V  F GG+   K  + L+     I+V TPGR+L   +  ++
Sbjct: 175 VVQIAKDAAALTKY-TGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEV 233

Query: 253 NLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHT--KQVMMFSATLSKEIRPVCKKFM 310
           +L +++  +LDE D+ML+ +     V++I R +P    +Q ++FSAT + ++  + K++ 
Sbjct: 234 HLDMVEVMVLDEADRMLD-MGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWT 292

Query: 311 HDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIAL 370
            DP  V ++ E       ++QH   +  ++K K L+ L+    + +V++F         +
Sbjct: 293 TDPAIVEIEPENV-ASDTVEQHVYAVAGSDKYKLLYNLVTQNPWERVMVFANRKDEVRRI 351

Query: 371 STLLSEQNFPAVSIHRGMTQEERLKKYQEFKD 402
              L +    A  +   + Q +R+K  + F++
Sbjct: 352 EERLVKDGINAAQLSGDVPQHKRIKTLEGFRE 383

Length = 475

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

 Score =  108 bits (273), Expect = 5e-26
 Identities = 73/267 (27%), Positives = 128/267 (47%), Gaps = 18/267 (6%)

Query: 146 AVLGMDILCQAKSGMGKTAVFVLATLQQL----ETTDSNVYVLVMCHTRELAFQISKEYE 201
           A+ G D+L  A +G GKTA F+L  LQ L            +L++  TRELA Q++ +  
Sbjct: 35  ALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELAMQVADQAR 94

Query: 202 RFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFI 261
             +K+ +++ +    GG+      E     N  IVV TPGR+L  ++ +  +   ++  I
Sbjct: 95  ELAKH-THLDIATITGGVAYMNHAEVFSE-NQDIVVATPGRLLQYIKEENFDCRAVETLI 152

Query: 262 LDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATL-SKEIRPVCKKFMHDPMEVYVD- 319
           LDE D+ML  +   +D++ I   +   KQ ++FSATL    ++   ++ ++DP+EV  + 
Sbjct: 153 LDEADRML-DMGFAQDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEP 211

Query: 320 ---DEAKLTLHGLQQHYVKLKENE-KNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLS 375
              +  K     + Q Y +  + E K   L  LL   E  + ++FV++  R   L+  L 
Sbjct: 212 SRRERKK-----IHQWYYRADDLEHKTALLCHLLKQPEVTRSIVFVRTRERVHELAGWLR 266

Query: 376 EQNFPAVSIHRGMTQEERLKKYQEFKD 402
           +       +   M Q +R +  +   D
Sbjct: 267 KAGINCCYLEGEMVQAKRNEAIKRLTD 293

Length = 434

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

 Score =  110 bits (276), Expect = 6e-26
 Identities = 84/270 (31%), Positives = 141/270 (52%), Gaps = 23/270 (8%)

Query: 146 AVLGMDILCQAKSGMGKTAVFVLATL-----QQLETTDSNVYVLVMCHTRELAFQISKEY 200
           A+ G D++  A++G GKT  F+L  +     Q L        VLV+  TRELA QI ++ 
Sbjct: 164 ALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQC 223

Query: 201 ERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHF 260
            +F    S I+  V +GG+P ++ + Y      +I++  PGR++  + +   NL  + + 
Sbjct: 224 NKFGA-SSKIRNTVAYGGVP-KRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYL 281

Query: 261 ILDECDKMLE---QLEMRRDVQEIFRSSPHTKQVMMFSATLSKEI----RPVCKKFMHDP 313
           +LDE D+ML+   + ++R+ V +I    P  +Q +M+SAT  KE+    R +CK    +P
Sbjct: 282 VLDEADRMLDMGFEPQIRKIVSQI---RP-DRQTLMWSATWPKEVQSLARDLCK---EEP 334

Query: 314 MEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVL--EFNQVVIFVKSVTRCIALS 371
           + V V        H ++Q    ++E+EK  KL  LL  +  + ++++IFV++      L+
Sbjct: 335 VHVNVGSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLT 394

Query: 372 TLLSEQNFPAVSIHRGMTQEERLKKYQEFK 401
             L    +PA+ IH    QEER     EFK
Sbjct: 395 KELRLDGWPALCIHGDKKQEERTWVLNEFK 424

Length = 545

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

 Score =  101 bits (254), Expect = 2e-23
 Identities = 62/192 (32%), Positives = 105/192 (54%), Gaps = 13/192 (6%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVY-------VLVMCHTRELAFQISKEYE 201
           G D+  QA++G GKT  F+ AT   L +  +           L+M  TRELA QI  + E
Sbjct: 45  GRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAE 104

Query: 202 RFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFI 261
             ++  + +K+G+ +GG    K  + L++    I++GT GR++   +   +NL  ++  +
Sbjct: 105 PLAQ-ATGLKLGLAYGGDGYDKQLKVLES-GVDILIGTTGRLIDYAKQNHINLGAIQVVV 162

Query: 262 LDECDKMLEQLEMRRDVQEIFRSSPHTKQ--VMMFSATLSKEIRPVCKKFMHDPMEVYVD 319
           LDE D+M + L   +D++ +FR  P   Q   M+FSATLS  +R +  + M++P  V V+
Sbjct: 163 LDEADRMFD-LGFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVE 221

Query: 320 DEAKLTLHGLQQ 331
            E K T H +++
Sbjct: 222 PEQK-TGHRIKE 232

Length = 423

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

 Score = 93.3 bits (232), Expect = 2e-20
 Identities = 70/263 (26%), Positives = 128/263 (48%), Gaps = 25/263 (9%)

Query: 146 AVLGMDILCQAKSGMGKTAVFVL------ATLQQLETTDS-NVYVLVMCHTRELAFQISK 198
           A+ G  +L  A +G GKTA F++       T++    ++  N   +V+  TREL  Q+  
Sbjct: 155 ALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVED 214

Query: 199 EYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLK 258
           + +   K +   K  +  GG  + + + Y      +++VGTPGR++ L+    + L  + 
Sbjct: 215 QAKVLGKGLP-FKTALVVGGDAMPQ-QLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVS 272

Query: 259 HFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
             +LDE D MLE+   R  V +IF++     QV++FSAT+S E+         D + + +
Sbjct: 273 VLVLDEVDCMLER-GFRDQVMQIFQALS-QPQVLLFSATVSPEVEKFASSLAKDIILISI 330

Query: 319 DDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQ--VVIFVKS------VTRCIAL 370
            +  +     ++Q  + ++  +K +KLF++L   +  +   V+FV S      +   I +
Sbjct: 331 GNPNRPN-KAVKQLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITV 389

Query: 371 STLLSEQNFPAVSIHRGMTQEER 393
            T L      A+SIH   + +ER
Sbjct: 390 VTGLK-----ALSIHGEKSMKER 407

Length = 518

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

 Score = 91.6 bits (227), Expect = 8e-20
 Identities = 65/228 (28%), Positives = 119/228 (52%), Gaps = 14/228 (6%)

Query: 146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNV-------YVLVMCHTRELAFQISK 198
           A+ G D+  QA++G GKT  F++A + +L +  +           L++  TRELA QI K
Sbjct: 43  ALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPTRELAIQIHK 102

Query: 199 EYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKL-NLSLL 257
           +  +F   +  ++  + +GG+   K  E L+     +++ TPGR++  V+  K+ +L   
Sbjct: 103 DAVKFGADLG-LRFALVYGGVDYDKQRELLQ-QGVDVIIATPGRLIDYVKQHKVVSLHAC 160

Query: 258 KHFILDECDKMLEQLEMRRDVQEIFRSSPH--TKQVMMFSATLSKEIRPVCKKFMHDPME 315
           +  +LDE D+M + L   +D++ + R  P   T+Q ++FSATLS  +  +  + M++P +
Sbjct: 161 EICVLDEADRMFD-LGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEK 219

Query: 316 VYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKS 363
           + V+ E        Q+ Y    + EK   L  LL   E  + ++FV +
Sbjct: 220 LVVETETITAARVRQRIYFP-ADEEKQTLLLGLLSRSEGARTMVFVNT 266

Length = 572

>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain

 Score = 68.3 bits (168), Expect = 1e-14
 Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 11/75 (14%)

Query: 74  YVSIHSSGFRDFLLKPEILRAIVDCWR-----ILVATNLFGRGMDIERVNIVFNYDMPED 128
              +H        L  E    I++ +R     +LVAT++ GRG+D+  VN+V NYD+P +
Sbjct: 10  VARLHGG------LSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPWN 63

Query: 129 SDTYLHRVARAGRFG 143
             +Y+ R+ RAGR G
Sbjct: 64  PASYIQRIGRAGRAG 78

The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. Length = 78

>gnl|CDD|238034 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

 Score = 68.8 bits (169), Expect = 4e-14
 Identities = 22/47 (46%), Positives = 32/47 (68%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKA 146
            +LVAT++  RG+D+  V++V NYD+P    +YL R+ RAGR G K 
Sbjct: 80  VVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKG 126

Length = 131

>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain

 Score = 64.9 bits (159), Expect = 2e-13
 Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 11/75 (14%)

Query: 74  YVSIHSSGFRDFLLKPEILRAIVDCWR-----ILVATNLFGRGMDIERVNIVFNYDMPED 128
              +H        L  E    I+D +      +LVAT++  RG+D+  V++V  YD+P  
Sbjct: 14  VARLHGG------LSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWS 67

Query: 129 SDTYLHRVARAGRFG 143
             +Y+ R+ RAGR G
Sbjct: 68  PASYIQRIGRAGRAG 82

Length = 82

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

 Score = 71.0 bits (174), Expect = 4e-13
 Identities = 24/46 (52%), Positives = 33/46 (71%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK 145
           R+LVAT++  RG+DI  V+ V NYD+P D + Y+HR+ R GR G K
Sbjct: 325 RVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRK 370

Length = 513

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

 Score = 67.9 bits (166), Expect = 2e-12
 Identities = 23/48 (47%), Positives = 37/48 (77%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV 147
           R+L+ T+L  RG+D+++V++V NYD+P   + Y+HR+ R+GRFG K V
Sbjct: 319 RVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGV 366

Length = 401

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

 Score = 65.7 bits (161), Expect = 1e-11
 Identities = 25/45 (55%), Positives = 34/45 (75%)

Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK 145
           +LVAT++  RG+DI+ V+ V N+DMP  +DTYLHR+ R GR G K
Sbjct: 298 VLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRK 342

Length = 434

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

 Score = 63.3 bits (154), Expect = 1e-10
 Identities = 23/43 (53%), Positives = 36/43 (83%)

Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG 143
           IL+AT++  RG+D+ER+++V NYD+P DS++Y+HR+ R GR G
Sbjct: 298 ILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAG 340

Length = 629

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

 Score = 60.3 bits (146), Expect = 9e-10
 Identities = 23/48 (47%), Positives = 34/48 (70%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV 147
           R+LVAT++ GRG+ I+ ++ V N+ +PED D Y+HR+ R GR G   V
Sbjct: 387 RVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGV 434

Length = 475

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

 Score = 59.2 bits (144), Expect = 1e-09
 Identities = 23/47 (48%), Positives = 31/47 (65%)

Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV 147
           ILVAT++  RG+ I  V  VFNYD+P+D + Y+HR+ R GR G    
Sbjct: 308 ILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGH 354

Length = 423

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

 Score = 58.7 bits (143), Expect = 3e-09
 Identities = 19/46 (41%), Positives = 32/46 (69%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK 145
            +LVAT++  RG+DI+ +  V NY++  D + ++HR+ R GR G+K
Sbjct: 294 SVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSK 339

Length = 460

>gnl|CDD|238034 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

 Score = 53.8 bits (130), Expect = 6e-09
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 2/74 (2%)

Query: 331 QHYVKLKENEKNKKLFELLD--VLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGM 388
           + YV   E+EK + L ELL   + +  +V+IF  S      L+ LL +      ++H   
Sbjct: 3   KQYVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDG 62

Query: 389 TQEERLKKYQEFKD 402
           +QEER +  ++F++
Sbjct: 63  SQEEREEVLKDFRE 76

Length = 131

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

 Score = 56.3 bits (136), Expect = 1e-08
 Identities = 19/47 (40%), Positives = 30/47 (63%)

Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV 147
           I++AT++  RG+D++ V  V N+D P   + Y+HR+ R GR G K  
Sbjct: 430 IMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGA 476

Length = 545

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

 Score = 56.1 bits (135), Expect = 2e-08
 Identities = 21/43 (48%), Positives = 31/43 (72%)

Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG 143
           ILVAT++  RG+ I+ V  V+NYD+P D++ Y+HR+ R  R G
Sbjct: 310 ILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLG 352

Length = 572

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

 Score = 52.5 bits (126), Expect = 2e-07
 Identities = 20/42 (47%), Positives = 30/42 (71%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR 141
           R+LVAT++  RG+DIE +  V NY++P   + Y+HR+ R GR
Sbjct: 297 RVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGR 338

Length = 456

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

 Score = 49.0 bits (117), Expect = 3e-06
 Identities = 29/88 (32%), Positives = 49/88 (55%), Gaps = 5/88 (5%)

Query: 57  ADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRA-IVDCWRILVATNLFGRGMDIE 115
           AD   +A+     +K   +SIH  G +    + E++++ +V    ++VAT + GRG+D+ 
Sbjct: 380 ADLLANAITVVTGLKA--LSIH--GEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLL 435

Query: 116 RVNIVFNYDMPEDSDTYLHRVARAGRFG 143
           RV  V  +DMP     Y+H++ RA R G
Sbjct: 436 RVRQVIIFDMPNTIKEYIHQIGRASRMG 463

Length = 518

>gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ

 Score = 46.6 bits (111), Expect = 2e-05
 Identities = 21/46 (45%), Positives = 28/46 (60%)

Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKA 146
           ++VATN FG G+D   V  V +YDMP + ++Y     RAGR G  A
Sbjct: 277 VMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPA 322

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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 591

>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function prediction only]

 Score = 44.7 bits (106), Expect = 9e-05
 Identities = 28/115 (24%), Positives = 53/115 (46%), Gaps = 10/115 (8%)

Query: 151 DILCQAKSGMGKTAVFVLATLQQL-ETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN 209
           ++L  A +G GKT + +LA L  L E     VY+      + LA +  +E+ R  +    
Sbjct: 49  NVLISAPTGSGKTLIALLAILSTLLEGGGKVVYI---VPLKALAEEKYEEFSRLEEL--G 103

Query: 210 IKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDE 264
           I+VG+  G   +  +          ++V TP ++ +L R +   +  +   ++DE
Sbjct: 104 IRVGISTGDYDLDDERLA----RYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDE 154

Length = 766

>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]

 Score = 43.6 bits (103), Expect = 2e-04
 Identities = 30/120 (25%), Positives = 50/120 (41%), Gaps = 22/120 (18%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
               +    +G GKT V   A        +     LV+  T+EL  Q ++  ++F   + 
Sbjct: 55  ERRGVIVLPTGAGKTVVAAEAI------AELKRSTLVLVPTKELLDQWAEALKKF--LLL 106

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHF---ILDEC 265
           N ++G++ GG   +K+ E  K     + V T   +  L R + L+  L   F   I DE 
Sbjct: 107 NDEIGIYGGG---EKELEPAK-----VTVAT---VQTLARRQLLDEFLGNEFGLIIFDEV 155

Length = 442

>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication, recombination, and repair]

 Score = 41.9 bits (99), Expect = 6e-04
 Identities = 20/48 (41%), Positives = 28/48 (58%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV 147
           +++VATN FG G+D   V  V +YD+P   ++Y     RAGR G  A 
Sbjct: 282 KVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAE 329

Length = 590

>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]

 Score = 41.2 bits (97), Expect = 0.001
 Identities = 70/302 (23%), Positives = 117/302 (38%), Gaps = 51/302 (16%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G +++    +G GKT  F+L  L  L    S   +L+   T  LA     + ER  + +S
Sbjct: 85  GRNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLY-PTNALAND---QAERLRELIS 140

Query: 209 N----IKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRI-LALVRNKKLNLSL---LKHF 260
           +    +  G + G  P  ++   +  + P I++  P  +   L+RN    L L   LK+ 
Sbjct: 141 DLPGKVTFGRYTGDTP-PEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYL 199

Query: 261 ILDECD----------KMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLS--KEIRPVCKK 308
           ++DE             +L    +RR +    R      Q++  SATL+   E     ++
Sbjct: 200 VVDELHTYRGVQGSEVALL----LRR-LLRRLRRYGSPLQIICTSATLANPGEF---AEE 251

Query: 309 FMHDPMEVYVDD----EAKLTLHGLQQHYVKLKENEKNKKLFEL-----LDVLEFNQVVI 359
                 EV VD+             +    +L E+ +   L EL     L V    Q ++
Sbjct: 252 LFGRDFEVPVDEDGSPRGLRYFVRREPPIRELAESIRRSALAELATLAALLVRNGIQTLV 311

Query: 360 FVKS-------VTRCIALSTLLSEQNFPAVSIHR-GMTQEERLKKYQEFKDFH-KGLAIT 410
           F +S                    +   AVS +R G+ +EER +   EFK+    G+  T
Sbjct: 312 FFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIAT 371

Query: 411 FA 412
            A
Sbjct: 372 NA 373

Length = 851

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	448
KOG0329|consensus	387		100.0
KOG0328|consensus	400		100.0
KOG0330|consensus	476		100.0
KOG0326|consensus	459		100.0
KOG0331|consensus	519		100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
KOG0338|consensus	691		100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
PTZ00110	545	helicase; Provisional	100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0343|consensus	758		100.0
KOG0340|consensus	442		100.0
KOG0327|consensus	397		100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
KOG0345|consensus	567		100.0
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0333|consensus	673		100.0
KOG0346|consensus	569		100.0
KOG0339|consensus	731		100.0
KOG0332|consensus	477		100.0
KOG0336|consensus	629		100.0
KOG0342|consensus	543		100.0
PTZ00424	401	helicase 45; Provisional	100.0
KOG0335|consensus	482		100.0
KOG0341|consensus	610		100.0
KOG4284|consensus	980		100.0
KOG0334|consensus	997		100.0
KOG0347|consensus	731		100.0
KOG0348|consensus	708		100.0
KOG0337|consensus	529		100.0
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	100.0
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	100.0
KOG0344|consensus	593		100.0
KOG0350|consensus	620		100.0
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	100.0
PRK13767	876	ATP-dependent helicase; Provisional	100.0
PRK02362	737	ski2-like helicase; Provisional	100.0
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	100.0
COG1201	814	Lhr Lhr-like helicases [General function predictio	100.0
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	100.0
PRK00254	720	ski2-like helicase; Provisional	100.0
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	100.0
PRK09401	1176	reverse gyrase; Reviewed	100.0
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	100.0
PRK01172	674	ski2-like helicase; Provisional	100.0
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.98
PRK10689	1147	transcription-repair coupling factor; Provisional	99.97
PRK14701	1638	reverse gyrase; Provisional	99.97
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.97
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.97
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.97
COG1205	851	Distinct helicase family with a unique C-terminal	99.97
KOG0349|consensus	725		99.96
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.96
COG1204	766	Superfamily II helicase [General function predicti	99.96
COG1202	830	Superfamily II helicase, archaea-specific [General	99.96
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.96
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.96
PHA02653	675	RNA helicase NPH-II; Provisional	99.96
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.96
PHA02558	501	uvsW UvsW helicase; Provisional	99.96
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.95
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.95
KOG0952|consensus	1230		99.95
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.94
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.94
PRK13766	773	Hef nuclease; Provisional	99.93
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.93
KOG0351|consensus	941		99.93
KOG0354|consensus	746		99.92
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.91
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.91
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.91
KOG0352|consensus	641		99.91
KOG0947|consensus	1248		99.9
PRK09694	878	helicase Cas3; Provisional	99.89
KOG0353|consensus	695		99.89
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.88
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.88
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.88
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.88
KOG0951|consensus	1674		99.87
KOG0948|consensus	1041		99.87
PRK05580	679	primosome assembly protein PriA; Validated	99.86
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.86
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.85
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.84
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.83
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.82
PRK04914	956	ATP-dependent helicase HepA; Validated	99.82
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.82
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.81
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.79
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.76
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.76
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.75
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.71
KOG0950|consensus	1008		99.69
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.69
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.66
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.66
KOG1123|consensus	776		99.64
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.63
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.59
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.59
COG4096	875	HsdR Type I site-specific restriction-modification	99.58
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.56
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.53
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.49
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.46
KOG0385|consensus	971		99.42
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.36
KOG0922|consensus	674		99.34
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.33
KOG0920|consensus	924		99.32
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.3
KOG0951|consensus	1674		99.3
CHL00122	870	secA preprotein translocase subunit SecA; Validate	99.23
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.22
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.21
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	99.21
KOG0949|consensus	1330		99.18
KOG0387|consensus	923		99.17
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	99.11
KOG4150|consensus	1034		99.11
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.09
KOG0351|consensus	941		99.08
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.07
KOG1000|consensus	689		99.07
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.06
KOG0392|consensus	1549		99.06
KOG0389|consensus	941		99.04
PRK05298	652	excinuclease ABC subunit B; Provisional	99.04
KOG0390|consensus	776		99.03
KOG0924|consensus	1042		99.02
KOG0384|consensus	1373		99.01
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.0
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.0
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.99
KOG0926|consensus	1172		98.99
KOG0923|consensus	902		98.98
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	98.96
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	98.94
KOG0953|consensus	700		98.89
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.85
KOG1002|consensus	791		98.84
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	98.83
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	98.8
KOG0925|consensus	699		98.71
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	98.68
KOG0353|consensus	695		98.62
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	98.59
PRK14873	665	primosome assembly protein PriA; Provisional	98.57
KOG4439|consensus	901		98.56
KOG0952|consensus	1230		98.54
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	98.53
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	98.51
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.47
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	98.45
COG4889	1518	Predicted helicase [General function prediction on	98.4
KOG0352|consensus	641		98.36
PRK15483	986	type III restriction-modification system StyLTI en	98.32
KOG2340|consensus	698		98.31
KOG0391|consensus	1958		98.25
COG0610	962	Type I site-specific restriction-modification syst	98.24
KOG0386|consensus	1157		98.17
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.12
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	98.02
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	97.97
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	97.95
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	97.86
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	97.82
KOG0333|consensus	673		97.81
KOG0388|consensus	1185		97.73
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	97.67
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.62
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	97.61
COG3587	985	Restriction endonuclease [Defense mechanisms]	97.59
PF13245	76	AAA_19: Part of AAA domain	97.55
PRK10536	262	hypothetical protein; Provisional	97.53
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	97.46
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	97.44
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	97.4
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	97.38
KOG0331|consensus	519		97.37
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.37
PRK10875	615	recD exonuclease V subunit alpha; Provisional	97.33
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	97.32
smart00490	82	HELICc helicase superfamily c-terminal domain.	97.31
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.28
KOG1802|consensus	935		97.25
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.2
KOG0989|consensus	346		97.19
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	97.17
KOG1803|consensus	649		97.13
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	97.06
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	97.03
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	97.03
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	97.01
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	96.97
KOG0336|consensus	629		96.95
PTZ00110	545	helicase; Provisional	96.94
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	96.94
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	96.91
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	96.89
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.89
PRK06526	254	transposase; Provisional	96.86
KOG0342|consensus	543		96.85
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	96.83
KOG0341|consensus	610		96.81
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	96.8
PRK08181	269	transposase; Validated	96.79
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	96.77
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	96.77
PRK04296	190	thymidine kinase; Provisional	96.76
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.76
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	96.73
KOG0348|consensus	708		96.71
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	96.7
smart00382	148	AAA ATPases associated with a variety of cellular	96.68
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.62
KOG0335|consensus	482		96.59
PRK14974	336	cell division protein FtsY; Provisional	96.57
PTZ00424	401	helicase 45; Provisional	96.53
KOG0330|consensus	476		96.52
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.51
KOG0921|consensus	1282		96.4
KOG0298|consensus	1394		96.39
KOG0345|consensus	567		96.39
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.37
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	96.37
KOG1132|consensus	945		96.36
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.34
PRK00149	450	dnaA chromosomal replication initiation protein; R	96.31
KOG1001|consensus	674		96.27
KOG0328|consensus	400		96.24
PRK05642	234	DNA replication initiation factor; Validated	96.21
KOG1015|consensus	1567		96.16
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	96.15
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	96.15
PRK06893	229	DNA replication initiation factor; Validated	96.07
PRK14087	450	dnaA chromosomal replication initiation protein; P	95.99
PHA02533	534	17 large terminase protein; Provisional	95.96
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	95.92
PRK00411	394	cdc6 cell division control protein 6; Reviewed	95.92
KOG0343|consensus	758		95.9
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	95.88
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	95.88
PRK08084	235	DNA replication initiation factor; Provisional	95.85
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	95.8
KOG0326|consensus	459		95.8
KOG0329|consensus	387		95.77
KOG0350|consensus	620		95.77
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	95.76
PLN03025	319	replication factor C subunit; Provisional	95.75
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	95.7
PRK06921	266	hypothetical protein; Provisional	95.68
COG1484	254	DnaC DNA replication protein [DNA replication, rec	95.66
PRK14088	440	dnaA chromosomal replication initiation protein; P	95.62
PRK08727	233	hypothetical protein; Validated	95.53
PRK13889	988	conjugal transfer relaxase TraA; Provisional	95.53
KOG0347|consensus	731		95.51
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	95.5
PRK12422	445	chromosomal replication initiation protein; Provis	95.5
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	95.48
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	95.45
KOG0338|consensus	691		95.45
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	95.44
PRK12377	248	putative replication protein; Provisional	95.42
PRK08116	268	hypothetical protein; Validated	95.4
PRK13767	876	ATP-dependent helicase; Provisional	95.38
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	95.38
PRK00771	437	signal recognition particle protein Srp54; Provisi	95.38
KOG0340|consensus	442		95.35
KOG0332|consensus	477		95.33
PRK09200	790	preprotein translocase subunit SecA; Reviewed	95.33
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	95.26
TIGR00376	637	DNA helicase, putative. The gene product may repre	95.24
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	95.17
PRK09183	259	transposase/IS protein; Provisional	95.16
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	95.13
PF13173	128	AAA_14: AAA domain	95.13
CHL00181	287	cbbX CbbX; Provisional	95.07
KOG0344|consensus	593		95.03
PHA02544	316	44 clamp loader, small subunit; Provisional	95.02
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	94.97
COG4626	546	Phage terminase-like protein, large subunit [Gener	94.94
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	94.93
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	94.9
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	94.9
PRK12402	337	replication factor C small subunit 2; Reviewed	94.89
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	94.88
PHA03368	738	DNA packaging terminase subunit 1; Provisional	94.79
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	94.77
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	94.77
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	94.75
PF00004	132	AAA: ATPase family associated with various cellula	94.75
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	94.75
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	94.74
KOG0991|consensus	333		94.73
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	94.72
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	94.62
smart00490	82	HELICc helicase superfamily c-terminal domain.	94.6
PRK00440	319	rfc replication factor C small subunit; Reviewed	94.57
PTZ00112	1164	origin recognition complex 1 protein; Provisional	94.56
PRK08903	227	DnaA regulatory inactivator Hda; Validated	94.55
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	94.54
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	94.5
KOG1805|consensus	1100		94.47
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	94.45
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	94.4
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	94.34
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	94.32
PRK06835	329	DNA replication protein DnaC; Validated	94.31
PRK07952	244	DNA replication protein DnaC; Validated	94.31
PHA02653	675	RNA helicase NPH-II; Provisional	94.28
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	94.24
PF05729	166	NACHT: NACHT domain	94.21
KOG4284|consensus	980		94.2
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	94.15
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	94.14
PRK13826	1102	Dtr system oriT relaxase; Provisional	94.06
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	94.06
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	94.06
PRK13833	323	conjugal transfer protein TrbB; Provisional	94.05
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	94.02
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	93.99
PRK07940	394	DNA polymerase III subunit delta'; Validated	93.97
PRK11054	684	helD DNA helicase IV; Provisional	93.96
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	93.96
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	93.96
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	93.94
PRK08533	230	flagellar accessory protein FlaH; Reviewed	93.93
PHA03333	752	putative ATPase subunit of terminase; Provisional	93.88
TIGR00064	272	ftsY signal recognition particle-docking protein F	93.83
PRK13342	413	recombination factor protein RarA; Reviewed	93.81
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	93.81
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	93.81
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	93.79
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	93.74
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	93.74
COG0593	408	DnaA ATPase involved in DNA replication initiation	93.68
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	93.65
KOG0327|consensus	397		93.63
COG3972	660	Superfamily I DNA and RNA helicases [General funct	93.62
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	93.58
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	93.53
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	93.45
PRK11823	446	DNA repair protein RadA; Provisional	93.36
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	93.34
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	93.34
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	93.22
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	93.2
PF02572	172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	93.19
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	93.18
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	93.15
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	93.14
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	93.1
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	93.08
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	93.07
PRK06904	472	replicative DNA helicase; Validated	93.05
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	92.87
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	92.87
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	92.86
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	92.86
TIGR00959	428	ffh signal recognition particle protein. This mode	92.86
PRK09112	351	DNA polymerase III subunit delta'; Validated	92.84
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	92.84
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	92.81
PRK05707	328	DNA polymerase III subunit delta'; Validated	92.8
KOG0391|consensus	1958		92.78
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	92.77
PRK04914	956	ATP-dependent helicase HepA; Validated	92.77
PRK07471	365	DNA polymerase III subunit delta'; Validated	92.75
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	92.71
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	92.71
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	92.7
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	92.69
PRK13851	344	type IV secretion system protein VirB11; Provision	92.64
KOG0738|consensus	491		92.6
PRK10867	433	signal recognition particle protein; Provisional	92.57
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	92.51
PRK13341	725	recombination factor protein RarA/unknown domain f	92.49
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	92.45
TIGR00767	415	rho transcription termination factor Rho. Members	92.39
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	92.37
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	92.34
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	92.21
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	92.17
KOG2170|consensus	344		92.13
KOG1133|consensus	821		92.12
PRK08006	471	replicative DNA helicase; Provisional	92.09
PRK04195	482	replication factor C large subunit; Provisional	92.08
KOG0058|consensus	716		92.07
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	92.06
KOG0741|consensus	744		92.05
PRK08939	306	primosomal protein DnaI; Reviewed	92.05
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	92.04
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	92.0
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	91.97
PHA00729	226	NTP-binding motif containing protein	91.92
PF03668	284	ATP_bind_2: P-loop ATPase protein family; InterPro	91.89
cd03115	173	SRP The signal recognition particle (SRP) mediates	91.72
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	91.69
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	91.66
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	91.64
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	91.61
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	91.57
PRK02362	737	ski2-like helicase; Provisional	91.55
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	91.52
KOG0339|consensus	731		91.5
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	91.42
PRK14701	1638	reverse gyrase; Provisional	91.42
PRK08840	464	replicative DNA helicase; Provisional	91.39
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	91.37
PRK04841	903	transcriptional regulator MalT; Provisional	91.31
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	91.3
PRK06067	234	flagellar accessory protein FlaH; Validated	91.3
KOG2228|consensus	408		91.24
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	91.23
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	91.17
PRK09376	416	rho transcription termination factor Rho; Provisio	91.05
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	91.02
PRK05748	448	replicative DNA helicase; Provisional	91.02
PRK07004	460	replicative DNA helicase; Provisional	91.01
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	90.99
PLN02165	334	adenylate isopentenyltransferase	90.99
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	90.91
KOG0742|consensus	630		90.89
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	90.89
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	90.86
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	90.81
KOG1016|consensus	1387		90.77
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	90.71
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	90.68
PHA03372	668	DNA packaging terminase subunit 1; Provisional	90.62
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	90.6
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	90.55
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	90.54
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	90.52
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	90.52
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	90.47
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	90.46
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	90.44
PRK07399	314	DNA polymerase III subunit delta'; Validated	90.41
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	90.37
COG2256	436	MGS1 ATPase related to the helicase subunit of the	90.35
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	90.34
PRK08769	319	DNA polymerase III subunit delta'; Validated	90.33
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	90.31
COG2109	198	BtuR ATP:corrinoid adenosyltransferase [Coenzyme m	90.31
TIGR02237	209	recomb_radB DNA repair and recombination protein R	90.24
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	90.17
KOG1131|consensus	755		90.16
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	90.07
COG3973	747	Superfamily I DNA and RNA helicases [General funct	90.03
PRK07414	178	cob(I)yrinic acid a,c-diamide adenosyltransferase;	89.97
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	89.9
PRK10689	1147	transcription-repair coupling factor; Provisional	89.89
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	89.89
KOG0743|consensus	457		89.76
TIGR00665	434	DnaB replicative DNA helicase. This model describe	89.71
PRK13897	606	type IV secretion system component VirD4; Provisio	89.7
KOG1513|consensus	1300		89.59
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	89.58
PTZ00293	211	thymidine kinase; Provisional	89.48
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	89.42
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	89.36
PRK08058	329	DNA polymerase III subunit delta'; Validated	89.19
PRK10416	318	signal recognition particle-docking protein FtsY;	89.03
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	88.96
PRK14873	665	primosome assembly protein PriA; Provisional	88.95
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	88.92
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	88.9
PRK09435	332	membrane ATPase/protein kinase; Provisional	88.61
KOG0346|consensus	569		88.57
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	88.5
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	88.48
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	88.45
PRK06871	325	DNA polymerase III subunit delta'; Validated	88.42
PRK06321	472	replicative DNA helicase; Provisional	88.4
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	88.35
PRK06964	342	DNA polymerase III subunit delta'; Validated	88.29
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	88.21
PRK08760	476	replicative DNA helicase; Provisional	88.2
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	88.13
KOG2227|consensus	529		88.08
PRK08506	472	replicative DNA helicase; Provisional	87.86
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	87.85
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	87.8
PRK00254	720	ski2-like helicase; Provisional	87.74
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	87.7
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	87.61
PRK09165	497	replicative DNA helicase; Provisional	87.54
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	87.54
PRK10865	857	protein disaggregation chaperone; Provisional	87.42

>KOG0329|consensus

Probab=100.00  E-value=1.6e-60  Score=421.61  Aligned_cols=372  Identities=69%  Similarity=1.022  Sum_probs=334.0

Q ss_pred             ccccCCCccccccccccccccchhhhhhhhccCceeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCccccccee
Q psy1548          40 NDDLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNI  119 (448)
Q Consensus        40 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~  119 (448)
                      .++++||+++++......   +....+....+|.|++.|++||+++.++|++++++.++|                    
T Consensus         5 e~dlldyeeeee~~~~~~---~~~~~~~~d~kgsyv~ihssgfrdfllkpellraivdcg--------------------   61 (387)
T KOG0329|consen    5 EEDLLDYEEEEEEQADQE---SAPAGPKKDKKGSYVSIHSSGFRDFLLKPELLRAIVDCG--------------------   61 (387)
T ss_pred             hhhhhcccccccccCCcc---CCCCCccccccCcEEEEeccchhhhhcCHHHHHHHHhcc--------------------
Confidence            568999988775544322   122234567889999999999999999999999999999                    


Q ss_pred             EeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHH
Q psy1548         120 VFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKE  199 (448)
Q Consensus       120 v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~  199 (448)
                         |++|+.+   |++      |||.+..|.|++++|.+|+|||++|.++.|+++++.++...++++|+||+||.|+.+.
T Consensus        62 ---fehpsev---qhe------cipqailgmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtrelafqi~~e  129 (387)
T KOG0329|consen   62 ---FEHPSEV---QHE------CIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTRELAFQISKE  129 (387)
T ss_pred             ---CCCchHh---hhh------hhhHHhhcchhheecccCCCceeeeehhhhhhcCCCCCeEEEEEEeccHHHHHHHHHH
Confidence               9999999   999      9999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHH
Q psy1548         200 YERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQ  279 (448)
Q Consensus       200 ~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~  279 (448)
                      +.+|++++|++++.+++||.++..+...+++ +|+|+|+||++++.+.+++.+++++++.+|+||||.|+++.+++.+++
T Consensus       130 y~rfskymP~vkvaVFfGG~~Ikkdee~lk~-~PhivVgTPGrilALvr~k~l~lk~vkhFvlDEcdkmle~lDMrRDvQ  208 (387)
T KOG0329|consen  130 YERFSKYMPSVKVSVFFGGLFIKKDEELLKN-CPHIVVGTPGRILALVRNRSLNLKNVKHFVLDECDKMLEQLDMRRDVQ  208 (387)
T ss_pred             HHHHHhhCCCceEEEEEcceeccccHHHHhC-CCeEEEcCcHHHHHHHHhccCchhhcceeehhhHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999988 699999999999999999999999999999999999999989999999


Q ss_pred             HHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEE
Q psy1548         280 EIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVI  359 (448)
Q Consensus       280 ~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~II  359 (448)
                      ++++..|+.+|+++||||++++++..+++||.+|..++++++...+.+++.|+|+.+++.+|...+.++++....++++|
T Consensus       209 Eifr~tp~~KQvmmfsatlskeiRpvC~kFmQdPmEi~vDdE~KLtLHGLqQ~YvkLke~eKNrkl~dLLd~LeFNQVvI  288 (387)
T KOG0329|consen  209 EIFRMTPHEKQVMMFSATLSKEIRPVCHKFMQDPMEIFVDDEAKLTLHGLQQYYVKLKENEKNRKLNDLLDVLEFNQVVI  288 (387)
T ss_pred             HHhhcCcccceeeeeeeecchhhHHHHHhhhcCchhhhccchhhhhhhhHHHHHHhhhhhhhhhhhhhhhhhhhhcceeE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EECccHHHHH----HHHHHHhCCCc----EEEEeCCCCHHH---HHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHh
Q psy1548         360 FVKSVTRCIA----LSTLLSEQNFP----AVSIHRGMTQEE---RLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRF  428 (448)
Q Consensus       360 F~~s~~~a~~----l~~~L~~~g~~----~~~lh~~~~~~e---R~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~  428 (448)
                      |+.++.+...    ++..|-.+|++    -+.++-+|+.+-   -.++-+.=+-|.+|.+|+|+++..|...|+.++++|
T Consensus       289 FvKsv~Rl~f~kr~vat~lfgrgmdiervNi~~NYdmp~~~DtYlHrv~rAgrfGtkglaitfvs~e~da~iLn~vqdRf  368 (387)
T KOG0329|consen  289 FVKSVQRLSFQKRLVATDLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNPVQDRF  368 (387)
T ss_pred             eeehhhhhhhhhhhHHhhhhccccCcccceeeeccCCCCCchHHHHHhhhhhccccccceeehhcchhhHHHhchhhHhh
Confidence            9999887442    44444444543    356677887643   233333334466999999999999999999999999


Q ss_pred             cCCCCCCCccccccccccC
Q psy1548         429 DVSISELPDEIDLSTYIEG  447 (448)
Q Consensus       429 ~~~~~~~p~~~~~~~~~~~  447 (448)
                      ++.|.+||+.++.++|+++
T Consensus       369 ~v~i~eLpdeid~s~y~~~  387 (387)
T KOG0329|consen  369 EVNIKELPDEIDFSTYEKT  387 (387)
T ss_pred             hccHhhcCcccchhhhhcC
Confidence            9999999999999998874

>KOG0328|consensus

Probab=100.00  E-value=7.1e-56  Score=397.31  Aligned_cols=324  Identities=34%  Similarity=0.573  Sum_probs=311.0

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      .+.|++++++.++++++...|                       |+.|+.+   |+.      ++|.+++|+||+.++.+
T Consensus        26 ~~~F~~Mgl~edlLrgiY~yG-----------------------fekPS~I---Qqr------Ai~~IlkGrdViaQaqS   73 (400)
T KOG0328|consen   26 IPTFDDMGLKEDLLRGIYAYG-----------------------FEKPSAI---QQR------AIPQILKGRDVIAQAQS   73 (400)
T ss_pred             ccchhhcCchHHHHHHHHHhc-----------------------cCCchHH---Hhh------hhhhhhcccceEEEecC
Confidence            457999999999999999999                       9999999   999      99999999999999999


Q ss_pred             CChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEE
Q psy1548         159 GMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVG  238 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~  238 (448)
                      |+|||.+|.+.+|+.+.-..+..++++++|||+|+.|+.+.+..++.++ ++.+..+.||.+..++...+..+ .+++.|
T Consensus        74 GTGKTa~~si~vlq~~d~~~r~tQ~lilsPTRELa~Qi~~vi~alg~~m-nvq~hacigg~n~gedikkld~G-~hvVsG  151 (400)
T KOG0328|consen   74 GTGKTATFSISVLQSLDISVRETQALILSPTRELAVQIQKVILALGDYM-NVQCHACIGGKNLGEDIKKLDYG-QHVVSG  151 (400)
T ss_pred             CCCceEEEEeeeeeecccccceeeEEEecChHHHHHHHHHHHHHhcccc-cceEEEEecCCccchhhhhhccc-ceEeeC
Confidence            9999999999999998887778899999999999999999999999999 99999999999998888888865 899999


Q ss_pred             cHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEE
Q psy1548         239 TPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV  318 (448)
Q Consensus       239 Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~  318 (448)
                      ||++++++++++.+.-+.++++|+||||.|++. +|..++-.+++++|+..|++++|||+|.++.+...+|+.+|+.+.+
T Consensus       152 tPGrv~dmikr~~L~tr~vkmlVLDEaDemL~k-gfk~Qiydiyr~lp~~~Qvv~~SATlp~eilemt~kfmtdpvrilv  230 (400)
T KOG0328|consen  152 TPGRVLDMIKRRSLRTRAVKMLVLDEADEMLNK-GFKEQIYDIYRYLPPGAQVVLVSATLPHEILEMTEKFMTDPVRILV  230 (400)
T ss_pred             CCchHHHHHHhccccccceeEEEeccHHHHHHh-hHHHHHHHHHHhCCCCceEEEEeccCcHHHHHHHHHhcCCceeEEE
Confidence            999999999999999999999999999999998 9999999999999999999999999999999999999999999999


Q ss_pred             cCcccccccceeEEEEEcCcch-HHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHH
Q psy1548         319 DDEAKLTLHGLQQHYVKLKENE-KNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKY  397 (448)
Q Consensus       319 ~~~~~~~~~~i~~~~~~~~~~~-k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l  397 (448)
                      ..+ ..+..+++++|+.++.++ |++.|.++.+.+.-.+.+|||||+..+..|.+.|++.++.+..+||+|+++||.+++
T Consensus       231 krd-eltlEgIKqf~v~ve~EewKfdtLcdLYd~LtItQavIFcnTk~kVdwLtekm~~~nftVssmHGDm~qkERd~im  309 (400)
T KOG0328|consen  231 KRD-ELTLEGIKQFFVAVEKEEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMEQKERDKIM  309 (400)
T ss_pred             ecC-CCchhhhhhheeeechhhhhHhHHHHHhhhhehheEEEEecccchhhHHHHHHHhhCceeeeccCCcchhHHHHHH
Confidence            888 788899999999998876 999999999999889999999999999999999999999999999999999999999


Q ss_pred             HHHhcCC----------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCC
Q psy1548         398 QEFKDFH----------------------------------------------KGLAITFASDENDAKILNNVQDRFDVS  431 (448)
Q Consensus       398 ~~F~~g~----------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~  431 (448)
                      ++|++|+                                              +|++|.|+.++ |...+++||+.+...
T Consensus       310 ~dFRsg~SrvLitTDVwaRGiDv~qVslviNYDLP~nre~YIHRIGRSGRFGRkGvainFVk~~-d~~~lrdieq~yst~  388 (400)
T KOG0328|consen  310 NDFRSGKSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSD-DLRILRDIEQYYSTQ  388 (400)
T ss_pred             HHhhcCCceEEEEechhhccCCcceeEEEEecCCCccHHHHhhhhccccccCCcceEEEEecHH-HHHHHHHHHHHHhhh
Confidence            9999999                                              89999999877 899999999999999


Q ss_pred             CCCCCccc
Q psy1548         432 ISELPDEI  439 (448)
Q Consensus       432 ~~~~p~~~  439 (448)
                      +.++|-++
T Consensus       389 i~emp~nv  396 (400)
T KOG0328|consen  389 IDEMPMNV  396 (400)
T ss_pred             cccccchh
Confidence            99999874

>KOG0330|consensus

Probab=100.00  E-value=1.3e-55  Score=411.61  Aligned_cols=323  Identities=29%  Similarity=0.488  Sum_probs=308.8

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      ..+|.++++.+++++++++.+                       |..|+++   |++      +||.++.|+|+|+.|.|
T Consensus        60 ~~sf~dLgv~~~L~~ac~~l~-----------------------~~~PT~I---Q~~------aiP~~L~g~dvIglAeT  107 (476)
T KOG0330|consen   60 FKSFADLGVHPELLEACQELG-----------------------WKKPTKI---QSE------AIPVALGGRDVIGLAET  107 (476)
T ss_pred             hcchhhcCcCHHHHHHHHHhC-----------------------cCCCchh---hhh------hcchhhCCCcEEEEecc
Confidence            357999999999999999999                       9999999   999      99999999999999999


Q ss_pred             CChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEE
Q psy1548         159 GMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVG  238 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~  238 (448)
                      |||||.+|++|+++.+...+..++++|++||||||.|+.+.+..++... ++++.++.||.+...+...+.+. |||+|+
T Consensus       108 GSGKT~afaLPIl~~LL~~p~~~~~lVLtPtRELA~QI~e~fe~Lg~~i-glr~~~lvGG~~m~~q~~~L~kk-PhilVa  185 (476)
T KOG0330|consen  108 GSGKTGAFALPILQRLLQEPKLFFALVLTPTRELAQQIAEQFEALGSGI-GLRVAVLVGGMDMMLQANQLSKK-PHILVA  185 (476)
T ss_pred             CCCchhhhHHHHHHHHHcCCCCceEEEecCcHHHHHHHHHHHHHhcccc-CeEEEEEecCchHHHHHHHhhcC-CCEEEe
Confidence            9999999999999999998888999999999999999999999999988 99999999999999998888886 999999


Q ss_pred             cHHHHHHHHH-CCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEE
Q psy1548         239 TPGRILALVR-NKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVY  317 (448)
Q Consensus       239 Tp~~l~~~l~-~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~  317 (448)
                      ||++|.+++. .+.+++..++++|+||||++++. +|...+..|++.+|..+|+++|||||+..+.++....+.+|..+.
T Consensus       186 TPGrL~dhl~~Tkgf~le~lk~LVlDEADrlLd~-dF~~~ld~ILk~ip~erqt~LfsATMt~kv~kL~rasl~~p~~v~  264 (476)
T KOG0330|consen  186 TPGRLWDHLENTKGFSLEQLKFLVLDEADRLLDM-DFEEELDYILKVIPRERQTFLFSATMTKKVRKLQRASLDNPVKVA  264 (476)
T ss_pred             CcHHHHHHHHhccCccHHHhHHHhhchHHhhhhh-hhHHHHHHHHHhcCccceEEEEEeecchhhHHHHhhccCCCeEEe
Confidence            9999999998 58899999999999999999998 999999999999999999999999999999999999999999999


Q ss_pred             EcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHH
Q psy1548         318 VDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKY  397 (448)
Q Consensus       318 ~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l  397 (448)
                      +... ..+.++++|+|+.++...|...|..+++...++++||||++...++.++-.|+..|+.+..+||.|++..|..++
T Consensus       265 ~s~k-y~tv~~lkQ~ylfv~~k~K~~yLV~ll~e~~g~s~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l  343 (476)
T KOG0330|consen  265 VSSK-YQTVDHLKQTYLFVPGKDKDTYLVYLLNELAGNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGAL  343 (476)
T ss_pred             ccch-hcchHHhhhheEeccccccchhHHHHHHhhcCCcEEEEEeccchHHHHHHHHHhcCcceecccchhhHHHHHHHH
Confidence            8877 678899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhcCC----------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCC
Q psy1548         398 QEFKDFH----------------------------------------------KGLAITFASDENDAKILNNVQDRFDVS  431 (448)
Q Consensus       398 ~~F~~g~----------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~  431 (448)
                      +.|++|.                                              +|.+|+|+|.. |.+...+||..++++
T Consensus       344 ~~Fk~~~r~iLv~TDVaSRGLDip~Vd~VVNyDiP~~skDYIHRvGRtaRaGrsG~~ItlVtqy-Dve~~qrIE~~~gkk  422 (476)
T KOG0330|consen  344 NKFKAGARSILVCTDVASRGLDIPHVDVVVNYDIPTHSKDYIHRVGRTARAGRSGKAITLVTQY-DVELVQRIEHALGKK  422 (476)
T ss_pred             HHHhccCCcEEEecchhcccCCCCCceEEEecCCCCcHHHHHHHcccccccCCCcceEEEEehh-hhHHHHHHHHHHhcC
Confidence            9999998                                              89999999986 999999999999998


Q ss_pred             CCCCCcc
Q psy1548         432 ISELPDE  438 (448)
Q Consensus       432 ~~~~p~~  438 (448)
                      ..+.+-.
T Consensus       423 l~~~~~~  429 (476)
T KOG0330|consen  423 LPEYKVD  429 (476)
T ss_pred             CCccCcc
Confidence            8774433

>KOG0326|consensus

Probab=100.00  E-value=5e-55  Score=397.88  Aligned_cols=330  Identities=31%  Similarity=0.506  Sum_probs=316.1

Q ss_pred             ccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeecc
Q psy1548          78 HSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAK  157 (448)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~ap  157 (448)
                      ...+|+++.+..+++.++.+.|                       |+.|+|+   |.+      +||.++.|+|++..|.
T Consensus        83 kG~efEd~~Lkr~LLmgIfe~G-----------------------~ekPSPi---Qee------sIPiaLtGrdiLaRaK  130 (459)
T KOG0326|consen   83 KGNEFEDYCLKRELLMGIFEKG-----------------------FEKPSPI---QEE------SIPIALTGRDILARAK  130 (459)
T ss_pred             cCccHHHhhhhHHHHHHHHHhc-----------------------cCCCCCc---ccc------ccceeecchhhhhhcc
Confidence            3457999999999999999999                       9999999   999      9999999999999999


Q ss_pred             CCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEE
Q psy1548         158 SGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVV  237 (448)
Q Consensus       158 TGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV  237 (448)
                      .|+|||.+|.+|+|..+.......+++|++|||+||.|+.+.++.+++.+ ++++.+.+||++..+++..+... .|++|
T Consensus       131 NGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPtrelALQtSqvc~~lskh~-~i~vmvttGGT~lrDDI~Rl~~~-VH~~v  208 (459)
T KOG0326|consen  131 NGTGKTAAYCIPVLEKIDPKKNVIQAIILVPTRELALQTSQVCKELSKHL-GIKVMVTTGGTSLRDDIMRLNQT-VHLVV  208 (459)
T ss_pred             CCCCCccceechhhhhcCccccceeEEEEeecchhhHHHHHHHHHHhccc-CeEEEEecCCcccccceeeecCc-eEEEE
Confidence            99999999999999999999899999999999999999999999999999 89999999999998888777765 89999


Q ss_pred             EcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEE
Q psy1548         238 GTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVY  317 (448)
Q Consensus       238 ~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~  317 (448)
                      +||++++++.+++...++++.++|+||||.+++. +|...++.++..+|+++|++++|||+|-.+..+..+++++|..|.
T Consensus       209 gTPGRIlDL~~KgVa~ls~c~~lV~DEADKlLs~-~F~~~~e~li~~lP~~rQillySATFP~tVk~Fm~~~l~kPy~IN  287 (459)
T KOG0326|consen  209 GTPGRILDLAKKGVADLSDCVILVMDEADKLLSV-DFQPIVEKLISFLPKERQILLYSATFPLTVKGFMDRHLKKPYEIN  287 (459)
T ss_pred             cCChhHHHHHhcccccchhceEEEechhhhhhch-hhhhHHHHHHHhCCccceeeEEecccchhHHHHHHHhccCcceee
Confidence            9999999999999999999999999999999998 999999999999999999999999999999999999999999998


Q ss_pred             EcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHH
Q psy1548         318 VDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKY  397 (448)
Q Consensus       318 ~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l  397 (448)
                      .-.+  .++.++.|+|.++.+.+|...|..+...+.-++.||||||..++|.+|+.+.+.|+.|.++|+.|-+++|.+++
T Consensus       288 LM~e--Ltl~GvtQyYafV~e~qKvhCLntLfskLqINQsIIFCNS~~rVELLAkKITelGyscyyiHakM~Q~hRNrVF  365 (459)
T KOG0326|consen  288 LMEE--LTLKGVTQYYAFVEERQKVHCLNTLFSKLQINQSIIFCNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVF  365 (459)
T ss_pred             hhhh--hhhcchhhheeeechhhhhhhHHHHHHHhcccceEEEeccchHhHHHHHHHHhccchhhHHHHHHHHhhhhhhh
Confidence            7666  78899999999999999999999999999889999999999999999999999999999999999999999999


Q ss_pred             HHHhcCC----------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCC
Q psy1548         398 QEFKDFH----------------------------------------------KGLAITFASDENDAKILNNVQDRFDVS  431 (448)
Q Consensus       398 ~~F~~g~----------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~  431 (448)
                      ++|++|+                                              -|++|+++|.+ |+..|.+||+.++.+
T Consensus       366 HdFr~G~crnLVctDL~TRGIDiqavNvVINFDfpk~aEtYLHRIGRsGRFGhlGlAInLitye-drf~L~~IE~eLGtE  444 (459)
T KOG0326|consen  366 HDFRNGKCRNLVCTDLFTRGIDIQAVNVVINFDFPKNAETYLHRIGRSGRFGHLGLAINLITYE-DRFNLYRIEQELGTE  444 (459)
T ss_pred             hhhhccccceeeehhhhhcccccceeeEEEecCCCCCHHHHHHHccCCccCCCcceEEEEEehh-hhhhHHHHHHHhccc
Confidence            9999998                                              79999999877 899999999999999


Q ss_pred             CCCCCccccccccc
Q psy1548         432 ISELPDEIDLSTYI  445 (448)
Q Consensus       432 ~~~~p~~~~~~~~~  445 (448)
                      |+++|..+|...|.
T Consensus       445 I~pip~~iDk~lyv  458 (459)
T KOG0326|consen  445 IKPIPSNIDKSLYV  458 (459)
T ss_pred             cccCCCcCCccccc
Confidence            99999999987663

>KOG0331|consensus

Probab=100.00  E-value=4.8e-54  Score=425.80  Aligned_cols=332  Identities=28%  Similarity=0.448  Sum_probs=306.1

Q ss_pred             ccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeecc
Q psy1548          78 HSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAK  157 (448)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~ap  157 (448)
                      ....|.++++++++...+...+                       |..|++|   |.+      .||.++.|+|++..|.
T Consensus        89 ~~~~f~~~~ls~~~~~~lk~~g-----------------------~~~PtpI---Qaq------~wp~~l~GrD~v~iA~  136 (519)
T KOG0331|consen   89 SSAAFQELGLSEELMKALKEQG-----------------------FEKPTPI---QAQ------GWPIALSGRDLVGIAR  136 (519)
T ss_pred             cchhhhcccccHHHHHHHHhcC-----------------------CCCCchh---hhc------ccceeccCCceEEEec
Confidence            4458999999999999999999                       9999999   999      9999999999999999


Q ss_pred             CCChhHHHHHHHHHHhhhc------cCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcC
Q psy1548         158 SGMGKTAVFVLATLQQLET------TDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTH  231 (448)
Q Consensus       158 TGsGKT~~~~l~~l~~l~~------~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~  231 (448)
                      ||||||++|++|++.++..      ...++++|||+||||||.|+...+..++..+ .+++.+++||.+...|...+.++
T Consensus       137 TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PTRELA~QV~~~~~~~~~~~-~~~~~cvyGG~~~~~Q~~~l~~g  215 (519)
T KOG0331|consen  137 TGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTRELAVQVQAEAREFGKSL-RLRSTCVYGGAPKGPQLRDLERG  215 (519)
T ss_pred             cCCcchhhhhhHHHHHHHhccccccCCCCCeEEEEcCcHHHHHHHHHHHHHHcCCC-CccEEEEeCCCCccHHHHHHhcC
Confidence            9999999999999999875      3457899999999999999999999999988 79999999999999999999997


Q ss_pred             CCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhC-CCCCeEEEEeccCCccHHHHHHHhc
Q psy1548         232 NPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSS-PHTKQVMMFSATLSKEIRPVCKKFM  310 (448)
Q Consensus       232 ~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l-~~~~q~i~~SAT~~~~~~~~~~~~l  310 (448)
                       .+|+|+||+++.++++.+.++++++.++|+||||+|++. +|.++++.|+..+ ++.+|++++|||||..++.++..|+
T Consensus       216 -vdiviaTPGRl~d~le~g~~~l~~v~ylVLDEADrMldm-GFe~qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl  293 (519)
T KOG0331|consen  216 -VDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEADRMLDM-GFEPQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFL  293 (519)
T ss_pred             -CcEEEeCChHHHHHHHcCCccccceeEEEeccHHhhhcc-ccHHHHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHh
Confidence             999999999999999999999999999999999999998 9999999999999 5566899999999999999999999


Q ss_pred             CCCeEEEEcCc-ccccccceeEEEEEcCcchHHHHHHHHHhhC---CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeC
Q psy1548         311 HDPMEVYVDDE-AKLTLHGLQQHYVKLKENEKNKKLFELLDVL---EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHR  386 (448)
Q Consensus       311 ~~~~~i~~~~~-~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~---~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~  386 (448)
                      .+|..+.+... ......++.|....++...|...|..+|...   ..+|+||||+|++.|+.|+..|+..++++..+||
T Consensus       294 ~~~~~i~ig~~~~~~a~~~i~qive~~~~~~K~~~l~~lL~~~~~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHG  373 (519)
T KOG0331|consen  294 NNPIQINVGNKKELKANHNIRQIVEVCDETAKLRKLGKLLEDISSDSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHG  373 (519)
T ss_pred             cCceEEEecchhhhhhhcchhhhhhhcCHHHHHHHHHHHHHHHhccCCCcEEEEecchhhHHHHHHHHHhcCcceeeecc
Confidence            99999988754 4567788999999999889999998888776   4669999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         387 GMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       387 ~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      +.++.+|..+|+.|++|+.  .|+++|+-.-+++  +|.+.--+-.+++|.+.+.|.++.||
T Consensus       374 d~sQ~eR~~~L~~FreG~~--~vLVATdVAaRGL--Di~dV~lVInydfP~~vEdYVHRiGR  431 (519)
T KOG0331|consen  374 DKSQSERDWVLKGFREGKS--PVLVATDVAARGL--DVPDVDLVINYDFPNNVEDYVHRIGR  431 (519)
T ss_pred             cccHHHHHHHHHhcccCCc--ceEEEcccccccC--CCccccEEEeCCCCCCHHHHHhhcCc
Confidence            9999999999999999995  7888888655554  56666667788999999999999998

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

Probab=100.00  E-value=7.5e-52  Score=425.63  Aligned_cols=331  Identities=33%  Similarity=0.530  Sum_probs=305.6

Q ss_pred             CCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCC
Q psy1548          80 SGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSG  159 (448)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTG  159 (448)
                      ..|.++++++.+++++.+.|                       |..|+++   |.+      +||.++.|+|++++|+||
T Consensus        29 ~~F~~l~l~~~ll~~l~~~g-----------------------f~~pt~I---Q~~------~IP~~l~g~Dvi~~A~TG   76 (513)
T COG0513          29 PEFASLGLSPELLQALKDLG-----------------------FEEPTPI---QLA------AIPLILAGRDVLGQAQTG   76 (513)
T ss_pred             CCHhhcCCCHHHHHHHHHcC-----------------------CCCCCHH---HHH------HHHHHhCCCCEEEECCCC
Confidence            67999999999999999999                       9999999   999      999999999999999999


Q ss_pred             ChhHHHHHHHHHHhhhc--cCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEE
Q psy1548         160 MGKTAVFVLATLQQLET--TDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVV  237 (448)
Q Consensus       160 sGKT~~~~l~~l~~l~~--~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV  237 (448)
                      ||||++|++|+++.+..  ......+||++||||||.|+++.+..+....+++++..++||.+...+...+..+ ++|+|
T Consensus        77 sGKT~Af~lP~l~~l~~~~~~~~~~aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~~-~~ivV  155 (513)
T COG0513          77 TGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRG-VDIVV  155 (513)
T ss_pred             ChHHHHHHHHHHHHHhcccccCCCceEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhcC-CCEEE
Confidence            99999999999999873  2222229999999999999999999999987568899999999999999888886 99999


Q ss_pred             EcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEE
Q psy1548         238 GTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVY  317 (448)
Q Consensus       238 ~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~  317 (448)
                      +||+++++++..+.+++++++++|+||||+|++. +|.+++..++..+|.+.|+++||||+|..+..+.+.++.+|..+.
T Consensus       156 aTPGRllD~i~~~~l~l~~v~~lVlDEADrmLd~-Gf~~~i~~I~~~~p~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~  234 (513)
T COG0513         156 ATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDM-GFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIE  234 (513)
T ss_pred             ECccHHHHHHHcCCcchhhcCEEEeccHhhhhcC-CCHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHccCCcEEE
Confidence            9999999999999999999999999999999998 999999999999999999999999999999999999999999888


Q ss_pred             EcCcc-cccccceeEEEEEcCcch-HHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHH
Q psy1548         318 VDDEA-KLTLHGLQQHYVKLKENE-KNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLK  395 (448)
Q Consensus       318 ~~~~~-~~~~~~i~~~~~~~~~~~-k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~  395 (448)
                      +.... ..+...+.|+++.+...+ |...|..+++.....++||||+|+..|+.|+..|...|+++..+||+|++++|.+
T Consensus       235 v~~~~~~~~~~~i~q~~~~v~~~~~k~~~L~~ll~~~~~~~~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~  314 (513)
T COG0513         235 VSVEKLERTLKKIKQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDR  314 (513)
T ss_pred             EccccccccccCceEEEEEeCCHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHH
Confidence            87442 237889999999999876 9999999999988889999999999999999999999999999999999999999


Q ss_pred             HHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         396 KYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       396 ~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      +++.|++|+  ..|+++|+-.-+++  +|.+.-.+-..++|.+.+.+.++.||
T Consensus       315 ~l~~F~~g~--~~vLVaTDvaaRGi--Di~~v~~VinyD~p~~~e~yvHRiGR  363 (513)
T COG0513         315 ALEKFKDGE--LRVLVATDVAARGL--DIPDVSHVINYDLPLDPEDYVHRIGR  363 (513)
T ss_pred             HHHHHHcCC--CCEEEEechhhccC--CccccceeEEccCCCCHHHheeccCc
Confidence            999999877  68999998755555  67777778889999999999999998

>KOG0338|consensus

Probab=100.00  E-value=2.1e-50  Score=387.59  Aligned_cols=329  Identities=29%  Similarity=0.495  Sum_probs=300.7

Q ss_pred             CCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCC
Q psy1548          80 SGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSG  159 (448)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTG  159 (448)
                      .+|.+|.|+..+++++...|                       |..|+||   |..      +||.++.|+|++.+|.||
T Consensus       181 ~sF~~mNLSRPlLka~~~lG-----------------------y~~PTpI---Q~a------~IPvallgkDIca~A~TG  228 (691)
T KOG0338|consen  181 ESFQSMNLSRPLLKACSTLG-----------------------YKKPTPI---QVA------TIPVALLGKDICACAATG  228 (691)
T ss_pred             hhHHhcccchHHHHHHHhcC-----------------------CCCCCch---hhh------cccHHhhcchhhheeccc
Confidence            47999999999999999999                       9999999   999      999999999999999999


Q ss_pred             ChhHHHHHHHHHHhhhccCC---CeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEE
Q psy1548         160 MGKTAVFVLATLQQLETTDS---NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV  236 (448)
Q Consensus       160 sGKT~~~~l~~l~~l~~~~~---~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~Il  236 (448)
                      ||||.+|++|+|.++...+.   ..++|||||||+|+.|++.+.++++.+. ++.++++.||.+...|...|+.. |+|+
T Consensus       229 sGKTAAF~lPiLERLlYrPk~~~~TRVLVL~PTRELaiQv~sV~~qlaqFt-~I~~~L~vGGL~lk~QE~~LRs~-PDIV  306 (691)
T KOG0338|consen  229 SGKTAAFALPILERLLYRPKKVAATRVLVLVPTRELAIQVHSVTKQLAQFT-DITVGLAVGGLDLKAQEAVLRSR-PDIV  306 (691)
T ss_pred             CCchhhhHHHHHHHHhcCcccCcceeEEEEeccHHHHHHHHHHHHHHHhhc-cceeeeeecCccHHHHHHHHhhC-CCEE
Confidence            99999999999999977654   3689999999999999999999999998 89999999999999999999886 9999


Q ss_pred             EEcHHHHHHHHHC-CCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeE
Q psy1548         237 VGTPGRILALVRN-KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPME  315 (448)
Q Consensus       237 V~Tp~~l~~~l~~-~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~  315 (448)
                      |+||+++.+++++ ..++++++..+|+||||+|++. +|..++.+|++.+|+++|.++|||||+..+++++.-.+..|+.
T Consensus       307 IATPGRlIDHlrNs~sf~ldsiEVLvlDEADRMLee-gFademnEii~lcpk~RQTmLFSATMteeVkdL~slSL~kPvr  385 (691)
T KOG0338|consen  307 IATPGRLIDHLRNSPSFNLDSIEVLVLDEADRMLEE-GFADEMNEIIRLCPKNRQTMLFSATMTEEVKDLASLSLNKPVR  385 (691)
T ss_pred             EecchhHHHHhccCCCccccceeEEEechHHHHHHH-HHHHHHHHHHHhccccccceeehhhhHHHHHHHHHhhcCCCeE
Confidence            9999999999977 5788999999999999999998 9999999999999999999999999999999999999999999


Q ss_pred             EEEcCcccccccceeEEEEEcCc---chHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHH
Q psy1548         316 VYVDDEAKLTLHGLQQHYVKLKE---NEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEE  392 (448)
Q Consensus       316 i~~~~~~~~~~~~i~~~~~~~~~---~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~e  392 (448)
                      +.+++. ......+.|.|+.+.+   ..+...|..++...-..++|||+.|++.|..+.-.|--.|+++.-+||.+++++
T Consensus       386 ifvd~~-~~~a~~LtQEFiRIR~~re~dRea~l~~l~~rtf~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGsLtQ~Q  464 (691)
T KOG0338|consen  386 IFVDPN-KDTAPKLTQEFIRIRPKREGDREAMLASLITRTFQDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGSLTQEQ  464 (691)
T ss_pred             EEeCCc-cccchhhhHHHheeccccccccHHHHHHHHHHhcccceEEEEehHHHHHHHHHHHHHhhchhhhhcccccHHH
Confidence            999888 6677888888887664   357788888887766678999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         393 RLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       393 R~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      |.+.++.|++++  +.++++|+-..+++  +|+..--+..+..|..++.|.++.||
T Consensus       465 RlesL~kFk~~e--idvLiaTDvAsRGL--DI~gV~tVINy~mP~t~e~Y~HRVGR  516 (691)
T KOG0338|consen  465 RLESLEKFKKEE--IDVLIATDVASRGL--DIEGVQTVINYAMPKTIEHYLHRVGR  516 (691)
T ss_pred             HHHHHHHHHhcc--CCEEEEechhhccC--CccceeEEEeccCchhHHHHHHHhhh
Confidence            999999999988  78999988755554  56655556677889998888888877

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=6.1e-49  Score=402.82  Aligned_cols=329  Identities=30%  Similarity=0.498  Sum_probs=300.6

Q ss_pred             CCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCC
Q psy1548          80 SGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSG  159 (448)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTG  159 (448)
                      .+|.++++++.+++++.+.|                       |..|+++   |++      +||.++.|+|++++||||
T Consensus         4 ~~f~~l~l~~~l~~~l~~~g-----------------------~~~~t~i---Q~~------ai~~~l~g~dvi~~a~TG   51 (460)
T PRK11776          4 TAFSTLPLPPALLANLNELG-----------------------YTEMTPI---QAQ------SLPAILAGKDVIAQAKTG   51 (460)
T ss_pred             CChhhcCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhcCCCEEEECCCC
Confidence            57999999999999999999                       9999999   999      999999999999999999


Q ss_pred             ChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEc
Q psy1548         160 MGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGT  239 (448)
Q Consensus       160 sGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~T  239 (448)
                      ||||++|++|+++.+......+++||++||++|+.|+.+.++.+....+++++..++|+.+...+...+..+ ++|+|+|
T Consensus        52 sGKT~a~~lpil~~l~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~~~-~~IvV~T  130 (460)
T PRK11776         52 SGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHG-AHIIVGT  130 (460)
T ss_pred             CcHHHHHHHHHHHHhhhccCCceEEEEeCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhcCC-CCEEEEC
Confidence            999999999999998766666789999999999999999999998776689999999999988887777764 8999999


Q ss_pred             HHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEc
Q psy1548         240 PGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVD  319 (448)
Q Consensus       240 p~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~  319 (448)
                      |+++.+++.++.+.+++++++|+||||+|++. +|...+..++..++...|++++|||+++.+..+...++.+|..+.+.
T Consensus       131 p~rl~~~l~~~~~~l~~l~~lViDEad~~l~~-g~~~~l~~i~~~~~~~~q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~  209 (460)
T PRK11776        131 PGRILDHLRKGTLDLDALNTLVLDEADRMLDM-GFQDAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVE  209 (460)
T ss_pred             hHHHHHHHHcCCccHHHCCEEEEECHHHHhCc-CcHHHHHHHHHhCCcccEEEEEEecCcHHHHHHHHHhcCCCEEEEEC
Confidence            99999999998889999999999999999998 99999999999999999999999999999999999999999988876


Q ss_pred             CcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHH
Q psy1548         320 DEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQE  399 (448)
Q Consensus       320 ~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~  399 (448)
                      ...  ....+.++++.+....|...+..++.....+++||||++++.|+.+++.|++.|+.+..+||+|++.+|..+++.
T Consensus       210 ~~~--~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~  287 (460)
T PRK11776        210 STH--DLPAIEQRFYEVSPDERLPALQRLLLHHQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVR  287 (460)
T ss_pred             cCC--CCCCeeEEEEEeCcHHHHHHHHHHHHhcCCCceEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHH
Confidence            652  345688999999988899999999988888899999999999999999999999999999999999999999999


Q ss_pred             HhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         400 FKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       400 F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      |++|+  ..|+++|+...+++  +|.+.-.+-..++|.+.+.+.++.||
T Consensus       288 F~~g~--~~vLVaTdv~~rGi--Di~~v~~VI~~d~p~~~~~yiqR~GR  332 (460)
T PRK11776        288 FANRS--CSVLVATDVAARGL--DIKALEAVINYELARDPEVHVHRIGR  332 (460)
T ss_pred             HHcCC--CcEEEEeccccccc--chhcCCeEEEecCCCCHhHhhhhccc
Confidence            99987  57888887655554  56666667778999999999999998

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=2.7e-48  Score=402.88  Aligned_cols=335  Identities=26%  Similarity=0.407  Sum_probs=302.2

Q ss_pred             cCceeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCc
Q psy1548          71 KGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGM  150 (448)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~  150 (448)
                      .+..++.+...|.++++++.+++++...+                       |..|+++   |.+      +||.+++|+
T Consensus       121 ~g~~~p~p~~~f~~~~l~~~l~~~l~~~g-----------------------~~~pt~i---Q~~------aip~~l~G~  168 (545)
T PTZ00110        121 AGENVPKPVVSFEYTSFPDYILKSLKNAG-----------------------FTEPTPI---QVQ------GWPIALSGR  168 (545)
T ss_pred             cCCCCCcccCCHhhcCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhcCC
Confidence            45566777789999999999999999999                       9999999   999      999999999


Q ss_pred             ceeeeccCCChhHHHHHHHHHHhhhcc-----CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhH
Q psy1548         151 DILCQAKSGMGKTAVFVLATLQQLETT-----DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE  225 (448)
Q Consensus       151 ~vli~apTGsGKT~~~~l~~l~~l~~~-----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~  225 (448)
                      |++++||||||||++|++|++..+...     ..++++|||+||++||.|+.+.++.+.... ++++.+++|+.+...+.
T Consensus       169 dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~~LIL~PTreLa~Qi~~~~~~~~~~~-~i~~~~~~gg~~~~~q~  247 (545)
T PTZ00110        169 DMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASS-KIRNTVAYGGVPKRGQI  247 (545)
T ss_pred             CEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcEEEEECChHHHHHHHHHHHHHHhccc-CccEEEEeCCCCHHHHH
Confidence            999999999999999999999876532     246789999999999999999999999877 89999999999888887


Q ss_pred             HHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHH
Q psy1548         226 EYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPV  305 (448)
Q Consensus       226 ~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~  305 (448)
                      ..+..+ ++|+|+||++|.+++..+...++++++||+||||+|+++ +|...+..++..+++..|++++|||+|.++..+
T Consensus       248 ~~l~~~-~~IlVaTPgrL~d~l~~~~~~l~~v~~lViDEAd~mld~-gf~~~i~~il~~~~~~~q~l~~SAT~p~~v~~l  325 (545)
T PTZ00110        248 YALRRG-VEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDM-GFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSL  325 (545)
T ss_pred             HHHHcC-CCEEEECHHHHHHHHHcCCCChhhCcEEEeehHHhhhhc-chHHHHHHHHHhCCCCCeEEEEEeCCCHHHHHH
Confidence            778775 899999999999999998888999999999999999998 999999999999999999999999999999999


Q ss_pred             HHHhcC-CCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhCCCcEE
Q psy1548         306 CKKFMH-DPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQNFPAV  382 (448)
Q Consensus       306 ~~~~l~-~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~  382 (448)
                      .+.++. +|..+.+.........++.+.+..+...+|...|..++...  ...++||||++++.|+.++..|+..|+++.
T Consensus       326 ~~~l~~~~~v~i~vg~~~l~~~~~i~q~~~~~~~~~k~~~L~~ll~~~~~~~~k~LIF~~t~~~a~~l~~~L~~~g~~~~  405 (545)
T PTZ00110        326 ARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPAL  405 (545)
T ss_pred             HHHHhccCCEEEEECCCccccCCCeeEEEEEEechhHHHHHHHHHHHhcccCCeEEEEecChHHHHHHHHHHHHcCCcEE
Confidence            998886 57777766553344567888888888888888888888765  467999999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHhcCC----------------------------------------------CceEEEEecChh
Q psy1548         383 SIHRGMTQEERLKKYQEFKDFH----------------------------------------------KGLAITFASDEN  416 (448)
Q Consensus       383 ~lh~~~~~~eR~~~l~~F~~g~----------------------------------------------~g~~I~~~t~~~  416 (448)
                      .+||+|++++|..++++|++|+                                              .|.+++|++.. 
T Consensus       406 ~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv~~rGIDi~~v~~VI~~d~P~s~~~yvqRiGRtGR~G~~G~ai~~~~~~-  484 (545)
T PTZ00110        406 CIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPD-  484 (545)
T ss_pred             EEECCCcHHHHHHHHHHHhcCCCcEEEEcchhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEECcc-
Confidence            9999999999999999999998                                              78999999887 


Q ss_pred             hHHHHHHHHHHhcCCCCCCCccccc
Q psy1548         417 DAKILNNVQDRFDVSISELPDEIDL  441 (448)
Q Consensus       417 d~~~l~~i~~~~~~~~~~~p~~~~~  441 (448)
                      |...++.+.+.+....+++|+++..
T Consensus       485 ~~~~~~~l~~~l~~~~q~vp~~l~~  509 (545)
T PTZ00110        485 KYRLARDLVKVLREAKQPVPPELEK  509 (545)
T ss_pred             hHHHHHHHHHHHHHccCCCCHHHHH
Confidence            7888999999999999999988653

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2.9e-48  Score=393.67  Aligned_cols=329  Identities=27%  Similarity=0.398  Sum_probs=294.5

Q ss_pred             CCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCC
Q psy1548          80 SGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSG  159 (448)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTG  159 (448)
                      ..|+++++++.+++++.+.|                       |..|+++   |++      +||.++.|+|++++||||
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g-----------------------~~~pt~i---Q~~------aip~il~g~dvi~~ApTG   55 (423)
T PRK04837          8 QKFSDFALHPQVVEALEKKG-----------------------FHNCTPI---QAL------ALPLTLAGRDVAGQAQTG   55 (423)
T ss_pred             CCHhhCCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhCCCcEEEECCCC
Confidence            57999999999999999999                       9999999   999      999999999999999999


Q ss_pred             ChhHHHHHHHHHHhhhcc-------CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCC
Q psy1548         160 MGKTAVFVLATLQQLETT-------DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHN  232 (448)
Q Consensus       160 sGKT~~~~l~~l~~l~~~-------~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~  232 (448)
                      ||||++|++|+++.+...       ..++++|||+||++||.|+.+.+..+.... ++++..++|+.....+...+..+ 
T Consensus        56 sGKTla~llp~l~~l~~~~~~~~~~~~~~~~lil~PtreLa~Qi~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~l~~~-  133 (423)
T PRK04837         56 TGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQAT-GLKLGLAYGGDGYDKQLKVLESG-  133 (423)
T ss_pred             chHHHHHHHHHHHHHHhcccccccccCCceEEEECCcHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHhcCC-
Confidence            999999999999887532       235789999999999999999999999888 89999999998877777777654 


Q ss_pred             CcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCC--CCeEEEEeccCCccHHHHHHHhc
Q psy1548         233 PQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPH--TKQVMMFSATLSKEIRPVCKKFM  310 (448)
Q Consensus       233 ~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~--~~q~i~~SAT~~~~~~~~~~~~l  310 (448)
                      ++|+|+||+++.+++..+.+.+++++++|+||||+++++ +|..++..++..++.  ..+.+++|||++..+..++..++
T Consensus       134 ~~IlV~TP~~l~~~l~~~~~~l~~v~~lViDEad~l~~~-~f~~~i~~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~  212 (423)
T PRK04837        134 VDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDL-GFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHM  212 (423)
T ss_pred             CCEEEECHHHHHHHHHcCCcccccccEEEEecHHHHhhc-ccHHHHHHHHHhCCCccceeEEEEeccCCHHHHHHHHHHC
Confidence            899999999999999998899999999999999999998 999999999999874  56789999999999999999999


Q ss_pred             CCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCH
Q psy1548         311 HDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQ  390 (448)
Q Consensus       311 ~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~  390 (448)
                      .+|..+.+... ......+.+.+.......|...|..++......++||||+++..|+.++..|...|+++..+||+|++
T Consensus       213 ~~p~~i~v~~~-~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~~  291 (423)
T PRK04837        213 NNPEYVEVEPE-QKTGHRIKEELFYPSNEEKMRLLQTLIEEEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQ  291 (423)
T ss_pred             CCCEEEEEcCC-CcCCCceeEEEEeCCHHHHHHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCCh
Confidence            99988887665 34556788888888888899999999987777899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         391 EERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       391 ~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      ++|..++++|++|+  +.|+++|+...+++  +|.+.-.+-..++|.+...+.++.||
T Consensus       292 ~~R~~~l~~F~~g~--~~vLVaTdv~~rGi--Dip~v~~VI~~d~P~s~~~yiqR~GR  345 (423)
T PRK04837        292 KKRLRILEEFTRGD--LDILVATDVAARGL--HIPAVTHVFNYDLPDDCEDYVHRIGR  345 (423)
T ss_pred             hHHHHHHHHHHcCC--CcEEEEechhhcCC--CccccCEEEEeCCCCchhheEecccc
Confidence            99999999999988  57888888655554  56666667778899999999999998

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=2.2e-48  Score=407.17  Aligned_cols=330  Identities=31%  Similarity=0.468  Sum_probs=298.5

Q ss_pred             CCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCC
Q psy1548          80 SGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSG  159 (448)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTG  159 (448)
                      ..|.++++++.+++++.+.|                       |..|+++   |++      +||.++.|+|+|++||||
T Consensus         6 ~~f~~l~L~~~ll~al~~~G-----------------------~~~ptpi---Q~~------ai~~ll~g~dvl~~ApTG   53 (629)
T PRK11634          6 TTFADLGLKAPILEALNDLG-----------------------YEKPSPI---QAE------CIPHLLNGRDVLGMAQTG   53 (629)
T ss_pred             CCHhhcCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHHcCCCEEEEcCCC
Confidence            46999999999999999999                       9999999   999      999999999999999999


Q ss_pred             ChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEc
Q psy1548         160 MGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGT  239 (448)
Q Consensus       160 sGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~T  239 (448)
                      +|||++|++|+++.+......+++||++||++|+.|+.+.+..+.+.++++.+..++|+.+...+...+..+ ++|+|+|
T Consensus        54 sGKT~af~lpll~~l~~~~~~~~~LIL~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~-~~IVVgT  132 (629)
T PRK11634         54 SGKTAAFSLPLLHNLDPELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQG-PQIVVGT  132 (629)
T ss_pred             CcHHHHHHHHHHHHhhhccCCCeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCC-CCEEEEC
Confidence            999999999999988766667799999999999999999999998887789999999999888887777665 8999999


Q ss_pred             HHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEc
Q psy1548         240 PGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVD  319 (448)
Q Consensus       240 p~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~  319 (448)
                      |+++.+++.++.+.++++++||+||||.|+++ +|...+..++..+|...|+++||||+|+.+..+.+.++.+|..+.+.
T Consensus       133 Pgrl~d~l~r~~l~l~~l~~lVlDEAd~ml~~-gf~~di~~Il~~lp~~~q~llfSAT~p~~i~~i~~~~l~~~~~i~i~  211 (629)
T PRK11634        133 PGRLLDHLKRGTLDLSKLSGLVLDEADEMLRM-GFIEDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQ  211 (629)
T ss_pred             HHHHHHHHHcCCcchhhceEEEeccHHHHhhc-ccHHHHHHHHHhCCCCCeEEEEEccCChhHHHHHHHHcCCCeEEEcc
Confidence            99999999998899999999999999999998 99999999999999999999999999999999999999999988776


Q ss_pred             CcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHH
Q psy1548         320 DEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQE  399 (448)
Q Consensus       320 ~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~  399 (448)
                      .. ......+.+.++.+....|...|..++......++||||+|+..|+.++..|.+.|+.+..+||+|++.+|.++++.
T Consensus       212 ~~-~~~~~~i~q~~~~v~~~~k~~~L~~~L~~~~~~~~IVF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~~  290 (629)
T PRK11634        212 SS-VTTRPDISQSYWTVWGMRKNEALVRFLEAEDFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLER  290 (629)
T ss_pred             Cc-cccCCceEEEEEEechhhHHHHHHHHHHhcCCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHHH
Confidence            55 44567788888888888899999999988877899999999999999999999999999999999999999999999


Q ss_pred             HhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         400 FKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       400 F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      |++|+  +.|+++|+-..+++  ++.+.-.+-..++|.+.+.+.++.||
T Consensus       291 Fr~G~--~~ILVATdv~arGI--Dip~V~~VI~~d~P~~~e~yvqRiGR  335 (629)
T PRK11634        291 LKDGR--LDILIATDVAARGL--DVERISLVVNYDIPMDSESYVHRIGR  335 (629)
T ss_pred             HhCCC--CCEEEEcchHhcCC--CcccCCEEEEeCCCCCHHHHHHHhcc
Confidence            99988  57888887544443  44444445567889999999999887

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=6.2e-48  Score=394.11  Aligned_cols=328  Identities=29%  Similarity=0.466  Sum_probs=293.2

Q ss_pred             CcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCC
Q psy1548          81 GFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGM  160 (448)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGs  160 (448)
                      +|+++++++.+++++.+.+                       |..|+++   |++      ++|.++.|+|+++++||||
T Consensus         2 ~f~~l~l~~~l~~~l~~~g-----------------------~~~pt~i---Q~~------ai~~il~g~dvlv~apTGs   49 (456)
T PRK10590          2 SFDSLGLSPDILRAVAEQG-----------------------YREPTPI---QQQ------AIPAVLEGRDLMASAQTGT   49 (456)
T ss_pred             CHHHcCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhCCCCEEEECCCCC
Confidence            6899999999999999999                       9999999   999      9999999999999999999


Q ss_pred             hhHHHHHHHHHHhhhccC------CCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCc
Q psy1548         161 GKTAVFVLATLQQLETTD------SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQ  234 (448)
Q Consensus       161 GKT~~~~l~~l~~l~~~~------~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~  234 (448)
                      |||++|++|+++.+....      ..+++|||+||++||.|+.+.++.+.... ++++..++|+.+...+...+..+ ++
T Consensus        50 GKTla~~lpil~~l~~~~~~~~~~~~~~aLil~PtreLa~Qi~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~-~~  127 (456)
T PRK10590         50 GKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYL-NIRSLVVFGGVSINPQMMKLRGG-VD  127 (456)
T ss_pred             cHHHHHHHHHHHHhhhcccccccCCCceEEEEeCcHHHHHHHHHHHHHHhccC-CCEEEEEECCcCHHHHHHHHcCC-Cc
Confidence            999999999999875432      23589999999999999999999999887 89999999999888777666654 89


Q ss_pred             EEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCe
Q psy1548         235 IVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPM  314 (448)
Q Consensus       235 IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~  314 (448)
                      |+|+||++|++++....+.++++++||+||||+|+++ +|...+..++..++...|++++|||+++++..++..++.+|.
T Consensus       128 IiV~TP~rL~~~~~~~~~~l~~v~~lViDEah~ll~~-~~~~~i~~il~~l~~~~q~l~~SAT~~~~~~~l~~~~~~~~~  206 (456)
T PRK10590        128 VLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDM-GFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPL  206 (456)
T ss_pred             EEEEChHHHHHHHHcCCcccccceEEEeecHHHHhcc-ccHHHHHHHHHhCCccCeEEEEeCCCcHHHHHHHHHHcCCCe
Confidence            9999999999999988888999999999999999998 999999999999999999999999999999999999999998


Q ss_pred             EEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHH
Q psy1548         315 EVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERL  394 (448)
Q Consensus       315 ~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~  394 (448)
                      .+.+... ......+.+++..++...|...+..++......++||||+++..|+.+++.|.+.|+++..+||+|++++|.
T Consensus       207 ~i~~~~~-~~~~~~i~~~~~~~~~~~k~~~l~~l~~~~~~~~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~  285 (456)
T PRK10590        207 EIEVARR-NTASEQVTQHVHFVDKKRKRELLSQMIGKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGART  285 (456)
T ss_pred             EEEEecc-cccccceeEEEEEcCHHHHHHHHHHHHHcCCCCcEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCCHHHHH
Confidence            8877655 344567888888888888888888888877778999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         395 KKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       395 ~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      ++++.|++|+  +.|+++|+...+++  +|.+.-.+-..++|.+...+.++.||
T Consensus       286 ~~l~~F~~g~--~~iLVaTdv~~rGi--Dip~v~~VI~~~~P~~~~~yvqR~GR  335 (456)
T PRK10590        286 RALADFKSGD--IRVLVATDIAARGL--DIEELPHVVNYELPNVPEDYVHRIGR  335 (456)
T ss_pred             HHHHHHHcCC--CcEEEEccHHhcCC--CcccCCEEEEeCCCCCHHHhhhhccc
Confidence            9999999987  57888887644443  45555556677889999899999998

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=9.8e-47  Score=392.57  Aligned_cols=322  Identities=25%  Similarity=0.408  Sum_probs=289.7

Q ss_pred             CCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCC
Q psy1548          80 SGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSG  159 (448)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTG  159 (448)
                      .+|.++++++.++++|.+.|                       |..|+++   |.+      +||.++.|+|+++++|||
T Consensus         9 ~~f~~l~l~~~l~~~L~~~g-----------------------~~~ptpi---Q~~------~ip~~l~G~Dvi~~ApTG   56 (572)
T PRK04537          9 LTFSSFDLHPALLAGLESAG-----------------------FTRCTPI---QAL------TLPVALPGGDVAGQAQTG   56 (572)
T ss_pred             CChhhcCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhCCCCEEEEcCCC
Confidence            46999999999999999999                       9999999   999      999999999999999999


Q ss_pred             ChhHHHHHHHHHHhhhcc-------CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCC
Q psy1548         160 MGKTAVFVLATLQQLETT-------DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHN  232 (448)
Q Consensus       160 sGKT~~~~l~~l~~l~~~-------~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~  232 (448)
                      ||||++|++|+++.+...       ...+++|||+||++|+.|+++.+..+.... ++++..++|+.....+...+..+ 
T Consensus        57 SGKTlafllpil~~l~~~~~~~~~~~~~~raLIl~PTreLa~Qi~~~~~~l~~~~-~i~v~~l~Gg~~~~~q~~~l~~~-  134 (572)
T PRK04537         57 TGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADL-GLRFALVYGGVDYDKQRELLQQG-  134 (572)
T ss_pred             CcHHHHHHHHHHHHHHhcccccccccCCceEEEEeCcHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHHhCC-
Confidence            999999999999987532       124799999999999999999999999887 89999999999888777767654 


Q ss_pred             CcEEEEcHHHHHHHHHCC-CCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCC--CCeEEEEeccCCccHHHHHHHh
Q psy1548         233 PQIVVGTPGRILALVRNK-KLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPH--TKQVMMFSATLSKEIRPVCKKF  309 (448)
Q Consensus       233 ~~IlV~Tp~~l~~~l~~~-~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~--~~q~i~~SAT~~~~~~~~~~~~  309 (448)
                      ++|+|+||++|++++... .+.+..+++|||||||+|+++ +|...+..+++.++.  ..|+++||||++..+..+...+
T Consensus       135 ~dIiV~TP~rL~~~l~~~~~~~l~~v~~lViDEAh~lld~-gf~~~i~~il~~lp~~~~~q~ll~SATl~~~v~~l~~~~  213 (572)
T PRK04537        135 VDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDL-GFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEH  213 (572)
T ss_pred             CCEEEECHHHHHHHHHhccccchhheeeeEecCHHHHhhc-chHHHHHHHHHhcccccCceEEEEeCCccHHHHHHHHHH
Confidence            899999999999998764 567899999999999999998 999999999999986  6899999999999999999999


Q ss_pred             cCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCC
Q psy1548         310 MHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMT  389 (448)
Q Consensus       310 l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~  389 (448)
                      +.+|..+.+... ......+.+.++.+...+|...+..++......++||||+|+..|+.+++.|.+.|+.+..+||+|+
T Consensus       214 l~~p~~i~v~~~-~~~~~~i~q~~~~~~~~~k~~~L~~ll~~~~~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~  292 (572)
T PRK04537        214 MNEPEKLVVETE-TITAARVRQRIYFPADEEKQTLLLGLLSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVP  292 (572)
T ss_pred             hcCCcEEEeccc-cccccceeEEEEecCHHHHHHHHHHHHhcccCCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCC
Confidence            999987776655 3456678888888888889999999998877889999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhcCC----------------------------------------------CceEEEEecChhhHHHHHH
Q psy1548         390 QEERLKKYQEFKDFH----------------------------------------------KGLAITFASDENDAKILNN  423 (448)
Q Consensus       390 ~~eR~~~l~~F~~g~----------------------------------------------~g~~I~~~t~~~d~~~l~~  423 (448)
                      +.+|.++++.|++|+                                              .|.+|+|++.. +...+..
T Consensus       293 ~~eR~~il~~Fr~G~~~VLVaTdv~arGIDip~V~~VInyd~P~s~~~yvqRiGRaGR~G~~G~ai~~~~~~-~~~~l~~  371 (572)
T PRK04537        293 QKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACER-YAMSLPD  371 (572)
T ss_pred             HHHHHHHHHHHHcCCCeEEEEehhhhcCCCccCCCEEEEcCCCCCHHHHhhhhcccccCCCCceEEEEecHH-HHHHHHH
Confidence            999999999999998                                              78999999886 6788999


Q ss_pred             HHHHhcCCCCCCCcc
Q psy1548         424 VQDRFDVSISELPDE  438 (448)
Q Consensus       424 i~~~~~~~~~~~p~~  438 (448)
                      |++.++..+...|..
T Consensus       372 i~~~~~~~~~~~~~~  386 (572)
T PRK04537        372 IEAYIEQKIPVEPVT  386 (572)
T ss_pred             HHHHHcCCCCccccC
Confidence            999998887655443

>KOG0343|consensus

Probab=100.00  E-value=3.1e-48  Score=375.71  Aligned_cols=330  Identities=25%  Similarity=0.398  Sum_probs=297.6

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      ...|.+++++...+++|.+.+                       |..|+.+   |+.      +||.++.|+|||..|.|
T Consensus        68 ~~kF~dlpls~~t~kgLke~~-----------------------fv~~tei---Q~~------~Ip~aL~G~DvlGAAkT  115 (758)
T KOG0343|consen   68 IKKFADLPLSQKTLKGLKEAK-----------------------FVKMTEI---QRD------TIPMALQGHDVLGAAKT  115 (758)
T ss_pred             hhhHHhCCCchHHHHhHhhcC-----------------------CccHHHH---HHh------hcchhccCccccccccc
Confidence            346999999999999999999                       9999999   999      99999999999999999


Q ss_pred             CChhHHHHHHHHHHhhhcc----CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCc
Q psy1548         159 GMGKTAVFVLATLQQLETT----DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQ  234 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~  234 (448)
                      |||||++|++|+|+.+...    ..|.-+|||+|||+||.|+++.+.+++++. ++..+++.||.....+...+..  .+
T Consensus       116 GSGKTLAFlvPvlE~L~r~kWs~~DGlGalIISPTRELA~QtFevL~kvgk~h-~fSaGLiiGG~~~k~E~eRi~~--mN  192 (758)
T KOG0343|consen  116 GSGKTLAFLVPVLEALYRLKWSPTDGLGALIISPTRELALQTFEVLNKVGKHH-DFSAGLIIGGKDVKFELERISQ--MN  192 (758)
T ss_pred             CCCceeeehHHHHHHHHHcCCCCCCCceeEEecchHHHHHHHHHHHHHHhhcc-ccccceeecCchhHHHHHhhhc--CC
Confidence            9999999999999987443    357789999999999999999999999998 9999999999987776666654  79


Q ss_pred             EEEEcHHHHHHHHHC-CCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCC
Q psy1548         235 IVVGTPGRILALVRN-KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDP  313 (448)
Q Consensus       235 IlV~Tp~~l~~~l~~-~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~  313 (448)
                      |+||||++|++.+.. ..++-.++.++|+||||+|++. +|...+..|+..+|+.+|+++||||-+..+.++++-.+.+|
T Consensus       193 ILVCTPGRLLQHmde~~~f~t~~lQmLvLDEADR~LDM-GFk~tL~~Ii~~lP~~RQTLLFSATqt~svkdLaRLsL~dP  271 (758)
T KOG0343|consen  193 ILVCTPGRLLQHMDENPNFSTSNLQMLVLDEADRMLDM-GFKKTLNAIIENLPKKRQTLLFSATQTKSVKDLARLSLKDP  271 (758)
T ss_pred             eEEechHHHHHHhhhcCCCCCCcceEEEeccHHHHHHH-hHHHHHHHHHHhCChhheeeeeecccchhHHHHHHhhcCCC
Confidence            999999999999876 5677899999999999999998 99999999999999999999999999999999999999999


Q ss_pred             eEEEEcCc-ccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhC--CCcEEEEeCCCCH
Q psy1548         314 MEVYVDDE-AKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQ--NFPAVSIHRGMTQ  390 (448)
Q Consensus       314 ~~i~~~~~-~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~--g~~~~~lh~~~~~  390 (448)
                      ..+.+... ...++.++.|+|+.++-.+|+..|..+++.+...++|||+.|.+++..++..+++.  |++...+||.|++
T Consensus       272 ~~vsvhe~a~~atP~~L~Q~y~~v~l~~Ki~~L~sFI~shlk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~Q  351 (758)
T KOG0343|consen  272 VYVSVHENAVAATPSNLQQSYVIVPLEDKIDMLWSFIKSHLKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMSQ  351 (758)
T ss_pred             cEEEEeccccccChhhhhheEEEEehhhHHHHHHHHHHhccccceEEEEehhhHHHHHHHHHHhcCCCCceeeeccchhH
Confidence            99988743 36788999999999999999999999999999999999999999999999999986  9999999999999


Q ss_pred             HHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         391 EERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       391 ~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      ..|..++.+|-+.+  .+|+|||+-..+++  ++...-++--.+.|.+.+-|-++.||
T Consensus       352 ~~R~ev~~~F~~~~--~~vLF~TDv~aRGL--DFpaVdwViQ~DCPedv~tYIHRvGR  405 (758)
T KOG0343|consen  352 KKRIEVYKKFVRKR--AVVLFCTDVAARGL--DFPAVDWVIQVDCPEDVDTYIHRVGR  405 (758)
T ss_pred             HHHHHHHHHHHHhc--ceEEEeehhhhccC--CCcccceEEEecCchhHHHHHHHhhh
Confidence            99999999998855  58999998654443  44444455556779998888888887

>KOG0340|consensus

Probab=100.00  E-value=1.2e-47  Score=354.45  Aligned_cols=324  Identities=28%  Similarity=0.437  Sum_probs=296.5

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      ..+|..+|+.+++.+.+...+                       ...|+++   |+.      |||.++.|+|+|.+|.|
T Consensus         6 ~~~F~~LGl~~Wlve~l~~l~-----------------------i~~pTpi---Q~~------cIpkILeGrdcig~AkT   53 (442)
T KOG0340|consen    6 AKPFSILGLSPWLVEQLKALG-----------------------IKKPTPI---QQA------CIPKILEGRDCIGCAKT   53 (442)
T ss_pred             cCchhhcCccHHHHHHHHHhc-----------------------CCCCCch---Hhh------hhHHHhccccccccccc
Confidence            467999999999999999999                       9999999   999      99999999999999999


Q ss_pred             CChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEE
Q psy1548         159 GMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVG  238 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~  238 (448)
                      |||||++|.+|+++++...+.+..++|++|||+|+.|+.++|..+++.+ ++++.+++||.+.-.+...+... ||++|+
T Consensus        54 GsGKT~AFaLPil~rLsedP~giFalvlTPTrELA~QiaEQF~alGk~l-~lK~~vivGG~d~i~qa~~L~~r-PHvVva  131 (442)
T KOG0340|consen   54 GSGKTAAFALPILNRLSEDPYGIFALVLTPTRELALQIAEQFIALGKLL-NLKVSVIVGGTDMIMQAAILSDR-PHVVVA  131 (442)
T ss_pred             CCCcchhhhHHHHHhhccCCCcceEEEecchHHHHHHHHHHHHHhcccc-cceEEEEEccHHHhhhhhhcccC-CCeEec
Confidence            9999999999999999999999999999999999999999999999998 99999999999988888888876 999999


Q ss_pred             cHHHHHHHHHCC----CCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCC--
Q psy1548         239 TPGRILALVRNK----KLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHD--  312 (448)
Q Consensus       239 Tp~~l~~~l~~~----~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~--  312 (448)
                      ||+++..++..+    ...+++++++|+||||++++. .|-..+..++..+|..+|.++||||+++.+..+...-...  
T Consensus       132 tPGRlad~l~sn~~~~~~~~~rlkflVlDEADrvL~~-~f~d~L~~i~e~lP~~RQtLlfSATitd~i~ql~~~~i~k~~  210 (442)
T KOG0340|consen  132 TPGRLADHLSSNLGVCSWIFQRLKFLVLDEADRVLAG-CFPDILEGIEECLPKPRQTLLFSATITDTIKQLFGCPITKSI  210 (442)
T ss_pred             CccccccccccCCccchhhhhceeeEEecchhhhhcc-chhhHHhhhhccCCCccceEEEEeehhhHHHHhhcCCccccc
Confidence            999999998765    245789999999999999998 9999999999999999999999999998887776655544  


Q ss_pred             CeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCC---CCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCC
Q psy1548         313 PMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLE---FNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMT  389 (448)
Q Consensus       313 ~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~---~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~  389 (448)
                      .......+. ..+...+.+.|+.++...|...|+.+++...   .+.++||+|+..+|+.|+..|+..++.+..+|+.|+
T Consensus       211 a~~~e~~~~-vstvetL~q~yI~~~~~vkdaYLv~~Lr~~~~~~~~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~  289 (442)
T KOG0340|consen  211 AFELEVIDG-VSTVETLYQGYILVSIDVKDAYLVHLLRDFENKENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMP  289 (442)
T ss_pred             ceEEeccCC-CCchhhhhhheeecchhhhHHHHHHHHhhhhhccCceEEEEeehhHHHHHHHHHHhhhceeeeehhhcch
Confidence            333343333 5678889999999999999999999997764   468999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhcCC----------------------------------------------CceEEEEecChhhHHHHHH
Q psy1548         390 QEERLKKYQEFKDFH----------------------------------------------KGLAITFASDENDAKILNN  423 (448)
Q Consensus       390 ~~eR~~~l~~F~~g~----------------------------------------------~g~~I~~~t~~~d~~~l~~  423 (448)
                      +.+|...+..|+++.                                              .|.+|+++|.. |.+++..
T Consensus       290 Q~eR~~aLsrFrs~~~~iliaTDVAsRGLDIP~V~LVvN~diPr~P~~yiHRvGRtARAGR~G~aiSivt~r-Dv~l~~a  368 (442)
T KOG0340|consen  290 QKERLAALSRFRSNAARILIATDVASRGLDIPTVELVVNHDIPRDPKDYIHRVGRTARAGRKGMAISIVTQR-DVELLQA  368 (442)
T ss_pred             HHHHHHHHHHHhhcCccEEEEechhhcCCCCCceeEEEecCCCCCHHHHHHhhcchhcccCCcceEEEechh-hHHHHHH
Confidence            999999999999998                                              89999999965 9999999


Q ss_pred             HHHHhcCCCCCCCccc
Q psy1548         424 VQDRFDVSISELPDEI  439 (448)
Q Consensus       424 i~~~~~~~~~~~p~~~  439 (448)
                      ||+..|.+..|.+...
T Consensus       369 iE~~igkKl~e~~~~~  384 (442)
T KOG0340|consen  369 IEEEIGKKLTEYNKVQ  384 (442)
T ss_pred             HHHHHhcccccccccc
Confidence            9999999999987663

>KOG0327|consensus

Probab=100.00  E-value=1.1e-47  Score=359.50  Aligned_cols=322  Identities=33%  Similarity=0.586  Sum_probs=306.0

Q ss_pred             CCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCC
Q psy1548          80 SGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSG  159 (448)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTG  159 (448)
                      .+|++++|+++|++++...|                       |+.|+.+   |+.      ||+....|.|+++++++|
T Consensus        26 dsfddm~L~e~LLrgiy~yG-----------------------FekPSaI---Qqr------aI~p~i~G~dv~~qaqsg   73 (397)
T KOG0327|consen   26 DSFDDMNLKESLLRGIYAYG-----------------------FEKPSAI---QQR------AILPCIKGHDVIAQAQSG   73 (397)
T ss_pred             hhhhhcCCCHHHHhHHHhhc-----------------------cCCchHH---Hhc------cccccccCCceeEeeecc
Confidence            48999999999999999999                       9999999   999      999999999999999999


Q ss_pred             ChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEc
Q psy1548         160 MGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGT  239 (448)
Q Consensus       160 sGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~T  239 (448)
                      +|||.+|.+++++.+.......++++++|+++|+.|+......++... ++++..+.|+.....+...+....++|+++|
T Consensus        74 TgKt~af~i~iLq~iD~~~ke~qalilaPtreLa~qi~~v~~~lg~~~-~~~v~~~igg~~~~~~~~~i~~~~~hivvGT  152 (397)
T KOG0327|consen   74 TGKTAAFLISILQQIDMSVKETQALILAPTRELAQQIQKVVRALGDHM-DVSVHACIGGTNVRREDQALLKDKPHIVVGT  152 (397)
T ss_pred             ccchhhhHHHHHhhcCcchHHHHHHHhcchHHHHHHHHHHHHhhhccc-ceeeeeecCcccchhhhhhhhccCceeecCC
Confidence            999999999999999887778899999999999999999999999888 9999999999988877766766668999999


Q ss_pred             HHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEc
Q psy1548         240 PGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVD  319 (448)
Q Consensus       240 p~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~  319 (448)
                      |+++.+++....+....++++|+||+|.|+.. +|..++..+++.+|++.|++++|||+|.++..+.++|+.+|..+.+.
T Consensus       153 pgrV~dml~~~~l~~~~iKmfvlDEaDEmLs~-gfkdqI~~if~~lp~~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vk  231 (397)
T KOG0327|consen  153 PGRVFDMLNRGSLSTDGIKMFVLDEADEMLSR-GFKDQIYDIFQELPSDVQVVLLSATMPSDVLEVTKKFMREPVRILVK  231 (397)
T ss_pred             chhHHHhhccccccccceeEEeecchHhhhcc-chHHHHHHHHHHcCcchhheeecccCcHHHHHHHHHhccCceEEEec
Confidence            99999999999888899999999999999998 99999999999999999999999999999999999999999999998


Q ss_pred             CcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHH
Q psy1548         320 DEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQE  399 (448)
Q Consensus       320 ~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~  399 (448)
                      .. ..+...++|+|..+..++|...|+.+.+  .-.+.+|||||++.+..+..+|..+|+.+.++||+|.+.+|..++.+
T Consensus       232 k~-~ltl~gikq~~i~v~k~~k~~~l~dl~~--~~~q~~if~nt~r~v~~l~~~L~~~~~~~s~~~~d~~q~~R~~~~~e  308 (397)
T KOG0327|consen  232 KD-ELTLEGIKQFYINVEKEEKLDTLCDLYR--RVTQAVIFCNTRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMRE  308 (397)
T ss_pred             ch-hhhhhheeeeeeeccccccccHHHHHHH--hhhcceEEecchhhHHHHHHHHhhCCceEEEeecccchhhhhHHHHH
Confidence            88 5789999999999999999999999999  45689999999999999999999999999999999999999999999


Q ss_pred             HhcCC----------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCCCC
Q psy1548         400 FKDFH----------------------------------------------KGLAITFASDENDAKILNNVQDRFDVSIS  433 (448)
Q Consensus       400 F~~g~----------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~~~  433 (448)
                      |+.|.                                              +|+.|++++.. |...++++++++++.+.
T Consensus       309 f~~gssrvlIttdl~argidv~~~slvinydlP~~~~~yihR~gr~gr~grkg~~in~v~~~-d~~~lk~ie~~y~~~i~  387 (397)
T KOG0327|consen  309 FRSGSSRVLITTDLLARGIDVQQVSLVVNYDLPARKENYIHRIGRAGRFGRKGVAINFVTEE-DVRDLKDIEKFYNTPIE  387 (397)
T ss_pred             hhcCCceEEeeccccccccchhhcceeeeeccccchhhhhhhcccccccCCCceeeeeehHh-hHHHHHhHHHhcCCcce
Confidence            99998                                              89999999877 89999999999999999


Q ss_pred             CCCccc
Q psy1548         434 ELPDEI  439 (448)
Q Consensus       434 ~~p~~~  439 (448)
                      |+|.+.
T Consensus       388 e~p~~~  393 (397)
T KOG0327|consen  388 ELPSNF  393 (397)
T ss_pred             ecccch
Confidence            999875

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

Probab=100.00  E-value=2.2e-46  Score=387.47  Aligned_cols=337  Identities=27%  Similarity=0.412  Sum_probs=299.4

Q ss_pred             ccCceeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeC
Q psy1548          70 VKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLG  149 (448)
Q Consensus        70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g  149 (448)
                      +.|..++.+...|.++++++.+++++...|                       |..|+++   |.+      +||.++.|
T Consensus       111 ~~g~~~p~pi~~f~~~~l~~~l~~~L~~~g-----------------------~~~ptpi---Q~~------aip~il~g  158 (518)
T PLN00206        111 VKGEAVPPPILSFSSCGLPPKLLLNLETAG-----------------------YEFPTPI---QMQ------AIPAALSG  158 (518)
T ss_pred             ecCCCCCchhcCHHhCCCCHHHHHHHHHcC-----------------------CCCCCHH---HHH------HHHHHhcC
Confidence            345667777788999999999999999999                       9999999   999      99999999


Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhc-------cCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccH
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLET-------TDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQ  222 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~-------~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~  222 (448)
                      +|+++++|||||||++|++|++..+..       ...++++|||+||++||.|+.+.++.+.+.. ++++..++||....
T Consensus       159 ~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~-~~~~~~~~gG~~~~  237 (518)
T PLN00206        159 RSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGL-PFKTALVVGGDAMP  237 (518)
T ss_pred             CCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCceEEEEeCCHHHHHHHHHHHHHHhCCC-CceEEEEECCcchH
Confidence            999999999999999999999987642       2246799999999999999999999998887 78899999998888


Q ss_pred             HhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccH
Q psy1548         223 KDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEI  302 (448)
Q Consensus       223 ~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~  302 (448)
                      .+...+..+ ++|+|+||++|.+++....+.++++++||+||||+|+++ +|+..+..++..++ ..|++++|||+++.+
T Consensus       238 ~q~~~l~~~-~~IiV~TPgrL~~~l~~~~~~l~~v~~lViDEad~ml~~-gf~~~i~~i~~~l~-~~q~l~~SATl~~~v  314 (518)
T PLN00206        238 QQLYRIQQG-VELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLER-GFRDQVMQIFQALS-QPQVLLFSATVSPEV  314 (518)
T ss_pred             HHHHHhcCC-CCEEEECHHHHHHHHHcCCccchheeEEEeecHHHHhhc-chHHHHHHHHHhCC-CCcEEEEEeeCCHHH
Confidence            887777665 899999999999999998889999999999999999998 99999999998885 579999999999999


Q ss_pred             HHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCC--CCeEEEEECccHHHHHHHHHHHh-CCC
Q psy1548         303 RPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLE--FNQVVIFVKSVTRCIALSTLLSE-QNF  379 (448)
Q Consensus       303 ~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~--~~~~IIF~~s~~~a~~l~~~L~~-~g~  379 (448)
                      ..++..++.++..+..... ......+.+.+..+....|...+.+++....  .+++||||+++..|+.+++.|.. .|+
T Consensus       315 ~~l~~~~~~~~~~i~~~~~-~~~~~~v~q~~~~~~~~~k~~~l~~~l~~~~~~~~~~iVFv~s~~~a~~l~~~L~~~~g~  393 (518)
T PLN00206        315 EKFASSLAKDIILISIGNP-NRPNKAVKQLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGL  393 (518)
T ss_pred             HHHHHHhCCCCEEEEeCCC-CCCCcceeEEEEeccchhHHHHHHHHHHhhcccCCCEEEEcCCchhHHHHHHHHhhccCc
Confidence            9999999999988887665 3445667888888888888888888887543  35899999999999999999975 599


Q ss_pred             cEEEEeCCCCHHHHHHHHHHHhcCC----------------------------------------------CceEEEEec
Q psy1548         380 PAVSIHRGMTQEERLKKYQEFKDFH----------------------------------------------KGLAITFAS  413 (448)
Q Consensus       380 ~~~~lh~~~~~~eR~~~l~~F~~g~----------------------------------------------~g~~I~~~t  413 (448)
                      .+..+||+|++++|..++++|++|+                                              .|.+++|++
T Consensus       394 ~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTdvl~rGiDip~v~~VI~~d~P~s~~~yihRiGRaGR~g~~G~ai~f~~  473 (518)
T PLN00206        394 KALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVN  473 (518)
T ss_pred             ceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEecHhhccCCcccCCEEEEeCCCCCHHHHHHhccccccCCCCeEEEEEEc
Confidence            9999999999999999999999999                                              789999998


Q ss_pred             ChhhHHHHHHHHHHhcCCCCCCCcccccccc
Q psy1548         414 DENDAKILNNVQDRFDVSISELPDEIDLSTY  444 (448)
Q Consensus       414 ~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~  444 (448)
                      .. +...+..+.+.+....+++|.++..+-+
T Consensus       474 ~~-~~~~~~~l~~~l~~~~~~vp~~l~~~~~  503 (518)
T PLN00206        474 EE-DRNLFPELVALLKSSGAAIPRELANSRY  503 (518)
T ss_pred             hh-HHHHHHHHHHHHHHcCCCCCHHHHhChh
Confidence            76 7888899999999999999998765443

>KOG0345|consensus

Probab=100.00  E-value=3e-47  Score=363.23  Aligned_cols=331  Identities=25%  Similarity=0.398  Sum_probs=295.0

Q ss_pred             CcccCC--CCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          81 GFRDFL--LKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        81 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      .|++++  |++++++++...|                       |...+|+   |..      +||.++.++||++.++|
T Consensus         5 ~~~~l~~~L~~~l~~~l~~~G-----------------------F~~mTpV---Qa~------tIPlll~~KDVvveavT   52 (567)
T KOG0345|consen    5 SFSSLAPPLSPWLLEALDESG-----------------------FEKMTPV---QAA------TIPLLLKNKDVVVEAVT   52 (567)
T ss_pred             chhhcCCCccHHHHHHHHhcC-----------------------CcccCHH---HHh------hhHHHhcCCceEEEcCC
Confidence            566655  5599999999999                       9999999   999      99999999999999999


Q ss_pred             CChhHHHHHHHHHHhhhcc-----CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCC
Q psy1548         159 GMGKTAVFVLATLQQLETT-----DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNP  233 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~-----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~  233 (448)
                      |||||++|++|++..+..+     +....+|||+|||||+.||.+.+..|...++++.+.++.||.....+...+.+.++
T Consensus        53 GSGKTlAFllP~le~i~rr~~~~~~~~vgalIIsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~  132 (567)
T KOG0345|consen   53 GSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGP  132 (567)
T ss_pred             CCCchhhHHHHHHHHHHhhccCCCccceeEEEecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCC
Confidence            9999999999999988332     22357999999999999999999999999889999999999999999999998889


Q ss_pred             cEEEEcHHHHHHHHHCC--CCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcC
Q psy1548         234 QIVVGTPGRILALVRNK--KLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMH  311 (448)
Q Consensus       234 ~IlV~Tp~~l~~~l~~~--~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~  311 (448)
                      +|+|||||+|.+++.+.  .+++.++.++|+||||++++. +|...+..|+..+|+.+++-+||||...++.++.+..+.
T Consensus       133 nIlVgTPGRL~di~~~~~~~l~~rsLe~LVLDEADrLldm-gFe~~~n~ILs~LPKQRRTGLFSATq~~~v~dL~raGLR  211 (567)
T KOG0345|consen  133 NILVGTPGRLLDILQREAEKLSFRSLEILVLDEADRLLDM-GFEASVNTILSFLPKQRRTGLFSATQTQEVEDLARAGLR  211 (567)
T ss_pred             cEEEeCchhHHHHHhchhhhccccccceEEecchHhHhcc-cHHHHHHHHHHhcccccccccccchhhHHHHHHHHhhcc
Confidence            99999999999999874  455679999999999999998 999999999999999999999999999999999999999


Q ss_pred             CCeEEEEcCccc-ccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhC--CCcEEEEeCCC
Q psy1548         312 DPMEVYVDDEAK-LTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQ--NFPAVSIHRGM  388 (448)
Q Consensus       312 ~~~~i~~~~~~~-~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~--g~~~~~lh~~~  388 (448)
                      +|+.+.+..... .++..+..+|+.|+..+|...|.+++.....+++|||++|...++..+..|...  +.++..+||.|
T Consensus       212 Npv~V~V~~k~~~~tPS~L~~~Y~v~~a~eK~~~lv~~L~~~~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHGK~  291 (567)
T KOG0345|consen  212 NPVRVSVKEKSKSATPSSLALEYLVCEADEKLSQLVHLLNNNKDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKM  291 (567)
T ss_pred             CceeeeecccccccCchhhcceeeEecHHHHHHHHHHHHhccccccEEEEecCcchHHHHHHHHHHHhCCCcEEEecchh
Confidence            999999877632 378889999999999999999999999998999999999999999999998875  67899999999


Q ss_pred             CHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         389 TQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       389 ~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      ++..|.++++.|++...  ++.|||+-..+++  +|-+.-.+--.+.|.+.+.+.++.||
T Consensus       292 ~q~~R~k~~~~F~~~~~--~vl~~TDVaARGl--Dip~iD~VvQ~DpP~~~~~FvHR~GR  347 (567)
T KOG0345|consen  292 SQKARAKVLEAFRKLSN--GVLFCTDVAARGL--DIPGIDLVVQFDPPKDPSSFVHRCGR  347 (567)
T ss_pred             cchhHHHHHHHHHhccC--ceEEeehhhhccC--CCCCceEEEecCCCCChhHHHhhcch
Confidence            99999999999999554  7888888644443  45555555556678888888888776

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=4.9e-46  Score=378.93  Aligned_cols=328  Identities=26%  Similarity=0.425  Sum_probs=287.6

Q ss_pred             CcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCC
Q psy1548          81 GFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGM  160 (448)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGs  160 (448)
                      .|+++++++.+++.+.+.|                       |..|+++   |++      ++|.++.|+|+++++|||+
T Consensus         2 ~f~~l~l~~~l~~~l~~~g-----------------------~~~p~~i---Q~~------ai~~~~~g~d~l~~apTGs   49 (434)
T PRK11192          2 TFSELELDESLLEALQDKG-----------------------YTRPTAI---QAE------AIPPALDGRDVLGSAPTGT   49 (434)
T ss_pred             CHhhcCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhCCCCEEEECCCCC
Confidence            6899999999999999999                       9999999   999      9999999999999999999


Q ss_pred             hhHHHHHHHHHHhhhcc----CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEE
Q psy1548         161 GKTAVFVLATLQQLETT----DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV  236 (448)
Q Consensus       161 GKT~~~~l~~l~~l~~~----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~Il  236 (448)
                      |||++|++|+++.+...    .+.+++||++||++|+.|+.+.+..+.... ++++..++|+.....+...+..+ ++|+
T Consensus        50 GKT~~~~lp~l~~l~~~~~~~~~~~~~lil~Pt~eLa~Q~~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~l~~~-~~Il  127 (434)
T PRK11192         50 GKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELAMQVADQARELAKHT-HLDIATITGGVAYMNHAEVFSEN-QDIV  127 (434)
T ss_pred             hHHHHHHHHHHHHHhhccccCCCCceEEEECCcHHHHHHHHHHHHHHHccC-CcEEEEEECCCCHHHHHHHhcCC-CCEE
Confidence            99999999999987532    234689999999999999999999999888 89999999999887776666554 8999


Q ss_pred             EEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCc-cHHHHHHHhcCCCeE
Q psy1548         237 VGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSK-EIRPVCKKFMHDPME  315 (448)
Q Consensus       237 V~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~-~~~~~~~~~l~~~~~  315 (448)
                      |+||++|++++..+.+.+.++++||+||||+|+++ +|...+..+...++...|+++||||++. .+..+...++.+|..
T Consensus       128 V~Tp~rl~~~~~~~~~~~~~v~~lViDEah~~l~~-~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~~~~~~~~  206 (434)
T PRK11192        128 VATPGRLLQYIKEENFDCRAVETLILDEADRMLDM-GFAQDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVE  206 (434)
T ss_pred             EEChHHHHHHHHcCCcCcccCCEEEEECHHHHhCC-CcHHHHHHHHHhCccccEEEEEEeecCHHHHHHHHHHHccCCEE
Confidence            99999999999999899999999999999999998 9999999999999999999999999985 478888889999998


Q ss_pred             EEEcCcccccccceeEEEEEcCc-chHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHH
Q psy1548         316 VYVDDEAKLTLHGLQQHYVKLKE-NEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERL  394 (448)
Q Consensus       316 i~~~~~~~~~~~~i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~  394 (448)
                      +..... .....++.+++..+.. ..|...|..+++.....++||||+++.+|+.++..|++.|+.+..+||+|++.+|.
T Consensus       207 i~~~~~-~~~~~~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~  285 (434)
T PRK11192        207 VEAEPS-RRERKKIHQWYYRADDLEHKTALLCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRN  285 (434)
T ss_pred             EEecCC-cccccCceEEEEEeCCHHHHHHHHHHHHhcCCCCeEEEEeCChHHHHHHHHHHHhCCCCEEEecCCCCHHHHH
Confidence            877665 3455677787777764 57888899988876778999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         395 KKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       395 ~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      .+++.|++|+  +.|+++|+...+++  ++.+.-.+-..++|.+.+.+.++.||
T Consensus       286 ~~l~~f~~G~--~~vLVaTd~~~~Gi--Dip~v~~VI~~d~p~s~~~yiqr~GR  335 (434)
T PRK11192        286 EAIKRLTDGR--VNVLVATDVAARGI--DIDDVSHVINFDMPRSADTYLHRIGR  335 (434)
T ss_pred             HHHHHHhCCC--CcEEEEccccccCc--cCCCCCEEEEECCCCCHHHHhhcccc
Confidence            9999999998  57788777544443  44444445556788888889999988

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=3.9e-45  Score=375.83  Aligned_cols=324  Identities=27%  Similarity=0.494  Sum_probs=292.1

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      ...|.++++++.+++++.+.|                       |..|+++   |.+      +|+.++.|+|+++++||
T Consensus        86 ~~~f~~~~l~~~l~~~l~~~g-----------------------~~~~~~i---Q~~------ai~~~~~G~dvi~~apT  133 (475)
T PRK01297         86 KTRFHDFNLAPELMHAIHDLG-----------------------FPYCTPI---QAQ------VLGYTLAGHDAIGRAQT  133 (475)
T ss_pred             CCCHhHCCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhCCCCEEEECCC
Confidence            347889999999999999999                       9999999   999      99999999999999999


Q ss_pred             CChhHHHHHHHHHHhhhccC-------CCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcC
Q psy1548         159 GMGKTAVFVLATLQQLETTD-------SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTH  231 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~~-------~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~  231 (448)
                      |||||++|++|+++.+....       +.+++|||+||++|+.|+.+.++.+.+.. ++++..++|+.+...+...+...
T Consensus       134 GSGKTlay~lpil~~l~~~~~~~~~~~~~~~aLil~PtreLa~Q~~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~~~~~  212 (475)
T PRK01297        134 GTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAALTKYT-GLNVMTFVGGMDFDKQLKQLEAR  212 (475)
T ss_pred             CChHHHHHHHHHHHHHHhcCcccccccCCceEEEEeCcHHHHHHHHHHHHHhhccC-CCEEEEEEccCChHHHHHHHhCC
Confidence            99999999999999886543       24689999999999999999999999887 89999999998888777777666


Q ss_pred             CCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCC--CCeEEEEeccCCccHHHHHHHh
Q psy1548         232 NPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPH--TKQVMMFSATLSKEIRPVCKKF  309 (448)
Q Consensus       232 ~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~--~~q~i~~SAT~~~~~~~~~~~~  309 (448)
                      .++|+|+||++|+.++..+...++++++|||||||++++. +|...+..+++.++.  ..|++++|||++.++..++..+
T Consensus       213 ~~~Iiv~TP~~Ll~~~~~~~~~l~~l~~lViDEah~l~~~-~~~~~l~~i~~~~~~~~~~q~i~~SAT~~~~~~~~~~~~  291 (475)
T PRK01297        213 FCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDM-GFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQW  291 (475)
T ss_pred             CCCEEEECHHHHHHHHHcCCcccccCceEEechHHHHHhc-ccHHHHHHHHHhCCCCCCceEEEEEeecCHHHHHHHHHh
Confidence            6899999999999999888888999999999999999998 999999999998864  5799999999999999999999


Q ss_pred             cCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCC
Q psy1548         310 MHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMT  389 (448)
Q Consensus       310 l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~  389 (448)
                      +.+|..+.+... .....++.+.+..+...+|...+..++......++||||+++++|+.+++.|.+.|+.+..+||+|+
T Consensus       292 ~~~~~~v~~~~~-~~~~~~~~~~~~~~~~~~k~~~l~~ll~~~~~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~  370 (475)
T PRK01297        292 TTDPAIVEIEPE-NVASDTVEQHVYAVAGSDKYKLLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVP  370 (475)
T ss_pred             ccCCEEEEeccC-cCCCCcccEEEEEecchhHHHHHHHHHHhcCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCC
Confidence            999988877665 4445667777777888889999999998877789999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhcCC----------------------------------------------CceEEEEecChhhHHHHHH
Q psy1548         390 QEERLKKYQEFKDFH----------------------------------------------KGLAITFASDENDAKILNN  423 (448)
Q Consensus       390 ~~eR~~~l~~F~~g~----------------------------------------------~g~~I~~~t~~~d~~~l~~  423 (448)
                      +++|.++++.|++|+                                              .|.+|+|++.+ |..++..
T Consensus       371 ~~~R~~~~~~Fr~G~~~vLvaT~~l~~GIDi~~v~~VI~~~~P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~~-d~~~~~~  449 (475)
T PRK01297        371 QHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGED-DAFQLPE  449 (475)
T ss_pred             HHHHHHHHHHHhCCCCcEEEEccccccCCcccCCCEEEEeCCCCCHHHHHHhhCccCCCCCCceEEEEecHH-HHHHHHH
Confidence            999999999999998                                              78899999876 8889999


Q ss_pred             HHHHhcCCC-CCCCcc
Q psy1548         424 VQDRFDVSI-SELPDE  438 (448)
Q Consensus       424 i~~~~~~~~-~~~p~~  438 (448)
                      +++.++.++ +++|..
T Consensus       450 ~~~~~~~~~~~~~~~~  465 (475)
T PRK01297        450 IEELLGRKISCEMPPA  465 (475)
T ss_pred             HHHHhCCCCcccCCcH
Confidence            999999997 576653

>KOG0333|consensus

Probab=100.00  E-value=9.3e-46  Score=356.86  Aligned_cols=335  Identities=26%  Similarity=0.403  Sum_probs=300.2

Q ss_pred             cCceeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCc
Q psy1548          71 KGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGM  150 (448)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~  150 (448)
                      +|..++-+..+|++.+++.++++.+...+                       |..|+++   |.+      ++|..+..+
T Consensus       236 kg~~lpnplrnwEE~~~P~e~l~~I~~~~-----------------------y~eptpI---qR~------aipl~lQ~r  283 (673)
T KOG0333|consen  236 KGGRLPNPLRNWEESGFPLELLSVIKKPG-----------------------YKEPTPI---QRQ------AIPLGLQNR  283 (673)
T ss_pred             cCCCCCccccChhhcCCCHHHHHHHHhcC-----------------------CCCCchH---HHh------hccchhccC
Confidence            34555566778999999999999999999                       9999999   999      999999999


Q ss_pred             ceeeeccCCChhHHHHHHHHHHhhhc---------cCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCccc
Q psy1548         151 DILCQAKSGMGKTAVFVLATLQQLET---------TDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPI  221 (448)
Q Consensus       151 ~vli~apTGsGKT~~~~l~~l~~l~~---------~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~  221 (448)
                      |+|..+.||||||++|++|++..+..         ...++.+++++|||+|++|+.+.-.+|++.+ ++++..+.||...
T Consensus       284 D~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~~~gpyaiilaptReLaqqIeeEt~kf~~~l-g~r~vsvigg~s~  362 (673)
T KOG0333|consen  284 DPIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEGPYAIILAPTRELAQQIEEETNKFGKPL-GIRTVSVIGGLSF  362 (673)
T ss_pred             CeeeEEeccCCccccchhhHHHHHHcCCCcchhhhcccCceeeeechHHHHHHHHHHHHHHhcccc-cceEEEEecccch
Confidence            99999999999999999999987632         3457899999999999999999999999998 8999999999999


Q ss_pred             HHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCC-------------
Q psy1548         222 QKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHT-------------  288 (448)
Q Consensus       222 ~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~-------------  288 (448)
                      .++...+..+ |+|+|+||++|.+.+.+..+-++++.++|+||||+|++. +|.+++..++..+|..             
T Consensus       363 EEq~fqls~g-ceiviatPgrLid~Lenr~lvl~qctyvvldeadrmiDm-gfE~dv~~iL~~mPssn~k~~tde~~~~~  440 (673)
T KOG0333|consen  363 EEQGFQLSMG-CEIVIATPGRLIDSLENRYLVLNQCTYVVLDEADRMIDM-GFEPDVQKILEQMPSSNAKPDTDEKEGEE  440 (673)
T ss_pred             hhhhhhhhcc-ceeeecCchHHHHHHHHHHHHhccCceEeccchhhhhcc-cccHHHHHHHHhCCccccCCCccchhhHH
Confidence            9888888887 999999999999999999999999999999999999998 9999999999988731             


Q ss_pred             ------------CeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCe
Q psy1548         289 ------------KQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQ  356 (448)
Q Consensus       289 ------------~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~  356 (448)
                                  +|.++||||+|+.+..+++.|+.+|+.+.+... ......++|.++.+..++|...|.+++.+.-..+
T Consensus       441 ~~~~~~~~~k~yrqT~mftatm~p~verlar~ylr~pv~vtig~~-gk~~~rveQ~v~m~~ed~k~kkL~eil~~~~~pp  519 (673)
T KOG0333|consen  441 RVRKNFSSSKKYRQTVMFTATMPPAVERLARSYLRRPVVVTIGSA-GKPTPRVEQKVEMVSEDEKRKKLIEILESNFDPP  519 (673)
T ss_pred             HHHhhcccccceeEEEEEecCCChHHHHHHHHHhhCCeEEEeccC-CCCccchheEEEEecchHHHHHHHHHHHhCCCCC
Confidence                        589999999999999999999999999999887 4456789999999999999999999999987779


Q ss_pred             EEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC--------------------------------
Q psy1548         357 VVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH--------------------------------  404 (448)
Q Consensus       357 ~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~--------------------------------  404 (448)
                      +|||+|+++.|+.||+.|.+.|+++..+||+-++++|..+++.|++|.                                
T Consensus       520 iIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTDvAgRGIDIpnVSlVinydmaksie  599 (673)
T KOG0333|consen  520 IIIFVNTKKGADALAKILEKAGYKVTTLHGGKSQEQRENALADFREGTGDILVATDVAGRGIDIPNVSLVINYDMAKSIE  599 (673)
T ss_pred             EEEEEechhhHHHHHHHHhhccceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEecccccCCCCCccceeeecchhhhHH
Confidence            999999999999999999999999999999999999999999999977                                


Q ss_pred             --------------CceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccc
Q psy1548         405 --------------KGLAITFASDENDAKILNNVQDRFDVSISELPDEIDL  441 (448)
Q Consensus       405 --------------~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~  441 (448)
                                    .|.+|+|+|..++.-+..-.+....-.....|.++.+
T Consensus       600 DYtHRIGRTgRAGk~GtaiSflt~~dt~v~ydLkq~l~es~~s~~P~Ela~  650 (673)
T KOG0333|consen  600 DYTHRIGRTGRAGKSGTAISFLTPADTAVFYDLKQALRESVKSHCPPELAN  650 (673)
T ss_pred             HHHHHhccccccccCceeEEEeccchhHHHHHHHHHHHHhhhccCChhhcc
Confidence                          8999999999854444444555555555566666543

>KOG0346|consensus

Probab=100.00  E-value=1.2e-45  Score=349.51  Aligned_cols=291  Identities=25%  Similarity=0.380  Sum_probs=266.1

Q ss_pred             CCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCC
Q psy1548          80 SGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSG  159 (448)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTG  159 (448)
                      .+|+++++++.+++++.+.|                       |..|+.+   |+.      +||.++.|+|++..|.||
T Consensus        19 ktFe~~gLD~RllkAi~~lG-----------------------~ekpTlI---Qs~------aIplaLEgKDvvarArTG   66 (569)
T KOG0346|consen   19 KTFEEFGLDSRLLKAITKLG-----------------------WEKPTLI---QSS------AIPLALEGKDVVARARTG   66 (569)
T ss_pred             ccHHHhCCCHHHHHHHHHhC-----------------------cCCcchh---hhc------ccchhhcCcceeeeeccC
Confidence            58999999999999999999                       9999999   999      999999999999999999


Q ss_pred             ChhHHHHHHHHHHhhhcc------CCCeEEEEeeccHHHHHHHHHHHHHhhccCC-CceEEEEEcCcccHHhHHHHhcCC
Q psy1548         160 MGKTAVFVLATLQQLETT------DSNVYVLVMCHTRELAFQISKEYERFSKYMS-NIKVGVFFGGLPIQKDEEYLKTHN  232 (448)
Q Consensus       160 sGKT~~~~l~~l~~l~~~------~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~-~~~v~~~~g~~~~~~~~~~l~~~~  232 (448)
                      ||||++|++|+++.+...      ..++.++|++||+|||+|++..+.++..+.+ .+++.-+..+.+.......+... 
T Consensus        67 SGKT~AYliPllqkll~~k~t~~~e~~~sa~iLvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d~-  145 (569)
T KOG0346|consen   67 SGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVILVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDL-  145 (569)
T ss_pred             CCchHHHHHHHHHHHHHhhhcccccccceeEEEechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHccC-
Confidence            999999999999988543      3568999999999999999999999887764 57777777666655555556554 


Q ss_pred             CcEEEEcHHHHHHHHHCCC-CcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcC
Q psy1548         233 PQIVVGTPGRILALVRNKK-LNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMH  311 (448)
Q Consensus       233 ~~IlV~Tp~~l~~~l~~~~-~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~  311 (448)
                      |+|+|+||++++.++..+. ..+..++++|+||||.++.. ||..++..+.+.+|+..|.++||||+++++..+.+-++.
T Consensus       146 pdIvV~TP~~ll~~~~~~~~~~~~~l~~LVvDEADLllsf-GYeedlk~l~~~LPr~~Q~~LmSATl~dDv~~LKkL~l~  224 (569)
T KOG0346|consen  146 PDIVVATPAKLLRHLAAGVLEYLDSLSFLVVDEADLLLSF-GYEEDLKKLRSHLPRIYQCFLMSATLSDDVQALKKLFLH  224 (569)
T ss_pred             CCeEEeChHHHHHHHhhccchhhhheeeEEechhhhhhhc-ccHHHHHHHHHhCCchhhheeehhhhhhHHHHHHHHhcc
Confidence            9999999999999998876 67889999999999999998 999999999999999999999999999999999999999


Q ss_pred             CCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhC-CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCH
Q psy1548         312 DPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVL-EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQ  390 (448)
Q Consensus       312 ~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~-~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~  390 (448)
                      +|+.+.....+...+..+.|+++.|++.+|+..++.+++.. -.+++|||+||..+|.+|.-.|.+.|++.+.++|.|+.
T Consensus       225 nPviLkl~e~el~~~dqL~Qy~v~cse~DKflllyallKL~LI~gKsliFVNtIdr~YrLkLfLeqFGiksciLNseLP~  304 (569)
T KOG0346|consen  225 NPVILKLTEGELPNPDQLTQYQVKCSEEDKFLLLYALLKLRLIRGKSLIFVNTIDRCYRLKLFLEQFGIKSCILNSELPA  304 (569)
T ss_pred             CCeEEEeccccCCCcccceEEEEEeccchhHHHHHHHHHHHHhcCceEEEEechhhhHHHHHHHHHhCcHhhhhcccccc
Confidence            99999988876667788999999999999999999998753 46799999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcCC
Q psy1548         391 EERLKKYQEFKDFH  404 (448)
Q Consensus       391 ~eR~~~l~~F~~g~  404 (448)
                      .-|.-++++|..|-
T Consensus       305 NSR~Hii~QFNkG~  318 (569)
T KOG0346|consen  305 NSRCHIIEQFNKGL  318 (569)
T ss_pred             cchhhHHHHhhCcc
Confidence            99999999999987

>KOG0339|consensus

Probab=100.00  E-value=8.6e-45  Score=348.56  Aligned_cols=333  Identities=26%  Similarity=0.392  Sum_probs=302.0

Q ss_pred             ccCceeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeC
Q psy1548          70 VKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLG  149 (448)
Q Consensus        70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g  149 (448)
                      +.|...+.+...|.+++++..|..++...-                       |..|+++   |.+      ++|.+++|
T Consensus       213 v~g~s~~rpvtsfeh~gfDkqLm~airk~E-----------------------y~kptpi---q~q------alptalsg  260 (731)
T KOG0339|consen  213 VSGSSPPRPVTSFEHFGFDKQLMTAIRKSE-----------------------YEKPTPI---QCQ------ALPTALSG  260 (731)
T ss_pred             eccCCCCCCcchhhhcCchHHHHHHHhhhh-----------------------cccCCcc---ccc------cccccccc
Confidence            345555666778999999999999999998                       9999999   999      99999999


Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhcc-----CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHh
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETT-----DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD  224 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~-----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~  224 (448)
                      ++|+-.|.||||||.+|++|++.++...     ..++..+|+|||++||.|++.++++|++.+ ++++.+++||.+..+|
T Consensus       261 rdvigIAktgSgktaAfi~pm~~himdq~eL~~g~gPi~vilvPTrela~Qi~~eaKkf~K~y-gl~~v~~ygGgsk~eQ  339 (731)
T KOG0339|consen  261 RDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVILVPTRELASQIFSEAKKFGKAY-GLRVVAVYGGGSKWEQ  339 (731)
T ss_pred             ccchheeeccCcchhHHHHHHHHHhcchhhhcCCCCCeEEEEeccHHHHHHHHHHHHHhhhhc-cceEEEeecCCcHHHH
Confidence            9999999999999999999999887432     457899999999999999999999999998 9999999999999999


Q ss_pred             HHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHH
Q psy1548         225 EEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRP  304 (448)
Q Consensus       225 ~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~  304 (448)
                      ...|+.+ +.|+|+||++|.++++.+..++.++.+|||||+++|++. +|..+++.|.....+.+|+++||||++..+..
T Consensus       340 ~k~Lk~g-~EivVaTPgRlid~VkmKatn~~rvS~LV~DEadrmfdm-Gfe~qVrSI~~hirpdrQtllFsaTf~~kIe~  417 (731)
T KOG0339|consen  340 SKELKEG-AEIVVATPGRLIDMVKMKATNLSRVSYLVLDEADRMFDM-GFEPQVRSIKQHIRPDRQTLLFSATFKKKIEK  417 (731)
T ss_pred             HHhhhcC-CeEEEechHHHHHHHHhhcccceeeeEEEEechhhhhcc-ccHHHHHHHHhhcCCcceEEEeeccchHHHHH
Confidence            9999965 999999999999999999999999999999999999998 99999999999999999999999999999999


Q ss_pred             HHHHhcCCCeEEEEcCcccccccceeEEEEEcCcc-hHHHHHHHHHhh-CCCCeEEEEECccHHHHHHHHHHHhCCCcEE
Q psy1548         305 VCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKEN-EKNKKLFELLDV-LEFNQVVIFVKSVTRCIALSTLLSEQNFPAV  382 (448)
Q Consensus       305 ~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~-~k~~~L~~ll~~-~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~  382 (448)
                      +++.++.+|+.+..... ......|.|.+..+.+. .|+.+|..-|.. ...+++|||+.-...++.++..|+-.|+++.
T Consensus       418 lard~L~dpVrvVqg~v-gean~dITQ~V~V~~s~~~Kl~wl~~~L~~f~S~gkvlifVTKk~~~e~i~a~Lklk~~~v~  496 (731)
T KOG0339|consen  418 LARDILSDPVRVVQGEV-GEANEDITQTVSVCPSEEKKLNWLLRHLVEFSSEGKVLIFVTKKADAEEIAANLKLKGFNVS  496 (731)
T ss_pred             HHHHHhcCCeeEEEeeh-hccccchhheeeeccCcHHHHHHHHHHhhhhccCCcEEEEEeccCCHHHHHHHhccccceee
Confidence            99999999999887765 44567788887777664 577777665544 3568999999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHhcCC----------------------------------------------CceEEEEecChh
Q psy1548         383 SIHRGMTQEERLKKYQEFKDFH----------------------------------------------KGLAITFASDEN  416 (448)
Q Consensus       383 ~lh~~~~~~eR~~~l~~F~~g~----------------------------------------------~g~~I~~~t~~~  416 (448)
                      .+||+|.+.+|.+++.+|+.+.                                              .|++-+++|.. 
T Consensus       497 llhgdkdqa~rn~~ls~fKkk~~~VlvatDvaargldI~~ikTVvnyD~ardIdththrigrtgRag~kGvayTlvTeK-  575 (731)
T KOG0339|consen  497 LLHGDKDQAERNEVLSKFKKKRKPVLVATDVAARGLDIPSIKTVVNYDFARDIDTHTHRIGRTGRAGEKGVAYTLVTEK-  575 (731)
T ss_pred             eecCchhhHHHHHHHHHHhhcCCceEEEeeHhhcCCCccccceeecccccchhHHHHHHhhhcccccccceeeEEechh-
Confidence            9999999999999999999996                                              89999999877 


Q ss_pred             hHHHHHHHHHHhcCCCCCCCccc
Q psy1548         417 DAKILNNVQDRFDVSISELPDEI  439 (448)
Q Consensus       417 d~~~l~~i~~~~~~~~~~~p~~~  439 (448)
                      |......+-+.+.-..+.+|+.+
T Consensus       576 Da~fAG~LVnnLe~agQnVP~~l  598 (731)
T KOG0339|consen  576 DAEFAGHLVNNLEGAGQNVPDEL  598 (731)
T ss_pred             hHHHhhHHHHHHhhccccCChHH
Confidence            77787888888888899999874

>KOG0332|consensus

Probab=100.00  E-value=6.7e-46  Score=344.78  Aligned_cols=328  Identities=27%  Similarity=0.466  Sum_probs=298.5

Q ss_pred             ccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeC--cceeee
Q psy1548          78 HSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLG--MDILCQ  155 (448)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g--~~vli~  155 (448)
                      ....|+++.|+|++++++..++                       |..|+.|   |..      ++|.++..  +|+|.+
T Consensus        88 S~ksFeeL~LkPellkgly~M~-----------------------F~kPskI---Qe~------aLPlll~~Pp~nlIaQ  135 (477)
T KOG0332|consen   88 SAKSFEELRLKPELLKGLYAMK-----------------------FQKPSKI---QET------ALPLLLAEPPQNLIAQ  135 (477)
T ss_pred             ccccHHhhCCCHHHHhHHHHhc-----------------------cCCcchH---HHh------hcchhhcCCchhhhhh
Confidence            4467999999999999999999                       9999999   999      99999985  899999


Q ss_pred             ccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcE
Q psy1548         156 AKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQI  235 (448)
Q Consensus       156 apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~I  235 (448)
                      +..|+|||.||.+.+|.++......|+++.|+||++||.|+.+.+.+.+++. +++..+...+..... -..+   ..+|
T Consensus       136 sqsGtGKTaaFvL~MLsrvd~~~~~PQ~iCLaPtrELA~Q~~eVv~eMGKf~-~ita~yair~sk~~r-G~~i---~eqI  210 (477)
T KOG0332|consen  136 SQSGTGKTAAFVLTMLSRVDPDVVVPQCICLAPTRELAPQTGEVVEEMGKFT-ELTASYAIRGSKAKR-GNKL---TEQI  210 (477)
T ss_pred             hcCCCchhHHHHHHHHHhcCccccCCCceeeCchHHHHHHHHHHHHHhcCce-eeeEEEEecCccccc-CCcc---hhhe
Confidence            9999999999999999999988888999999999999999999999999998 888888876652111 1111   2589


Q ss_pred             EEEcHHHHHHHHHC-CCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCe
Q psy1548         236 VVGTPGRILALVRN-KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPM  314 (448)
Q Consensus       236 lV~Tp~~l~~~l~~-~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~  314 (448)
                      +|+||+.+.+++.. +.+.+..++.+|+||||.|++..||.++-..|++.+|+++|+++||||+...+..++...++++.
T Consensus       211 viGTPGtv~Dlm~klk~id~~kikvfVlDEAD~Mi~tqG~~D~S~rI~~~lP~~~QllLFSATf~e~V~~Fa~kivpn~n  290 (477)
T KOG0332|consen  211 VIGTPGTVLDLMLKLKCIDLEKIKVFVLDEADVMIDTQGFQDQSIRIMRSLPRNQQLLLFSATFVEKVAAFALKIVPNAN  290 (477)
T ss_pred             eeCCCccHHHHHHHHHhhChhhceEEEecchhhhhhcccccccchhhhhhcCCcceEEeeechhHHHHHHHHHHhcCCCc
Confidence            99999999999887 88899999999999999999877899999999999999999999999999999999999999999


Q ss_pred             EEEEcCcccccccceeEEEEEcCc-chHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHH
Q psy1548         315 EVYVDDEAKLTLHGLQQHYVKLKE-NEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEER  393 (448)
Q Consensus       315 ~i~~~~~~~~~~~~i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR  393 (448)
                      .+.+..+ .....+|+|+|+.|.. ++|++.|.++.....-++.||||.|++.|..|+..|++.|..|.++||+|+-++|
T Consensus       291 ~i~Lk~e-el~L~~IkQlyv~C~~~~~K~~~l~~lyg~~tigqsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~~~~R  369 (477)
T KOG0332|consen  291 VIILKRE-ELALDNIKQLYVLCACRDDKYQALVNLYGLLTIGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLTVEQR  369 (477)
T ss_pred             eeeeehh-hccccchhhheeeccchhhHHHHHHHHHhhhhhhheEEEEeehhhHHHHHHHHHhcCceeEEeeccchhHHH
Confidence            9999888 7788999999999986 5799999999888888999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCC----------------------------------------------------CceEEEEecChhhHHHH
Q psy1548         394 LKKYQEFKDFH----------------------------------------------------KGLAITFASDENDAKIL  421 (448)
Q Consensus       394 ~~~l~~F~~g~----------------------------------------------------~g~~I~~~t~~~d~~~l  421 (448)
                      ..++++|++|+                                                    +|++|+|+.+..+.+++
T Consensus       370 ~~ii~~Fr~g~~kVLitTnV~ARGiDv~qVs~VvNydlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~s~~~m  449 (477)
T KOG0332|consen  370 AAIIDRFREGKEKVLITTNVCARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINLVDDKDSMNIM  449 (477)
T ss_pred             HHHHHHHhcCcceEEEEechhhcccccceEEEEEecCCccccCCCCCHHHHHHHhcccccccccceEEEeecccCcHHHH
Confidence            99999999998                                                    89999999999999999


Q ss_pred             HHHHHHhcCCCCCC-Cccccccc
Q psy1548         422 NNVQDRFDVSISEL-PDEIDLST  443 (448)
Q Consensus       422 ~~i~~~~~~~~~~~-p~~~~~~~  443 (448)
                      +.||+.|+..+..+ |++++.++
T Consensus       450 n~iq~~F~~~i~~~~~~d~~E~e  472 (477)
T KOG0332|consen  450 NKIQKHFNMKIKRLDPDDLDELE  472 (477)
T ss_pred             HHHHHHHhhcceecCCccHHHHH
Confidence            99999998877766 55555443

>KOG0336|consensus

Probab=100.00  E-value=9.9e-46  Score=346.88  Aligned_cols=334  Identities=25%  Similarity=0.381  Sum_probs=304.4

Q ss_pred             eeeccCCcc-cCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCccee
Q psy1548          75 VSIHSSGFR-DFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDIL  153 (448)
Q Consensus        75 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vl  153 (448)
                      .+.+.-.|+ .|+-.+++++.+.+.|                       |..|+|+   |.+      +||.++.|.|++
T Consensus       214 IPnP~ctFddAFq~~pevmenIkK~G-----------------------FqKPtPI---qSQ------aWPI~LQG~Dli  261 (629)
T KOG0336|consen  214 IPNPVCTFDDAFQCYPEVMENIKKTG-----------------------FQKPTPI---QSQ------AWPILLQGIDLI  261 (629)
T ss_pred             CCCCcCcHHHHHhhhHHHHHHHHhcc-----------------------CCCCCcc---hhc------ccceeecCcceE
Confidence            344445565 4678899999999999                       9999999   999      999999999999


Q ss_pred             eeccCCChhHHHHHHHHHHhhhc------cCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHH
Q psy1548         154 CQAKSGMGKTAVFVLATLQQLET------TDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEY  227 (448)
Q Consensus       154 i~apTGsGKT~~~~l~~l~~l~~------~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~  227 (448)
                      ..|.||+|||++|++|.+.++..      ...++.+|+++||++|+.|+.-++.+++-.  +.+..+++|+.....+...
T Consensus       262 GVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptreLalqie~e~~kysyn--g~ksvc~ygggnR~eqie~  339 (629)
T KOG0336|consen  262 GVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTRELALQIEGEVKKYSYN--GLKSVCVYGGGNRNEQIED  339 (629)
T ss_pred             EEEecCCCcCHHHhccceeeeeccchhhhccCCCceEEEeccHHHHHHHHhHHhHhhhc--CcceEEEecCCCchhHHHH
Confidence            99999999999999998876643      235789999999999999999888887654  8899999999999999999


Q ss_pred             HhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHH
Q psy1548         228 LKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCK  307 (448)
Q Consensus       228 l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~  307 (448)
                      ++.+ .+|+|+||++|.++...+.+++.++.++|+||||+|++. +|.+++.+++-...+++|+++.|||||+.++.++.
T Consensus       340 lkrg-veiiiatPgrlndL~~~n~i~l~siTYlVlDEADrMLDM-gFEpqIrkilldiRPDRqtvmTSATWP~~VrrLa~  417 (629)
T KOG0336|consen  340 LKRG-VEIIIATPGRLNDLQMDNVINLASITYLVLDEADRMLDM-GFEPQIRKILLDIRPDRQTVMTSATWPEGVRRLAQ  417 (629)
T ss_pred             HhcC-ceEEeeCCchHhhhhhcCeeeeeeeEEEEecchhhhhcc-cccHHHHHHhhhcCCcceeeeecccCchHHHHHHH
Confidence            9987 999999999999999999999999999999999999998 99999999999999999999999999999999999


Q ss_pred             HhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhC-CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeC
Q psy1548         308 KFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVL-EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHR  386 (448)
Q Consensus       308 ~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~-~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~  386 (448)
                      .|+++|..+.+...+-...+.++|.++...+.+|...+..++... ...++||||..+..|+.|...|.-.|+.+-.+||
T Consensus       418 sY~Kep~~v~vGsLdL~a~~sVkQ~i~v~~d~~k~~~~~~f~~~ms~ndKvIiFv~~K~~AD~LSSd~~l~gi~~q~lHG  497 (629)
T KOG0336|consen  418 SYLKEPMIVYVGSLDLVAVKSVKQNIIVTTDSEKLEIVQFFVANMSSNDKVIIFVSRKVMADHLSSDFCLKGISSQSLHG  497 (629)
T ss_pred             HhhhCceEEEecccceeeeeeeeeeEEecccHHHHHHHHHHHHhcCCCceEEEEEechhhhhhccchhhhcccchhhccC
Confidence            999999999998886677788999998888889999999998876 4569999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         387 GMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       387 ~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      +-.+.+|+.+++.|++|+  +-|+++|+-..+++  ++.+..++-.+++|-+++.+.++.||
T Consensus       498 ~r~Q~DrE~al~~~ksG~--vrILvaTDlaSRGl--Dv~DiTHV~NyDFP~nIeeYVHRvGr  555 (629)
T KOG0336|consen  498 NREQSDREMALEDFKSGE--VRILVATDLASRGL--DVPDITHVYNYDFPRNIEEYVHRVGR  555 (629)
T ss_pred             ChhhhhHHHHHHhhhcCc--eEEEEEechhhcCC--CchhcceeeccCCCccHHHHHHHhcc
Confidence            999999999999999998  78888888766665  88899999999999999999988887

>KOG0342|consensus

Probab=100.00  E-value=6.7e-46  Score=356.27  Aligned_cols=332  Identities=27%  Similarity=0.420  Sum_probs=296.2

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      ...|.+..+++..++++.++|                       |...+++   |+.      .+|.++.|+|+++.|.|
T Consensus        81 ~~~f~~~~LS~~t~kAi~~~G-----------------------F~~MT~V---Q~~------ti~pll~gkDvl~~AKT  128 (543)
T KOG0342|consen   81 TFRFEEGSLSPLTLKAIKEMG-----------------------FETMTPV---QQK------TIPPLLEGKDVLAAAKT  128 (543)
T ss_pred             hhHhhccccCHHHHHHHHhcC-----------------------ccchhHH---HHh------hcCccCCCccceeeecc
Confidence            456889999999999999999                       9999999   999      99999999999999999


Q ss_pred             CChhHHHHHHHHHHhhhcc----CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCc
Q psy1548         159 GMGKTAVFVLATLQQLETT----DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQ  234 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~  234 (448)
                      |+|||++|++|+++.+...    ..+..++|+||||+||.|++.+++.+..+.+...+..+.||.........+.. +++
T Consensus       129 GtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k-~~n  207 (543)
T KOG0342|consen  129 GTGKTLAFLLPAIELLRKLKFKPRNGTGVLIICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVK-GCN  207 (543)
T ss_pred             CCCceeeehhHHHHHHHhcccCCCCCeeEEEecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhc-ccc
Confidence            9999999999999987543    35678999999999999999999999998878999999999999888888888 599


Q ss_pred             EEEEcHHHHHHHHHC-CCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcC-C
Q psy1548         235 IVVGTPGRILALVRN-KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMH-D  312 (448)
Q Consensus       235 IlV~Tp~~l~~~l~~-~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~-~  312 (448)
                      |+|+|||+|++++.+ +.+.+.+++++|+||||++++. +|+.++..|++.+|..+|.++||||.+++++++++-.+. +
T Consensus       208 iliATPGRLlDHlqNt~~f~~r~~k~lvlDEADrlLd~-GF~~di~~Ii~~lpk~rqt~LFSAT~~~kV~~l~~~~L~~d  286 (543)
T KOG0342|consen  208 ILIATPGRLLDHLQNTSGFLFRNLKCLVLDEADRLLDI-GFEEDVEQIIKILPKQRQTLLFSATQPSKVKDLARGALKRD  286 (543)
T ss_pred             EEEeCCchHHhHhhcCCcchhhccceeEeecchhhhhc-ccHHHHHHHHHhccccceeeEeeCCCcHHHHHHHHHhhcCC
Confidence            999999999999987 4556688899999999999998 999999999999999999999999999999999987665 5


Q ss_pred             CeEEEEcCcc-cccccceeEEEEEcCcchHHHHHHHHHhhCCC-CeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCH
Q psy1548         313 PMEVYVDDEA-KLTLHGLQQHYVKLKENEKNKKLFELLDVLEF-NQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQ  390 (448)
Q Consensus       313 ~~~i~~~~~~-~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~-~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~  390 (448)
                      |..+.+.+.. ..+...+.|-|+.++...++-.+..+++.+.. .++||||+|...+..++..|+...++|..+||++++
T Consensus       287 ~~~v~~~d~~~~~The~l~Qgyvv~~~~~~f~ll~~~LKk~~~~~KiiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~Q  366 (543)
T KOG0342|consen  287 PVFVNVDDGGERETHERLEQGYVVAPSDSRFSLLYTFLKKNIKRYKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQKQ  366 (543)
T ss_pred             ceEeecCCCCCcchhhcccceEEeccccchHHHHHHHHHHhcCCceEEEEechhhHHHHHHHHHhhcCCchhhhhcCCcc
Confidence            8888776553 35677899999999999899999999998866 799999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         391 EERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       391 ~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      ..|..+..+|++.++  +|++||+-.-+++  ++-+.-++-=.+.|++...|-++.||
T Consensus       367 ~kRT~~~~~F~kaes--gIL~cTDVaARGl--D~P~V~~VvQ~~~P~d~~~YIHRvGR  420 (543)
T KOG0342|consen  367 NKRTSTFFEFCKAES--GILVCTDVAARGL--DIPDVDWVVQYDPPSDPEQYIHRVGR  420 (543)
T ss_pred             cccchHHHHHhhccc--ceEEecchhhccC--CCCCceEEEEeCCCCCHHHHHHHhcc
Confidence            999999999999885  7888888755554  55555555556778888888888887

>PTZ00424 helicase 45; Provisional

Probab=100.00  E-value=7.6e-44  Score=359.71  Aligned_cols=324  Identities=32%  Similarity=0.546  Sum_probs=290.4

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      ...|+++++++.+++++...+                       |..|+++   |.+      +|+.++.|+|+++++||
T Consensus        27 ~~~~~~l~l~~~~~~~l~~~~-----------------------~~~~~~~---Q~~------ai~~i~~~~d~ii~apT   74 (401)
T PTZ00424         27 VDSFDALKLNEDLLRGIYSYG-----------------------FEKPSAI---QQR------GIKPILDGYDTIGQAQS   74 (401)
T ss_pred             cCCHhhCCCCHHHHHHHHHcC-----------------------CCCCCHH---HHH------HHHHHhCCCCEEEECCC
Confidence            467999999999999999999                       9999999   999      99999999999999999


Q ss_pred             CChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEE
Q psy1548         159 GMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVG  238 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~  238 (448)
                      |||||++|++|+++.+.....+.++||++|+++|+.|+.+.+..+.... ++.+..+.|+.....+...+..+ ++|+|+
T Consensus        75 GsGKT~~~~l~~l~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~-~~Ivv~  152 (401)
T PTZ00424         75 GTGKTATFVIAALQLIDYDLNACQALILAPTRELAQQIQKVVLALGDYL-KVRCHACVGGTVVRDDINKLKAG-VHMVVG  152 (401)
T ss_pred             CChHHHHHHHHHHHHhcCCCCCceEEEECCCHHHHHHHHHHHHHHhhhc-CceEEEEECCcCHHHHHHHHcCC-CCEEEE
Confidence            9999999999999988765566799999999999999999999998776 78888889998777666666665 899999


Q ss_pred             cHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEE
Q psy1548         239 TPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV  318 (448)
Q Consensus       239 Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~  318 (448)
                      ||+++.+++.++...+++++++|+||||++.++ ++...+..+++.+++..|++++|||+++.+..+...++.+|..+.+
T Consensus       153 Tp~~l~~~l~~~~~~l~~i~lvViDEah~~~~~-~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~  231 (401)
T PTZ00424        153 TPGRVYDMIDKRHLRVDDLKLFILDEADEMLSR-GFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILV  231 (401)
T ss_pred             CcHHHHHHHHhCCcccccccEEEEecHHHHHhc-chHHHHHHHHhhCCCCcEEEEEEecCCHHHHHHHHHHcCCCEEEEe
Confidence            999999999888888999999999999999998 8999999999999999999999999999999999999999988776


Q ss_pred             cCcccccccceeEEEEEcCc-chHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHH
Q psy1548         319 DDEAKLTLHGLQQHYVKLKE-NEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKY  397 (448)
Q Consensus       319 ~~~~~~~~~~i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l  397 (448)
                      ... .....++.+++..+.. ..+...+..++......++||||+++++|+.+++.|...++.+..+||+|++++|..++
T Consensus       232 ~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ivF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~  310 (401)
T PTZ00424        232 KKD-ELTLEGIRQFYVAVEKEEWKFDTLCDLYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIM  310 (401)
T ss_pred             CCC-CcccCCceEEEEecChHHHHHHHHHHHHHhcCCCeEEEEecCcHHHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHH
Confidence            554 3456677777777765 34677788888777778999999999999999999999999999999999999999999


Q ss_pred             HHHhcCC----------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCC
Q psy1548         398 QEFKDFH----------------------------------------------KGLAITFASDENDAKILNNVQDRFDVS  431 (448)
Q Consensus       398 ~~F~~g~----------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~  431 (448)
                      +.|++|+                                              .|.+++|+++. |...++.+++.++..
T Consensus       311 ~~f~~g~~~vLvaT~~l~~GiDip~v~~VI~~~~p~s~~~y~qr~GRagR~g~~G~~i~l~~~~-~~~~~~~~e~~~~~~  389 (401)
T PTZ00424        311 REFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPD-DIEQLKEIERHYNTQ  389 (401)
T ss_pred             HHHHcCCCCEEEEcccccCCcCcccCCEEEEECCCCCHHHEeecccccccCCCCceEEEEEcHH-HHHHHHHHHHHHCCc
Confidence            9999998                                              78899999876 889999999999999


Q ss_pred             CCCCCccc
Q psy1548         432 ISELPDEI  439 (448)
Q Consensus       432 ~~~~p~~~  439 (448)
                      +.++|...
T Consensus       390 ~~~~~~~~  397 (401)
T PTZ00424        390 IEEMPMEV  397 (401)
T ss_pred             ccccCcch
Confidence            99987664

>KOG0335|consensus

Probab=100.00  E-value=1.1e-45  Score=360.50  Aligned_cols=342  Identities=27%  Similarity=0.394  Sum_probs=306.6

Q ss_pred             hhccCceeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeee
Q psy1548          68 KEVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV  147 (448)
Q Consensus        68 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~  147 (448)
                      .++.|.+.+.+..+|.+-.+...+...+...+                       |..|+++   |+.      +||.+.
T Consensus        62 v~~~G~~~p~~i~~f~~~~l~~~l~~ni~~~~-----------------------~~~ptpv---Qk~------sip~i~  109 (482)
T KOG0335|consen   62 VKVSGRDVPPHIPTFDEAILGEALAGNIKRSG-----------------------YTKPTPV---QKY------SIPIIS  109 (482)
T ss_pred             eeccCCccCCCcccccccchhHHHhhcccccc-----------------------ccCCCcc---eee------ccceee
Confidence            34567788888889998889999999999999                       9999999   999      999999


Q ss_pred             eCcceeeeccCCChhHHHHHHHHHHhhhccC----------CCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEc
Q psy1548         148 LGMDILCQAKSGMGKTAVFVLATLQQLETTD----------SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFG  217 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l~~l~~l~~~~----------~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g  217 (448)
                      .|++++++|+||||||.+|++|++..+....          ..++++|++|||+||.|+++.++++.... .+++...+|
T Consensus       110 ~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~Qi~nea~k~~~~s-~~~~~~~yg  188 (482)
T KOG0335|consen  110 GGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALILAPTRELVDQIYNEARKFSYLS-GMKSVVVYG  188 (482)
T ss_pred             cCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCCCCCCceEEEeCcHHHhhHHHHHHHhhcccc-cceeeeeeC
Confidence            9999999999999999999999999875442          25899999999999999999999999887 899999999


Q ss_pred             CcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCC----CCeEEE
Q psy1548         218 GLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPH----TKQVMM  293 (448)
Q Consensus       218 ~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~----~~q~i~  293 (448)
                      +.+...+...+..+ ++|+|+||++|.+++..+.+.+.+++++|+||||+|++..+|.+++..++..+..    ..|.++
T Consensus       189 g~~~~~q~~~~~~g-cdIlvaTpGrL~d~~e~g~i~l~~~k~~vLDEADrMlD~mgF~p~Ir~iv~~~~~~~~~~~qt~m  267 (482)
T KOG0335|consen  189 GTDLGAQLRFIKRG-CDILVATPGRLKDLIERGKISLDNCKFLVLDEADRMLDEMGFEPQIRKIVEQLGMPPKNNRQTLL  267 (482)
T ss_pred             CcchhhhhhhhccC-ccEEEecCchhhhhhhcceeehhhCcEEEecchHHhhhhccccccHHHHhcccCCCCccceeEEE
Confidence            99888888888876 9999999999999999999999999999999999999944999999999988753    789999


Q ss_pred             EeccCCccHHHHHHHhcCC-CeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCC----CC-----eEEEEECc
Q psy1548         294 FSATLSKEIRPVCKKFMHD-PMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLE----FN-----QVVIFVKS  363 (448)
Q Consensus       294 ~SAT~~~~~~~~~~~~l~~-~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~----~~-----~~IIF~~s  363 (448)
                      ||||+|..+..++..++.+ ...+.+... .....++.|...++.+.+|...|.+++....    .+     +++|||.+
T Consensus       268 FSAtfp~~iq~l~~~fl~~~yi~laV~rv-g~~~~ni~q~i~~V~~~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt  346 (482)
T KOG0335|consen  268 FSATFPKEIQRLAADFLKDNYIFLAVGRV-GSTSENITQKILFVNEMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVET  346 (482)
T ss_pred             EeccCChhhhhhHHHHhhccceEEEEeee-ccccccceeEeeeecchhhHHHHHHHhhcccCCcccCCcccceEEEEeec
Confidence            9999999999999988886 666666666 5577899999999999999999999997653    23     79999999


Q ss_pred             cHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccc
Q psy1548         364 VTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLST  443 (448)
Q Consensus       364 ~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~  443 (448)
                      ++.|..++..|...++++..+||+.++.+|.+.++.|+.|+.  -+.++|.-..+++  +|..--++...++|.+++.+.
T Consensus       347 ~~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~al~~Fr~g~~--pvlVaT~VaaRGl--Di~~V~hVInyDmP~d~d~Yv  422 (482)
T KOG0335|consen  347 KRGADELAAFLSSNGYPAKSIHGDRTQIEREQALNDFRNGKA--PVLVATNVAARGL--DIPNVKHVINYDMPADIDDYV  422 (482)
T ss_pred             cchhhHHHHHHhcCCCCceeecchhhhhHHHHHHHHhhcCCc--ceEEEehhhhcCC--CCCCCceeEEeecCcchhhHH
Confidence            999999999999999999999999999999999999999994  6778887655555  666667788999999999999


Q ss_pred             cccCC
Q psy1548         444 YIEGR  448 (448)
Q Consensus       444 ~~~~~  448 (448)
                      +++||
T Consensus       423 HRIGR  427 (482)
T KOG0335|consen  423 HRIGR  427 (482)
T ss_pred             Hhccc
Confidence            99998

>KOG0341|consensus

Probab=100.00  E-value=4.2e-46  Score=347.26  Aligned_cols=339  Identities=25%  Similarity=0.373  Sum_probs=301.4

Q ss_pred             ccCceeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeC
Q psy1548          70 VKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLG  149 (448)
Q Consensus        70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g  149 (448)
                      ++|...+.+..+|.++.++..+++.+.+.|                       +..|+++   |-+      -+|.+++|
T Consensus       160 veGd~ipPPIksF~eMKFP~~~L~~lk~KG-----------------------I~~PTpI---QvQ------GlPvvLsG  207 (610)
T KOG0341|consen  160 VEGDDIPPPIKSFKEMKFPKPLLRGLKKKG-----------------------IVHPTPI---QVQ------GLPVVLSG  207 (610)
T ss_pred             eeCCCCCCchhhhhhccCCHHHHHHHHhcC-----------------------CCCCCce---eec------CcceEeec
Confidence            567788888899999999999999999999                       9999999   999      99999999


Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhc--------cCCCeEEEEeeccHHHHHHHHHHHHHhhccC-----CCceEEEEE
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLET--------TDSNVYVLVMCHTRELAFQISKEYERFSKYM-----SNIKVGVFF  216 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~--------~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-----~~~~v~~~~  216 (448)
                      +|+|..|-||||||++|.+|++.....        ...++..||+||+|+||.|+++.+..+...+     |.+++.++.
T Consensus       208 RDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~Lci  287 (610)
T KOG0341|consen  208 RDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCI  287 (610)
T ss_pred             CceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCCCeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhh
Confidence            999999999999999999998765422        2457899999999999999999888776533     578999999


Q ss_pred             cCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEec
Q psy1548         217 GGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSA  296 (448)
Q Consensus       217 g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SA  296 (448)
                      ||.+...+....+.+ .||+|+||++|.+++..+.+++.-++++++||||+|++. +|..++..++..+...+|.++|||
T Consensus       288 GG~~v~eql~~v~~G-vHivVATPGRL~DmL~KK~~sLd~CRyL~lDEADRmiDm-GFEddir~iF~~FK~QRQTLLFSA  365 (610)
T KOG0341|consen  288 GGVPVREQLDVVRRG-VHIVVATPGRLMDMLAKKIMSLDACRYLTLDEADRMIDM-GFEDDIRTIFSFFKGQRQTLLFSA  365 (610)
T ss_pred             cCccHHHHHHHHhcC-eeEEEcCcchHHHHHHHhhccHHHHHHhhhhhHHHHhhc-cchhhHHHHHHHHhhhhheeeeec
Confidence            999999999999887 999999999999999999999999999999999999998 999999999999999999999999


Q ss_pred             cCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHh
Q psy1548         297 TLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSE  376 (448)
Q Consensus       297 T~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~  376 (448)
                      |||..++.+++.-+..|+.+.+....... -++.|.+.++..+.|.-.|.+-+.+.. .+++|||..+..++.+.++|--
T Consensus       366 TMP~KIQ~FAkSALVKPvtvNVGRAGAAs-ldViQevEyVkqEaKiVylLeCLQKT~-PpVLIFaEkK~DVD~IhEYLLl  443 (610)
T KOG0341|consen  366 TMPKKIQNFAKSALVKPVTVNVGRAGAAS-LDVIQEVEYVKQEAKIVYLLECLQKTS-PPVLIFAEKKADVDDIHEYLLL  443 (610)
T ss_pred             cccHHHHHHHHhhcccceEEecccccccc-hhHHHHHHHHHhhhhhhhHHHHhccCC-CceEEEeccccChHHHHHHHHH
Confidence            99999999999999999999998875443 445555556677777777777776543 5899999999999999999999


Q ss_pred             CCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         377 QNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       377 ~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      .|..+..+|||-.+++|...++.|+.|++  .++++|+-...++  ++.++-++-.+++|++++++.+++||
T Consensus       444 KGVEavaIHGGKDQedR~~ai~afr~gkK--DVLVATDVASKGL--DFp~iqHVINyDMP~eIENYVHRIGR  511 (610)
T KOG0341|consen  444 KGVEAVAIHGGKDQEDRHYAIEAFRAGKK--DVLVATDVASKGL--DFPDIQHVINYDMPEEIENYVHRIGR  511 (610)
T ss_pred             ccceeEEeecCcchhHHHHHHHHHhcCCC--ceEEEecchhccC--CCccchhhccCCChHHHHHHHHHhcc
Confidence            99999999999999999999999999995  7777777544443  66777788889999999999999998

>KOG4284|consensus

Probab=100.00  E-value=5.5e-43  Score=344.18  Aligned_cols=297  Identities=29%  Similarity=0.464  Sum_probs=277.6

Q ss_pred             ceeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcce
Q psy1548          73 AYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDI  152 (448)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~v  152 (448)
                      +..+....+|+++.++.+++.+|...+                       |..|+++   |..      +||.++.+.|+
T Consensus        18 DV~~~~~~~fe~l~l~r~vl~glrrn~-----------------------f~~ptki---Qaa------AIP~~~~kmDl   65 (980)
T KOG4284|consen   18 DVQSNCTPGFEQLALWREVLLGLRRNA-----------------------FALPTKI---QAA------AIPAIFSKMDL   65 (980)
T ss_pred             ccccCCCCCHHHHHHHHHHHHHHHhhc-----------------------ccCCCch---hhh------hhhhhhcccce
Confidence            344556679999999999999999999                       9999999   999      99999999999


Q ss_pred             eeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCC
Q psy1548         153 LCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHN  232 (448)
Q Consensus       153 li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~  232 (448)
                      ||++..|+|||++|.+.+++.+..+...++++||+|||+++.|+.+.+.+++..+.+.+|.++.||++...+...++.  
T Consensus        66 iVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~PTREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rlk~--  143 (980)
T KOG4284|consen   66 IVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTPTREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRLKQ--  143 (980)
T ss_pred             EEEecCCCCceEEEEeeeehhcCcccCcceeEEEecchhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhhhh--
Confidence            999999999999999999999988888899999999999999999999999998879999999999998888887776  


Q ss_pred             CcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCC
Q psy1548         233 PQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHD  312 (448)
Q Consensus       233 ~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~  312 (448)
                      ++|+|||||++..++..+.+++++++++|+||||.+.+...|..++..|+..+|..+|++++|||.|..+...+.++|.+
T Consensus       144 ~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEADkL~~t~sfq~~In~ii~slP~~rQv~a~SATYp~nLdn~Lsk~mrd  223 (980)
T KOG4284|consen  144 TRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEADKLMDTESFQDDINIIINSLPQIRQVAAFSATYPRNLDNLLSKFMRD  223 (980)
T ss_pred             ceEEecCchHHHHHHHhcCCCccceeEEEeccHHhhhchhhHHHHHHHHHHhcchhheeeEEeccCchhHHHHHHHHhcc
Confidence            68999999999999999999999999999999999998548999999999999999999999999999999999999999


Q ss_pred             CeEEEEcCcccccccceeEEEEEcCcc--------hHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEE
Q psy1548         313 PMEVYVDDEAKLTLHGLQQHYVKLKEN--------EKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSI  384 (448)
Q Consensus       313 ~~~i~~~~~~~~~~~~i~~~~~~~~~~--------~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~l  384 (448)
                      |..+..... ...+-+|+|+++.+.+-        .|++.|..+++..+..++||||+...+|+-++.+|+..|++|.++
T Consensus       224 p~lVr~n~~-d~~L~GikQyv~~~~s~nnsveemrlklq~L~~vf~~ipy~QAlVF~~~~sra~~~a~~L~ssG~d~~~I  302 (980)
T KOG4284|consen  224 PALVRFNAD-DVQLFGIKQYVVAKCSPNNSVEEMRLKLQKLTHVFKSIPYVQALVFCDQISRAEPIATHLKSSGLDVTFI  302 (980)
T ss_pred             cceeecccC-CceeechhheeeeccCCcchHHHHHHHHHHHHHHHhhCchHHHHhhhhhhhhhhHHHHHhhccCCCeEEe
Confidence            999998777 56778999998876543        388999999999999999999999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHhcCC
Q psy1548         385 HRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       385 h~~~~~~eR~~~l~~F~~g~  404 (448)
                      .|.|++.+|..+++.++...
T Consensus       303 SgaM~Q~~Rl~a~~~lr~f~  322 (980)
T KOG4284|consen  303 SGAMSQKDRLLAVDQLRAFR  322 (980)
T ss_pred             ccccchhHHHHHHHHhhhce
Confidence            99999999999999999877

>KOG0334|consensus

Probab=100.00  E-value=8.6e-43  Score=362.06  Aligned_cols=336  Identities=27%  Similarity=0.433  Sum_probs=305.3

Q ss_pred             hhccCceeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeee
Q psy1548          68 KEVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV  147 (448)
Q Consensus        68 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~  147 (448)
                      ..+.+..++.+..+|.+.++...++..+++.+                       |..|++|   |.+      +||+++
T Consensus       353 i~v~g~~~pkpv~sW~q~gl~~~il~tlkkl~-----------------------y~k~~~I---Q~q------AiP~Im  400 (997)
T KOG0334|consen  353 IKVKGKECPKPVTSWTQCGLSSKILETLKKLG-----------------------YEKPTPI---QAQ------AIPAIM  400 (997)
T ss_pred             eeeccCCCCcccchHhhCCchHHHHHHHHHhc-----------------------CCCCcch---hhh------hcchhc
Confidence            34566678888889999999999999999999                       9999999   999      999999


Q ss_pred             eCcceeeeccCCChhHHHHHHHHHHhhhcc-----CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccH
Q psy1548         148 LGMDILCQAKSGMGKTAVFVLATLQQLETT-----DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQ  222 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l~~l~~l~~~-----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~  222 (448)
                      +|+|||.+|.||||||++|++|++.++...     ..||.+||++||++|+.|+.+.++.|.+.+ ++++.+++|+....
T Consensus       401 sGrdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~aPtrela~QI~r~~~kf~k~l-~ir~v~vygg~~~~  479 (997)
T KOG0334|consen  401 SGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILAPTRELAMQIHREVRKFLKLL-GIRVVCVYGGSGIS  479 (997)
T ss_pred             cCcceEEeeccCCccchhhhcchhhhhhcCCChhhCCCceEEEEcCCHHHHHHHHHHHHHHHhhc-CceEEEecCCccHH
Confidence            999999999999999999999999766332     358999999999999999999999999998 99999999999999


Q ss_pred             HhHHHHhcCCCcEEEEcHHHHHHHHHCCCC---cCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCC
Q psy1548         223 KDEEYLKTHNPQIVVGTPGRILALVRNKKL---NLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLS  299 (448)
Q Consensus       223 ~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~---~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~  299 (448)
                      .++..++++ +.|+||||+++.+++..+.-   ++.++.++|+||||+|++. +|.+++..|+..+++.+|++++|||+|
T Consensus       480 ~qiaelkRg-~eIvV~tpGRmiD~l~~n~grvtnlrR~t~lv~deaDrmfdm-gfePq~~~Ii~nlrpdrQtvlfSatfp  557 (997)
T KOG0334|consen  480 QQIAELKRG-AEIVVCTPGRMIDILCANSGRVTNLRRVTYLVLDEADRMFDM-GFEPQITRILQNLRPDRQTVLFSATFP  557 (997)
T ss_pred             HHHHHHhcC-CceEEeccchhhhhHhhcCCccccccccceeeechhhhhhee-ccCcccchHHhhcchhhhhhhhhhhhh
Confidence            999999998 99999999999998866544   4555569999999999987 999999999999999999999999999


Q ss_pred             ccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcC-cchHHHHHHHHHhhC-CCCeEEEEECccHHHHHHHHHHHhC
Q psy1548         300 KEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLK-ENEKNKKLFELLDVL-EFNQVVIFVKSVTRCIALSTLLSEQ  377 (448)
Q Consensus       300 ~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~-~~~k~~~L~~ll~~~-~~~~~IIF~~s~~~a~~l~~~L~~~  377 (448)
                      ..++.+++..+..|+.+.+... ......+.+.+..+. +.+|+..|.++|... ..+++||||.+...|..+...|.+.
T Consensus       558 r~m~~la~~vl~~Pveiiv~~~-svV~k~V~q~v~V~~~e~eKf~kL~eLl~e~~e~~~tiiFv~~qe~~d~l~~~L~~a  636 (997)
T KOG0334|consen  558 RSMEALARKVLKKPVEIIVGGR-SVVCKEVTQVVRVCAIENEKFLKLLELLGERYEDGKTIIFVDKQEKADALLRDLQKA  636 (997)
T ss_pred             HHHHHHHHHhhcCCeeEEEccc-eeEeccceEEEEEecCchHHHHHHHHHHHHHhhcCCEEEEEcCchHHHHHHHHHHhc
Confidence            9999999999999999888766 556678889988888 789999999999764 5679999999999999999999999


Q ss_pred             CCcEEEEeCCCCHHHHHHHHHHHhcCC----------------------------------------------CceEEEE
Q psy1548         378 NFPAVSIHRGMTQEERLKKYQEFKDFH----------------------------------------------KGLAITF  411 (448)
Q Consensus       378 g~~~~~lh~~~~~~eR~~~l~~F~~g~----------------------------------------------~g~~I~~  411 (448)
                      |+++..+||+.++.+|..++++|+++.                                              +|.+++|
T Consensus       637 g~~~~slHGgv~q~dR~sti~dfK~~~~~LLvaTsvvarGLdv~~l~Lvvnyd~pnh~edyvhR~gRTgragrkg~AvtF  716 (997)
T KOG0334|consen  637 GYNCDSLHGGVDQHDRSSTIEDFKNGVVNLLVATSVVARGLDVKELILVVNYDFPNHYEDYVHRVGRTGRAGRKGAAVTF  716 (997)
T ss_pred             CcchhhhcCCCchHHHHhHHHHHhccCceEEEehhhhhcccccccceEEEEcccchhHHHHHHHhcccccCCccceeEEE
Confidence            999999999999999999999999998                                              8999999


Q ss_pred             ecChhhHHHHHHHHHHhcCCCCCCCcccc
Q psy1548         412 ASDENDAKILNNVQDRFDVSISELPDEID  440 (448)
Q Consensus       412 ~t~~~d~~~l~~i~~~~~~~~~~~p~~~~  440 (448)
                      ++.. +..+.-.|.+.+...-+.+|..+.
T Consensus       717 i~p~-q~~~a~dl~~al~~~~~~~P~~l~  744 (997)
T KOG0334|consen  717 ITPD-QLKYAGDLCKALELSKQPVPKLLQ  744 (997)
T ss_pred             eChH-HhhhHHHHHHHHHhccCCCchHHH
Confidence            9984 778888999999888888887654

>KOG0347|consensus

Probab=100.00  E-value=4.6e-43  Score=339.80  Aligned_cols=329  Identities=28%  Similarity=0.459  Sum_probs=284.4

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeC-cceeeecc
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLG-MDILCQAK  157 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g-~~vli~ap  157 (448)
                      .+.|..+.++.+++++|...|                       |..|++|   |..      .+|.+..| .|++..|.
T Consensus       180 vsAW~~l~lp~~iL~aL~~~g-----------------------Fs~Pt~I---Qsl------~lp~ai~gk~DIlGaAe  227 (731)
T KOG0347|consen  180 VSAWKNLFLPMEILRALSNLG-----------------------FSRPTEI---QSL------VLPAAIRGKVDILGAAE  227 (731)
T ss_pred             hHHHhcCCCCHHHHHHHHhcC-----------------------CCCCccc---hhh------cccHhhccchhcccccc
Confidence            456999999999999999999                       9999999   999      99999999 79999999


Q ss_pred             CCChhHHHHHHHHHHhhhcc-----------CCCeE--EEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHh
Q psy1548         158 SGMGKTAVFVLATLQQLETT-----------DSNVY--VLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD  224 (448)
Q Consensus       158 TGsGKT~~~~l~~l~~l~~~-----------~~~~~--~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~  224 (448)
                      ||||||++|.+|++..+...           ..+++  +||++|||+||.|+.+.+..+.... ++++..++||.....|
T Consensus       228 TGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t-~i~v~si~GGLavqKQ  306 (731)
T KOG0347|consen  228 TGSGKTLAFGIPIVERLLESSDDSQELSNTSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKT-QIRVASITGGLAVQKQ  306 (731)
T ss_pred             cCCCceeeecchhhhhhhhccchHhhhhhHHhccCcceeEEecChHHHHHHHHHHHHHhcccc-CeEEEEeechhHHHHH
Confidence            99999999999999955332           12344  9999999999999999999999987 9999999999999999


Q ss_pred             HHHHhcCCCcEEEEcHHHHHHHHHCCCC---cCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCC-----CCCeEEEEec
Q psy1548         225 EEYLKTHNPQIVVGTPGRILALVRNKKL---NLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSP-----HTKQVMMFSA  296 (448)
Q Consensus       225 ~~~l~~~~~~IlV~Tp~~l~~~l~~~~~---~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~-----~~~q~i~~SA  296 (448)
                      .+.+.. +|+|+|+|||+|+.++..+..   .+++++++|+||+|+|++. +.-..+..+++.+.     +..|.+.|||
T Consensus       307 qRlL~~-~p~IVVATPGRlweli~e~n~~l~~~k~vkcLVlDEaDRmvek-ghF~Els~lL~~L~e~~~~~qrQTlVFSA  384 (731)
T KOG0347|consen  307 QRLLNQ-RPDIVVATPGRLWELIEEDNTHLGNFKKVKCLVLDEADRMVEK-GHFEELSKLLKHLNEEQKNRQRQTLVFSA  384 (731)
T ss_pred             HHHHhc-CCCEEEecchHHHHHHHhhhhhhhhhhhceEEEEccHHHHhhh-ccHHHHHHHHHHhhhhhcccccceEEEEE
Confidence            888877 599999999999999988655   5788999999999999998 88888999888775     3569999999


Q ss_pred             cCCc---------------------cHHHHHHH--hcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCC
Q psy1548         297 TLSK---------------------EIRPVCKK--FMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLE  353 (448)
Q Consensus       297 T~~~---------------------~~~~~~~~--~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~  353 (448)
                      |++-                     .++.++..  +...|..|...+. ..+...+....+.|+..+|.-.|+.+|..++
T Consensus       385 Tlt~~~~~~~~~~~k~~~k~~~~~~kiq~Lmk~ig~~~kpkiiD~t~q-~~ta~~l~Es~I~C~~~eKD~ylyYfl~ryP  463 (731)
T KOG0347|consen  385 TLTLVLQQPLSSSRKKKDKEDELNAKIQHLMKKIGFRGKPKIIDLTPQ-SATASTLTESLIECPPLEKDLYLYYFLTRYP  463 (731)
T ss_pred             EeehhhcChhHHhhhccchhhhhhHHHHHHHHHhCccCCCeeEecCcc-hhHHHHHHHHhhcCCccccceeEEEEEeecC
Confidence            9643                     12223222  3346777777666 5566777777888888888888888887765


Q ss_pred             CCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCC
Q psy1548         354 FNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSIS  433 (448)
Q Consensus       354 ~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~  433 (448)
                       |++|||||+...+.+|+-.|+..+++...+|+.|.+.+|.+.+++|++..+  +++++|+-.-+++  +|...-++..+
T Consensus       464 -GrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA~M~QKqRLknLEkF~~~~~--~VLiaTDVAARGL--DIp~V~HVIHY  538 (731)
T KOG0347|consen  464 -GRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHASMIQKQRLKNLEKFKQSPS--GVLIATDVAARGL--DIPGVQHVIHY  538 (731)
T ss_pred             -CceEEEechHHHHHHHHHHHhhcCCCCchhhHHHHHHHHHHhHHHHhcCCC--eEEEeehhhhccC--CCCCcceEEEe
Confidence             689999999999999999999999999999999999999999999999774  7888888766666  88888899999


Q ss_pred             CCCccccccccccCC
Q psy1548         434 ELPDEIDLSTYIEGR  448 (448)
Q Consensus       434 ~~p~~~~~~~~~~~~  448 (448)
                      .+|-..+.|.++-||
T Consensus       539 qVPrtseiYVHRSGR  553 (731)
T KOG0347|consen  539 QVPRTSEIYVHRSGR  553 (731)
T ss_pred             ecCCccceeEecccc
Confidence            999999999999887

>KOG0348|consensus

Probab=100.00  E-value=2e-42  Score=334.40  Aligned_cols=334  Identities=26%  Similarity=0.391  Sum_probs=273.8

Q ss_pred             eccCCcccCCCCHHHHHHHhh-ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeee
Q psy1548          77 IHSSGFRDFLLKPEILRAIVD-CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQ  155 (448)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~  155 (448)
                      +....|..+|+++.+...|.. ++                       +..|+.+   |++      +||.++.|+|++|.
T Consensus       133 fts~~f~~LGL~~~lv~~L~~~m~-----------------------i~~pTsV---Qkq------~IP~lL~grD~lV~  180 (708)
T KOG0348|consen  133 FTSAAFASLGLHPHLVSHLNTKMK-----------------------ISAPTSV---QKQ------AIPVLLEGRDALVR  180 (708)
T ss_pred             cccccchhcCCCHHHHHHHHHHhc-----------------------cCccchH---hhc------chhhhhcCcceEEE
Confidence            456789999999999999965 46                       8999999   999      99999999999999


Q ss_pred             ccCCChhHHHHHHHHHHhhhc------cCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHh
Q psy1548         156 AKSGMGKTAVFVLATLQQLET------TDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK  229 (448)
Q Consensus       156 apTGsGKT~~~~l~~l~~l~~------~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~  229 (448)
                      ++||||||++|++|+++.+..      +..|+.+||++||||||.|+++.+.++.+.+-=+-.+.+.||.....+...++
T Consensus       181 aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLR  260 (708)
T KOG0348|consen  181 AQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLR  260 (708)
T ss_pred             cCCCCcccHHHHHHHHHHHHhcCccccccCCceEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHh
Confidence            999999999999999998743      34678999999999999999999999988652345577889988888888888


Q ss_pred             cCCCcEEEEcHHHHHHHHHC-CCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhC-------------CCCCeEEEEe
Q psy1548         230 THNPQIVVGTPGRILALVRN-KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSS-------------PHTKQVMMFS  295 (448)
Q Consensus       230 ~~~~~IlV~Tp~~l~~~l~~-~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l-------------~~~~q~i~~S  295 (448)
                      .| ++|+|+|||+|.+.+++ ..+.+++++|+|+||+|++++. ||..++..|++.+             |+..|-+++|
T Consensus       261 KG-iNILIgTPGRLvDHLknT~~i~~s~LRwlVlDEaDrlleL-Gfekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlS  338 (708)
T KOG0348|consen  261 KG-INILIGTPGRLVDHLKNTKSIKFSRLRWLVLDEADRLLEL-GFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLS  338 (708)
T ss_pred             cC-ceEEEcCchHHHHHHhccchheeeeeeEEEecchhHHHhc-cchhhHHHHHHHHhhccchhcccccccHHHHhHhhh
Confidence            87 99999999999999987 6788999999999999999998 9999999998876             2245889999


Q ss_pred             ccCCccHHHHHHHhcCCCeEEEEcCcc------------------------cccccceeEEEEEcCcchHHHHHHHHHhh
Q psy1548         296 ATLSKEIRPVCKKFMHDPMEVYVDDEA------------------------KLTLHGLQQHYVKLKENEKNKKLFELLDV  351 (448)
Q Consensus       296 AT~~~~~~~~~~~~l~~~~~i~~~~~~------------------------~~~~~~i~~~~~~~~~~~k~~~L~~ll~~  351 (448)
                      ||+++.+..+....++||+.|..+...                        ...+..+.|.|..+++.-++-.|..+|.+
T Consensus       339 ATLtd~V~rLa~~sLkDpv~I~ld~s~~~~~p~~~a~~ev~~~~~~~~l~~~~iPeqL~qry~vVPpKLRLV~Laa~L~~  418 (708)
T KOG0348|consen  339 ATLTDGVNRLADLSLKDPVYISLDKSHSQLNPKDKAVQEVDDGPAGDKLDSFAIPEQLLQRYTVVPPKLRLVALAALLLN  418 (708)
T ss_pred             hhhHHHHHHHhhccccCceeeeccchhhhcCcchhhhhhcCCcccccccccccCcHHhhhceEecCCchhHHHHHHHHHH
Confidence            999999999999999999988832110                        12345678889999998888777777755


Q ss_pred             C----CCCeEEEEECccHHHHHHHHHHHhC----------------------CCcEEEEeCCCCHHHHHHHHHHHhcCCC
Q psy1548         352 L----EFNQVVIFVKSVTRCIALSTLLSEQ----------------------NFPAVSIHRGMTQEERLKKYQEFKDFHK  405 (448)
Q Consensus       352 ~----~~~~~IIF~~s~~~a~~l~~~L~~~----------------------g~~~~~lh~~~~~~eR~~~l~~F~~g~~  405 (448)
                      .    ...++|||+.+.+.++.=+..|...                      +..+.-+||+|++++|..+++.|...+.
T Consensus       419 ~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~~~~s~g~~~l~~~~k~~rLHGsm~QeeRts~f~~Fs~~~~  498 (708)
T KOG0348|consen  419 KVKFEEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSGAPDSEGLPPLFMDLKFYRLHGSMEQEERTSVFQEFSHSRR  498 (708)
T ss_pred             HhhhhhhceeEEEEechhHHHHHHHHHHhhhhcccccccCCcccCCChhhhhcceEEEecCchhHHHHHHHHHhhccccc
Confidence            3    4558999999999999988877642                      3358899999999999999999999775


Q ss_pred             ceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         406 GLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       406 g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                        +|++||+-.-+++  ++-+.-.+.-++-|...+.+.++.||
T Consensus       499 --~VLLcTDVAaRGL--DlP~V~~vVQYd~P~s~adylHRvGR  537 (708)
T KOG0348|consen  499 --AVLLCTDVAARGL--DLPHVGLVVQYDPPFSTADYLHRVGR  537 (708)
T ss_pred             --eEEEehhhhhccC--CCCCcCeEEEeCCCCCHHHHHHHhhh
Confidence              6999998643332  22222222234446666677777776

>KOG0337|consensus

Probab=100.00  E-value=2.6e-40  Score=311.83  Aligned_cols=322  Identities=25%  Similarity=0.384  Sum_probs=294.9

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      +.+|..++|+..+++++.+.|                       |+.|+|+   |+.      .+|.++.|+|++..+-|
T Consensus        20 ~g~fqsmgL~~~v~raI~kkg-----------------------~~~ptpi---qRK------TipliLe~~dvv~mart   67 (529)
T KOG0337|consen   20 SGGFQSMGLDYKVLRAIHKKG-----------------------FNTPTPI---QRK------TIPLILEGRDVVGMART   67 (529)
T ss_pred             CCCccccCCCHHHHHHHHHhh-----------------------cCCCCch---hcc------cccceeeccccceeeec
Confidence            678999999999999999999                       9999999   999      99999999999999999


Q ss_pred             CChhHHHHHHHHHHhhhcc-CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEE
Q psy1548         159 GMGKTAVFVLATLQQLETT-DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVV  237 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV  237 (448)
                      |||||.||++|+++.+... ..+.+++++.||++|+.|+.+.++.+++.. ++++.+++|+....++...+..+ |||++
T Consensus        68 gsgktaaf~ipm~e~Lk~~s~~g~RalilsptreLa~qtlkvvkdlgrgt-~lr~s~~~ggD~~eeqf~~l~~n-pDii~  145 (529)
T KOG0337|consen   68 GSGKTAAFLIPMIEKLKSHSQTGLRALILSPTRELALQTLKVVKDLGRGT-KLRQSLLVGGDSIEEQFILLNEN-PDIII  145 (529)
T ss_pred             CCcchhhHHHHHHHHHhhccccccceeeccCcHHHHHHHHHHHHHhcccc-chhhhhhcccchHHHHHHHhccC-CCEEE
Confidence            9999999999999998654 356899999999999999999999999998 99999999999999888888765 99999


Q ss_pred             EcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEE
Q psy1548         238 GTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVY  317 (448)
Q Consensus       238 ~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~  317 (448)
                      +||++++.+.-+-.+.++.+.|+|+||+|.+++. +|..++.+++..+|...|.++||||+|..+.++.+..+.+|..+.
T Consensus       146 ATpgr~~h~~vem~l~l~sveyVVfdEadrlfem-gfqeql~e~l~rl~~~~QTllfSatlp~~lv~fakaGl~~p~lVR  224 (529)
T KOG0337|consen  146 ATPGRLLHLGVEMTLTLSSVEYVVFDEADRLFEM-GFQEQLHEILSRLPESRQTLLFSATLPRDLVDFAKAGLVPPVLVR  224 (529)
T ss_pred             ecCceeeeeehheeccccceeeeeehhhhHHHhh-hhHHHHHHHHHhCCCcceEEEEeccCchhhHHHHHccCCCCceEE
Confidence            9999999887776788999999999999999998 999999999999999999999999999999999999999999999


Q ss_pred             EcCcccccccceeEEEEEcCcchHHHHHHHHHhhCC-CCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHH
Q psy1548         318 VDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLE-FNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKK  396 (448)
Q Consensus       318 ~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~-~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~  396 (448)
                      ++-+ ......++..+..+.+++|...|..++...- ..+++|||.|..+++.+...|+..|+.+..++|.|.+..|..-
T Consensus       225 ldve-tkise~lk~~f~~~~~a~K~aaLl~il~~~~~~~~t~vf~~tk~hve~~~~ll~~~g~~~s~iysslD~~aRk~~  303 (529)
T KOG0337|consen  225 LDVE-TKISELLKVRFFRVRKAEKEAALLSILGGRIKDKQTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKIN  303 (529)
T ss_pred             eehh-hhcchhhhhheeeeccHHHHHHHHHHHhccccccceeEEecccchHHHHHHHHHhcCCCccccccccChHhhhhc
Confidence            7776 4456778889999999999999999998763 4589999999999999999999999999999999999999999


Q ss_pred             HHHHhcCC----------------------------------------------CceEEEEecChhhHHHHHHHHHHhcC
Q psy1548         397 YQEFKDFH----------------------------------------------KGLAITFASDENDAKILNNVQDRFDV  430 (448)
Q Consensus       397 l~~F~~g~----------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~  430 (448)
                      +.+|+.++                                              .|.+.+|++.. |..++-+++.+++.
T Consensus       304 ~~~F~~~k~~~lvvTdvaaRG~diplldnvinyd~p~~~klFvhRVgr~aragrtg~aYs~V~~~-~~~yl~DL~lflgr  382 (529)
T KOG0337|consen  304 GRDFRGRKTSILVVTDVAARGLDIPLLDNVINYDFPPDDKLFVHRVGRVARAGRTGRAYSLVAST-DDPYLLDLQLFLGR  382 (529)
T ss_pred             cccccCCccceEEEehhhhccCCCccccccccccCCCCCceEEEEecchhhccccceEEEEEecc-cchhhhhhhhhcCC
Confidence            99999988                                              78889999877 66677788888887


Q ss_pred             CCCCCCc
Q psy1548         431 SISELPD  437 (448)
Q Consensus       431 ~~~~~p~  437 (448)
                      ++...+.
T Consensus       383 ~~~~~~~  389 (529)
T KOG0337|consen  383 PLIFAIS  389 (529)
T ss_pred             ceeeccc
Confidence            6655443

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

Probab=100.00  E-value=4.9e-39  Score=343.04  Aligned_cols=314  Identities=15%  Similarity=0.212  Sum_probs=246.1

Q ss_pred             CCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHH
Q psy1548          86 LLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAV  165 (448)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~  165 (448)
                      .+++.+.+++.+.|                       |..|+++   |.+      ++|.++.|+|+++++|||||||++
T Consensus        20 ~l~~~l~~~L~~~g-----------------------~~~p~~~---Q~~------ai~~il~G~nvvv~apTGSGKTla   67 (742)
T TIGR03817        20 WAHPDVVAALEAAG-----------------------IHRPWQH---QAR------AAELAHAGRHVVVATGTASGKSLA   67 (742)
T ss_pred             cCCHHHHHHHHHcC-----------------------CCcCCHH---HHH------HHHHHHCCCCEEEECCCCCcHHHH
Confidence            37899999999999                       9999999   999      999999999999999999999999


Q ss_pred             HHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHH
Q psy1548         166 FVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILA  245 (448)
Q Consensus       166 ~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~  245 (448)
                      |++|+++.+... .+.++|||+||++|+.|+.+.++.+. .. ++++..+.|+.+. .+...+..+ ++|+|+||+++..
T Consensus        68 ~~LPiL~~l~~~-~~~~aL~l~PtraLa~q~~~~l~~l~-~~-~i~v~~~~Gdt~~-~~r~~i~~~-~~IivtTPd~L~~  142 (742)
T TIGR03817        68 YQLPVLSALADD-PRATALYLAPTKALAADQLRAVRELT-LR-GVRPATYDGDTPT-EERRWAREH-ARYVLTNPDMLHR  142 (742)
T ss_pred             HHHHHHHHHhhC-CCcEEEEEcChHHHHHHHHHHHHHhc-cC-CeEEEEEeCCCCH-HHHHHHhcC-CCEEEEChHHHHH
Confidence            999999998664 35699999999999999999999987 33 7888888888764 344455554 8999999999875


Q ss_pred             HHHCC----CCcCCCeeEEEecchhHHHhhhhhHHHHHHHHH-------hCCCCCeEEEEeccCCccHHHHHHHhcCCCe
Q psy1548         246 LVRNK----KLNLSLLKHFILDECDKMLEQLEMRRDVQEIFR-------SSPHTKQVMMFSATLSKEIRPVCKKFMHDPM  314 (448)
Q Consensus       246 ~l~~~----~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~-------~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~  314 (448)
                      .+...    ...+++++++|+||||.|.+  .|...+..+++       ..+.+.|++++|||+++.. +++.+++..|.
T Consensus       143 ~~L~~~~~~~~~l~~l~~vViDEah~~~g--~fg~~~~~il~rL~ri~~~~g~~~q~i~~SATi~n~~-~~~~~l~g~~~  219 (742)
T TIGR03817       143 GILPSHARWARFLRRLRYVVIDECHSYRG--VFGSHVALVLRRLRRLCARYGASPVFVLASATTADPA-AAASRLIGAPV  219 (742)
T ss_pred             hhccchhHHHHHHhcCCEEEEeChhhccC--ccHHHHHHHHHHHHHHHHhcCCCCEEEEEecCCCCHH-HHHHHHcCCCe
Confidence            43221    12378999999999999865  35555444433       3456789999999999875 46778888886


Q ss_pred             EEEEcCcccccccceeEEEEEcCc-----------------chHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhC
Q psy1548         315 EVYVDDEAKLTLHGLQQHYVKLKE-----------------NEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQ  377 (448)
Q Consensus       315 ~i~~~~~~~~~~~~i~~~~~~~~~-----------------~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~  377 (448)
                      .+. ... . .+....+...+.+.                 .++...+..+++.  +.++||||+|++.|+.++..|++.
T Consensus       220 ~~i-~~~-~-~~~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~l~~l~~~--~~~~IVF~~sr~~ae~l~~~l~~~  294 (742)
T TIGR03817       220 VAV-TED-G-SPRGARTVALWEPPLTELTGENGAPVRRSASAEAADLLADLVAE--GARTLTFVRSRRGAELVAAIARRL  294 (742)
T ss_pred             EEE-CCC-C-CCcCceEEEEecCCccccccccccccccchHHHHHHHHHHHHHC--CCCEEEEcCCHHHHHHHHHHHHHH
Confidence            543 222 1 12222222222211                 2355566666664  569999999999999999998763


Q ss_pred             --------CCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         378 --------NFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       378 --------g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                              +..+..+||+|++++|.+++++|++|+  +.+.++|+.-.+++  +|.+.--+-..++|.+...+.++.||
T Consensus       295 l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~f~~G~--i~vLVaTd~lerGI--DI~~vd~VI~~~~P~s~~~y~qRiGR  369 (742)
T TIGR03817       295 LGEVDPDLAERVAAYRAGYLPEDRRELERALRDGE--LLGVATTNALELGV--DISGLDAVVIAGFPGTRASLWQQAGR  369 (742)
T ss_pred             HHhhccccccchhheecCCCHHHHHHHHHHHHcCC--ceEEEECchHhccC--CcccccEEEEeCCCCCHHHHHHhccc
Confidence                    567899999999999999999999998  57888888655555  66666667788899999999999998

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.

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=100.00  E-value=4.9e-36  Score=307.38  Aligned_cols=302  Identities=17%  Similarity=0.164  Sum_probs=224.6

Q ss_pred             eeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHH
Q psy1548         118 NIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQIS  197 (448)
Q Consensus       118 ~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~  197 (448)
                      ..+++|..|+++   |++      +++.++.|+|+++++|||+|||++|++|++..      +..+||++|+++|+.|+.
T Consensus         4 ~~~~g~~~~r~~---Q~~------ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~------~~~~lVi~P~~~L~~dq~   68 (470)
T TIGR00614         4 KTVFGLSSFRPV---QLE------VINAVLLGRDCFVVMPTGGGKSLCYQLPALCS------DGITLVISPLISLMEDQV   68 (470)
T ss_pred             HhhcCCCCCCHH---HHH------HHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHc------CCcEEEEecHHHHHHHHH
Confidence            344568999998   999      99999999999999999999999999999863      347999999999999988


Q ss_pred             HHHHHhhccCCCceEEEEEcCcccHHhH---HHHhcCCCcEEEEcHHHHHHHH-HCCCC-cCCCeeEEEecchhHHHhh-
Q psy1548         198 KEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTHNPQIVVGTPGRILALV-RNKKL-NLSLLKHFILDECDKMLEQ-  271 (448)
Q Consensus       198 ~~~~~~~~~~~~~~v~~~~g~~~~~~~~---~~l~~~~~~IlV~Tp~~l~~~l-~~~~~-~~~~i~~lViDEah~l~~~-  271 (448)
                      +.+..+     ++.+..+.++.......   ..+..+.++|+++||+++.... ....+ ...+++++||||||++.+| 
T Consensus        69 ~~l~~~-----gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~~iViDEaH~i~~~g  143 (470)
T TIGR00614        69 LQLKAS-----GIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWG  143 (470)
T ss_pred             HHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCcCEEEEeCCcccCccc
Confidence            887754     67777777776544322   2334556899999999975321 00111 4678999999999999987 


Q ss_pred             hhhHHHHHHH--HHhCCCCCeEEEEeccCCccHHHHHHHhc--CCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHH
Q psy1548         272 LEMRRDVQEI--FRSSPHTKQVMMFSATLSKEIRPVCKKFM--HDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFE  347 (448)
Q Consensus       272 ~~~~~~~~~i--~~~l~~~~q~i~~SAT~~~~~~~~~~~~l--~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~  347 (448)
                      .+|+..+..+  +....++.|++++|||+++.+...+...+  .+|..+.....    .+++...... ........+..
T Consensus       144 ~~fr~~~~~l~~l~~~~~~~~~l~lTAT~~~~~~~di~~~l~l~~~~~~~~s~~----r~nl~~~v~~-~~~~~~~~l~~  218 (470)
T TIGR00614       144 HDFRPDYKALGSLKQKFPNVPIMALTATASPSVREDILRQLNLKNPQIFCTSFD----RPNLYYEVRR-KTPKILEDLLR  218 (470)
T ss_pred             cccHHHHHHHHHHHHHcCCCceEEEecCCCHHHHHHHHHHcCCCCCcEEeCCCC----CCCcEEEEEe-CCccHHHHHHH
Confidence            2477777665  23333577899999999998766655543  35554433222    2334322222 22234555666


Q ss_pred             HHh-hCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHH
Q psy1548         348 LLD-VLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQD  426 (448)
Q Consensus       348 ll~-~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~  426 (448)
                      ++. ...+.++||||+|+++|+.++..|++.|+.+..+||+|++++|.+++++|++|+  +.|+++|+...+++  ++.+
T Consensus       219 ~l~~~~~~~~~IIF~~s~~~~e~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~--~~vLVaT~~~~~GI--D~p~  294 (470)
T TIGR00614       219 FIRKEFKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDE--IQVVVATVAFGMGI--NKPD  294 (470)
T ss_pred             HHHHhcCCCceEEEECcHHHHHHHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHHHcCC--CcEEEEechhhccC--Cccc
Confidence            665 445567799999999999999999999999999999999999999999999987  57788887543433  4444


Q ss_pred             HhcCCCCCCCccccccccccCC
Q psy1548         427 RFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       427 ~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      .--+-...+|.++..+.++.||
T Consensus       295 V~~VI~~~~P~s~~~y~Qr~GR  316 (470)
T TIGR00614       295 VRFVIHYSLPKSMESYYQESGR  316 (470)
T ss_pred             ceEEEEeCCCCCHHHHHhhhcC
Confidence            4455667889999999999998

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

>KOG0344|consensus

Probab=100.00  E-value=7.9e-36  Score=293.27  Aligned_cols=336  Identities=25%  Similarity=0.309  Sum_probs=282.7

Q ss_pred             ccCceeeeccCCccc----CCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccccee
Q psy1548          70 VKGAYVSIHSSGFRD----FLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK  145 (448)
Q Consensus        70 ~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~  145 (448)
                      +.|...+.....|.+    +..++.+++.+.+.+                       |..|+++   |.+      ++|.
T Consensus       122 v~G~~~~~~l~~f~~lt~~~~~~~~ll~nl~~~~-----------------------F~~Pt~i---q~~------aipv  169 (593)
T KOG0344|consen  122 VDGFHLPPPLLSFSDLTYDYSMNKRLLENLQELG-----------------------FDEPTPI---QKQ------AIPV  169 (593)
T ss_pred             ccCCCCCCccccccccchhhhhcHHHHHhHhhCC-----------------------CCCCCcc---cch------hhhh
Confidence            345454555556664    667899999999999                       9999999   999      9999


Q ss_pred             eeeCcceeeeccCCChhHHHHHHHHHHhhhcc-----CCCeEEEEeeccHHHHHHHHHHHHHhh--ccCCCceEEEEEcC
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETT-----DSNVYVLVMCHTRELAFQISKEYERFS--KYMSNIKVGVFFGG  218 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~-----~~~~~~lil~Pt~~L~~q~~~~~~~~~--~~~~~~~v~~~~g~  218 (448)
                      ++.+++++.++|||+|||++|.+|+++++...     ..+.+++|+.||++|+.|++.++.++.  ... ..++..+...
T Consensus       170 fl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t-~~~a~~~~~~  248 (593)
T KOG0344|consen  170 FLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQEKHKVGLRALILSPTRELAAQIYREMRKYSIDEGT-SLRAAQFSKP  248 (593)
T ss_pred             hhcccceEEeccCCCcchhhhhhHHHHHHHHhhcccCccceEEEEecchHHHHHHHHHHHHhcCCCCCC-chhhhhcccc
Confidence            99999999999999999999999999988432     467899999999999999999999998  444 4444444333


Q ss_pred             cccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCC--CcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCC-CCCeEEEEe
Q psy1548         219 LPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK--LNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSP-HTKQVMMFS  295 (448)
Q Consensus       219 ~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~--~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~-~~~q~i~~S  295 (448)
                      .........+....++|+|+||-++..++..+.  +++..+.++|+||+|++.+...|..++..|+..+. ++..+-+||
T Consensus       249 ~~~~qk~a~~~~~k~dili~TP~ri~~~~~~~~~~idl~~V~~lV~dEaD~lfe~~~f~~Qla~I~sac~s~~i~~a~FS  328 (593)
T KOG0344|consen  249 AYPSQKPAFLSDEKYDILISTPMRIVGLLGLGKLNIDLSKVEWLVVDEADLLFEPEFFVEQLADIYSACQSPDIRVALFS  328 (593)
T ss_pred             cchhhccchhHHHHHHHHhcCHHHHHHHhcCCCccchhheeeeEeechHHhhhChhhHHHHHHHHHHHhcCcchhhhhhh
Confidence            221222222222237999999999999998865  78999999999999999886578999999988765 566788999


Q ss_pred             ccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCc-chHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHH
Q psy1548         296 ATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKE-NEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLL  374 (448)
Q Consensus       296 AT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L  374 (448)
                      ||++..+++++...+.++..+.+... ......+.|..+.+.+ ..|.-++..++...-..+++||+.+.++|..|+..|
T Consensus       329 at~~~~VEE~~~~i~~~~~~vivg~~-~sa~~~V~QelvF~gse~~K~lA~rq~v~~g~~PP~lIfVQs~eRak~L~~~L  407 (593)
T KOG0344|consen  329 ATISVYVEEWAELIKSDLKRVIVGLR-NSANETVDQELVFCGSEKGKLLALRQLVASGFKPPVLIFVQSKERAKQLFEEL  407 (593)
T ss_pred             ccccHHHHHHHHHhhccceeEEEecc-hhHhhhhhhhheeeecchhHHHHHHHHHhccCCCCeEEEEecHHHHHHHHHHh
Confidence            99999999999999999999988777 4456678787777765 568999999999887779999999999999999999


Q ss_pred             -HhCCCcEEEEeCCCCHHHHHHHHHHHhcCC----------------------------------------------Cce
Q psy1548         375 -SEQNFPAVSIHRGMTQEERLKKYQEFKDFH----------------------------------------------KGL  407 (448)
Q Consensus       375 -~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~----------------------------------------------~g~  407 (448)
                       .-.++++.++||+.++.+|.++++.|+.|+                                              .|.
T Consensus       408 ~~~~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTdll~RGiDf~gvn~VInyD~p~s~~syihrIGRtgRag~~g~  487 (593)
T KOG0344|consen  408 EIYDNINVDVIHGERSQKQRDETMERFRIGKIWVLICTDLLARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGRSGK  487 (593)
T ss_pred             hhccCcceeeEecccchhHHHHHHHHHhccCeeEEEehhhhhccccccCcceEEecCCCchhHHHHHHhhccCCCCCCcc
Confidence             556899999999999999999999999999                                              899


Q ss_pred             EEEEecChhhHHHHHHHHHHhcCCCCCCCcccc
Q psy1548         408 AITFASDENDAKILNNVQDRFDVSISELPDEID  440 (448)
Q Consensus       408 ~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~  440 (448)
                      +|+|.|++ |.+.++.|........+++|.++.
T Consensus       488 Aitfytd~-d~~~ir~iae~~~~sG~evpe~~m  519 (593)
T KOG0344|consen  488 AITFYTDQ-DMPRIRSIAEVMEQSGCEVPEKIM  519 (593)
T ss_pred             eEEEeccc-cchhhhhHHHHHHHcCCcchHHHH
Confidence            99999987 999999999999999999999864

>KOG0350|consensus

Probab=100.00  E-value=7.1e-36  Score=287.22  Aligned_cols=311  Identities=23%  Similarity=0.312  Sum_probs=258.7

Q ss_pred             ccCCCCchhhhhhhccccccceee---------eeCcceeeeccCCChhHHHHHHHHHHhhhcc-CCCeEEEEeeccHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKA---------VLGMDILCQAKSGMGKTAVFVLATLQQLETT-DSNVYVLVMCHTREL  192 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~---------~~g~~vli~apTGsGKT~~~~l~~l~~l~~~-~~~~~~lil~Pt~~L  192 (448)
                      ...-+|+   |..      .+|.+         ..++|+.|.||||||||++|.+|+++.+..+ -+..+++||+||++|
T Consensus       157 is~~FPV---Q~a------Vlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~LRavVivPtr~L  227 (620)
T KOG0350|consen  157 ISRLFPV---QYA------VLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTREL  227 (620)
T ss_pred             cccccch---HHH------HHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHHHccCCccceEEEEEeeHHHH
Confidence            6777788   877      66555         3478999999999999999999999998766 355899999999999


Q ss_pred             HHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCC----cEEEEcHHHHHHHHHC-CCCcCCCeeEEEecchhH
Q psy1548         193 AFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNP----QIVVGTPGRILALVRN-KKLNLSLLKHFILDECDK  267 (448)
Q Consensus       193 ~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~----~IlV~Tp~~l~~~l~~-~~~~~~~i~~lViDEah~  267 (448)
                      +.|+++.+.++.... ++.|+.+.|..+...+...+....+    +|+|+||++|.+.+.+ +.+++++++++||||||+
T Consensus       228 ~~QV~~~f~~~~~~t-gL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~LrfLVIDEADR  306 (620)
T KOG0350|consen  228 ALQVYDTFKRLNSGT-GLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNNTKSFDLKHLRFLVIDEADR  306 (620)
T ss_pred             HHHHHHHHHHhccCC-ceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhccCCCCcchhhceEEEechHHH
Confidence            999999999999988 8999999999998888888876656    9999999999999984 789999999999999999


Q ss_pred             HHhhhhhHHHHHHHHHhCC----------------------------------CCCeEEEEeccCCccHHHHHHHhcCCC
Q psy1548         268 MLEQLEMRRDVQEIFRSSP----------------------------------HTKQVMMFSATLSKEIRPVCKKFMHDP  313 (448)
Q Consensus       268 l~~~~~~~~~~~~i~~~l~----------------------------------~~~q~i~~SAT~~~~~~~~~~~~l~~~  313 (448)
                      |++. .|-..+..++..+.                                  +..+.+.+|||+...-..+...-+..|
T Consensus       307 ll~q-sfQ~Wl~~v~~~~~~~k~~~~~~nii~~~~~~~pt~~~e~~t~~~~~~~~l~kL~~satLsqdP~Kl~~l~l~~P  385 (620)
T KOG0350|consen  307 LLDQ-SFQEWLDTVMSLCKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKLYPPLWKLVFSATLSQDPSKLKDLTLHIP  385 (620)
T ss_pred             HHHH-HHHHHHHHHHHHhCCchhhcChhhhhhhcccCCchhhHHHHhhcCCcCchhHhhhcchhhhcChHHHhhhhcCCC
Confidence            9987 66555555443322                                  122468899999888788887778888


Q ss_pred             eEEEEcC---cccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHH----hCCCcEEEEeC
Q psy1548         314 MEVYVDD---EAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLS----EQNFPAVSIHR  386 (448)
Q Consensus       314 ~~i~~~~---~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~----~~g~~~~~lh~  386 (448)
                      ....+..   .....+..+.++++.++...|.-.++.++......++|+|+++...+.+++..|+    +..+++..+.|
T Consensus       386 rl~~v~~~~~~ryslp~~l~~~~vv~~~~~kpl~~~~lI~~~k~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~  465 (620)
T KOG0350|consen  386 RLFHVSKPLIGRYSLPSSLSHRLVVTEPKFKPLAVYALITSNKLNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTG  465 (620)
T ss_pred             ceEEeecccceeeecChhhhhceeecccccchHhHHHHHHHhhcceEEEEecchHHHHHHHHHHHHHhccccchhhhhhh
Confidence            6555442   2234567788888888888899999999999989999999999999999999887    34678888999


Q ss_pred             CCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         387 GMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       387 ~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      +++...|.+.++.|..|+  +-+++|++.--+++  ++-+.-++-.++.|.+.-.+.++.||
T Consensus       466 ~l~~k~r~k~l~~f~~g~--i~vLIcSD~laRGi--Dv~~v~~VINYd~P~~~ktyVHR~GR  523 (620)
T KOG0350|consen  466 QLNGKRRYKMLEKFAKGD--INVLICSDALARGI--DVNDVDNVINYDPPASDKTYVHRAGR  523 (620)
T ss_pred             hhhHHHHHHHHHHHhcCC--ceEEEehhhhhcCC--cccccceEeecCCCchhhHHHHhhcc
Confidence            999999999999999977  78888888644443  66667777788899988888888887

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

Probab=100.00  E-value=1.1e-35  Score=316.68  Aligned_cols=298  Identities=17%  Similarity=0.162  Sum_probs=222.9

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      |..++++   |++      +|+.++.|+|+++.+|||+|||+||++|++..      +..+|||+|+++|+.++...+..
T Consensus       458 ~~sFRp~---Q~e------aI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~------~GiTLVISPLiSLmqDQV~~L~~  522 (1195)
T PLN03137        458 NHSFRPN---QRE------IINATMSGYDVFVLMPTGGGKSLTYQLPALIC------PGITLVISPLVSLIQDQIMNLLQ  522 (1195)
T ss_pred             CCCCCHH---HHH------HHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc------CCcEEEEeCHHHHHHHHHHHHHh
Confidence            7778888   999      99999999999999999999999999999864      34799999999999865555544


Q ss_pred             hhccCCCceEEEEEcCcccHHhHHHHhc-----CCCcEEEEcHHHHHH---HHHC--CCCcCCCeeEEEecchhHHHhh-
Q psy1548         203 FSKYMSNIKVGVFFGGLPIQKDEEYLKT-----HNPQIVVGTPGRILA---LVRN--KKLNLSLLKHFILDECDKMLEQ-  271 (448)
Q Consensus       203 ~~~~~~~~~v~~~~g~~~~~~~~~~l~~-----~~~~IlV~Tp~~l~~---~l~~--~~~~~~~i~~lViDEah~l~~~-  271 (448)
                      .     ++++..+.++.....+...+..     +.++|+|+||+++..   ++..  .......+.+|||||||++++| 
T Consensus       523 ~-----GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~LslIVIDEAHcVSqWG  597 (1195)
T PLN03137        523 A-----NIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARFVIDEAHCVSQWG  597 (1195)
T ss_pred             C-----CCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhccccceeccCcchhhhhcc
Confidence            2     7888899998887666554432     568999999999852   2221  1112345889999999999998 


Q ss_pred             hhhHHHHHHH--HHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcch-HHHHHHHH
Q psy1548         272 LEMRRDVQEI--FRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENE-KNKKLFEL  348 (448)
Q Consensus       272 ~~~~~~~~~i--~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~-k~~~L~~l  348 (448)
                      ++|++.+..+  ++...+..|++++|||++..+...+...+.....+.....  ...+++...  .+.... ....+..+
T Consensus       598 hDFRpdYr~L~~Lr~~fp~vPilALTATAT~~V~eDI~~~L~l~~~~vfr~S--f~RpNL~y~--Vv~k~kk~le~L~~~  673 (1195)
T PLN03137        598 HDFRPDYQGLGILKQKFPNIPVLALTATATASVKEDVVQALGLVNCVVFRQS--FNRPNLWYS--VVPKTKKCLEDIDKF  673 (1195)
T ss_pred             cchHHHHHHHHHHHHhCCCCCeEEEEecCCHHHHHHHHHHcCCCCcEEeecc--cCccceEEE--EeccchhHHHHHHHH
Confidence            3488888764  4444457889999999999888766655542222211111  223344322  222222 24556666


Q ss_pred             HhhC-CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHH
Q psy1548         349 LDVL-EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDR  427 (448)
Q Consensus       349 l~~~-~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~  427 (448)
                      +... ...+.||||+|++.|+.++..|++.|+.+..|||+|++++|..++++|++|+  +.|+++|....+++  ++.+.
T Consensus       674 I~~~~~~esgIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F~~Ge--i~VLVATdAFGMGI--DkPDV  749 (1195)
T PLN03137        674 IKENHFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDE--INIICATVAFGMGI--NKPDV  749 (1195)
T ss_pred             HHhcccCCCceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHHhcCC--CcEEEEechhhcCC--CccCC
Confidence            6543 3568999999999999999999999999999999999999999999999988  57778887643433  44444


Q ss_pred             hcCCCCCCCccccccccccCC
Q psy1548         428 FDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       428 ~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      --|-...+|.+++.+.++.||
T Consensus       750 R~VIHydlPkSiEsYyQriGR  770 (1195)
T PLN03137        750 RFVIHHSLPKSIEGYHQECGR  770 (1195)
T ss_pred             cEEEEcCCCCCHHHHHhhhcc
Confidence            446678889999999999998

>PRK13767 ATP-dependent helicase; Provisional

Probab=100.00  E-value=4.5e-35  Score=318.53  Aligned_cols=318  Identities=19%  Similarity=0.231  Sum_probs=226.7

Q ss_pred             CCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHH
Q psy1548          87 LKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVF  166 (448)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~  166 (448)
                      +++.+.+|+.+ +                       |..|+++   |.+      +||.++.|+|++++||||||||++|
T Consensus        18 l~~~v~~~~~~-~-----------------------~~~~tpi---Q~~------Ai~~il~g~nvli~APTGSGKTlaa   64 (876)
T PRK13767         18 LRPYVREWFKE-K-----------------------FGTFTPP---QRY------AIPLIHEGKNVLISSPTGSGKTLAA   64 (876)
T ss_pred             cCHHHHHHHHH-c-----------------------cCCCCHH---HHH------HHHHHHcCCCEEEECCCCCcHHHHH
Confidence            56777777665 6                       8889999   999      9999999999999999999999999


Q ss_pred             HHHHHHhhhcc------CCCeEEEEeeccHHHHHHHHHHHHH-------hh----ccCCCceEEEEEcCcccHHhHHHHh
Q psy1548         167 VLATLQQLETT------DSNVYVLVMCHTRELAFQISKEYER-------FS----KYMSNIKVGVFFGGLPIQKDEEYLK  229 (448)
Q Consensus       167 ~l~~l~~l~~~------~~~~~~lil~Pt~~L~~q~~~~~~~-------~~----~~~~~~~v~~~~g~~~~~~~~~~l~  229 (448)
                      .+|+++.+...      ..+.++||++|+++|+.|+++.+..       +.    ...+++++...+|+.+.......+.
T Consensus        65 ~Lpil~~l~~~~~~~~~~~~~~~LyIsPtraLa~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l~  144 (876)
T PRK13767         65 FLAIIDELFRLGREGELEDKVYCLYVSPLRALNNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLK  144 (876)
T ss_pred             HHHHHHHHHhhccccCCCCCeEEEEEcCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHHh
Confidence            99999887532      2457899999999999999876552       22    2333678899999988666655555


Q ss_pred             cCCCcEEEEcHHHHHHHHHCCCC--cCCCeeEEEecchhHHHhhhhhHHHHH----HHHHhCCCCCeEEEEeccCCccHH
Q psy1548         230 THNPQIVVGTPGRILALVRNKKL--NLSLLKHFILDECDKMLEQLEMRRDVQ----EIFRSSPHTKQVMMFSATLSKEIR  303 (448)
Q Consensus       230 ~~~~~IlV~Tp~~l~~~l~~~~~--~~~~i~~lViDEah~l~~~~~~~~~~~----~i~~~l~~~~q~i~~SAT~~~~~~  303 (448)
                      + +++|+|+||+++..++....+  .++++++||+||+|.+.+. .+...+.    .+....+...|++++|||+++. .
T Consensus       145 ~-~p~IlVtTPE~L~~ll~~~~~~~~l~~l~~VVIDE~H~l~~~-~RG~~l~~~L~rL~~l~~~~~q~IglSATl~~~-~  221 (876)
T PRK13767        145 K-PPHILITTPESLAILLNSPKFREKLRTVKWVIVDEIHSLAEN-KRGVHLSLSLERLEELAGGEFVRIGLSATIEPL-E  221 (876)
T ss_pred             C-CCCEEEecHHHHHHHhcChhHHHHHhcCCEEEEechhhhccC-ccHHHHHHHHHHHHHhcCCCCeEEEEecccCCH-H
Confidence            4 489999999999888866543  4789999999999999865 4444433    3444444678999999999763 3


Q ss_pred             HHHHHhcC-------CCeEEEEcCcccccccceeEE-----EEEcCcch----HHHHHHHHHhhCCCCeEEEEECccHHH
Q psy1548         304 PVCKKFMH-------DPMEVYVDDEAKLTLHGLQQH-----YVKLKENE----KNKKLFELLDVLEFNQVVIFVKSVTRC  367 (448)
Q Consensus       304 ~~~~~~l~-------~~~~i~~~~~~~~~~~~i~~~-----~~~~~~~~----k~~~L~~ll~~~~~~~~IIF~~s~~~a  367 (448)
                      ++..++..       .+..+. ... ......+...     ........    ....+..+++.  ++++||||||+..|
T Consensus       222 ~va~~L~~~~~~~~~r~~~iv-~~~-~~k~~~i~v~~p~~~l~~~~~~~~~~~l~~~L~~~i~~--~~~~LVF~nTr~~a  297 (876)
T PRK13767        222 EVAKFLVGYEDDGEPRDCEIV-DAR-FVKPFDIKVISPVDDLIHTPAEEISEALYETLHELIKE--HRTTLIFTNTRSGA  297 (876)
T ss_pred             HHHHHhcCccccCCCCceEEE-ccC-CCccceEEEeccCccccccccchhHHHHHHHHHHHHhc--CCCEEEEeCCHHHH
Confidence            44443322       122221 111 0001111110     00111111    22334444433  56899999999999


Q ss_pred             HHHHHHHHhC------CCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccc
Q psy1548         368 IALSTLLSEQ------NFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDL  441 (448)
Q Consensus       368 ~~l~~~L~~~------g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~  441 (448)
                      +.++..|++.      +..+.++||+|++++|..+++.|++|+  +.+.+||+.-+.++  +|.+.--+-....|.+...
T Consensus       298 e~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~--i~vLVaTs~Le~GI--Dip~Vd~VI~~~~P~sv~~  373 (876)
T PRK13767        298 ERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGE--LKVVVSSTSLELGI--DIGYIDLVVLLGSPKSVSR  373 (876)
T ss_pred             HHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCC--CeEEEECChHHhcC--CCCCCcEEEEeCCCCCHHH
Confidence            9999999873      467999999999999999999999998  57888887644443  3433333444567888888


Q ss_pred             cccccCC
Q psy1548         442 STYIEGR  448 (448)
Q Consensus       442 ~~~~~~~  448 (448)
                      +.++.||
T Consensus       374 ylQRiGR  380 (876)
T PRK13767        374 LLQRIGR  380 (876)
T ss_pred             HHHhccc
Confidence            8888887

>PRK02362 ski2-like helicase; Provisional

Probab=100.00  E-value=6.3e-35  Score=314.20  Aligned_cols=318  Identities=19%  Similarity=0.237  Sum_probs=229.0

Q ss_pred             CcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccccee-eeeCcceeeeccCC
Q psy1548          81 GFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK-AVLGMDILCQAKSG  159 (448)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~-~~~g~~vli~apTG  159 (448)
                      .|+++++++.+++++.+.|                       +..|+++   |.+      +++. +..|+|+++++|||
T Consensus         2 ~~~~l~lp~~~~~~l~~~g-----------------------~~~l~p~---Q~~------ai~~~~~~g~nvlv~APTG   49 (737)
T PRK02362          2 KIAELPLPEGVIEFYEAEG-----------------------IEELYPP---QAE------AVEAGLLDGKNLLAAIPTA   49 (737)
T ss_pred             ChhhcCCCHHHHHHHHhCC-----------------------CCcCCHH---HHH------HHHHHHhCCCcEEEECCCc
Confidence            5889999999999999999                       9999999   999      9987 77899999999999


Q ss_pred             ChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEc
Q psy1548         160 MGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGT  239 (448)
Q Consensus       160 sGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~T  239 (448)
                      ||||++|.+|++..+..   +.+++|++|+++|+.|+++.++.+.. + ++++..++|+......  .+  +.++|+|+|
T Consensus        50 SGKTlia~lail~~l~~---~~kal~i~P~raLa~q~~~~~~~~~~-~-g~~v~~~tGd~~~~~~--~l--~~~~IiV~T  120 (737)
T PRK02362         50 SGKTLIAELAMLKAIAR---GGKALYIVPLRALASEKFEEFERFEE-L-GVRVGISTGDYDSRDE--WL--GDNDIIVAT  120 (737)
T ss_pred             chHHHHHHHHHHHHHhc---CCcEEEEeChHHHHHHHHHHHHHhhc-C-CCEEEEEeCCcCcccc--cc--CCCCEEEEC
Confidence            99999999999998853   45899999999999999999998754 3 7899999998754332  12  237999999


Q ss_pred             HHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHh---CCCCCeEEEEeccCCccHHHHHHHhcCC----
Q psy1548         240 PGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRS---SPHTKQVMMFSATLSKEIRPVCKKFMHD----  312 (448)
Q Consensus       240 p~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~---l~~~~q~i~~SAT~~~~~~~~~~~~l~~----  312 (448)
                      |+++..++++...++++++++|+||+|.+.+. +++..++.++..   .++..|++++|||+++. .++..++...    
T Consensus       121 pek~~~llr~~~~~l~~v~lvViDE~H~l~d~-~rg~~le~il~rl~~~~~~~qii~lSATl~n~-~~la~wl~~~~~~~  198 (737)
T PRK02362        121 SEKVDSLLRNGAPWLDDITCVVVDEVHLIDSA-NRGPTLEVTLAKLRRLNPDLQVVALSATIGNA-DELADWLDAELVDS  198 (737)
T ss_pred             HHHHHHHHhcChhhhhhcCEEEEECccccCCC-cchHHHHHHHHHHHhcCCCCcEEEEcccCCCH-HHHHHHhCCCcccC
Confidence            99999999877677899999999999999876 777777766544   45678999999999763 4444443221    


Q ss_pred             ---CeEEE--EcCcccccccceeEEEEEcCc-chHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCC--------
Q psy1548         313 ---PMEVY--VDDEAKLTLHGLQQHYVKLKE-NEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQN--------  378 (448)
Q Consensus       313 ---~~~i~--~~~~~~~~~~~i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g--------  378 (448)
                         |+.+.  +.......... .+..+.... ......+.+.+.  .++++||||+|++.|+.++..|.+..        
T Consensus       199 ~~rpv~l~~~v~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~--~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~  275 (737)
T PRK02362        199 EWRPIDLREGVFYGGAIHFDD-SQREVEVPSKDDTLNLVLDTLE--EGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAE  275 (737)
T ss_pred             CCCCCCCeeeEecCCeecccc-ccccCCCccchHHHHHHHHHHH--cCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHH
Confidence               11111  00000000000 011111111 223333444333  46799999999999999998886431        


Q ss_pred             ----------------------------CcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHH---
Q psy1548         379 ----------------------------FPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDR---  427 (448)
Q Consensus       379 ----------------------------~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~---  427 (448)
                                                  ..+.++||+|++++|..+++.|++|.  +.|+++|+.-..++  ++...   
T Consensus       276 ~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gva~hHagl~~~eR~~ve~~Fr~G~--i~VLvaT~tla~Gv--nlPa~~VV  351 (737)
T PRK02362        276 RAELAELAEEIREVSDTETSKDLADCVAKGAAFHHAGLSREHRELVEDAFRDRL--IKVISSTPTLAAGL--NLPARRVI  351 (737)
T ss_pred             HHHHHHHHHHHHhccCccccHHHHHHHHhCEEeecCCCCHHHHHHHHHHHHcCC--CeEEEechhhhhhc--CCCceEEE
Confidence                                        35889999999999999999999988  67777777533332  11111   


Q ss_pred             ------hcCCCCCCCccccccccccCC
Q psy1548         428 ------FDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       428 ------~~~~~~~~p~~~~~~~~~~~~  448 (448)
                            |+-.....|-....+.+|.||
T Consensus       352 I~~~~~yd~~~g~~~~s~~~y~Qm~GR  378 (737)
T PRK02362        352 IRDYRRYDGGAGMQPIPVLEYHQMAGR  378 (737)
T ss_pred             EecceeecCCCCceeCCHHHHHHHhhc
Confidence                  111111235555567788887

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

Probab=100.00  E-value=1.5e-34  Score=303.63  Aligned_cols=298  Identities=17%  Similarity=0.229  Sum_probs=221.5

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCc-ceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEE-eeccHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGM-DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLV-MCHTRELAFQISKEY  200 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~-~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~li-l~Pt~~L~~q~~~~~  200 (448)
                      |. |+++   |.+      ++|.++.|+ ++++++|||||||.++.++++.. ......++.|+ ++|||+|+.|+++.+
T Consensus        14 ~~-Ptpi---Q~~------~i~~il~G~~~v~~~apTGSGKTaa~aafll~~-~~~~~~~~rLv~~vPtReLa~Qi~~~~   82 (844)
T TIGR02621        14 YS-PFPW---QLS------LAERFVAGQPPESCSTPTGLGKTSIIAAWLLAV-EIGAKVPRRLVYVVNRRTVVDQVTEEA   82 (844)
T ss_pred             CC-CCHH---HHH------HHHHHHcCCCcceEecCCCCcccHHHHHhhccc-cccccccceEEEeCchHHHHHHHHHHH
Confidence            76 9998   999      999999998 68888999999999776555532 23333445555 679999999999999


Q ss_pred             HHhhccCC----------------------CceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCC------
Q psy1548         201 ERFSKYMS----------------------NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKL------  252 (448)
Q Consensus       201 ~~~~~~~~----------------------~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~------  252 (448)
                      +++++.++                      ++++..++||.+...+...+..+ ++|+|+|++.    +.++.+      
T Consensus        83 ~~~~k~l~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~-p~IIVgT~D~----i~sr~L~~gYg~  157 (844)
T TIGR02621        83 EKIGERLPDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHR-PAVIVGTVDM----IGSRLLFSGYGC  157 (844)
T ss_pred             HHHHHHhcccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCC-CcEEEECHHH----HcCCcccccccc
Confidence            99998652                      38899999999999998888775 8999999654    444443      


Q ss_pred             ----------cCCCeeEEEecchhHHHhhhhhHHHHHHHHHhC--CCC---CeEEEEeccCCccHHHHHHHhcCCCeEEE
Q psy1548         253 ----------NLSLLKHFILDECDKMLEQLEMRRDVQEIFRSS--PHT---KQVMMFSATLSKEIRPVCKKFMHDPMEVY  317 (448)
Q Consensus       253 ----------~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l--~~~---~q~i~~SAT~~~~~~~~~~~~l~~~~~i~  317 (448)
                                .+++++++|+||||  ++. +|...+..|++.+  ++.   .|+++||||++.++.++...++.++..+.
T Consensus       158 ~~~~~pi~ag~L~~v~~LVLDEAD--Ld~-gF~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~~l~~~~~~~p~~i~  234 (844)
T TIGR02621       158 GFKSRPLHAGFLGQDALIVHDEAH--LEP-AFQELLKQIMNEQQRPPDFLPLRVVELTATSRTDGPDRTTLLSAEDYKHP  234 (844)
T ss_pred             ccccccchhhhhccceEEEEehhh--hcc-ccHHHHHHHHHhcccCcccccceEEEEecCCCccHHHHHHHHccCCceee
Confidence                      26889999999999  565 8999999999965  432   69999999999998888888888887666


Q ss_pred             EcCcccccccceeEEEEEcCcchHHHHHHHHH---hhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHH
Q psy1548         318 VDDEAKLTLHGLQQHYVKLKENEKNKKLFELL---DVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERL  394 (448)
Q Consensus       318 ~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll---~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~  394 (448)
                      +... .....++.++ +.++...|...+...+   ....++++||||||++.|+.+++.|++.++  ..+||+|++.+|.
T Consensus       235 V~~~-~l~a~ki~q~-v~v~~e~Kl~~lv~~L~~ll~e~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~q~dR~  310 (844)
T TIGR02621       235 VLKK-RLAAKKIVKL-VPPSDEKFLSTMVKELNLLMKDSGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLRGAERD  310 (844)
T ss_pred             cccc-cccccceEEE-EecChHHHHHHHHHHHHHHHhhCCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCCHHHHh
Confidence            5443 4445566664 3444444544433322   123457899999999999999999999887  8999999999999


Q ss_pred             -----HHHHHHhc----CC-----CceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         395 -----KKYQEFKD----FH-----KGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       395 -----~~l~~F~~----g~-----~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                           +++++|++    |+     .|..|+++|+--++++  +|..  +.-+.++. .++.+.++.||
T Consensus       311 ~~~~~~il~~Fk~~~~~g~~~~~~~g~~ILVATdVaerGL--DId~--d~VI~d~a-P~esyIQRiGR  373 (844)
T TIGR02621       311 DLVKKEIFNRFLPQMLSGSRARPQQGTVYLVCTSAGEVGV--NISA--DHLVCDLA-PFESMQQRFGR  373 (844)
T ss_pred             hHHHHHHHHHHhccccccccccccccceEEeccchhhhcc--cCCc--ceEEECCC-CHHHHHHHhcc
Confidence                 88999987    43     3456777776433333  3321  22222221 14566777776

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.

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

Probab=100.00  E-value=6.1e-34  Score=297.57  Aligned_cols=285  Identities=20%  Similarity=0.244  Sum_probs=225.1

Q ss_pred             CCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHH
Q psy1548          87 LKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVF  166 (448)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~  166 (448)
                      +++.+.+|+...                        |..|++.   |.+      +||.+.+|+|+|+.||||||||+++
T Consensus         8 l~~~v~~~~~~~------------------------~~~~t~~---Q~~------a~~~i~~G~nvLiiAPTGsGKTeAA   54 (814)
T COG1201           8 LDPRVREWFKRK------------------------FTSLTPP---QRY------AIPEIHSGENVLIIAPTGSGKTEAA   54 (814)
T ss_pred             cCHHHHHHHHHh------------------------cCCCCHH---HHH------HHHHHhCCCceEEEcCCCCChHHHH
Confidence            678888888775                        7899999   999      9999999999999999999999999


Q ss_pred             HHHHHHhhhcc-----CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHH
Q psy1548         167 VLATLQQLETT-----DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPG  241 (448)
Q Consensus       167 ~l~~l~~l~~~-----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~  241 (448)
                      .+|+++.+...     ..+..+|||+|.++|.+++.+.++.+...+ ++.+.+.+|+++..+..... ..+|||+|+||+
T Consensus        55 fLpil~~l~~~~~~~~~~~i~~lYIsPLkALn~Di~~rL~~~~~~~-G~~v~vRhGDT~~~er~r~~-~~PPdILiTTPE  132 (814)
T COG1201          55 FLPVINELLSLGKGKLEDGIYALYISPLKALNNDIRRRLEEPLREL-GIEVAVRHGDTPQSEKQKML-KNPPHILITTPE  132 (814)
T ss_pred             HHHHHHHHHhccCCCCCCceEEEEeCcHHHHHHHHHHHHHHHHHHc-CCccceecCCCChHHhhhcc-CCCCcEEEeChh
Confidence            99999988665     346899999999999999999999999998 99999999999866554444 447999999999


Q ss_pred             HHHHHHHCCCC--cCCCeeEEEecchhHHHhhhhhHHHHH----HHHHhCCCCCeEEEEeccCCccHHHHHHHhcCC--C
Q psy1548         242 RILALVRNKKL--NLSLLKHFILDECDKMLEQLEMRRDVQ----EIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHD--P  313 (448)
Q Consensus       242 ~l~~~l~~~~~--~~~~i~~lViDEah~l~~~~~~~~~~~----~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~--~  313 (448)
                      .|.-++....+  .+.+++++|+||+|.+.+. ..+.++.    .+....+ +.|.|++|||..+ ..+..+++...  +
T Consensus       133 sL~lll~~~~~r~~l~~vr~VIVDEiHel~~s-KRG~~Lsl~LeRL~~l~~-~~qRIGLSATV~~-~~~varfL~g~~~~  209 (814)
T COG1201         133 SLAILLNSPKFRELLRDVRYVIVDEIHALAES-KRGVQLALSLERLRELAG-DFQRIGLSATVGP-PEEVAKFLVGFGDP  209 (814)
T ss_pred             HHHHHhcCHHHHHHhcCCcEEEeehhhhhhcc-ccchhhhhhHHHHHhhCc-ccEEEeehhccCC-HHHHHHHhcCCCCc
Confidence            99988876433  4799999999999999876 5444444    3333334 8899999999974 45666665554  3


Q ss_pred             eEEEEcCcccccccceeEEEEEcCc---------chHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCC-CcEEE
Q psy1548         314 MEVYVDDEAKLTLHGLQQHYVKLKE---------NEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQN-FPAVS  383 (448)
Q Consensus       314 ~~i~~~~~~~~~~~~i~~~~~~~~~---------~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g-~~~~~  383 (448)
                      ..|......    ............         ..-...+.++++.+.  .+|||+||+..|+.++..|++.+ .++..
T Consensus       210 ~~Iv~~~~~----k~~~i~v~~p~~~~~~~~~~~~~~~~~i~~~v~~~~--ttLIF~NTR~~aE~l~~~L~~~~~~~i~~  283 (814)
T COG1201         210 CEIVDVSAA----KKLEIKVISPVEDLIYDEELWAALYERIAELVKKHR--TTLIFTNTRSGAERLAFRLKKLGPDIIEV  283 (814)
T ss_pred             eEEEEcccC----CcceEEEEecCCccccccchhHHHHHHHHHHHhhcC--cEEEEEeChHHHHHHHHHHHHhcCCceee
Confidence            444332221    122222222221         124556666776654  89999999999999999999986 89999


Q ss_pred             EeCCCCHHHHHHHHHHHhcCCCceEEEEecChhh
Q psy1548         384 IHRGMTQEERLKKYQEFKDFHKGLAITFASDEND  417 (448)
Q Consensus       384 lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d  417 (448)
                      +||.++.+.|..+.++|++|+  +...+||+.-+
T Consensus       284 HHgSlSre~R~~vE~~lk~G~--lravV~TSSLE  315 (814)
T COG1201         284 HHGSLSRELRLEVEERLKEGE--LKAVVATSSLE  315 (814)
T ss_pred             ecccccHHHHHHHHHHHhcCC--ceEEEEccchh
Confidence            999999999999999999998  67777777533

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=100.00  E-value=4.7e-34  Score=300.38  Aligned_cols=296  Identities=16%  Similarity=0.153  Sum_probs=221.4

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      |..|+++   |++      +++.++.|+|+++.+|||+|||++|++|++..      ...+||++|+++|+.|+.+.++.
T Consensus        23 ~~~~r~~---Q~~------ai~~il~g~dvlv~apTGsGKTl~y~lpal~~------~g~tlVisPl~sL~~dqv~~l~~   87 (607)
T PRK11057         23 YQQFRPG---QQE------IIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL------DGLTLVVSPLISLMKDQVDQLLA   87 (607)
T ss_pred             CCCCCHH---HHH------HHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc------CCCEEEEecHHHHHHHHHHHHHH
Confidence            8888888   999      99999999999999999999999999999864      23799999999999998888876


Q ss_pred             hhccCCCceEEEEEcCcccHHhH---HHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhh-hhhHHHH
Q psy1548         203 FSKYMSNIKVGVFFGGLPIQKDE---EYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQ-LEMRRDV  278 (448)
Q Consensus       203 ~~~~~~~~~v~~~~g~~~~~~~~---~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~-~~~~~~~  278 (448)
                      +     ++.+..+.++.......   ..+..+..+++++||+++........+...+++++||||||++.+| .+|++.+
T Consensus        88 ~-----gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~~~l~~~~l~~iVIDEaH~i~~~G~~fr~~y  162 (607)
T PRK11057         88 N-----GVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLEHLAHWNPALLAVDEAHCISQWGHDFRPEY  162 (607)
T ss_pred             c-----CCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHHHHHhhCCCCEEEEeCccccccccCcccHHH
Confidence            4     56777777766544432   2344566899999999986422212233457899999999999987 2477776


Q ss_pred             HHHH--HhCCCCCeEEEEeccCCccHHHHHHHhc--CCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCC
Q psy1548         279 QEIF--RSSPHTKQVMMFSATLSKEIRPVCKKFM--HDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEF  354 (448)
Q Consensus       279 ~~i~--~~l~~~~q~i~~SAT~~~~~~~~~~~~l--~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~  354 (448)
                      ..+.  ....++.+++++|||+++.....+...+  .+|...... .   ..+++.  +..+....+...+..++....+
T Consensus       163 ~~L~~l~~~~p~~~~v~lTAT~~~~~~~di~~~l~l~~~~~~~~~-~---~r~nl~--~~v~~~~~~~~~l~~~l~~~~~  236 (607)
T PRK11057        163 AALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQISS-F---DRPNIR--YTLVEKFKPLDQLMRYVQEQRG  236 (607)
T ss_pred             HHHHHHHHhCCCCcEEEEecCCChhHHHHHHHHhCCCCeEEEECC-C---CCCcce--eeeeeccchHHHHHHHHHhcCC
Confidence            5542  2223578899999999988765544433  455443321 1   123332  2233344456667777777778


Q ss_pred             CeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCC
Q psy1548         355 NQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISE  434 (448)
Q Consensus       355 ~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~  434 (448)
                      +++||||+|+++|+.++..|++.|+.+..+||+|++++|.++++.|++|+  +.|.++|+...+++  ++.+.--+-..+
T Consensus       237 ~~~IIFc~tr~~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~--~~VLVaT~a~~~GI--Dip~V~~VI~~d  312 (607)
T PRK11057        237 KSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDD--LQIVVATVAFGMGI--NKPNVRFVVHFD  312 (607)
T ss_pred             CCEEEEECcHHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCC--CCEEEEechhhccC--CCCCcCEEEEeC
Confidence            89999999999999999999999999999999999999999999999987  56777777533332  333333344577


Q ss_pred             CCccccccccccCC
Q psy1548         435 LPDEIDLSTYIEGR  448 (448)
Q Consensus       435 ~p~~~~~~~~~~~~  448 (448)
                      +|.+++.+.++.||
T Consensus       313 ~P~s~~~y~Qr~GR  326 (607)
T PRK11057        313 IPRNIESYYQETGR  326 (607)
T ss_pred             CCCCHHHHHHHhhh
Confidence            78888888898887

>PRK00254 ski2-like helicase; Provisional

Probab=100.00  E-value=1.3e-33  Score=303.33  Aligned_cols=287  Identities=14%  Similarity=0.191  Sum_probs=220.6

Q ss_pred             CcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccccee-eeeCcceeeeccCC
Q psy1548          81 GFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK-AVLGMDILCQAKSG  159 (448)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~-~~~g~~vli~apTG  159 (448)
                      .|+++++++.+.+.+.+.|                       |..|+++   |.+      +++. ++.|+|+++++|||
T Consensus         2 ~~~~l~l~~~~~~~l~~~g-----------------------~~~l~~~---Q~~------ai~~~~~~g~nvlv~apTG   49 (720)
T PRK00254          2 KVDELRVDERIKRVLKERG-----------------------IEELYPP---QAE------ALKSGVLEGKNLVLAIPTA   49 (720)
T ss_pred             cHHHcCCCHHHHHHHHhCC-----------------------CCCCCHH---HHH------HHHHHHhCCCcEEEECCCC
Confidence            5788999999999999999                       9999999   999      9986 78899999999999


Q ss_pred             ChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEc
Q psy1548         160 MGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGT  239 (448)
Q Consensus       160 sGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~T  239 (448)
                      ||||++|.+|++..+...  +.++||++|+++|+.|+++.+..+.. + ++++..++|+.+....  .+  +.++|+|+|
T Consensus        50 sGKT~~~~l~il~~l~~~--~~~~l~l~P~~aLa~q~~~~~~~~~~-~-g~~v~~~~Gd~~~~~~--~~--~~~~IiV~T  121 (720)
T PRK00254         50 SGKTLVAEIVMVNKLLRE--GGKAVYLVPLKALAEEKYREFKDWEK-L-GLRVAMTTGDYDSTDE--WL--GKYDIIIAT  121 (720)
T ss_pred             cHHHHHHHHHHHHHHHhc--CCeEEEEeChHHHHHHHHHHHHHHhh-c-CCEEEEEeCCCCCchh--hh--ccCCEEEEc
Confidence            999999999999887543  45899999999999999999988753 4 7899999998764332  22  248999999


Q ss_pred             HHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEc
Q psy1548         240 PGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVD  319 (448)
Q Consensus       240 p~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~  319 (448)
                      |+++..+++....++++++++|+||+|.+.+. ++...+..++..++...|++++|||+++. .++..+ +..+.... .
T Consensus       122 pe~~~~ll~~~~~~l~~l~lvViDE~H~l~~~-~rg~~le~il~~l~~~~qiI~lSATl~n~-~~la~w-l~~~~~~~-~  197 (720)
T PRK00254        122 AEKFDSLLRHGSSWIKDVKLVVADEIHLIGSY-DRGATLEMILTHMLGRAQILGLSATVGNA-EELAEW-LNAELVVS-D  197 (720)
T ss_pred             HHHHHHHHhCCchhhhcCCEEEEcCcCccCCc-cchHHHHHHHHhcCcCCcEEEEEccCCCH-HHHHHH-hCCccccC-C
Confidence            99999999877777899999999999999887 88899999999998899999999999863 566554 33222111 0


Q ss_pred             Ccccccc-cc-eeEEEEEcCcc-------hHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhC-------------
Q psy1548         320 DEAKLTL-HG-LQQHYVKLKEN-------EKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQ-------------  377 (448)
Q Consensus       320 ~~~~~~~-~~-i~~~~~~~~~~-------~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~-------------  377 (448)
                      .. .... .. ..+.+......       .....+.+.+.  .++++||||+|++.|+.++..|.+.             
T Consensus       198 ~r-pv~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~--~~~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~  274 (720)
T PRK00254        198 WR-PVKLRKGVFYQGFLFWEDGKIERFPNSWESLVYDAVK--KGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRAL  274 (720)
T ss_pred             CC-CCcceeeEecCCeeeccCcchhcchHHHHHHHHHHHH--hCCCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHH
Confidence            00 0000 00 11111111111       11233444444  3678999999999999888766421             


Q ss_pred             --------------------CCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChh
Q psy1548         378 --------------------NFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDEN  416 (448)
Q Consensus       378 --------------------g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~  416 (448)
                                          ...+.++||+|++++|..+++.|++|.  +.|.++|+.-
T Consensus       275 ~~~~~~~~~~~~~~~L~~~l~~gv~~hHagl~~~eR~~ve~~F~~G~--i~VLvaT~tL  331 (720)
T PRK00254        275 KELADSLEENPTNEKLKKALRGGVAFHHAGLGRTERVLIEDAFREGL--IKVITATPTL  331 (720)
T ss_pred             HHHHHHHhcCCCcHHHHHHHhhCEEEeCCCCCHHHHHHHHHHHHCCC--CeEEEeCcHH
Confidence                                235899999999999999999999987  6777777753

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=100.00  E-value=2.5e-34  Score=302.95  Aligned_cols=297  Identities=17%  Similarity=0.217  Sum_probs=228.6

Q ss_pred             eeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHH
Q psy1548         121 FNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEY  200 (448)
Q Consensus       121 ~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~  200 (448)
                      |+|..++++   |.+      +++.++.|+|+++++|||+|||++|++|++..      +..++|++|+++|+.|+.+.+
T Consensus         9 fg~~~fr~~---Q~~------~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~------~g~~lVisPl~sL~~dq~~~l   73 (591)
T TIGR01389         9 FGYDDFRPG---QEE------IISHVLDGRDVLVVMPTGGGKSLCYQVPALLL------KGLTVVISPLISLMKDQVDQL   73 (591)
T ss_pred             cCCCCCCHH---HHH------HHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc------CCcEEEEcCCHHHHHHHHHHH
Confidence            448888888   999      99999999999999999999999999999853      236899999999999988888


Q ss_pred             HHhhccCCCceEEEEEcCcccHHhH---HHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhh-hhhHH
Q psy1548         201 ERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQ-LEMRR  276 (448)
Q Consensus       201 ~~~~~~~~~~~v~~~~g~~~~~~~~---~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~-~~~~~  276 (448)
                      +.+     ++.+..+.++.+.....   ..+..+..+|+++||+++........+...++++|||||||++.+| .+|++
T Consensus        74 ~~~-----gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~~l~~~~l~~iViDEaH~i~~~g~~frp  148 (591)
T TIGR01389        74 RAA-----GVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLNMLQRIPIALVAVDEAHCVSQWGHDFRP  148 (591)
T ss_pred             HHc-----CCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHHHHhcCCCCEEEEeCCcccccccCccHH
Confidence            774     67777888877655433   2345566899999999986543333344678899999999999887 34888


Q ss_pred             HHHHHHH---hCCCCCeEEEEeccCCccHHHHHHHhcC--CCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhh
Q psy1548         277 DVQEIFR---SSPHTKQVMMFSATLSKEIRPVCKKFMH--DPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDV  351 (448)
Q Consensus       277 ~~~~i~~---~l~~~~q~i~~SAT~~~~~~~~~~~~l~--~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~  351 (448)
                      .+..+..   .++ ..+++++|||++..+...+...+.  ++..+.. .   ....++.  +.......+...+.+++..
T Consensus       149 ~y~~l~~l~~~~~-~~~vi~lTAT~~~~~~~~i~~~l~~~~~~~~~~-~---~~r~nl~--~~v~~~~~~~~~l~~~l~~  221 (591)
T TIGR01389       149 EYQRLGSLAERFP-QVPRIALTATADAETRQDIRELLRLADANEFIT-S---FDRPNLR--FSVVKKNNKQKFLLDYLKK  221 (591)
T ss_pred             HHHHHHHHHHhCC-CCCEEEEEeCCCHHHHHHHHHHcCCCCCCeEec-C---CCCCCcE--EEEEeCCCHHHHHHHHHHh
Confidence            7776643   343 456999999999988776666654  3333321 1   1223332  2233345567778888887


Q ss_pred             CCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCC
Q psy1548         352 LEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVS  431 (448)
Q Consensus       352 ~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~  431 (448)
                      ..+.++||||+|++.|+.+++.|...|+++..+||+|++++|..+++.|++|+  +.|.++|....+++  ++.+.--+-
T Consensus       222 ~~~~~~IIf~~sr~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F~~g~--~~vlVaT~a~~~GI--D~p~v~~VI  297 (591)
T TIGR01389       222 HRGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDD--VKVMVATNAFGMGI--DKPNVRFVI  297 (591)
T ss_pred             cCCCCEEEEECcHHHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHHHcCC--CcEEEEechhhccC--cCCCCCEEE
Confidence            77789999999999999999999999999999999999999999999999987  67888887643333  333333455


Q ss_pred             CCCCCccccccccccCC
Q psy1548         432 ISELPDEIDLSTYIEGR  448 (448)
Q Consensus       432 ~~~~p~~~~~~~~~~~~  448 (448)
                      ...+|.+++.+.++.||
T Consensus       298 ~~~~p~s~~~y~Q~~GR  314 (591)
T TIGR01389       298 HYDMPGNLESYYQEAGR  314 (591)
T ss_pred             EcCCCCCHHHHhhhhcc
Confidence            67789999999999988

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.

>PRK09401 reverse gyrase; Reviewed

Probab=100.00  E-value=6.1e-32  Score=298.00  Aligned_cols=259  Identities=20%  Similarity=0.262  Sum_probs=202.9

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .|+++   |+.      ++|.++.|+|++++||||+|||+ |.++++..+..  .+.+++||+||++|+.|+.+.++.++
T Consensus        80 ~pt~i---Q~~------~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~--~g~~alIL~PTreLa~Qi~~~l~~l~  147 (1176)
T PRK09401         80 KPWSL---QRT------WAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAK--KGKKSYIIFPTRLLVEQVVEKLEKFG  147 (1176)
T ss_pred             CCcHH---HHH------HHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHh--cCCeEEEEeccHHHHHHHHHHHHHHh
Confidence            78888   999      99999999999999999999996 55555554433  36689999999999999999999999


Q ss_pred             ccCCCceEEEEEcCccc-----HHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhh--------
Q psy1548         205 KYMSNIKVGVFFGGLPI-----QKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQ--------  271 (448)
Q Consensus       205 ~~~~~~~v~~~~g~~~~-----~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~--------  271 (448)
                      ... ++.+..++|+...     ......+..+.++|+|+||++|.+.+.  .+...+++++|+||||+|+++        
T Consensus       148 ~~~-~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~--~l~~~~~~~lVvDEaD~~L~~~k~id~~l  224 (1176)
T PRK09401        148 EKV-GCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFD--ELPKKKFDFVFVDDVDAVLKSSKNIDKLL  224 (1176)
T ss_pred             hhc-CceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHH--hccccccCEEEEEChHHhhhcccchhhHH
Confidence            877 7888777776542     223344555669999999999998876  455667999999999999863        


Q ss_pred             --hhhH-HHHHHHHHhCCC------------------------CCeEEEEeccCCcc-HHHHHHHhcCCCeEEEEcCccc
Q psy1548         272 --LEMR-RDVQEIFRSSPH------------------------TKQVMMFSATLSKE-IRPVCKKFMHDPMEVYVDDEAK  323 (448)
Q Consensus       272 --~~~~-~~~~~i~~~l~~------------------------~~q~i~~SAT~~~~-~~~~~~~~l~~~~~i~~~~~~~  323 (448)
                        .||. .++..++..++.                        ..|++++|||+++. +..   .++.++..+.+... .
T Consensus       225 ~~lGF~~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~~~~~---~l~~~ll~~~v~~~-~  300 (1176)
T PRK09401        225 YLLGFSEEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRV---KLFRELLGFEVGSP-V  300 (1176)
T ss_pred             HhCCCCHHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCccchHH---HHhhccceEEecCc-c
Confidence              2674 677777777654                        67999999999875 332   22344444555444 3


Q ss_pred             ccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHH---HHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHH
Q psy1548         324 LTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTR---CIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEF  400 (448)
Q Consensus       324 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~---a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F  400 (448)
                      ....++.+.|+.++  +|...|..+++... .++||||+++..   |+.+++.|++.|+++..+||+|     .+.+++|
T Consensus       301 ~~~rnI~~~yi~~~--~k~~~L~~ll~~l~-~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l-----~~~l~~F  372 (1176)
T PRK09401        301 FYLRNIVDSYIVDE--DSVEKLVELVKRLG-DGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF-----ERKFEKF  372 (1176)
T ss_pred             cccCCceEEEEEcc--cHHHHHHHHHHhcC-CCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH-----HHHHHHH
Confidence            45678888888766  67778888887664 579999999887   9999999999999999999999     2346999


Q ss_pred             hcCCCceEEE
Q psy1548         401 KDFHKGLAIT  410 (448)
Q Consensus       401 ~~g~~g~~I~  410 (448)
                      ++|+..+.|.
T Consensus       373 ~~G~~~VLVa  382 (1176)
T PRK09401        373 EEGEVDVLVG  382 (1176)
T ss_pred             HCCCCCEEEE
Confidence            9999544444

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=100.00  E-value=2.1e-31  Score=294.72  Aligned_cols=285  Identities=19%  Similarity=0.216  Sum_probs=205.2

Q ss_pred             eeccCCChhHHHHHHHHHHhhhcc----------CCCeEEEEeeccHHHHHHHHHHHHHhh-----------ccCCCceE
Q psy1548         154 CQAKSGMGKTAVFVLATLQQLETT----------DSNVYVLVMCHTRELAFQISKEYERFS-----------KYMSNIKV  212 (448)
Q Consensus       154 i~apTGsGKT~~~~l~~l~~l~~~----------~~~~~~lil~Pt~~L~~q~~~~~~~~~-----------~~~~~~~v  212 (448)
                      |++|||||||++|.+|+++.+...          ..+.++|||+|+++|+.|+.+.++...           ....++++
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~~~~~~~~~~~~raLYISPLKALa~Dv~~~L~~pl~~i~~~~~~~g~~~~~i~V   80 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIPLKGIADERRRRGETEVNLRV   80 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccccccccccCCCCEEEEEeChHHHHHHHHHHHHHHHHhhhhhhhhcccccCceEE
Confidence            579999999999999999988543          235799999999999999999887521           11127899


Q ss_pred             EEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCC-CCcCCCeeEEEecchhHHHhhhh----hHHHHHHHHHhCCC
Q psy1548         213 GVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNK-KLNLSLLKHFILDECDKMLEQLE----MRRDVQEIFRSSPH  287 (448)
Q Consensus       213 ~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~-~~~~~~i~~lViDEah~l~~~~~----~~~~~~~i~~~l~~  287 (448)
                      ...+|+++..++...+.+ +++|+|+||++|..++.++ ...++++++|||||+|.+.+. .    +...+..+...++.
T Consensus        81 ~vrtGDt~~~eR~rll~~-ppdILVTTPEsL~~LLtsk~r~~L~~Vr~VIVDE~H~L~g~-kRG~~Lel~LeRL~~l~~~  158 (1490)
T PRK09751         81 GIRTGDTPAQERSKLTRN-PPDILITTPESLYLMLTSRARETLRGVETVIIDEVHAVAGS-KRGAHLALSLERLDALLHT  158 (1490)
T ss_pred             EEEECCCCHHHHHHHhcC-CCCEEEecHHHHHHHHhhhhhhhhccCCEEEEecHHHhccc-ccccHHHHHHHHHHHhCCC
Confidence            999999987766555554 5899999999999987654 346899999999999999864 3    34455666666777


Q ss_pred             CCeEEEEeccCCccHHHHHHHhcC-CCeEEEEcCcccccccceeEEEEEcCcchH--------------------H-HHH
Q psy1548         288 TKQVMMFSATLSKEIRPVCKKFMH-DPMEVYVDDEAKLTLHGLQQHYVKLKENEK--------------------N-KKL  345 (448)
Q Consensus       288 ~~q~i~~SAT~~~~~~~~~~~~l~-~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k--------------------~-~~L  345 (448)
                      +.|+|++|||+++ .+++++++.. .|..+.....  .....+... +......+                    . ...
T Consensus       159 ~~QrIgLSATI~n-~eevA~~L~g~~pv~Iv~~~~--~r~~~l~v~-vp~~d~~~~~~~~~~~~~~~~~~r~~~i~~~v~  234 (1490)
T PRK09751        159 SAQRIGLSATVRS-ASDVAAFLGGDRPVTVVNPPA--MRHPQIRIV-VPVANMDDVSSVASGTGEDSHAGREGSIWPYIE  234 (1490)
T ss_pred             CCeEEEEEeeCCC-HHHHHHHhcCCCCEEEECCCC--CcccceEEE-EecCchhhccccccccccccchhhhhhhhHHHH
Confidence            8999999999987 4566655443 3555533222  122223221 22111100                    0 011


Q ss_pred             HHHHhh-CCCCeEEEEECccHHHHHHHHHHHhCC---------------------------------CcEEEEeCCCCHH
Q psy1548         346 FELLDV-LEFNQVVIFVKSVTRCIALSTLLSEQN---------------------------------FPAVSIHRGMTQE  391 (448)
Q Consensus       346 ~~ll~~-~~~~~~IIF~~s~~~a~~l~~~L~~~g---------------------------------~~~~~lh~~~~~~  391 (448)
                      ..++.. ...+++||||||+..|+.++..|++..                                 +.+..+||+|+++
T Consensus       235 ~~il~~i~~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSke  314 (1490)
T PRK09751        235 TGILDEVLRHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKE  314 (1490)
T ss_pred             HHHHHHHhcCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHH
Confidence            122222 235789999999999999999997641                                 1257899999999


Q ss_pred             HHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         392 ERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       392 eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      +|..+++.|++|+  +.+.+||+.-+.++  +|...-.+...+.|.++..+.+|.||
T Consensus       315 eR~~IE~~fK~G~--LrvLVATssLELGI--DIg~VDlVIq~gsP~sVas~LQRiGR  367 (1490)
T PRK09751        315 QRAITEQALKSGE--LRCVVATSSLELGI--DMGAVDLVIQVATPLSVASGLQRIGR  367 (1490)
T ss_pred             HHHHHHHHHHhCC--ceEEEeCcHHHccC--CcccCCEEEEeCCCCCHHHHHHHhCC
Confidence            9999999999998  57888888654444  45555555556778888888999988

>PRK01172 ski2-like helicase; Provisional

Probab=100.00  E-value=1.6e-31  Score=285.76  Aligned_cols=283  Identities=15%  Similarity=0.205  Sum_probs=210.0

Q ss_pred             CcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCC
Q psy1548          81 GFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGM  160 (448)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGs  160 (448)
                      .|+++++++++++++.+.+                       |. ++++   |.+      +++.+..|+|+++++||||
T Consensus         2 ~~~~~~l~~~~~~~~~~~~-----------------------~~-l~~~---Q~~------ai~~l~~~~nvlv~apTGS   48 (674)
T PRK01172          2 KISDLGYDDEFLNLFTGND-----------------------FE-LYDH---QRM------AIEQLRKGENVIVSVPTAA   48 (674)
T ss_pred             cHhhcCCCHHHHHHHhhCC-----------------------CC-CCHH---HHH------HHHHHhcCCcEEEECCCCc
Confidence            5788999999999999888                       76 6777   999      9999999999999999999


Q ss_pred             hhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcH
Q psy1548         161 GKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTP  240 (448)
Q Consensus       161 GKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp  240 (448)
                      |||+++.++++..+..   +.+++|++|+++|+.|+++.++++.. . +.++...+|+......  .+ . .++|+|+||
T Consensus        49 GKTl~a~lail~~l~~---~~k~v~i~P~raLa~q~~~~~~~l~~-~-g~~v~~~~G~~~~~~~--~~-~-~~dIiv~Tp  119 (674)
T PRK01172         49 GKTLIAYSAIYETFLA---GLKSIYIVPLRSLAMEKYEELSRLRS-L-GMRVKISIGDYDDPPD--FI-K-RYDVVILTS  119 (674)
T ss_pred             hHHHHHHHHHHHHHHh---CCcEEEEechHHHHHHHHHHHHHHhh-c-CCeEEEEeCCCCCChh--hh-c-cCCEEEECH
Confidence            9999999999987754   34899999999999999999988753 3 7888888888654322  12 2 379999999


Q ss_pred             HHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHH---hCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEE
Q psy1548         241 GRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFR---SSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVY  317 (448)
Q Consensus       241 ~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~---~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~  317 (448)
                      +++..++.+....+.+++++|+||+|.+.+. ++...++.++.   ..++..|++++|||+++. .++.+++.....  .
T Consensus       120 ek~~~l~~~~~~~l~~v~lvViDEaH~l~d~-~rg~~le~ll~~~~~~~~~~riI~lSATl~n~-~~la~wl~~~~~--~  195 (674)
T PRK01172        120 EKADSLIHHDPYIINDVGLIVADEIHIIGDE-DRGPTLETVLSSARYVNPDARILALSATVSNA-NELAQWLNASLI--K  195 (674)
T ss_pred             HHHHHHHhCChhHHhhcCEEEEecchhccCC-CccHHHHHHHHHHHhcCcCCcEEEEeCccCCH-HHHHHHhCCCcc--C
Confidence            9999998887777899999999999998876 66666666544   456788999999999763 555554322211  0


Q ss_pred             EcCcccccccceeEEEE-----EcCcch-HHHHHHHHHhh--CCCCeEEEEECccHHHHHHHHHHHhC-----C------
Q psy1548         318 VDDEAKLTLHGLQQHYV-----KLKENE-KNKKLFELLDV--LEFNQVVIFVKSVTRCIALSTLLSEQ-----N------  378 (448)
Q Consensus       318 ~~~~~~~~~~~i~~~~~-----~~~~~~-k~~~L~~ll~~--~~~~~~IIF~~s~~~a~~l~~~L~~~-----g------  378 (448)
                        ..  ..+..+.....     ...... ....+..++..  ..++++||||++++.|+.++..|.+.     .      
T Consensus       196 --~~--~r~vpl~~~i~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~  271 (674)
T PRK01172        196 --SN--FRPVPLKLGILYRKRLILDGYERSQVDINSLIKETVNDGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSE  271 (674)
T ss_pred             --CC--CCCCCeEEEEEecCeeeecccccccccHHHHHHHHHhCCCcEEEEeccHHHHHHHHHHHHHhhhhccccccccc
Confidence              00  00111111110     111111 11112233322  24679999999999999999988653     1      


Q ss_pred             --------------CcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         379 --------------FPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       379 --------------~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                                    ..+.++||+|++++|..+++.|++|.  +.|.++|+.
T Consensus       272 ~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~~f~~g~--i~VLvaT~~  320 (674)
T PRK01172        272 NNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRY--IKVIVATPT  320 (674)
T ss_pred             ccccccHHHHHHHhcCEEEecCCCCHHHHHHHHHHHHcCC--CeEEEecch
Confidence                          24788999999999999999999987  577777764

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.98  E-value=8e-31  Score=282.89  Aligned_cols=263  Identities=17%  Similarity=0.133  Sum_probs=202.7

Q ss_pred             eeccCCCCchhhhhhhccccccceeeeeC------cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHH
Q psy1548         121 FNYDMPEDSDTYLHRVARAGRFGTKAVLG------MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAF  194 (448)
Q Consensus       121 ~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g------~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~  194 (448)
                      ++|. |++.   |+.      +++.++.+      +|++++||||+|||.+|++|++..+..   +.+++|++||++||.
T Consensus       448 ~~f~-~T~~---Q~~------aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~---g~qvlvLvPT~~LA~  514 (926)
T TIGR00580       448 FPFE-ETPD---QLK------AIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLD---GKQVAVLVPTTLLAQ  514 (926)
T ss_pred             CCCC-CCHH---HHH------HHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHh---CCeEEEEeCcHHHHH
Confidence            3464 7888   999      99998875      799999999999999999999988754   358999999999999


Q ss_pred             HHHHHHHHhhccCCCceEEEEEcCcccHHh---HHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhh
Q psy1548         195 QISKEYERFSKYMSNIKVGVFFGGLPIQKD---EEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQ  271 (448)
Q Consensus       195 q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~---~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~  271 (448)
                      |+++.++++...+ ++++..++|+.+..++   ...+..+.++|+||||..    + .+.+.+++++++||||+|++.. 
T Consensus       515 Q~~~~f~~~~~~~-~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~l----l-~~~v~f~~L~llVIDEahrfgv-  587 (926)
T TIGR00580       515 QHFETFKERFANF-PVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKL----L-QKDVKFKDLGLLIIDEEQRFGV-  587 (926)
T ss_pred             HHHHHHHHHhccC-CcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHH----h-hCCCCcccCCEEEeecccccch-
Confidence            9999999988877 7889889887764433   334556679999999943    2 3456789999999999997532 


Q ss_pred             hhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhh
Q psy1548         272 LEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDV  351 (448)
Q Consensus       272 ~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~  351 (448)
                           .....++.++.+.|+++||||+.+....+....+.++..+...+..   ...+..++...........+...+. 
T Consensus       588 -----~~~~~L~~~~~~~~vL~~SATpiprtl~~~l~g~~d~s~I~~~p~~---R~~V~t~v~~~~~~~i~~~i~~el~-  658 (926)
T TIGR00580       588 -----KQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPED---RLPVRTFVMEYDPELVREAIRRELL-  658 (926)
T ss_pred             -----hHHHHHHhcCCCCCEEEEecCCCHHHHHHHHhcCCCcEEEecCCCC---ccceEEEEEecCHHHHHHHHHHHHH-
Confidence                 2344556677789999999998777666666666677766654442   2235555443332211222222222 


Q ss_pred             CCCCeEEEEECccHHHHHHHHHHHhC--CCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         352 LEFNQVVIFVKSVTRCIALSTLLSEQ--NFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       352 ~~~~~~IIF~~s~~~a~~l~~~L~~~--g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                       .+++++||||+++.++.+++.|++.  ++++..+||+|++++|.+++++|++|+  ..|+++|+-
T Consensus       659 -~g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~Gk--~~ILVaT~i  721 (926)
T TIGR00580       659 -RGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGE--FQVLVCTTI  721 (926)
T ss_pred             -cCCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHcCC--CCEEEECCh
Confidence             4679999999999999999999985  789999999999999999999999998  578888775

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.

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.97  E-value=1.6e-29  Score=278.27  Aligned_cols=261  Identities=15%  Similarity=0.133  Sum_probs=205.6

Q ss_pred             eccCCCCchhhhhhhccccccceeeeeC------cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHH
Q psy1548         122 NYDMPEDSDTYLHRVARAGRFGTKAVLG------MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ  195 (448)
Q Consensus       122 ~~~~p~~~~~yQ~~~~~~~~~~~~~~~g------~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q  195 (448)
                      +| .|++.   |++      +|+.++.+      +|++++++||+|||.+|+.+++..+.   .+.+++|++||++||.|
T Consensus       598 ~~-~~T~~---Q~~------aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~---~g~qvlvLvPT~eLA~Q  664 (1147)
T PRK10689        598 PF-ETTPD---QAQ------AINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE---NHKQVAVLVPTTLLAQQ  664 (1147)
T ss_pred             CC-CCCHH---HHH------HHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHH---cCCeEEEEeCcHHHHHH
Confidence            35 68888   999      99999887      89999999999999999988877653   35689999999999999


Q ss_pred             HHHHHHHhhccCCCceEEEEEcCcccHHhHHH---HhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhh
Q psy1548         196 ISKEYERFSKYMSNIKVGVFFGGLPIQKDEEY---LKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQL  272 (448)
Q Consensus       196 ~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~---l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~  272 (448)
                      +++.+++..... ++++..++|+.+..++...   +..+.++|+||||+.+    . ..+.+++++++||||+|++..  
T Consensus       665 ~~~~f~~~~~~~-~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL----~-~~v~~~~L~lLVIDEahrfG~--  736 (1147)
T PRK10689        665 HYDNFRDRFANW-PVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLL----Q-SDVKWKDLGLLIVDEEHRFGV--  736 (1147)
T ss_pred             HHHHHHHhhccC-CceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHH----h-CCCCHhhCCEEEEechhhcch--
Confidence            999999877666 6888888888776665443   3445689999999643    2 345678999999999998722  


Q ss_pred             hhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcc-hHHHHHHHHHhh
Q psy1548         273 EMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKEN-EKNKKLFELLDV  351 (448)
Q Consensus       273 ~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~-~k~~~L~~ll~~  351 (448)
                      .    ....++.++.++|+++||||+.+....++...+.++..+...+...   ..+++++...... .+...+.++.  
T Consensus       737 ~----~~e~lk~l~~~~qvLl~SATpiprtl~l~~~gl~d~~~I~~~p~~r---~~v~~~~~~~~~~~~k~~il~el~--  807 (1147)
T PRK10689        737 R----HKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARR---LAVKTFVREYDSLVVREAILREIL--  807 (1147)
T ss_pred             h----HHHHHHhcCCCCcEEEEcCCCCHHHHHHHHhhCCCcEEEecCCCCC---CCceEEEEecCcHHHHHHHHHHHh--
Confidence            2    2344577788999999999998888888888888888877655422   2344444433322 2333333443  


Q ss_pred             CCCCeEEEEECccHHHHHHHHHHHhC--CCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         352 LEFNQVVIFVKSVTRCIALSTLLSEQ--NFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       352 ~~~~~~IIF~~s~~~a~~l~~~L~~~--g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                       .+++++||||+++.++.+++.|++.  +..+..+||+|++++|.+++++|++|+  ..|+++|+-
T Consensus       808 -r~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk--~~VLVaTdI  870 (1147)
T PRK10689        808 -RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQR--FNVLVCTTI  870 (1147)
T ss_pred             -cCCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHhcC--CCEEEECch
Confidence             3679999999999999999999987  789999999999999999999999998  577777764

>PRK14701 reverse gyrase; Provisional

Probab=99.97  E-value=8.2e-30  Score=286.72  Aligned_cols=265  Identities=17%  Similarity=0.173  Sum_probs=206.4

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      | .|+++   |++      ++|.++.|+|++++||||+|||++++++++...   ..+.+++||+||++|+.|+.+.++.
T Consensus        78 ~-~pt~i---Q~~------~i~~il~G~d~li~APTGsGKTl~~~~~al~~~---~~g~~aLVl~PTreLa~Qi~~~l~~  144 (1638)
T PRK14701         78 F-EFWSI---QKT------WAKRILRGKSFSIVAPTGMGKSTFGAFIALFLA---LKGKKCYIILPTTLLVKQTVEKIES  144 (1638)
T ss_pred             C-CCCHH---HHH------HHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHH---hcCCeEEEEECHHHHHHHHHHHHHH
Confidence            8 59999   999      999999999999999999999997766665442   2356899999999999999999999


Q ss_pred             hhccCC-CceEEEEEcCcccHHhH---HHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhh-------
Q psy1548         203 FSKYMS-NIKVGVFFGGLPIQKDE---EYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQ-------  271 (448)
Q Consensus       203 ~~~~~~-~~~v~~~~g~~~~~~~~---~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~-------  271 (448)
                      ++..++ ++++..++|+.+...+.   ..+..+.++|+|+||+++.+.+... . ..+++++|+||||+|++|       
T Consensus       145 l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l-~-~~~i~~iVVDEAD~ml~~~knid~~  222 (1638)
T PRK14701        145 FCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEM-K-HLKFDFIFVDDVDAFLKASKNIDRS  222 (1638)
T ss_pred             HHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHH-h-hCCCCEEEEECceeccccccccchh
Confidence            987652 46777888988766553   3455666999999999998766532 1 267899999999999863       


Q ss_pred             ---hhhHHHHHH----HHH----------------------hCCCCCe-EEEEeccCCccHHHHHHHhcCCCeEEEEcCc
Q psy1548         272 ---LEMRRDVQE----IFR----------------------SSPHTKQ-VMMFSATLSKEIRPVCKKFMHDPMEVYVDDE  321 (448)
Q Consensus       272 ---~~~~~~~~~----i~~----------------------~l~~~~q-~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~  321 (448)
                         .+|.+++..    +++                      .+++..| ++++|||+++.  .....++.++..+.+...
T Consensus       223 L~llGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~~r--~~~~~l~~~~l~f~v~~~  300 (1638)
T PRK14701        223 LQLLGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGKAK--GDRVKLYRELLGFEVGSG  300 (1638)
T ss_pred             hhcCCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCCch--hHHHHHhhcCeEEEecCC
Confidence               378877764    332                      2344555 67799999864  112234567777777665


Q ss_pred             ccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHH---HHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHH
Q psy1548         322 AKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTR---CIALSTLLSEQNFPAVSIHRGMTQEERLKKYQ  398 (448)
Q Consensus       322 ~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~---a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~  398 (448)
                       .....++.+.|+.+....| ..+..+++.. +.++||||+|++.   |+.+++.|++.|+++..+||+     |..+++
T Consensus       301 -~~~lr~i~~~yi~~~~~~k-~~L~~ll~~~-g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~~-----R~~~l~  372 (1638)
T PRK14701        301 -RSALRNIVDVYLNPEKIIK-EHVRELLKKL-GKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSAK-----NKKGFD  372 (1638)
T ss_pred             -CCCCCCcEEEEEECCHHHH-HHHHHHHHhC-CCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecch-----HHHHHH
Confidence             4566788899887766655 5677888776 4689999999875   589999999999999999995     899999


Q ss_pred             HHhcCCCceEEEEecC
Q psy1548         399 EFKDFHKGLAITFASD  414 (448)
Q Consensus       399 ~F~~g~~g~~I~~~t~  414 (448)
                      +|++|+.  .|+++|.
T Consensus       373 ~F~~G~~--~VLVaT~  386 (1638)
T PRK14701        373 LFEEGEI--DYLIGVA  386 (1638)
T ss_pred             HHHcCCC--CEEEEec
Confidence            9999994  5666663

>cd00268 DEADc DEAD-box helicases

Probab=99.97  E-value=6.8e-30  Score=233.63  Aligned_cols=200  Identities=38%  Similarity=0.650  Sum_probs=181.1

Q ss_pred             cccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCCh
Q psy1548          82 FRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMG  161 (448)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsG  161 (448)
                      |+++++++.+.+.+.+.+                       +..|++.   |++      +++.+..|+|+++.+|||+|
T Consensus         1 ~~~~~~~~~i~~~l~~~~-----------------------~~~~~~~---Q~~------~~~~~~~~~~~li~~~TG~G   48 (203)
T cd00268           1 FEELGLSPELLRGIYALG-----------------------FEKPTPI---QAR------AIPPLLSGRDVIGQAQTGSG   48 (203)
T ss_pred             CCcCCCCHHHHHHHHHcC-----------------------CCCCCHH---HHH------HHHHHhcCCcEEEECCCCCc
Confidence            678899999999999998                       8888888   999      99999999999999999999


Q ss_pred             hHHHHHHHHHHhhhcc--CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEc
Q psy1548         162 KTAVFVLATLQQLETT--DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGT  239 (448)
Q Consensus       162 KT~~~~l~~l~~l~~~--~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~T  239 (448)
                      ||++|++|+++.+...  ..+++++|++|+++|+.|+...++.+.... ++++..+.|+.+.......+.. .++|+|+|
T Consensus        49 KT~~~~~~~l~~~~~~~~~~~~~viii~p~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~-~~~iiv~T  126 (203)
T cd00268          49 KTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQIAEVARKLGKHT-NLKVVVIYGGTSIDKQIRKLKR-GPHIVVAT  126 (203)
T ss_pred             HHHHHHHHHHHHHHhhcccCCceEEEEcCCHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHhcC-CCCEEEEC
Confidence            9999999999988776  467799999999999999999999998776 7899999999887666555553 48999999


Q ss_pred             HHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEE
Q psy1548         240 PGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEV  316 (448)
Q Consensus       240 p~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i  316 (448)
                      |+++.+++.+....+.+++++|+||+|.+.+. ++...+..+++.++..+|++++|||+++....++..++.+|..+
T Consensus       127 ~~~l~~~l~~~~~~~~~l~~lIvDE~h~~~~~-~~~~~~~~~~~~l~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~  202 (203)
T cd00268         127 PGRLLDLLERGKLDLSKVKYLVLDEADRMLDM-GFEDQIREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRI  202 (203)
T ss_pred             hHHHHHHHHcCCCChhhCCEEEEeChHHhhcc-ChHHHHHHHHHhCCcccEEEEEeccCCHHHHHHHHHHCCCCEEe
Confidence            99999999888888899999999999999887 89999999999999999999999999999999999999988765

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.

>TIGR01054 rgy reverse gyrase

Probab=99.97  E-value=2.5e-29  Score=277.77  Aligned_cols=262  Identities=18%  Similarity=0.289  Sum_probs=198.1

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      ...|+++   |+.      ++|.++.|+|++++||||+|||+ |.+|+...+..  .+++++|++||++||.|+.+.++.
T Consensus        76 g~~p~~i---Q~~------~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~--~g~~vLIL~PTreLa~Qi~~~l~~  143 (1171)
T TIGR01054        76 GSEPWSI---QKM------WAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAK--KGKRCYIILPTTLLVIQVAEKISS  143 (1171)
T ss_pred             CCCCcHH---HHH------HHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHh--cCCeEEEEeCHHHHHHHHHHHHHH
Confidence            4479999   999      99999999999999999999996 66777665543  356899999999999999999999


Q ss_pred             hhccCCCceE---EEEEcCcccHHh---HHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhh-----
Q psy1548         203 FSKYMSNIKV---GVFFGGLPIQKD---EEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQ-----  271 (448)
Q Consensus       203 ~~~~~~~~~v---~~~~g~~~~~~~---~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~-----  271 (448)
                      +.... ++.+   +.++|+.+...+   ...+.++.++|+|+||++|.+.+..  +.. +++++|+||||+|+++     
T Consensus       144 l~~~~-~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~--l~~-~~~~iVvDEaD~~L~~~k~vd  219 (1171)
T TIGR01054       144 LAEKA-GVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDE--LGP-KFDFIFVDDVDALLKASKNVD  219 (1171)
T ss_pred             HHHhc-CCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHH--hcC-CCCEEEEeChHhhhhccccHH
Confidence            98766 5543   356788776554   2344556699999999999887764  212 8899999999999873     


Q ss_pred             -----hhhHHH-HHHH----------------------HHhCCCCCe--EEEEecc-CCccHHHHHHHhcCCCeEEEEcC
Q psy1548         272 -----LEMRRD-VQEI----------------------FRSSPHTKQ--VMMFSAT-LSKEIRPVCKKFMHDPMEVYVDD  320 (448)
Q Consensus       272 -----~~~~~~-~~~i----------------------~~~l~~~~q--~i~~SAT-~~~~~~~~~~~~l~~~~~i~~~~  320 (448)
                           .||..+ +..+                      ++.+++.+|  ++++||| +|..+..   .++.++..+.+..
T Consensus       220 ~il~llGF~~e~i~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~li~~SAT~~p~~~~~---~l~r~ll~~~v~~  296 (1171)
T TIGR01054       220 KLLKLLGFSEELIEKAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRGCLIVSSATGRPRGKRA---KLFRELLGFEVGG  296 (1171)
T ss_pred             HHHHHcCCCHHHHHHHHHHhhhccccchHHHHHHHHHHHHhhhhccCcEEEEEeCCCCccccHH---HHcccccceEecC
Confidence                 256653 4443                      233455555  6778999 5655432   2344555566555


Q ss_pred             cccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECcc---HHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHH
Q psy1548         321 EAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSV---TRCIALSTLLSEQNFPAVSIHRGMTQEERLKKY  397 (448)
Q Consensus       321 ~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~---~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l  397 (448)
                      . .....++.+.|.....  +...|.++++.. +.++||||+++   +.|+.+++.|++.|+++..+||+|++    .++
T Consensus       297 ~-~~~~r~I~~~~~~~~~--~~~~L~~ll~~l-~~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~~----~~l  368 (1171)
T TIGR01054       297 G-SDTLRNVVDVYVEDED--LKETLLEIVKKL-GTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKPK----EDY  368 (1171)
T ss_pred             c-cccccceEEEEEeccc--HHHHHHHHHHHc-CCCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCCH----HHH
Confidence            4 4456788888876554  345677777765 36799999999   99999999999999999999999973    789


Q ss_pred             HHHhcCCCceEEEEec
Q psy1548         398 QEFKDFHKGLAITFAS  413 (448)
Q Consensus       398 ~~F~~g~~g~~I~~~t  413 (448)
                      ++|++|+.  .|+++|
T Consensus       369 ~~Fr~G~~--~vLVat  382 (1171)
T TIGR01054       369 EKFAEGEI--DVLIGV  382 (1171)
T ss_pred             HHHHcCCC--CEEEEe
Confidence            99999995  455553

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.

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.97  E-value=4.5e-29  Score=265.52  Aligned_cols=259  Identities=19%  Similarity=0.182  Sum_probs=186.6

Q ss_pred             CCCchhhhhhhccccccceeeeeC------cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHH
Q psy1548         126 PEDSDTYLHRVARAGRFGTKAVLG------MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKE  199 (448)
Q Consensus       126 p~~~~~yQ~~~~~~~~~~~~~~~g------~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~  199 (448)
                      |++.   |++      +++.+..+      ++++++||||||||++|++|++..+.   .+.+++|++||++||.|+++.
T Consensus       262 lt~~---Q~~------ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~---~g~q~lilaPT~~LA~Q~~~~  329 (681)
T PRK10917        262 LTGA---QKR------VVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIE---AGYQAALMAPTEILAEQHYEN  329 (681)
T ss_pred             CCHH---HHH------HHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHH---cCCeEEEEeccHHHHHHHHHH
Confidence            5555   999      99998886      48999999999999999999998774   356899999999999999999


Q ss_pred             HHHhhccCCCceEEEEEcCcccHHh---HHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHH
Q psy1548         200 YERFSKYMSNIKVGVFFGGLPIQKD---EEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRR  276 (448)
Q Consensus       200 ~~~~~~~~~~~~v~~~~g~~~~~~~---~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~  276 (448)
                      ++++...+ ++++..++|+.+....   ...+..+.++|+||||+.+..     ...+++++++|+||+|++..  ..+.
T Consensus       330 l~~l~~~~-~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~v~~~~l~lvVIDE~Hrfg~--~qr~  401 (681)
T PRK10917        330 LKKLLEPL-GIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQD-----DVEFHNLGLVIIDEQHRFGV--EQRL  401 (681)
T ss_pred             HHHHHhhc-CcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcc-----cchhcccceEEEechhhhhH--HHHH
Confidence            99999887 8999999999875433   345566679999999987643     34578999999999998643  2222


Q ss_pred             HHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchH-HHHHHHHHhhCCCC
Q psy1548         277 DVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEK-NKKLFELLDVLEFN  355 (448)
Q Consensus       277 ~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k-~~~L~~ll~~~~~~  355 (448)
                          .+.......++++||||+.+....+......++..+...+.   ....+...+.......+ .+.+...+  ..++
T Consensus       402 ----~l~~~~~~~~iL~~SATp~prtl~~~~~g~~~~s~i~~~p~---~r~~i~~~~~~~~~~~~~~~~i~~~~--~~g~  472 (681)
T PRK10917        402 ----ALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPP---GRKPITTVVIPDSRRDEVYERIREEI--AKGR  472 (681)
T ss_pred             ----HHHhcCCCCCEEEEeCCCCHHHHHHHHcCCCceEEEecCCC---CCCCcEEEEeCcccHHHHHHHHHHHH--HcCC
Confidence                23334556789999999876644433221122222221111   12234444433222222 12233333  2466


Q ss_pred             eEEEEECcc--------HHHHHHHHHHHhC--CCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         356 QVVIFVKSV--------TRCIALSTLLSEQ--NFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       356 ~~IIF~~s~--------~~a~~l~~~L~~~--g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                      +++|||+..        ..++.+++.|++.  ++++..+||+|++++|.+++++|++|+  +.|+++|+-
T Consensus       473 q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~--~~ILVaT~v  540 (681)
T PRK10917        473 QAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGE--IDILVATTV  540 (681)
T ss_pred             cEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCC--CCEEEECcc
Confidence            999999964        4566778888775  578999999999999999999999987  567777764

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

Probab=99.97  E-value=5.9e-29  Score=266.82  Aligned_cols=306  Identities=20%  Similarity=0.221  Sum_probs=232.6

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      ...+.+.   |.+      ++..+.+|+|++|++|||||||.+|++|+++.+...+.. ++|+|.||++|++++.+.+++
T Consensus        68 ~~~lY~H---Q~~------A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a-~AL~lYPtnALa~DQ~~rl~~  137 (851)
T COG1205          68 IERLYSH---QVD------ALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSA-RALLLYPTNALANDQAERLRE  137 (851)
T ss_pred             cccccHH---HHH------HHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcCc-cEEEEechhhhHhhHHHHHHH
Confidence            5554444   999      999999999999999999999999999999999887655 899999999999999999999


Q ss_pred             hhccCC-CceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCC----CcCCCeeEEEecchhHHHhhhhhHHH
Q psy1548         203 FSKYMS-NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK----LNLSLLKHFILDECDKMLEQLEMRRD  277 (448)
Q Consensus       203 ~~~~~~-~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~----~~~~~i~~lViDEah~l~~~~~~~~~  277 (448)
                      +...++ ++.+..+.|+++..... .+..++|+|+++||++|..++....    ..++++++||+||+|..-.  .|+..
T Consensus       138 ~~~~~~~~v~~~~y~Gdt~~~~r~-~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYrG--v~GS~  214 (851)
T COG1205         138 LISDLPGKVTFGRYTGDTPPEERR-AIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRG--VQGSE  214 (851)
T ss_pred             HHHhCCCcceeeeecCCCChHHHH-HHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceeccc--cchhH
Confidence            999885 58888888988755544 4455569999999999988554422    3357899999999996644  45555


Q ss_pred             HHHHHHh-------CCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcC---------cchH
Q psy1548         278 VQEIFRS-------SPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLK---------ENEK  341 (448)
Q Consensus       278 ~~~i~~~-------l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~---------~~~k  341 (448)
                      +..+++.       .+.+.|+|+.|||+.+. .+++..+........++..  ..+...+......+         ...+
T Consensus       215 vA~llRRL~~~~~~~~~~~q~i~~SAT~~np-~e~~~~l~~~~f~~~v~~~--g~~~~~~~~~~~~p~~~~~~~~~r~s~  291 (851)
T COG1205         215 VALLLRRLLRRLRRYGSPLQIICTSATLANP-GEFAEELFGRDFEVPVDED--GSPRGLRYFVRREPPIRELAESIRRSA  291 (851)
T ss_pred             HHHHHHHHHHHHhccCCCceEEEEeccccCh-HHHHHHhcCCcceeeccCC--CCCCCceEEEEeCCcchhhhhhcccch
Confidence            5555444       34578999999999766 5666777766666543333  23444555555544         1234


Q ss_pred             HHHHHHHHhhC--CCCeEEEEECccHHHHHHH----HHHHhCC----CcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEE
Q psy1548         342 NKKLFELLDVL--EFNQVVIFVKSVTRCIALS----TLLSEQN----FPAVSIHRGMTQEERLKKYQEFKDFHKGLAITF  411 (448)
Q Consensus       342 ~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~----~~L~~~g----~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~  411 (448)
                      ...+..++...  .+-++|+|+.++..++.++    ..+...+    ..+..++++|..++|.++..+|++|+  +.+.+
T Consensus       292 ~~~~~~~~~~~~~~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~~~g~--~~~~~  369 (851)
T COG1205         292 LAELATLAALLVRNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGE--LLGVI  369 (851)
T ss_pred             HHHHHHHHHHHHHcCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHHhcCC--ccEEe
Confidence            44444444332  4569999999999999998    4454555    56899999999999999999999998  34445


Q ss_pred             ecChhhHHHHHHHHHHhcCCCCCCCc-cccccccccCC
Q psy1548         412 ASDENDAKILNNVQDRFDVSISELPD-EIDLSTYIEGR  448 (448)
Q Consensus       412 ~t~~~d~~~l~~i~~~~~~~~~~~p~-~~~~~~~~~~~  448 (448)
                      .|..  .+.--+|.+...+..+..|. ..-.+.++.||
T Consensus       370 st~A--lelgidiG~ldavi~~g~P~~s~~~~~Q~~GR  405 (851)
T COG1205         370 ATNA--LELGIDIGSLDAVIAYGYPGVSVLSFRQRAGR  405 (851)
T ss_pred             cchh--hhhceeehhhhhHhhcCCCCchHHHHHHhhhh
Confidence            4554  44445889999999999999 66778888776

>KOG0349|consensus

Probab=99.96  E-value=6.2e-29  Score=235.44  Aligned_cols=258  Identities=25%  Similarity=0.414  Sum_probs=204.7

Q ss_pred             CeEEEEeeccHHHHHHHHHHHHHhhccC--CCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCe
Q psy1548         180 NVYVLVMCHTRELAFQISKEYERFSKYM--SNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLL  257 (448)
Q Consensus       180 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~--~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i  257 (448)
                      .+.++|+-|+++|+.|.+..+++|..+.  |.++..++.||.....|...++++ .+|+|+||+++.+++..+.+.+.++
T Consensus       286 ap~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g-~~ivvGtpgRl~~~is~g~~~lt~c  364 (725)
T KOG0349|consen  286 APEAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDG-THIVVGTPGRLLQPISKGLVTLTHC  364 (725)
T ss_pred             CcceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcC-ceeeecCchhhhhhhhccceeeeee
Confidence            4789999999999999999888877665  356777889998888899899887 8999999999999999999999999


Q ss_pred             eEEEecchhHHHhhhhhHHHHHHHHHhCCC------CCeEEEEeccCCc-cHHHHHHHhcCCCeEEEEcCccccccccee
Q psy1548         258 KHFILDECDKMLEQLEMRRDVQEIFRSSPH------TKQVMMFSATLSK-EIRPVCKKFMHDPMEVYVDDEAKLTLHGLQ  330 (448)
Q Consensus       258 ~~lViDEah~l~~~~~~~~~~~~i~~~l~~------~~q~i~~SAT~~~-~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~  330 (448)
                      +++|+||++.++.. ++-+.+..+...+|+      ..|.+.+|||+.. ++.++..+.|.-|..+....+ ...+..+.
T Consensus       365 rFlvlDead~lL~q-gy~d~I~r~h~qip~~tsdg~rlq~~vCsatlh~feVkk~~ervmhfptwVdLkge-D~vpetvH  442 (725)
T KOG0349|consen  365 RFLVLDEADLLLGQ-GYDDKIYRFHGQIPHMTSDGFRLQSPVCSATLHIFEVKKVGERVMHFPTWVDLKGE-DLVPETVH  442 (725)
T ss_pred             EEEEecchhhhhhc-ccHHHHHHHhccchhhhcCCcccccceeeeEEeEEEeeehhhhhccCceeEecccc-cccchhhc
Confidence            99999999999997 888888888777663      4589999999864 577788888888988887666 34444444


Q ss_pred             EEEEEcCcc----------------------------------h-----HHHHHHHHHhhCCCCeEEEEECccHHHHHHH
Q psy1548         331 QHYVKLKEN----------------------------------E-----KNKKLFELLDVLEFNQVVIFVKSVTRCIALS  371 (448)
Q Consensus       331 ~~~~~~~~~----------------------------------~-----k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~  371 (448)
                      +....+.+.                                  +     |-+.-...++.+.-.++||||.|+..|+.|.
T Consensus       443 hvv~lv~p~~d~sw~~lr~~i~td~vh~kdn~~pg~~Spe~~s~a~kilkgEy~v~ai~~h~mdkaiifcrtk~dcDnLe  522 (725)
T KOG0349|consen  443 HVVKLVCPSVDGSWCDLRQFIETDKVHTKDNLLPGQVSPENPSSATKILKGEYGVVAIRRHAMDKAIIFCRTKQDCDNLE  522 (725)
T ss_pred             cceeecCCccCccHHHHhhhhccCCcccccccccccCCCCChhhhhHHhcCchhhhhhhhhccCceEEEEeccccchHHH
Confidence            443332210                                  0     1111122334445568999999999999999


Q ss_pred             HHHHhCC---CcEEEEeCCCCHHHHHHHHHHHhcCC--------------------------------------------
Q psy1548         372 TLLSEQN---FPAVSIHRGMTQEERLKKYQEFKDFH--------------------------------------------  404 (448)
Q Consensus       372 ~~L~~~g---~~~~~lh~~~~~~eR~~~l~~F~~g~--------------------------------------------  404 (448)
                      +.|.+.|   +.+.++||+..++||..-++.|+.+.                                            
T Consensus       523 r~~~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvkflictdvaargldi~g~p~~invtlpd~k~nyvhrigrvgra  602 (725)
T KOG0349|consen  523 RMMNQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLPFMINVTLPDDKTNYVHRIGRVGRA  602 (725)
T ss_pred             HHHHHcCCccceeEEEecCCChhHHHHHHHhhhhcCeEEEEEehhhhccccccCCceEEEEecCcccchhhhhhhccchh
Confidence            9998874   58999999999999999999999988                                            


Q ss_pred             --CceEEEEecCh-------------------------------hhHHHHHHHHHHhcCCCCCCCcccc
Q psy1548         405 --KGLAITFASDE-------------------------------NDAKILNNVQDRFDVSISELPDEID  440 (448)
Q Consensus       405 --~g~~I~~~t~~-------------------------------~d~~~l~~i~~~~~~~~~~~p~~~~  440 (448)
                        .|++|+++.+.                               .+..+|.+||+.+++.|+++-.+++
T Consensus       603 ermglaislvat~~ekvwyh~c~srgr~c~nt~l~e~~gc~iwyne~~llaeve~hln~ti~qv~~~~~  671 (725)
T KOG0349|consen  603 ERMGLAISLVATVPEKVWYHWCKSRGRSCNNTNLTEVRGCCIWYNEPNLLAEVEDHLNITIQQVDKTMD  671 (725)
T ss_pred             hhcceeEEEeeccchheeehhhhccCCcccCCccccccceEEEeCchhHHHHHHHhhcceeeeeCCCCC
Confidence              56666666442                               1577888999999999998876655

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

Probab=99.96  E-value=1.1e-29  Score=257.08  Aligned_cols=299  Identities=18%  Similarity=0.173  Sum_probs=217.4

Q ss_pred             eeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHH
Q psy1548         121 FNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEY  200 (448)
Q Consensus       121 ~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~  200 (448)
                      ++|....+-   |++      +|..+++|+|+++..|||+|||+||.+|++-.      ..-+|||+|..+|..++.+.+
T Consensus        13 fGy~~FR~g---Q~e------vI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~------~G~TLVVSPLiSLM~DQV~~l   77 (590)
T COG0514          13 FGYASFRPG---QQE------IIDALLSGKDTLVVMPTGGGKSLCYQIPALLL------EGLTLVVSPLISLMKDQVDQL   77 (590)
T ss_pred             hCccccCCC---HHH------HHHHHHcCCcEEEEccCCCCcchHhhhHHHhc------CCCEEEECchHHHHHHHHHHH
Confidence            346666677   999      99999999999999999999999999999875      227999999999999888888


Q ss_pred             HHhhccCCCceEEEEEcCcccHHh---HHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhh-hhhHH
Q psy1548         201 ERFSKYMSNIKVGVFFGGLPIQKD---EEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQ-LEMRR  276 (448)
Q Consensus       201 ~~~~~~~~~~~v~~~~g~~~~~~~---~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~-~~~~~  276 (448)
                      +..     ++.+..+.+..+..+.   ...+..+..++++-+|+++..---.+.+.-..+.++||||||++.+| ++|++
T Consensus        78 ~~~-----Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~L~~~~i~l~vIDEAHCiSqWGhdFRP  152 (590)
T COG0514          78 EAA-----GIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRP  152 (590)
T ss_pred             HHc-----CceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHHHHHHhCCCceEEechHHHHhhcCCccCH
Confidence            775     6788888777654443   33456667899999999986432222222456778999999999999 45999


Q ss_pred             HHHHHHHhCC--CCCeEEEEeccCCccHHHHHHHhcC--CCeEEEEcCcccccccceeEEEEEcC-cchHHHHHHHHHhh
Q psy1548         277 DVQEIFRSSP--HTKQVMMFSATLSKEIRPVCKKFMH--DPMEVYVDDEAKLTLHGLQQHYVKLK-ENEKNKKLFELLDV  351 (448)
Q Consensus       277 ~~~~i~~~l~--~~~q~i~~SAT~~~~~~~~~~~~l~--~~~~i~~~~~~~~~~~~i~~~~~~~~-~~~k~~~L~~ll~~  351 (448)
                      .+..+-....  ++.+++++|||.++.+...+...+.  .+..+....    ..+++........ ...+...+.+ ...
T Consensus       153 ~Y~~lg~l~~~~~~~p~~AlTATA~~~v~~DI~~~L~l~~~~~~~~sf----dRpNi~~~v~~~~~~~~q~~fi~~-~~~  227 (590)
T COG0514         153 DYRRLGRLRAGLPNPPVLALTATATPRVRDDIREQLGLQDANIFRGSF----DRPNLALKVVEKGEPSDQLAFLAT-VLP  227 (590)
T ss_pred             hHHHHHHHHhhCCCCCEEEEeCCCChHHHHHHHHHhcCCCcceEEecC----CCchhhhhhhhcccHHHHHHHHHh-hcc
Confidence            9998754332  3788999999999998887776554  443433322    2344433322222 2233333332 124


Q ss_pred             CCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCC
Q psy1548         352 LEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVS  431 (448)
Q Consensus       352 ~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~  431 (448)
                      ...+..||||.|++.++.++++|...|+++..||+||+.++|..+.+.|..++  +.|.++|...=+++  +-.+.--+.
T Consensus       228 ~~~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f~~~~--~~iiVAT~AFGMGI--dKpdVRfVi  303 (590)
T COG0514         228 QLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDE--IKVMVATNAFGMGI--DKPDVRFVI  303 (590)
T ss_pred             ccCCCeEEEEeeHHhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHHHHhcCC--CcEEEEeccccCcc--CCCCceEEE
Confidence            45567999999999999999999999999999999999999999999999877  57777777421111  111111145


Q ss_pred             CCCCCccccccccccCC
Q psy1548         432 ISELPDEIDLSTYIEGR  448 (448)
Q Consensus       432 ~~~~p~~~~~~~~~~~~  448 (448)
                      +..+|.+++.+-+=.||
T Consensus       304 H~~lP~s~EsYyQE~GR  320 (590)
T COG0514         304 HYDLPGSIESYYQETGR  320 (590)
T ss_pred             EecCCCCHHHHHHHHhh
Confidence            66778887766655554

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.96  E-value=1e-28  Score=261.57  Aligned_cols=265  Identities=20%  Similarity=0.221  Sum_probs=199.4

Q ss_pred             hhhhccccccceee-eeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCce
Q psy1548         133 LHRVARAGRFGTKA-VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIK  211 (448)
Q Consensus       133 Q~~~~~~~~~~~~~-~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~  211 (448)
                      |++      ++... ..|+|+|+++|||||||+.+++.+++.+...  +.+++|+||+++||.+.++.+++|...  +++
T Consensus        36 qq~------av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~--~~k~vYivPlkALa~Ek~~~~~~~~~~--Gir  105 (766)
T COG1204          36 QQE------AVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG--GGKVVYIVPLKALAEEKYEEFSRLEEL--GIR  105 (766)
T ss_pred             HHH------HhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc--CCcEEEEeChHHHHHHHHHHhhhHHhc--CCE
Confidence            777      55444 4469999999999999999999999988765  458999999999999999999955443  899


Q ss_pred             EEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCC---CC
Q psy1548         212 VGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSP---HT  288 (448)
Q Consensus       212 v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~---~~  288 (448)
                      +...+|+.+....  .+.  .++|+|+||+++-.++++...+...++++|+||+|.+.+. ..++.++.+.....   ..
T Consensus       106 V~~~TgD~~~~~~--~l~--~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~-~RG~~lE~iv~r~~~~~~~  180 (766)
T COG1204         106 VGISTGDYDLDDE--RLA--RYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDR-TRGPVLESIVARMRRLNEL  180 (766)
T ss_pred             EEEecCCcccchh--hhc--cCCEEEEchHHhhHhhhcCcchhhcccEEEEeeeeecCCc-ccCceehhHHHHHHhhCcc
Confidence            9999999875442  222  3799999999999999998888999999999999988775 57777777766554   34


Q ss_pred             CeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchH-------HHHHHHHHhhC-CCCeEEEE
Q psy1548         289 KQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEK-------NKKLFELLDVL-EFNQVVIF  360 (448)
Q Consensus       289 ~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k-------~~~L~~ll~~~-~~~~~IIF  360 (448)
                      .|++++|||+|+. .+++.+.-.++......+..........+.+.......|       ...+...+... .+++++||
T Consensus       181 ~rivgLSATlpN~-~evA~wL~a~~~~~~~rp~~l~~~v~~~~~~~~~~~~~k~~~~~~~~~~~~~v~~~~~~~~qvLvF  259 (766)
T COG1204         181 IRIVGLSATLPNA-EEVADWLNAKLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNLALELVLESLAEGGQVLVF  259 (766)
T ss_pred             eEEEEEeeecCCH-HHHHHHhCCcccccCCCCcccccCCccceEEEEecCccccccccchHHHHHHHHHHHhcCCeEEEE
Confidence            7999999999865 567777666655333333322222333344443332222       23333333333 46799999


Q ss_pred             ECccHHHHHHHHHHHhC---------------------C----------------CcEEEEeCCCCHHHHHHHHHHHhcC
Q psy1548         361 VKSVTRCIALSTLLSEQ---------------------N----------------FPAVSIHRGMTQEERLKKYQEFKDF  403 (448)
Q Consensus       361 ~~s~~~a~~l~~~L~~~---------------------g----------------~~~~~lh~~~~~~eR~~~l~~F~~g  403 (448)
                      |+|++.+...|+.|.+.                     +                ..+.++|+||+.++|.-+.+.|+.|
T Consensus       260 v~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~~GvafHhAGL~~~~R~~vE~~Fr~g  339 (766)
T COG1204         260 VHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRGVAFHHAGLPREDRQLVEDAFRKG  339 (766)
T ss_pred             EecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHHhCccccccCCCHHHHHHHHHHHhcC
Confidence            99999999999999830                     0                1278899999999999999999998


Q ss_pred             CCceEEEEecCh
Q psy1548         404 HKGLAITFASDE  415 (448)
Q Consensus       404 ~~g~~I~~~t~~  415 (448)
                      +  +.|.++|+.
T Consensus       340 ~--ikVlv~TpT  349 (766)
T COG1204         340 K--IKVLVSTPT  349 (766)
T ss_pred             C--ceEEEechH
Confidence            8  677777764

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

Probab=99.96  E-value=1.6e-28  Score=240.05  Aligned_cols=283  Identities=20%  Similarity=0.202  Sum_probs=226.2

Q ss_pred             ccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccccee-eeeCcceeeec
Q psy1548          78 HSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK-AVLGMDILCQA  156 (448)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~-~~~g~~vli~a  156 (448)
                      +....+++.++++..+-+...|                       +....|+   |..      ++.. ++.|+|.++.+
T Consensus       192 ~r~~vdeLdipe~fk~~lk~~G-----------------------~~eLlPV---Q~l------aVe~GLLeG~nllVVS  239 (830)
T COG1202         192 ERVPVDELDIPEKFKRMLKREG-----------------------IEELLPV---QVL------AVEAGLLEGENLLVVS  239 (830)
T ss_pred             ccccccccCCcHHHHHHHHhcC-----------------------cceecch---hhh------hhhhccccCCceEEEe
Confidence            3445788999999999999999                       9999999   999      6643 67899999999


Q ss_pred             cCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHH---hcCCC
Q psy1548         157 KSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL---KTHNP  233 (448)
Q Consensus       157 pTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l---~~~~~  233 (448)
                      +|+||||++.-++-+..+...  +.+.|+++|..+||+|-++.|+.-...+ ++++..-.|-..+.......   ..-.+
T Consensus       240 aTasGKTLIgElAGi~~~l~~--g~KmlfLvPLVALANQKy~dF~~rYs~L-glkvairVG~srIk~~~~pv~~~t~~dA  316 (830)
T COG1202         240 ATASGKTLIGELAGIPRLLSG--GKKMLFLVPLVALANQKYEDFKERYSKL-GLKVAIRVGMSRIKTREEPVVVDTSPDA  316 (830)
T ss_pred             ccCCCcchHHHhhCcHHHHhC--CCeEEEEehhHHhhcchHHHHHHHhhcc-cceEEEEechhhhcccCCccccCCCCCC
Confidence            999999999998888877654  3479999999999999999998766666 78887777755433321111   11137


Q ss_pred             cEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHH---HHHHhCCCCCeEEEEeccCCccHHHHHHHhc
Q psy1548         234 QIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQ---EIFRSSPHTKQVMMFSATLSKEIRPVCKKFM  310 (448)
Q Consensus       234 ~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~---~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l  310 (448)
                      ||+|||.+-+-.+++.+ -.+.++..+||||+|.+-+. ..+..+.   .-++.+-+..|+|.+|||+.+. .++++.+.
T Consensus       317 DIIVGTYEGiD~lLRtg-~~lgdiGtVVIDEiHtL~de-ERG~RLdGLI~RLr~l~~~AQ~i~LSATVgNp-~elA~~l~  393 (830)
T COG1202         317 DIIVGTYEGIDYLLRTG-KDLGDIGTVVIDEIHTLEDE-ERGPRLDGLIGRLRYLFPGAQFIYLSATVGNP-EELAKKLG  393 (830)
T ss_pred             cEEEeechhHHHHHHcC-CcccccceEEeeeeeeccch-hcccchhhHHHHHHHhCCCCeEEEEEeecCCh-HHHHHHhC
Confidence            99999999999999887 56899999999999987664 4444444   4455566789999999999766 67777776


Q ss_pred             CCCeEEEEcCcccccccceeEEEEEcC-cchHHHHHHHHHhhC--------CCCeEEEEECccHHHHHHHHHHHhCCCcE
Q psy1548         311 HDPMEVYVDDEAKLTLHGLQQHYVKLK-ENEKNKKLFELLDVL--------EFNQVVIFVKSVTRCIALSTLLSEQNFPA  381 (448)
Q Consensus       311 ~~~~~i~~~~~~~~~~~~i~~~~~~~~-~~~k~~~L~~ll~~~--------~~~~~IIF~~s~~~a~~l~~~L~~~g~~~  381 (448)
                      ..++.+.      ..+..+..+.+.+. ..+|.+.+..+++..        -.+++|||++|+..|..++..|...|+++
T Consensus       394 a~lV~y~------~RPVplErHlvf~~~e~eK~~ii~~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG~~a  467 (830)
T COG1202         394 AKLVLYD------ERPVPLERHLVFARNESEKWDIIARLVKREFSTESSKGYRGQTIVFTYSRRRCHELADALTGKGLKA  467 (830)
T ss_pred             CeeEeec------CCCCChhHeeeeecCchHHHHHHHHHHHHHHhhhhccCcCCceEEEecchhhHHHHHHHhhcCCccc
Confidence            6665543      23445666666666 678888888877542        24699999999999999999999999999


Q ss_pred             EEEeCCCCHHHHHHHHHHHhcCC
Q psy1548         382 VSIHRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       382 ~~lh~~~~~~eR~~~l~~F~~g~  404 (448)
                      .+||+||+..+|..+...|.+++
T Consensus       468 ~pYHaGL~y~eRk~vE~~F~~q~  490 (830)
T COG1202         468 APYHAGLPYKERKSVERAFAAQE  490 (830)
T ss_pred             ccccCCCcHHHHHHHHHHHhcCC
Confidence            99999999999999999999998

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.96  E-value=3.3e-28  Score=257.20  Aligned_cols=260  Identities=22%  Similarity=0.229  Sum_probs=183.9

Q ss_pred             CCCCchhhhhhhccccccceeeeeC------cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHH
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLG------MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK  198 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g------~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~  198 (448)
                      .|++.   |++      +++.++.+      .+.+++||||||||++|++|++..+..   +.+++|++||++||.|+++
T Consensus       235 ~lt~~---Q~~------ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~---g~qvlilaPT~~LA~Q~~~  302 (630)
T TIGR00643       235 KLTRA---QKR------VVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEA---GYQVALMAPTEILAEQHYN  302 (630)
T ss_pred             CCCHH---HHH------HHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHc---CCcEEEECCHHHHHHHHHH
Confidence            45666   999      99988876      368999999999999999999988753   5589999999999999999


Q ss_pred             HHHHhhccCCCceEEEEEcCcccHH---hHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhH
Q psy1548         199 EYERFSKYMSNIKVGVFFGGLPIQK---DEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMR  275 (448)
Q Consensus       199 ~~~~~~~~~~~~~v~~~~g~~~~~~---~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~  275 (448)
                      .++++...+ ++++..++|+.....   ....+..+.++|+|+||+.+.+     ...+.+++++|+||+|++..  ..+
T Consensus       303 ~~~~l~~~~-gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~-----~~~~~~l~lvVIDEaH~fg~--~qr  374 (630)
T TIGR00643       303 SLRNLLAPL-GIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE-----KVEFKRLALVIIDEQHRFGV--EQR  374 (630)
T ss_pred             HHHHHhccc-CcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc-----cccccccceEEEechhhccH--HHH
Confidence            999998877 899999999987654   3445566678999999987643     35578999999999998643  222


Q ss_pred             HHHHHHHHhCC--CCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhh--
Q psy1548         276 RDVQEIFRSSP--HTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDV--  351 (448)
Q Consensus       276 ~~~~~i~~~l~--~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~--  351 (448)
                      ..+.   ....  ...++++||||+.+....+.....-+...+...+.   ....+...+.  ....+ ..+...+..  
T Consensus       375 ~~l~---~~~~~~~~~~~l~~SATp~prtl~l~~~~~l~~~~i~~~p~---~r~~i~~~~~--~~~~~-~~~~~~i~~~l  445 (630)
T TIGR00643       375 KKLR---EKGQGGFTPHVLVMSATPIPRTLALTVYGDLDTSIIDELPP---GRKPITTVLI--KHDEK-DIVYEFIEEEI  445 (630)
T ss_pred             HHHH---HhcccCCCCCEEEEeCCCCcHHHHHHhcCCcceeeeccCCC---CCCceEEEEe--CcchH-HHHHHHHHHHH
Confidence            2222   2222  26789999999766543332211111111111111   1123333332  22223 333333332  


Q ss_pred             CCCCeEEEEECcc--------HHHHHHHHHHHhC--CCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         352 LEFNQVVIFVKSV--------TRCIALSTLLSEQ--NFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       352 ~~~~~~IIF~~s~--------~~a~~l~~~L~~~--g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                      ..+++++|||+..        ..++.+++.|++.  ++++..+||+|++++|..++++|++|+  ..|+++|+-
T Consensus       446 ~~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~--~~ILVaT~v  517 (630)
T TIGR00643       446 AKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGE--VDILVATTV  517 (630)
T ss_pred             HhCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCC--CCEEEECce
Confidence            2467899999876        4567788888764  788999999999999999999999988  466666664

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.96  E-value=1.7e-28  Score=244.10  Aligned_cols=255  Identities=18%  Similarity=0.217  Sum_probs=171.5

Q ss_pred             ceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccH--------
Q psy1548         151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQ--------  222 (448)
Q Consensus       151 ~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~--------  222 (448)
                      ++++++|||||||++|++|++..+... .+.+++|++|+++|+.|+++.+..+.+    ..++.++|+....        
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~-~~~~ii~v~P~~~L~~q~~~~l~~~f~----~~~~~~~~~~~~~~~~~~~~~   75 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQ-KADRVIIALPTRATINAMYRRAKELFG----SNLGLLHSSSSFKRIKEMGDS   75 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhC-CCCeEEEEeehHHHHHHHHHHHHHHhC----cccEEeeccHHHHHHhccCCc
Confidence            589999999999999999999876543 345899999999999999999998753    2344444433210        


Q ss_pred             ---HhH-HHHhc-----CCCcEEEEcHHHHHHHHHCCC----CcCC--CeeEEEecchhHHHhhhhhHHHHHHHHHhCC-
Q psy1548         223 ---KDE-EYLKT-----HNPQIVVGTPGRILALVRNKK----LNLS--LLKHFILDECDKMLEQLEMRRDVQEIFRSSP-  286 (448)
Q Consensus       223 ---~~~-~~l~~-----~~~~IlV~Tp~~l~~~l~~~~----~~~~--~i~~lViDEah~l~~~~~~~~~~~~i~~~l~-  286 (448)
                         ... .....     ...+|+|+||+++...+....    ..+.  ..+++|+||+|.+.+. ++.. +..+++.++ 
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~-~~~~-l~~~l~~l~~  153 (358)
T TIGR01587        76 EEFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEY-TLAL-ILAVLEVLKD  153 (358)
T ss_pred             hhHHHHHHHHhhchhhhhhCCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHH-HHHH-HHHHHHHHHH
Confidence               000 00001     125799999999988765521    1111  2378999999999875 4333 555555554 


Q ss_pred             CCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEc--CcchHHHHHHHHHhhC-CCCeEEEEECc
Q psy1548         287 HTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKL--KENEKNKKLFELLDVL-EFNQVVIFVKS  363 (448)
Q Consensus       287 ~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~--~~~~k~~~L~~ll~~~-~~~~~IIF~~s  363 (448)
                      .+.|++++|||+|+.+.+++..+...+........ . ......+.+..+  ....+...+..+++.. .++++||||+|
T Consensus       154 ~~~~~i~~SATlp~~l~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~lVf~~t  231 (358)
T TIGR01587       154 NDVPILLMSATLPKFLKEYAEKIGYVEFNEPLDLK-E-ERRFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAIIVNT  231 (358)
T ss_pred             cCCCEEEEecCchHHHHHHHhcCCCcccccCCCCc-c-ccccccccceeeccccccCHHHHHHHHHHhhCCCeEEEEECC
Confidence            47899999999997777776655433221111111 0 000112222222  2234555666666543 46799999999


Q ss_pred             cHHHHHHHHHHHhCCC--cEEEEeCCCCHHHHHHH----HHHHhcCCCceEEEEecChh
Q psy1548         364 VTRCIALSTLLSEQNF--PAVSIHRGMTQEERLKK----YQEFKDFHKGLAITFASDEN  416 (448)
Q Consensus       364 ~~~a~~l~~~L~~~g~--~~~~lh~~~~~~eR~~~----l~~F~~g~~g~~I~~~t~~~  416 (448)
                      +++|+.+++.|++.+.  .+..+||+|++.+|.++    ++.|++|+  ..|.++|+.-
T Consensus       232 ~~~~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~--~~ilvaT~~~  288 (358)
T TIGR01587       232 VDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNE--KFVIVATQVI  288 (358)
T ss_pred             HHHHHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCC--CeEEEECcch
Confidence            9999999999998766  59999999999999764    89999877  4667777643

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.

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.96  E-value=7.3e-28  Score=251.87  Aligned_cols=302  Identities=17%  Similarity=0.200  Sum_probs=205.4

Q ss_pred             CCHHHHHHHhhcccee-EeeccccCCcccccceeEeeccCCCCc---------hhhhhhhccccccceeeeeCcceeeec
Q psy1548          87 LKPEILRAIVDCWRIL-VATNLFGRGMDIERVNIVFNYDMPEDS---------DTYLHRVARAGRFGTKAVLGMDILCQA  156 (448)
Q Consensus        87 ~~~~~~~~~~~~~~~~-~~~~~~~~~~d~~~~~~v~~~~~p~~~---------~~yQ~~~~~~~~~~~~~~~g~~vli~a  156 (448)
                      ++..+++++.+.|..+ +-++-.+.-.+...+     |..|.|.         ...|++      +++.+++|++++++|
T Consensus       118 ~~~~~~~g~~~~~n~~~~~~~~~~~~~~~~~~-----~~n~~~~~~~~l~~~~~~iQ~q------il~~i~~gkdvIv~A  186 (675)
T PHA02653        118 FDEYILRGLVEGGNALGIFSNNVGSKKDTIGI-----LGNPEPFSKIPLASLQPDVQLK------IFEAWISRKPVVLTG  186 (675)
T ss_pred             ccHHHHhhHhhcCceeeeeccCcccccccccc-----cCCCCccccccCCchhHHHHHH------HHHHHHhCCCEEEEC
Confidence            4578888888776322 333333322211111     2222221         234788      999999999999999


Q ss_pred             cCCChhHHH---------HHHHHHHhhh---ccCCCeEEEEeeccHHHHHHHHHHHHHhhcc--CCCceEEEEEcCcccH
Q psy1548         157 KSGMGKTAV---------FVLATLQQLE---TTDSNVYVLVMCHTRELAFQISKEYERFSKY--MSNIKVGVFFGGLPIQ  222 (448)
Q Consensus       157 pTGsGKT~~---------~~l~~l~~l~---~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~--~~~~~v~~~~g~~~~~  222 (448)
                      +||||||.+         |++|.+..+.   ....+.++++++|+++||.|+...+.+..++  .++..+.+.+|+.+. 
T Consensus       187 ~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~~vg~~~~~g~~v~v~~Gg~~~-  265 (675)
T PHA02653        187 GTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLKSLGFDEIDGSPISLKYGSIPD-  265 (675)
T ss_pred             CCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHHHhCccccCCceEEEEECCcch-
Confidence            999999987         4455555442   2334568999999999999999988876654  236778888999862 


Q ss_pred             HhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCC-CCCeEEEEeccCCcc
Q psy1548         223 KDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSP-HTKQVMMFSATLSKE  301 (448)
Q Consensus       223 ~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~-~~~q~i~~SAT~~~~  301 (448)
                      ........ ..+|+|+|++.       ....+++++++|+||||.+... +  +.+..+++..+ ..+|+++||||++.+
T Consensus       266 ~~~~t~~k-~~~Ilv~T~~L-------~l~~L~~v~~VVIDEaHEr~~~-~--DllL~llk~~~~~~rq~ILmSATl~~d  334 (675)
T PHA02653        266 ELINTNPK-PYGLVFSTHKL-------TLNKLFDYGTVIIDEVHEHDQI-G--DIIIAVARKHIDKIRSLFLMTATLEDD  334 (675)
T ss_pred             HHhhcccC-CCCEEEEeCcc-------cccccccCCEEEccccccCccc-h--hHHHHHHHHhhhhcCEEEEEccCCcHh
Confidence            22122222 37899999752       1124788999999999998664 2  44555555443 345999999999988


Q ss_pred             HHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcC----------cchHHHHHHHHHhh--CCCCeEEEEECccHHHHH
Q psy1548         302 IRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLK----------ENEKNKKLFELLDV--LEFNQVVIFVKSVTRCIA  369 (448)
Q Consensus       302 ~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~----------~~~k~~~L~~ll~~--~~~~~~IIF~~s~~~a~~  369 (448)
                      +..+ ..++.+|..+.+...   +...++++|....          ...+...+..+...  ..++++||||+++.+|+.
T Consensus       335 v~~l-~~~~~~p~~I~I~gr---t~~pV~~~yi~~~~~~~~~~~y~~~~k~~~l~~L~~~~~~~~g~iLVFlpg~~ei~~  410 (675)
T PHA02653        335 RDRI-KEFFPNPAFVHIPGG---TLFPISEVYVKNKYNPKNKRAYIEEEKKNIVTALKKYTPPKGSSGIVFVASVSQCEE  410 (675)
T ss_pred             HHHH-HHHhcCCcEEEeCCC---cCCCeEEEEeecCcccccchhhhHHHHHHHHHHHHHhhcccCCcEEEEECcHHHHHH
Confidence            8776 578888888876432   3456777776433          12233333333322  235689999999999999


Q ss_pred             HHHHHHhC--CCcEEEEeCCCCHHHHHHHHHHH-hcCCCceEEEEecChhhHH
Q psy1548         370 LSTLLSEQ--NFPAVSIHRGMTQEERLKKYQEF-KDFHKGLAITFASDENDAK  419 (448)
Q Consensus       370 l~~~L~~~--g~~~~~lh~~~~~~eR~~~l~~F-~~g~~g~~I~~~t~~~d~~  419 (448)
                      +++.|++.  ++.+..+||+|++.  .+++++| ++|+  ..|.++|+-.+.+
T Consensus       411 l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk--~kILVATdIAERG  459 (675)
T PHA02653        411 YKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSKN--PSIIISTPYLESS  459 (675)
T ss_pred             HHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccCc--eeEEeccChhhcc
Confidence            99999987  79999999999985  5677887 5655  4677777754443

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.96  E-value=2.8e-27  Score=233.90  Aligned_cols=291  Identities=15%  Similarity=0.111  Sum_probs=195.2

Q ss_pred             hhhhhccccccceeeeeCcc--eeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccC--
Q psy1548         132 YLHRVARAGRFGTKAVLGMD--ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYM--  207 (448)
Q Consensus       132 yQ~~~~~~~~~~~~~~~g~~--vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~--  207 (448)
                      +|.+      +++.+..+.+  +++.+|||||||.+|++|++..      ..++++++|+++|++|+++.++.+...+  
T Consensus         1 hQ~~------~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~~------~~~~~~~~P~~aL~~~~~~~~~~~~~~~~~   68 (357)
T TIGR03158         1 HQVA------TFEALQSKDADIIFNTAPTGAGKTLAWLTPLLHG------ENDTIALYPTNALIEDQTEAIKEFVDVFKP   68 (357)
T ss_pred             CHHH------HHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHHc------CCCEEEEeChHHHHHHHHHHHHHHHHhcCC
Confidence            4888      8999998874  7899999999999999999852      2368999999999999999999887543  


Q ss_pred             -CCceEEEEEcCcccHHh-------------------HHHHhcCCCcEEEEcHHHHHHHHHCC----C-C---cCCCeeE
Q psy1548         208 -SNIKVGVFFGGLPIQKD-------------------EEYLKTHNPQIVVGTPGRILALVRNK----K-L---NLSLLKH  259 (448)
Q Consensus       208 -~~~~v~~~~g~~~~~~~-------------------~~~l~~~~~~IlV~Tp~~l~~~l~~~----~-~---~~~~i~~  259 (448)
                       .+..+..+.|.......                   ........++|+++||+.+..+++..    . .   .+.++++
T Consensus        69 ~~~~~v~~~~g~~~~d~~~~~~~~~~~~~g~~~~~~~r~~~~~~~p~illT~p~~l~~llr~~~~~~~~~~~~~~~~~~~  148 (357)
T TIGR03158        69 ERDVNLLHVSKATLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLTRFAYIDRGDIAAGFYTKFST  148 (357)
T ss_pred             CCCceEEEecCCchHHHHHhhhhhcccCccchhhhhHHHHHhcCCCCEEEecHHHHHHHHhhhccCcccchhhhhcCCCE
Confidence             14556666665322100                   01112235899999999998776531    1 1   2478999


Q ss_pred             EEecchhHHHhhh----hhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHh--cCCCeEEEEcCcc-----------
Q psy1548         260 FILDECDKMLEQL----EMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKF--MHDPMEVYVDDEA-----------  322 (448)
Q Consensus       260 lViDEah~l~~~~----~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~--l~~~~~i~~~~~~-----------  322 (448)
                      +|+||+|.+..+.    -+.-....+++......+++++|||+++.+...+...  +..|.........           
T Consensus       149 iV~DE~H~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~lSAT~~~~~~~~l~~~~~~~~~~~~v~g~~~~~~~~~~~~~~  228 (357)
T TIGR03158       149 VIFDEFHLYDAKQLVGMLFLLAYMQLIRFFECRRKFVFLSATPDPALILRLQNAKQAGVKIAPIDGEKYQFPDNPELEAD  228 (357)
T ss_pred             EEEecccccCcccchhhhhhhHHHHHHHhhhcCCcEEEEecCCCHHHHHHHHhccccCceeeeecCcccccCCChhhhcc
Confidence            9999999875430    1112333444444445799999999998877777664  4444433222200           


Q ss_pred             ------cccccceeEEEEEcCcchHHHHHHHHHh-------hCCCCeEEEEECccHHHHHHHHHHHhCC--CcEEEEeCC
Q psy1548         323 ------KLTLHGLQQHYVKLKENEKNKKLFELLD-------VLEFNQVVIFVKSVTRCIALSTLLSEQN--FPAVSIHRG  387 (448)
Q Consensus       323 ------~~~~~~i~~~~~~~~~~~k~~~L~~ll~-------~~~~~~~IIF~~s~~~a~~l~~~L~~~g--~~~~~lh~~  387 (448)
                            ....+.+.+.+.. ....|...+..+++       ...++++||||||++.|+.++..|++.|  +.+..+||.
T Consensus       229 ~~~~~~~~~~~~i~~~~~~-~~~~~~~~l~~l~~~i~~~~~~~~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~  307 (357)
T TIGR03158       229 NKTQSFRPVLPPVELELIP-APDFKEEELSELAEEVIERFRQLPGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGF  307 (357)
T ss_pred             ccccccceeccceEEEEEe-CCchhHHHHHHHHHHHHHHHhccCCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecC
Confidence                  0111355555554 33344443333222       2356799999999999999999999864  578899999


Q ss_pred             CCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         388 MTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       388 ~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      +++.+|.++.        ...|.++|+--++++  +|... .+ +.+ |.+.+.+.++.||
T Consensus       308 ~~~~~R~~~~--------~~~iLVaTdv~~rGi--Di~~~-~v-i~~-p~~~~~yiqR~GR  355 (357)
T TIGR03158       308 APKKDRERAM--------QFDILLGTSTVDVGV--DFKRD-WL-IFS-ARDAAAFWQRLGR  355 (357)
T ss_pred             CCHHHHHHhc--------cCCEEEEecHHhccc--CCCCc-eE-EEC-CCCHHHHhhhccc
Confidence            9999997653        247888887544443  33322 12 233 7778888899998

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.

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.96  E-value=4.8e-27  Score=242.40  Aligned_cols=292  Identities=15%  Similarity=0.121  Sum_probs=188.2

Q ss_pred             CchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccC
Q psy1548         128 DSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYM  207 (448)
Q Consensus       128 ~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  207 (448)
                      ..++||++      +++.++.+++.++++|||+|||+++...+...+.  ....++||++||++|+.|+.+.++++....
T Consensus       114 ~~r~~Q~~------av~~~l~~~~~il~apTGsGKT~i~~~l~~~~~~--~~~~~vLilvpt~eL~~Q~~~~l~~~~~~~  185 (501)
T PHA02558        114 EPHWYQYD------AVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLE--NYEGKVLIIVPTTSLVTQMIDDFVDYRLFP  185 (501)
T ss_pred             CCCHHHHH------HHHHHHhcCceEEEeCCCCCHHHHHHHHHHHHHh--cCCCeEEEEECcHHHHHHHHHHHHHhcccc
Confidence            45666999      9999999999999999999999976543222222  233489999999999999999999987543


Q ss_pred             CCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCC
Q psy1548         208 SNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPH  287 (448)
Q Consensus       208 ~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~  287 (448)
                       ...+..+.+|....        ...+|+|+||+++.+...   ..+++++++|+||||++... .    +..++..+++
T Consensus       186 -~~~~~~i~~g~~~~--------~~~~I~VaT~qsl~~~~~---~~~~~~~~iIvDEaH~~~~~-~----~~~il~~~~~  248 (501)
T PHA02558        186 -REAMHKIYSGTAKD--------TDAPIVVSTWQSAVKQPK---EWFDQFGMVIVDECHLFTGK-S----LTSIITKLDN  248 (501)
T ss_pred             -ccceeEEecCcccC--------CCCCEEEeeHHHHhhchh---hhccccCEEEEEchhcccch-h----HHHHHHhhhc
Confidence             45565666665422        136899999999876432   24678999999999988664 3    4566677777


Q ss_pred             CCeEEEEeccCCccHHHHHH-HhcCCCeEEEEcCcc-----cccccceeEEE---------------------EEcCcch
Q psy1548         288 TKQVMMFSATLSKEIRPVCK-KFMHDPMEVYVDDEA-----KLTLHGLQQHY---------------------VKLKENE  340 (448)
Q Consensus       288 ~~q~i~~SAT~~~~~~~~~~-~~l~~~~~i~~~~~~-----~~~~~~i~~~~---------------------~~~~~~~  340 (448)
                      ..++++||||+++....... ..+-.|....+....     ......+....                     .......
T Consensus       249 ~~~~lGLTATp~~~~~~~~~~~~~fG~i~~~v~~~~li~~g~l~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  328 (501)
T PHA02558        249 CKFKFGLTGSLRDGKANILQYVGLFGDIFKPVTTSQLMEEGQVTDLKINSIFLRYPDEDRVKLKGEDYQEEIKYITSHTK  328 (501)
T ss_pred             cceEEEEeccCCCccccHHHHHHhhCCceEEecHHHHHhCCCcCCceEEEEeccCCHHHhhhhcccchHHHHHHHhccHH
Confidence            78999999998654221111 001112222211100     00000000000                     0112223


Q ss_pred             HHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecC-hhh
Q psy1548         341 KNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASD-END  417 (448)
Q Consensus       341 k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~-~~d  417 (448)
                      +...+..++...  .+.+++|||++.++|+.+++.|++.|.++..+||+|++++|..+++.|++|+.  .++++|. --.
T Consensus       329 Rn~~I~~~~~~~~~~~~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~~--~vLvaT~~~l~  406 (501)
T PHA02558        329 RNKWIANLALKLAKKGENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKG--IIIVASYGVFS  406 (501)
T ss_pred             HHHHHHHHHHHHHhcCCCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCCC--eEEEEEcceec
Confidence            444444444332  35689999999999999999999999999999999999999999999998763  4555552 111


Q ss_pred             HHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         418 AKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       418 ~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      ++.  ++.+.-.+-+...|.+...+.|+.||
T Consensus       407 eG~--Dip~ld~vIl~~p~~s~~~~~QriGR  435 (501)
T PHA02558        407 TGI--SIKNLHHVIFAHPSKSKIIVLQSIGR  435 (501)
T ss_pred             ccc--ccccccEEEEecCCcchhhhhhhhhc
Confidence            111  22222222223334445556677776

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.95  E-value=4e-27  Score=252.34  Aligned_cols=255  Identities=16%  Similarity=0.201  Sum_probs=191.0

Q ss_pred             cceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh-hccCCCceEEEEEcCcc
Q psy1548         142 FGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF-SKYMSNIKVGVFFGGLP  220 (448)
Q Consensus       142 ~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~-~~~~~~~~v~~~~g~~~  220 (448)
                      .+..+.++++++++||||||||.+|.+++++....   ..+++++.|+|++|.|+.+.+... .... +..++..+++..
T Consensus        13 i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~~---~~~ilvlqPrR~aA~qia~rva~~l~~~~-g~~VGy~vr~~~   88 (812)
T PRK11664         13 LLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGI---NGKIIMLEPRRLAARNVAQRLAEQLGEKP-GETVGYRMRAES   88 (812)
T ss_pred             HHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCCc---CCeEEEECChHHHHHHHHHHHHHHhCccc-CceEEEEecCcc
Confidence            45566678999999999999999999999976422   248999999999999999988654 3333 677777776653


Q ss_pred             cHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhH-HHhhhhh-HHHHHHHHHhCCCCCeEEEEeccC
Q psy1548         221 IQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDK-MLEQLEM-RRDVQEIFRSSPHTKQVMMFSATL  298 (448)
Q Consensus       221 ~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~-l~~~~~~-~~~~~~i~~~l~~~~q~i~~SAT~  298 (448)
                      ...      . ..+|+|+||+++++++..+ ..++++++|||||+|. .++. ++ ...+..+++.++++.|+++||||+
T Consensus        89 ~~~------~-~t~I~v~T~G~Llr~l~~d-~~L~~v~~IIlDEaHER~l~~-Dl~L~ll~~i~~~lr~~lqlilmSATl  159 (812)
T PRK11664         89 KVG------P-NTRLEVVTEGILTRMIQRD-PELSGVGLVILDEFHERSLQA-DLALALLLDVQQGLRDDLKLLIMSATL  159 (812)
T ss_pred             ccC------C-CCcEEEEChhHHHHHHhhC-CCcCcCcEEEEcCCCcccccc-chHHHHHHHHHHhCCccceEEEEecCC
Confidence            221      1 2689999999999988764 4689999999999996 3332 22 223445667778889999999999


Q ss_pred             CccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHH-----HHHHHHhhCCCCeEEEEECccHHHHHHHHH
Q psy1548         299 SKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNK-----KLFELLDVLEFNQVVIFVKSVTRCIALSTL  373 (448)
Q Consensus       299 ~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~-----~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~  373 (448)
                      +.+  . ...++.++..+.....    ...++++|..++..++..     .+..++.. ..+++||||++..+++.+++.
T Consensus       160 ~~~--~-l~~~~~~~~~I~~~gr----~~pV~~~y~~~~~~~~~~~~v~~~l~~~l~~-~~g~iLVFlpg~~ei~~l~~~  231 (812)
T PRK11664        160 DND--R-LQQLLPDAPVIVSEGR----SFPVERRYQPLPAHQRFDEAVARATAELLRQ-ESGSLLLFLPGVGEIQRVQEQ  231 (812)
T ss_pred             CHH--H-HHHhcCCCCEEEecCc----cccceEEeccCchhhhHHHHHHHHHHHHHHh-CCCCEEEEcCCHHHHHHHHHH
Confidence            865  2 3466666555544322    234677777666555543     34444443 357899999999999999999


Q ss_pred             HHh---CCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHH
Q psy1548         374 LSE---QNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAK  419 (448)
Q Consensus       374 L~~---~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~  419 (448)
                      |++   .++.+..+||+|++++|.++++.|++|+  ..|.++|+-.+.+
T Consensus       232 L~~~~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~--rkVlvATnIAErs  278 (812)
T PRK11664        232 LASRVASDVLLCPLYGALSLAEQQKAILPAPAGR--RKVVLATNIAETS  278 (812)
T ss_pred             HHHhccCCceEEEeeCCCCHHHHHHHhccccCCC--eEEEEecchHHhc
Confidence            987   5788999999999999999999999887  5788888754443

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.95  E-value=6.7e-27  Score=250.14  Aligned_cols=255  Identities=14%  Similarity=0.180  Sum_probs=190.2

Q ss_pred             cceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh-ccCCCceEEEEEcCcc
Q psy1548         142 FGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS-KYMSNIKVGVFFGGLP  220 (448)
Q Consensus       142 ~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~-~~~~~~~v~~~~g~~~  220 (448)
                      .+..+..+.+++++|+||||||.+|.+++++...   .+.+++++.|+|++|.|+.+.+.... ... +..++...++..
T Consensus        10 i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~---~~~~ilvlqPrR~aA~qiA~rva~~~~~~~-g~~VGy~vr~~~   85 (819)
T TIGR01970        10 LRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPG---IGGKIIMLEPRRLAARSAAQRLASQLGEAV-GQTVGYRVRGEN   85 (819)
T ss_pred             HHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhc---cCCeEEEEeCcHHHHHHHHHHHHHHhCCCc-CcEEEEEEcccc
Confidence            4555667889999999999999999999998752   24589999999999999999885443 333 566666655432


Q ss_pred             cHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhH-HHhhhhhHH-HHHHHHHhCCCCCeEEEEeccC
Q psy1548         221 IQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDK-MLEQLEMRR-DVQEIFRSSPHTKQVMMFSATL  298 (448)
Q Consensus       221 ~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~-l~~~~~~~~-~~~~i~~~l~~~~q~i~~SAT~  298 (448)
                      .      ... ..+|+|+||++|++++..+ ..++++++|||||+|. +++. ++.- .+..+...++++.|+++||||+
T Consensus        86 ~------~s~-~t~I~v~T~G~Llr~l~~d-~~L~~v~~VIiDEaHER~L~~-Dl~L~ll~~i~~~lr~dlqlIlmSATl  156 (819)
T TIGR01970        86 K------VSR-RTRLEVVTEGILTRMIQDD-PELDGVGALIFDEFHERSLDA-DLGLALALDVQSSLREDLKILAMSATL  156 (819)
T ss_pred             c------cCC-CCcEEEECCcHHHHHHhhC-cccccCCEEEEeccchhhhcc-chHHHHHHHHHHhcCCCceEEEEeCCC
Confidence            1      112 3789999999999998764 4689999999999994 6664 5433 3345566678889999999999


Q ss_pred             CccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHH-----HHHHHHHhhCCCCeEEEEECccHHHHHHHHH
Q psy1548         299 SKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKN-----KKLFELLDVLEFNQVVIFVKSVTRCIALSTL  373 (448)
Q Consensus       299 ~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~-----~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~  373 (448)
                      +...   ...++.++..+.+...    ...++++|......++.     ..+..++.. ..+++||||++..+++.+++.
T Consensus       157 ~~~~---l~~~l~~~~vI~~~gr----~~pVe~~y~~~~~~~~~~~~v~~~l~~~l~~-~~g~iLVFlpg~~eI~~l~~~  228 (819)
T TIGR01970       157 DGER---LSSLLPDAPVVESEGR----SFPVEIRYLPLRGDQRLEDAVSRAVEHALAS-ETGSILVFLPGQAEIRRVQEQ  228 (819)
T ss_pred             CHHH---HHHHcCCCcEEEecCc----ceeeeeEEeecchhhhHHHHHHHHHHHHHHh-cCCcEEEEECCHHHHHHHHHH
Confidence            8653   3566666555554332    23466777666554442     233444443 357899999999999999999


Q ss_pred             HHh---CCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHH
Q psy1548         374 LSE---QNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAK  419 (448)
Q Consensus       374 L~~---~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~  419 (448)
                      |++   .++.+..+||+|++++|.++++.|++|+  ..|.++|+-.+.+
T Consensus       229 L~~~~~~~~~v~pLHg~L~~~eq~~~~~~~~~G~--rkVlVATnIAErg  275 (819)
T TIGR01970       229 LAERLDSDVLICPLYGELSLAAQDRAIKPDPQGR--RKVVLATNIAETS  275 (819)
T ss_pred             HHhhcCCCcEEEEecCCCCHHHHHHHHhhcccCC--eEEEEecchHhhc
Confidence            987   4789999999999999999999999987  4677777754433

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.

>KOG0952|consensus

Probab=99.95  E-value=1.1e-26  Score=240.76  Aligned_cols=265  Identities=22%  Similarity=0.308  Sum_probs=200.3

Q ss_pred             EeeccCCCCchhhhhhhccccccceeeee-CcceeeeccCCChhHHHHHHHHHHhhhc-------cCCCeEEEEeeccHH
Q psy1548         120 VFNYDMPEDSDTYLHRVARAGRFGTKAVL-GMDILCQAKSGMGKTAVFVLATLQQLET-------TDSNVYVLVMCHTRE  191 (448)
Q Consensus       120 v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~-g~~vli~apTGsGKT~~~~l~~l~~l~~-------~~~~~~~lil~Pt~~  191 (448)
                      +++|...+.+   |.+      ++|.+.. ..|+||+||||+|||..|++.+|..+..       .++..+++||+|+++
T Consensus       105 ~f~f~~fN~i---QS~------vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKA  175 (1230)
T KOG0952|consen  105 FFSFEEFNRI---QSE------VFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKA  175 (1230)
T ss_pred             cccHHHHHHH---HHH------hhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHH
Confidence            4567788888   999      9998876 5799999999999999999999998864       235679999999999


Q ss_pred             HHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCC---CcCCCeeEEEecchhHH
Q psy1548         192 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK---LNLSLLKHFILDECDKM  268 (448)
Q Consensus       192 L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~---~~~~~i~~lViDEah~l  268 (448)
                      ||.++.+.+.+=...+ +++|..++|++......  ...  ++|+|+||+++--..++..   -.++.++++||||+|.+
T Consensus       176 La~Em~~~~~kkl~~~-gi~v~ELTGD~ql~~te--i~~--tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHlL  250 (1230)
T KOG0952|consen  176 LAAEMVDKFSKKLAPL-GISVRELTGDTQLTKTE--IAD--TQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHLL  250 (1230)
T ss_pred             HHHHHHHHHhhhcccc-cceEEEecCcchhhHHH--HHh--cCEEEecccceeeeeeeeccchhhhhheeeEEeeeehhh
Confidence            9999776665544444 89999999998766544  332  7999999999754443322   23578999999999977


Q ss_pred             HhhhhhHHHHHHHHHhC-------CCCCeEEEEeccCCccHHHHHHHhcCCCeE-EEEcCcccccccceeEEEEEcCcc-
Q psy1548         269 LEQLEMRRDVQEIFRSS-------PHTKQVMMFSATLSKEIRPVCKKFMHDPME-VYVDDEAKLTLHGLQQHYVKLKEN-  339 (448)
Q Consensus       269 ~~~~~~~~~~~~i~~~l-------~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~-i~~~~~~~~~~~~i~~~~~~~~~~-  339 (448)
                      .+  ..++.++.|+.++       ....+++++|||+|+- .+++.++-.+|.. +...+. ...+..+.+.++..+.. 
T Consensus       251 hd--~RGpvlEtiVaRtlr~vessqs~IRivgLSATlPN~-eDvA~fL~vn~~~glfsFd~-~yRPvpL~~~~iG~k~~~  326 (1230)
T KOG0952|consen  251 HD--DRGPVLETIVARTLRLVESSQSMIRIVGLSATLPNY-EDVARFLRVNPYAGLFSFDQ-RYRPVPLTQGFIGIKGKK  326 (1230)
T ss_pred             cC--cccchHHHHHHHHHHHHHhhhhheEEEEeeccCCCH-HHHHHHhcCCCccceeeecc-cccccceeeeEEeeeccc
Confidence            66  6777787776554       3466899999999865 5666666555433 333333 45667778877776654 


Q ss_pred             --h--------HHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhC----C-------------------CcEEEEeC
Q psy1548         340 --E--------KNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQ----N-------------------FPAVSIHR  386 (448)
Q Consensus       340 --~--------k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~----g-------------------~~~~~lh~  386 (448)
                        .        ..+.+.+.+.  .+.+++|||.+++.+...|+.|.+.    |                   .....+|+
T Consensus       327 ~~~~~~~~d~~~~~kv~e~~~--~g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhA  404 (1230)
T KOG0952|consen  327 NRQQKKNIDEVCYDKVVEFLQ--EGHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHA  404 (1230)
T ss_pred             chhhhhhHHHHHHHHHHHHHH--cCCeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhccc
Confidence              1        1222333333  4679999999999999999998652    1                   12678999


Q ss_pred             CCCHHHHHHHHHHHhcCC
Q psy1548         387 GMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       387 ~~~~~eR~~~l~~F~~g~  404 (448)
                      ||...+|..+...|+.|.
T Consensus       405 Gm~r~DR~l~E~~F~~G~  422 (1230)
T KOG0952|consen  405 GMLRSDRQLVEKEFKEGH  422 (1230)
T ss_pred             ccchhhHHHHHHHHhcCC
Confidence            999999999999999998

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

Probab=99.94  E-value=9.1e-26  Score=219.40  Aligned_cols=160  Identities=17%  Similarity=0.253  Sum_probs=134.1

Q ss_pred             CchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccC
Q psy1548         128 DSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYM  207 (448)
Q Consensus       128 ~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  207 (448)
                      ..+.||..      ....++.+ |.||+.|||.|||+.+++-+...+.+.++  ++|+++||+.|+.|..+.|+++.+..
T Consensus        15 e~R~YQ~~------i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~~~--kvlfLAPTKPLV~Qh~~~~~~v~~ip   85 (542)
T COG1111          15 EPRLYQLN------IAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWFGG--KVLFLAPTKPLVLQHAEFCRKVTGIP   85 (542)
T ss_pred             cHHHHHHH------HHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhcCC--eEEEecCCchHHHHHHHHHHHHhCCC
Confidence            44888998      55555544 99999999999999999999888877654  89999999999999999999998765


Q ss_pred             CCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCC
Q psy1548         208 SNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPH  287 (448)
Q Consensus       208 ~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~  287 (448)
                       .-.+..++|..+..+....+.+  .+|+|+||+.+.+-+..+.+++.++.++|+||||+-.+. ..+..+.+......+
T Consensus        86 -~~~i~~ltGev~p~~R~~~w~~--~kVfvaTPQvveNDl~~Grid~~dv~~lifDEAHRAvGn-yAYv~Va~~y~~~~k  161 (542)
T COG1111          86 -EDEIAALTGEVRPEEREELWAK--KKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHRAVGN-YAYVFVAKEYLRSAK  161 (542)
T ss_pred             -hhheeeecCCCChHHHHHHHhh--CCEEEeccHHHHhHHhcCccChHHceEEEechhhhccCc-chHHHHHHHHHHhcc
Confidence             6788999999987766665555  589999999999999999999999999999999998887 555555555555567


Q ss_pred             CCeEEEEeccCCc
Q psy1548         288 TKQVMMFSATLSK  300 (448)
Q Consensus       288 ~~q~i~~SAT~~~  300 (448)
                      ++.++++|||...
T Consensus       162 ~~~ilgLTASPGs  174 (542)
T COG1111         162 NPLILGLTASPGS  174 (542)
T ss_pred             CceEEEEecCCCC
Confidence            7789999999644

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

Probab=99.94  E-value=6.6e-26  Score=200.79  Aligned_cols=165  Identities=27%  Similarity=0.465  Sum_probs=140.9

Q ss_pred             hhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCc
Q psy1548         131 TYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI  210 (448)
Q Consensus       131 ~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~  210 (448)
                      ++|++      +++.+..|+++++.+|||+|||++|++|+++.+... ...++++++|+++|+.|+.+.+..+.... ++
T Consensus         2 ~~Q~~------~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~-~~~~~lii~P~~~l~~q~~~~~~~~~~~~-~~   73 (169)
T PF00270_consen    2 PLQQE------AIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEG-KDARVLIIVPTRALAEQQFERLRKFFSNT-NV   73 (169)
T ss_dssp             HHHHH------HHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT-SSSEEEEEESSHHHHHHHHHHHHHHTTTT-TS
T ss_pred             HHHHH------HHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccC-CCceEEEEeeccccccccccccccccccc-cc
Confidence            35999      999999999999999999999999999999988776 44599999999999999999999998875 78


Q ss_pred             eEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCC--CC
Q psy1548         211 KVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSP--HT  288 (448)
Q Consensus       211 ~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~--~~  288 (448)
                      ++..++|+............+.++|+|+||+++.+++.....++.+++++|+||+|.+..+ .+...+..++..+.  .+
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~iViDE~h~l~~~-~~~~~~~~i~~~~~~~~~  152 (169)
T PF00270_consen   74 RVVLLHGGQSISEDQREVLSNQADILVTTPEQLLDLISNGKINISRLSLIVIDEAHHLSDE-TFRAMLKSILRRLKRFKN  152 (169)
T ss_dssp             SEEEESTTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSSTGTTESEEEEETHHHHHHT-THHHHHHHHHHHSHTTTT
T ss_pred             ccccccccccccccccccccccccccccCcchhhccccccccccccceeeccCcccccccc-cHHHHHHHHHHHhcCCCC
Confidence            9999999887553333222434899999999999999986667788999999999999997 88888999888873  36


Q ss_pred             CeEEEEeccCCccHHH
Q psy1548         289 KQVMMFSATLSKEIRP  304 (448)
Q Consensus       289 ~q~i~~SAT~~~~~~~  304 (448)
                      .|++++|||+++.+++
T Consensus       153 ~~~i~~SAT~~~~~~~  168 (169)
T PF00270_consen  153 IQIILLSATLPSNVEK  168 (169)
T ss_dssp             SEEEEEESSSTHHHHH
T ss_pred             CcEEEEeeCCChhHhh
Confidence            8999999999966554

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=99.93  E-value=1.3e-24  Score=236.52  Aligned_cols=272  Identities=21%  Similarity=0.305  Sum_probs=191.4

Q ss_pred             chhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCC
Q psy1548         129 SDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS  208 (448)
Q Consensus       129 ~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  208 (448)
                      .++||++      +...++.+ |+++++|||+|||+++++++...+.  ..+.++|||+||++|+.|+.+.++.+.... 
T Consensus        16 ~r~yQ~~------~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~--~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~-   85 (773)
T PRK13766         16 ARLYQQL------LAATALKK-NTLVVLPTGLGKTAIALLVIAERLH--KKGGKVLILAPTKPLVEQHAEFFRKFLNIP-   85 (773)
T ss_pred             ccHHHHH------HHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHH--hCCCeEEEEeCcHHHHHHHHHHHHHHhCCC-
Confidence            4788999      77666666 9999999999999999999888763  234589999999999999999999887543 


Q ss_pred             CceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCC
Q psy1548         209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHT  288 (448)
Q Consensus       209 ~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~  288 (448)
                      +.++..++|+.+..... .+... .+|+|+||+.+...+..+.+.+.+++++|+||||++... .....+...+....+.
T Consensus        86 ~~~v~~~~g~~~~~~r~-~~~~~-~~iiv~T~~~l~~~l~~~~~~~~~~~liVvDEaH~~~~~-~~~~~i~~~~~~~~~~  162 (773)
T PRK13766         86 EEKIVVFTGEVSPEKRA-ELWEK-AKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGN-YAYVYIAERYHEDAKN  162 (773)
T ss_pred             CceEEEEeCCCCHHHHH-HHHhC-CCEEEECHHHHHHHHHcCCCChhhCcEEEEECCcccccc-ccHHHHHHHHHhcCCC
Confidence            45788888887655433 33333 689999999998888888888899999999999998765 3334444445455556


Q ss_pred             CeEEEEeccCCcc---HHHHHHHhcCCCeEEEEcCc--------------------cc----------------------
Q psy1548         289 KQVMMFSATLSKE---IRPVCKKFMHDPMEVYVDDE--------------------AK----------------------  323 (448)
Q Consensus       289 ~q~i~~SAT~~~~---~~~~~~~~l~~~~~i~~~~~--------------------~~----------------------  323 (448)
                      .++++||||+...   +..++..+......+.....                    ..                      
T Consensus       163 ~~il~lTaTP~~~~~~i~~~~~~L~i~~v~~~~~~~~~v~~~~~~~~v~~~~v~l~~~~~~i~~~l~~~~~~~l~~l~~~  242 (773)
T PRK13766        163 PLVLGLTASPGSDEEKIKEVCENLGIEHVEVRTEDDPDVKPYVHKVKIEWVRVELPEELKEIRDLLNEALKDRLKKLKEL  242 (773)
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHhCCceEEEEcCCCChhHHhhhccceeEEEEeCCcHHHHHHHHHHHHHHHHHHHHHHHC
Confidence            7899999997433   22223332211111000000                    00                      


Q ss_pred             -cc--cc-------------ceeEE-------------------------------------------------------
Q psy1548         324 -LT--LH-------------GLQQH-------------------------------------------------------  332 (448)
Q Consensus       324 -~~--~~-------------~i~~~-------------------------------------------------------  332 (448)
                       ..  ..             .+...                                                       
T Consensus       243 ~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~y~~~l~~~~~~~~~~~~  322 (773)
T PRK13766        243 GVIVSISPDVSKKELLGLQKKLQQEIANDDSEGYEAISILAEAMKLRHAVELLETQGVEALRRYLERLREEARSSGGSKA  322 (773)
T ss_pred             CCcccCCCCcCHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHhhccccCCcHH
Confidence             00  00             00000                                                       


Q ss_pred             -----------------EEEcCcchHHHHHHHHHhh----CCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCC----
Q psy1548         333 -----------------YVKLKENEKNKKLFELLDV----LEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRG----  387 (448)
Q Consensus       333 -----------------~~~~~~~~k~~~L~~ll~~----~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~----  387 (448)
                                       ........|...|.++++.    ..++++||||+++..|+.|++.|...|+++..+||.    
T Consensus       323 ~~~l~~~~~~~~~~~~~~~~~~~~pK~~~L~~il~~~~~~~~~~kvlIF~~~~~t~~~L~~~L~~~~~~~~~~~g~~~~~  402 (773)
T PRK13766        323 SKRLVEDPRFRKAVRKAKELDIEHPKLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKD  402 (773)
T ss_pred             HHHHHhCHHHHHHHHHHHhcccCChHHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHhCCCceEEEEcccccc
Confidence                             0001112356666666644    456799999999999999999999999999999986    


Q ss_pred             ----CCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         388 ----MTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       388 ----~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                          |++.+|.++++.|++|+  ..++++|+.
T Consensus       403 ~~~~~~~~~r~~~~~~F~~g~--~~vLvaT~~  432 (773)
T PRK13766        403 GDKGMSQKEQIEILDKFRAGE--FNVLVSTSV  432 (773)
T ss_pred             ccCCCCHHHHHHHHHHHHcCC--CCEEEECCh
Confidence                99999999999999987  456666654

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.93  E-value=7.5e-25  Score=226.06  Aligned_cols=300  Identities=19%  Similarity=0.169  Sum_probs=216.2

Q ss_pred             cCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         124 DMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       124 ~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      -.|+++   |..      ++|.++.|+  |+.+.||+|||++|.+|++.....   +..++|++||++||.|.++.+..+
T Consensus       102 ~~p~~V---Q~~------~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~---G~~v~VvTptreLA~qdae~~~~l  167 (656)
T PRK12898        102 QRHFDV---QLM------GGLALLSGR--LAEMQTGEGKTLTATLPAGTAALA---GLPVHVITVNDYLAERDAELMRPL  167 (656)
T ss_pred             CCCChH---HHH------HHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhc---CCeEEEEcCcHHHHHHHHHHHHHH
Confidence            378899   999      999999999  999999999999999999987543   458999999999999999999999


Q ss_pred             hccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHH-HHHHHCCC-------------------------CcCCCe
Q psy1548         204 SKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRI-LALVRNKK-------------------------LNLSLL  257 (448)
Q Consensus       204 ~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l-~~~l~~~~-------------------------~~~~~i  257 (448)
                      ...+ ++++++++|+.+..  ...... .++|+|||...+ .++|+.+.                         .-...+
T Consensus       168 ~~~l-Glsv~~i~gg~~~~--~r~~~y-~~dIvygT~~e~~FDyLrd~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~r~~  243 (656)
T PRK12898        168 YEAL-GLTVGCVVEDQSPD--ERRAAY-GADITYCTNKELVFDYLRDRLALGQRASDARLALESLHGRSSRSTQLLLRGL  243 (656)
T ss_pred             Hhhc-CCEEEEEeCCCCHH--HHHHHc-CCCEEEECCCchhhhhccccccccccccchhhhhhhhccccCchhhhccccc
Confidence            9988 99999999997633  333333 389999999887 44443321                         113557


Q ss_pred             eEEEecchhHHHhh--------------h---hhHHHHHHHHHhC--------------------------------C--
Q psy1548         258 KHFILDECDKMLEQ--------------L---EMRRDVQEIFRSS--------------------------------P--  286 (448)
Q Consensus       258 ~~lViDEah~l~~~--------------~---~~~~~~~~i~~~l--------------------------------~--  286 (448)
                      .+.|+||+|.++=+              .   .+......+.+.+                                +  
T Consensus       244 ~~aIvDEvDSiLiDeartpliis~~~~~~~~~~~y~~~~~~~~~l~~~~~y~~d~~~~~v~lt~~g~~~~e~~~~~l~~~  323 (656)
T PRK12898        244 HFAIVDEADSVLIDEARTPLIISAPAKEADEAEVYRQALELAAQLKEGEDYTIDAAEKRIELTEAGRARIAELAESLPPA  323 (656)
T ss_pred             ceeEeecccceeeccCCCceEEECCCCCCchhHHHHHHHHHHHhcCCCCceEEECCCCeEEEcHHHHHHHHHHhCcchhh
Confidence            78999999965321              0   0100001010000                                0  


Q ss_pred             ----------------------CC--------------------------------------------------------
Q psy1548         287 ----------------------HT--------------------------------------------------------  288 (448)
Q Consensus       287 ----------------------~~--------------------------------------------------------  288 (448)
                                            .+                                                        
T Consensus       324 ~~~~~~~~~~i~~Al~A~~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~w~~GLhQaieaKE~v~i~~e~~t~a~It~q~  403 (656)
T PRK12898        324 WRGAVRREELVRQALSALHLFRRDEHYIVRDGKVVIVDEFTGRVMPDRSWEDGLHQMIEAKEGCELTDPRETLARITYQR  403 (656)
T ss_pred             cccchHHHHHHHHHHHHHHHHhcCCceEEECCeEEEEECCCCeECCCCCcChHHHHHHHHhcCCCCCcCceeeeeehHHH
Confidence                                  00                                                        


Q ss_pred             -----CeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhC--CCCeEEEEE
Q psy1548         289 -----KQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVL--EFNQVVIFV  361 (448)
Q Consensus       289 -----~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~--~~~~~IIF~  361 (448)
                           .++.+||||.+....++...|..++..|.....   ......+.++.+...+|...|..++...  .+.++||||
T Consensus       404 ~Fr~Y~kl~GmTGTa~~~~~El~~~y~l~vv~IPt~kp---~~r~~~~~~v~~t~~~K~~aL~~~i~~~~~~~~pvLIft  480 (656)
T PRK12898        404 FFRRYLRLAGMTGTAREVAGELWSVYGLPVVRIPTNRP---SQRRHLPDEVFLTAAAKWAAVAARVRELHAQGRPVLVGT  480 (656)
T ss_pred             HHHhhHHHhcccCcChHHHHHHHHHHCCCeEEeCCCCC---ccceecCCEEEeCHHHHHHHHHHHHHHHHhcCCCEEEEe
Confidence                 135799999998888888888888766655443   2233445567777888999999998764  256899999


Q ss_pred             CccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHH----HHHHH--HHhcCCCCCC
Q psy1548         362 KSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKI----LNNVQ--DRFDVSISEL  435 (448)
Q Consensus       362 ~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~----l~~i~--~~~~~~~~~~  435 (448)
                      +|++.++.++..|.+.|+++..+||++.+.+  +.+..|+.++ | .|+++|+-.-+++    ...+.  .-+.+-..++
T Consensus       481 ~t~~~se~L~~~L~~~gi~~~~Lhg~~~~rE--~~ii~~ag~~-g-~VlVATdmAgRGtDI~l~~~V~~~GGLhVI~~d~  556 (656)
T PRK12898        481 RSVAASERLSALLREAGLPHQVLNAKQDAEE--AAIVARAGQR-G-RITVATNMAGRGTDIKLEPGVAARGGLHVILTER  556 (656)
T ss_pred             CcHHHHHHHHHHHHHCCCCEEEeeCCcHHHH--HHHHHHcCCC-C-cEEEEccchhcccCcCCccchhhcCCCEEEEcCC
Confidence            9999999999999999999999999966544  4455554333 3 4778877432332    11221  1135777889


Q ss_pred             CccccccccccCC
Q psy1548         436 PDEIDLSTYIEGR  448 (448)
Q Consensus       436 p~~~~~~~~~~~~  448 (448)
                      |++...+.++.||
T Consensus       557 P~s~r~y~hr~GR  569 (656)
T PRK12898        557 HDSARIDRQLAGR  569 (656)
T ss_pred             CCCHHHHHHhccc
Confidence            9998888888887

>KOG0351|consensus

Probab=99.93  E-value=1.3e-25  Score=239.83  Aligned_cols=294  Identities=15%  Similarity=0.101  Sum_probs=210.4

Q ss_pred             hhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCC
Q psy1548         130 DTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  209 (448)
Q Consensus       130 ~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  209 (448)
                      ++.|++      ++...+.|+|+++.+|||.||++||.+|++-.      ++.+|||.|..+|++.+...+...     +
T Consensus       266 R~~Q~e------aI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~------~gitvVISPL~SLm~DQv~~L~~~-----~  328 (941)
T KOG0351|consen  266 RPNQLE------AINATLSGKDCFVLMPTGGGKSLCYQLPALLL------GGVTVVISPLISLMQDQVTHLSKK-----G  328 (941)
T ss_pred             ChhHHH------HHHHHHcCCceEEEeecCCceeeEeecccccc------CCceEEeccHHHHHHHHHHhhhhc-----C
Confidence            344999      99999999999999999999999999998753      338999999999998865555321     7


Q ss_pred             ceEEEEEcCcccHHhH---HHHhcC--CCcEEEEcHHHHHHH--HHCCCCcCCC---eeEEEecchhHHHhh-hhhHHHH
Q psy1548         210 IKVGVFFGGLPIQKDE---EYLKTH--NPQIVVGTPGRILAL--VRNKKLNLSL---LKHFILDECDKMLEQ-LEMRRDV  278 (448)
Q Consensus       210 ~~v~~~~g~~~~~~~~---~~l~~~--~~~IlV~Tp~~l~~~--l~~~~~~~~~---i~~lViDEah~l~~~-~~~~~~~  278 (448)
                      +....+.++.....+.   ..+..+  ..+|++.||+++...  +......+..   +.++||||||++..| ++||+.+
T Consensus       329 I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWgHdFRp~Y  408 (941)
T KOG0351|consen  329 IPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWGHDFRPSY  408 (941)
T ss_pred             cceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhhcccccHHH
Confidence            8888888887765433   234444  579999999998542  1222222333   889999999999999 6799999


Q ss_pred             HHHHHhC--CCCCeEEEEeccCCccHHHHHHHhcC--CCeEEEEcCcccccccceeEEEEEcCcchH-HHHHHHHHhhCC
Q psy1548         279 QEIFRSS--PHTKQVMMFSATLSKEIRPVCKKFMH--DPMEVYVDDEAKLTLHGLQQHYVKLKENEK-NKKLFELLDVLE  353 (448)
Q Consensus       279 ~~i~~~l--~~~~q~i~~SAT~~~~~~~~~~~~l~--~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k-~~~L~~ll~~~~  353 (448)
                      ..+....  .+.+.+|++|||.+..+++.+...+.  +|..+..    .....|+...+..-..... ...+...-..++
T Consensus       409 k~l~~l~~~~~~vP~iALTATAT~~v~~DIi~~L~l~~~~~~~~----sfnR~NL~yeV~~k~~~~~~~~~~~~~~~~~~  484 (941)
T KOG0351|consen  409 KRLGLLRIRFPGVPFIALTATATERVREDVIRSLGLRNPELFKS----SFNRPNLKYEVSPKTDKDALLDILEESKLRHP  484 (941)
T ss_pred             HHHHHHHhhCCCCCeEEeehhccHHHHHHHHHHhCCCCcceecc----cCCCCCceEEEEeccCccchHHHHHHhhhcCC
Confidence            9874433  23478999999999988887666554  5553332    2335666555544432222 333333334456


Q ss_pred             CCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCC
Q psy1548         354 FNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSIS  433 (448)
Q Consensus       354 ~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~  433 (448)
                      ...+||||.++..|+.++..|++.|+.+..||+||+..+|..+.+.|..++.  -|.++|=.  .++.-+-.+.--+...
T Consensus       485 ~~s~IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~w~~~~~--~VivATVA--FGMGIdK~DVR~ViH~  560 (941)
T KOG0351|consen  485 DQSGIIYCLSRKECEQVSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSDKI--RVIVATVA--FGMGIDKPDVRFVIHY  560 (941)
T ss_pred             CCCeEEEeCCcchHHHHHHHHHHhchhhHhhhcCCCHHHHHHHHHHHhcCCC--eEEEEEee--ccCCCCCCceeEEEEC
Confidence            7799999999999999999999999999999999999999999999999983  33333322  1111111222235667


Q ss_pred             CCCccccccccccCC
Q psy1548         434 ELPDEIDLSTYIEGR  448 (448)
Q Consensus       434 ~~p~~~~~~~~~~~~  448 (448)
                      .+|.+++.+-+=.||
T Consensus       561 ~lPks~E~YYQE~GR  575 (941)
T KOG0351|consen  561 SLPKSFEGYYQEAGR  575 (941)
T ss_pred             CCchhHHHHHHhccc
Confidence            778887766554444

>KOG0354|consensus

Probab=99.92  E-value=1.2e-23  Score=215.82  Aligned_cols=167  Identities=16%  Similarity=0.200  Sum_probs=131.0

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      |..+.++|+||.+      ....++ |+|+||++|||+|||++++..+++.+++.+. .++++++|++.|+.|+...+..
T Consensus        57 ~p~~~~lR~YQ~e------ivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~-~KiVF~aP~~pLv~QQ~a~~~~  128 (746)
T KOG0354|consen   57 YPTNLELRNYQEE------LVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPK-GKVVFLAPTRPLVNQQIACFSI  128 (746)
T ss_pred             ccCcccccHHHHH------HhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCc-ceEEEeeCCchHHHHHHHHHhh
Confidence            6667778999999      887888 9999999999999999999999999998877 5999999999999998755554


Q ss_pred             hhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCc-CCCeeEEEecchhHHHhhhhhHHHHHHH
Q psy1548         203 FSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLN-LSLLKHFILDECDKMLEQLEMRRDVQEI  281 (448)
Q Consensus       203 ~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~-~~~i~~lViDEah~l~~~~~~~~~~~~i  281 (448)
                      ++.   ...+....||.........+.. ..+|+|+||+.+.+.+.++... ++.+.++||||||+-...+.+...+...
T Consensus       129 ~~~---~~~~T~~l~~~~~~~~r~~i~~-s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra~kn~~Y~~Vmr~~  204 (746)
T KOG0354|consen  129 YLI---PYSVTGQLGDTVPRSNRGEIVA-SKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRTSKNHPYNNIMREY  204 (746)
T ss_pred             ccC---cccceeeccCccCCCchhhhhc-ccceEEeChHhhhhhcccccccccceEEEEEEcccccccccccHHHHHHHH
Confidence            443   2455555666433333333333 3799999999999999876554 5999999999999988875566666666


Q ss_pred             HHhCCCCCeEEEEeccCCcc
Q psy1548         282 FRSSPHTKQVMMFSATLSKE  301 (448)
Q Consensus       282 ~~~l~~~~q~i~~SAT~~~~  301 (448)
                      +..-....|++++|||+..+
T Consensus       205 l~~k~~~~qILgLTASpG~~  224 (746)
T KOG0354|consen  205 LDLKNQGNQILGLTASPGSK  224 (746)
T ss_pred             HHhhhccccEEEEecCCCcc
Confidence            66655566999999996553

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.91  E-value=1.8e-23  Score=220.28  Aligned_cols=298  Identities=16%  Similarity=0.156  Sum_probs=205.4

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .|+++   |..      +++.+..|+  ++.+.||+|||+++++|++.....   +..++|++||+.||.|.++.+..+.
T Consensus        78 ~p~~v---Ql~------~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~---G~~v~VvTpt~~LA~qd~e~~~~l~  143 (790)
T PRK09200         78 RPYDV---QLI------GALVLHEGN--IAEMQTGEGKTLTATMPLYLNALE---GKGVHLITVNDYLAKRDAEEMGQVY  143 (790)
T ss_pred             CCchH---HHH------hHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHc---CCCeEEEeCCHHHHHHHHHHHHHHH
Confidence            78888   999      888888887  999999999999999999855443   4579999999999999999999999


Q ss_pred             ccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHH-HHHHHCCC------CcCCCeeEEEecchhHHHhh------
Q psy1548         205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRI-LALVRNKK------LNLSLLKHFILDECDKMLEQ------  271 (448)
Q Consensus       205 ~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l-~~~l~~~~------~~~~~i~~lViDEah~l~~~------  271 (448)
                      ..+ +++++++.|+.+...+.....  .++|+||||+++ .+++....      ..+..+.++|+||||.|+=+      
T Consensus       144 ~~l-Gl~v~~i~g~~~~~~~r~~~y--~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEaDsiLiDea~tpl  220 (790)
T PRK09200        144 EFL-GLTVGLNFSDIDDASEKKAIY--EADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEIDSILLDEAQTPL  220 (790)
T ss_pred             hhc-CCeEEEEeCCCCcHHHHHHhc--CCCEEEECCccccchhHHhccccchhhhcccccceEEEeccccceeccCCCce
Confidence            998 999999999987433333332  389999999999 55554322      34578899999999977522      


Q ss_pred             ---------hhhHHHHHHHHHhCCCC--------C---------------------------------------------
Q psy1548         272 ---------LEMRRDVQEIFRSSPHT--------K---------------------------------------------  289 (448)
Q Consensus       272 ---------~~~~~~~~~i~~~l~~~--------~---------------------------------------------  289 (448)
                               .........+...+...        .                                             
T Consensus       221 iisg~~~~~~~~y~~~~~~~~~l~~~~dy~~d~~~~~~~lt~~g~~~~e~~~~i~~l~~~~~~~~~~~i~~Al~A~~~~~  300 (790)
T PRK09200        221 IISGKPRVQSNLYHIAAKFVKTLEEDVDYEFDEEKKEVWLTDQGIEKAESYFGIDNLYSLEHQVLYRHIILALRAHVLFK  300 (790)
T ss_pred             eeeCCCccccHHHHHHHHHHHhcccCCCeEEecCCCeEEecHhHHHHHHHhcCCccccChhhhHHHHHHHHHHHHHHHhh
Confidence                     01122222222222110        0                                             


Q ss_pred             ----------------------------------------------------------------eEEEEeccCCccHHHH
Q psy1548         290 ----------------------------------------------------------------QVMMFSATLSKEIRPV  305 (448)
Q Consensus       290 ----------------------------------------------------------------q~i~~SAT~~~~~~~~  305 (448)
                                                                                      ++.+||.|......++
T Consensus       301 ~d~dYiV~~~~v~ivD~~TGr~~~gr~~s~GlhQaieaKe~v~i~~e~~t~a~It~q~~fr~Y~kl~GmTGTa~t~~~e~  380 (790)
T PRK09200        301 RDVDYIVYDGEIVLVDRFTGRVLPGRKLQDGLHQAIEAKEGVEITEENRTMASITIQNLFRMFPKLSGMTGTAKTEEKEF  380 (790)
T ss_pred             cCCcEEEECCEEEEEECCCCcCCCCCccChHHHHHHHHhcCCCcCCCceehhhhhHHHHHHHhHHHhccCCCChHHHHHH
Confidence                                                                            2244444443333333


Q ss_pred             HHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhCCCcEEE
Q psy1548         306 CKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQNFPAVS  383 (448)
Q Consensus       306 ~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~  383 (448)
                      ...|.- ++ +.+++. ......-....+.+...+|...+...+...  .+.++||||+|++.++.++..|.+.|+++..
T Consensus       381 ~~~Y~l-~v-~~IPt~-kp~~r~d~~~~i~~~~~~K~~al~~~i~~~~~~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~  457 (790)
T PRK09200        381 FEVYNM-EV-VQIPTN-RPIIRIDYPDKVFVTLDEKYKAVIEEVKERHETGRPVLIGTGSIEQSETFSKLLDEAGIPHNL  457 (790)
T ss_pred             HHHhCC-cE-EECCCC-CCcccccCCCeEEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCCEEE
Confidence            332221 11 111111 110010111234456678999998888653  5679999999999999999999999999999


Q ss_pred             EeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHH---HHH-----hcCCCCCCCccccccccccCC
Q psy1548         384 IHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNV---QDR-----FDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       384 lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i---~~~-----~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      +||++.+.++..+...++.|    .|+++|+-.-+++  +|   ...     +.+-..++|.+...+.++.||
T Consensus       458 L~~~~~~~e~~~i~~ag~~g----~VlIATdmAgRG~--DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~GR  524 (790)
T PRK09200        458 LNAKNAAKEAQIIAEAGQKG----AVTVATNMAGRGT--DIKLGEGVHELGGLAVIGTERMESRRVDLQLRGR  524 (790)
T ss_pred             ecCCccHHHHHHHHHcCCCC----eEEEEccchhcCc--CCCcccccccccCcEEEeccCCCCHHHHHHhhcc
Confidence            99999998888777776543    5788877432332  33   122     356677899998888888887

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.91  E-value=4.9e-23  Score=213.83  Aligned_cols=300  Identities=19%  Similarity=0.201  Sum_probs=204.3

Q ss_pred             cCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         124 DMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       124 ~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      -.|+++   |..      ..+.+..|+  ++.++||+|||++|.+|++.....   +..+.|++||..||.|..+.+..+
T Consensus        55 ~~p~~v---Qli------g~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~---G~~V~VvTpt~~LA~qdae~~~~l  120 (745)
T TIGR00963        55 MRPFDV---QLI------GGIALHKGK--IAEMKTGEGKTLTATLPAYLNALT---GKGVHVVTVNDYLAQRDAEWMGQV  120 (745)
T ss_pred             CCccch---HHh------hhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHh---CCCEEEEcCCHHHHHHHHHHHHHH
Confidence            368888   999      877777776  999999999999999999533332   336999999999999999999999


Q ss_pred             hccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHH-HHHHHCC------CCcCCCeeEEEecchhHHHhh-----
Q psy1548         204 SKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRI-LALVRNK------KLNLSLLKHFILDECDKMLEQ-----  271 (448)
Q Consensus       204 ~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l-~~~l~~~------~~~~~~i~~lViDEah~l~~~-----  271 (448)
                      ...+ ++++++++|+.+...+...+   .++|+||||+++ .++++.+      ...+..+.++|+||+|.|+-+     
T Consensus       121 ~~~L-GLsv~~i~g~~~~~~r~~~y---~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs~LIDeaRtp  196 (745)
T TIGR00963       121 YRFL-GLSVGLILSGMSPEERREAY---ACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDSILIDEARTP  196 (745)
T ss_pred             hccC-CCeEEEEeCCCCHHHHHHhc---CCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHHHHhHHhhhhH
Confidence            9998 89999999998765444333   379999999999 8888765      346788999999999988652     


Q ss_pred             ---hh-------hHHHHHHHHHhCCC---------C--------------------------------------------
Q psy1548         272 ---LE-------MRRDVQEIFRSSPH---------T--------------------------------------------  288 (448)
Q Consensus       272 ---~~-------~~~~~~~i~~~l~~---------~--------------------------------------------  288 (448)
                         .+       .......+.+.+..         .                                            
T Consensus       197 Liisg~~~~~~~ly~~a~~i~r~L~~~~dy~~de~~k~v~Lt~~G~~~~e~~~~~~~ly~~~~~~~~~~i~~Al~A~~l~  276 (745)
T TIGR00963       197 LIISGPAEKSTELYLQANRFAKALEKEVHYEVDEKNRAVLLTEKGIKKAEDLLGVDNLYDLENSPLIHYINNALKAKELF  276 (745)
T ss_pred             HhhcCCCCCchHHHHHHHHHHHhhccCCCeEEecCCCceeECHHHHHHHHHHcCCccccChhhhHHHHHHHHHHHHHHHH
Confidence               00       01111111111110         0                                            


Q ss_pred             ----------------------------------------------------------------CeEEEEeccCCccHHH
Q psy1548         289 ----------------------------------------------------------------KQVMMFSATLSKEIRP  304 (448)
Q Consensus       289 ----------------------------------------------------------------~q~i~~SAT~~~~~~~  304 (448)
                                                                                      .++.+||.|...+..+
T Consensus       277 ~~d~dYiV~d~~V~ivD~~TGR~~~gr~ws~GLhQaiEaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~te~~E  356 (745)
T TIGR00963       277 EKDVDYIVRDGEVVIVDEFTGRIMEGRRWSDGLHQAIEAKEGVEIQNENQTLATITYQNFFRLYEKLSGMTGTAKTEEEE  356 (745)
T ss_pred             hcCCcEEEECCEEEEEECCCCcCCCCCccchHHHHHHHHhcCCCcCCCceeeeeeeHHHHHhhCchhhccCCCcHHHHHH
Confidence                                                                            0234455554433333


Q ss_pred             HHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhh--CCCCeEEEEECccHHHHHHHHHHHhCCCcEE
Q psy1548         305 VCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDV--LEFNQVVIFVKSVTRCIALSTLLSEQNFPAV  382 (448)
Q Consensus       305 ~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~--~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~  382 (448)
                      +...|.-+-+.  +++........ ....+.....+|..++...+..  ..+.++||||+|.+.++.++..|.+.|++..
T Consensus       357 ~~~iY~l~vv~--IPtnkp~~R~d-~~d~i~~t~~~k~~ai~~~i~~~~~~grpvLV~t~si~~se~ls~~L~~~gi~~~  433 (745)
T TIGR00963       357 FEKIYNLEVVV--VPTNRPVIRKD-LSDLVYKTEEEKWKAVVDEIKERHAKGQPVLVGTTSVEKSELLSNLLKERGIPHN  433 (745)
T ss_pred             HHHHhCCCEEE--eCCCCCeeeee-CCCeEEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCeE
Confidence            33333222111  11110000011 1112344556788887776633  3567999999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHH---HHHHHH--HhcCCCCCCCccccccccccCC
Q psy1548         383 SIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKI---LNNVQD--RFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       383 ~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~---l~~i~~--~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      .+|++  +.+|...+..|..+.  ..|+++|+-.-++.   +..+..  -+.+...++|++.....++.||
T Consensus       434 ~Lna~--q~~rEa~ii~~ag~~--g~VtIATnmAgRGtDI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~GR  500 (745)
T TIGR00963       434 VLNAK--NHEREAEIIAQAGRK--GAVTIATNMAGRGTDIKLEEVKELGGLYVIGTERHESRRIDNQLRGR  500 (745)
T ss_pred             EeeCC--hHHHHHHHHHhcCCC--ceEEEEeccccCCcCCCccchhhcCCcEEEecCCCCcHHHHHHHhcc
Confidence            99999  889999999998766  37777776322221   011211  3567777888887777787777

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.

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.91  E-value=5.2e-23  Score=214.92  Aligned_cols=259  Identities=16%  Similarity=0.106  Sum_probs=173.2

Q ss_pred             cceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcc-
Q psy1548         142 FGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLP-  220 (448)
Q Consensus       142 ~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~-  220 (448)
                      ..+.+..|  .++.++||+|||++|++|++.....   +..++|++|+++||.|+.+.+..+...+ ++++++++++.. 
T Consensus        78 g~l~l~~G--~Iaem~TGeGKTLta~Lpa~l~aL~---g~~V~VVTpn~yLA~Rdae~m~~l~~~L-GLsv~~~~~~s~~  151 (762)
T TIGR03714        78 GAIVLHQG--NIAEMKTGEGKTLTATMPLYLNALT---GKGAMLVTTNDYLAKRDAEEMGPVYEWL-GLTVSLGVVDDPD  151 (762)
T ss_pred             HHHHhcCC--ceeEecCCcchHHHHHHHHHHHhhc---CCceEEeCCCHHHHHHHHHHHHHHHhhc-CCcEEEEECCCCc
Confidence            44444444  7999999999999999998766543   3369999999999999999999999998 999998887632 


Q ss_pred             --cHHhHHHHhcCCCcEEEEcHHHH-HHHHHC------CCCcCCCeeEEEecchhHHHhh---------------hhhHH
Q psy1548         221 --IQKDEEYLKTHNPQIVVGTPGRI-LALVRN------KKLNLSLLKHFILDECDKMLEQ---------------LEMRR  276 (448)
Q Consensus       221 --~~~~~~~l~~~~~~IlV~Tp~~l-~~~l~~------~~~~~~~i~~lViDEah~l~~~---------------~~~~~  276 (448)
                        ...+...... .++|++|||+++ .+++..      ....+..+.++|+||||.|+-+               .....
T Consensus       152 ~~~~~~~rr~~y-~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDsILiDeartpliisg~~~~~~~~y~  230 (762)
T TIGR03714       152 EEYDANEKRKIY-NSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDSVLLDSAQTPLVISGAPRVQSNLYH  230 (762)
T ss_pred             cccCHHHHHHhC-CCCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhhHhhccCcCCeeeeCCCccchHHHH
Confidence              2222222223 489999999999 455532      2344678999999999988643               11222


Q ss_pred             HHHHHHHhCCCC--------------------------------------------------------------------
Q psy1548         277 DVQEIFRSSPHT--------------------------------------------------------------------  288 (448)
Q Consensus       277 ~~~~i~~~l~~~--------------------------------------------------------------------  288 (448)
                      ....+.+.+...                                                                    
T Consensus       231 ~~~~~v~~l~~~~dy~~d~~~~~v~lt~~G~~~~e~~~~~~~l~~~~~~~~~~~i~~al~A~~~~~~d~dYiV~~~~v~i  310 (762)
T TIGR03714       231 IADTFVRTLKEDVDYIFKKDKKEVWLTDKGIEKAEQYFKIDNLYSEEYFELVRHINLALRAHYLFKRNKDYVVTNGEVVL  310 (762)
T ss_pred             HHHHHHHhcCCCCCeEEEcCCCeeeecHhHHHHHHHHcCCCccCChhhHHHHHHHHHHHHHHHHHhcCCceEEECCEEEE
Confidence            222222222210                                                                    


Q ss_pred             -------------------------------------------------CeEEEEeccCCccHHHHHHHhcCCCeEEEEc
Q psy1548         289 -------------------------------------------------KQVMMFSATLSKEIRPVCKKFMHDPMEVYVD  319 (448)
Q Consensus       289 -------------------------------------------------~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~  319 (448)
                                                                       .++.+||.|...+..++...|.- ++ +.++
T Consensus       311 vD~~TGr~~~gr~~~~GLhQaieaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~~~~~Ef~~iY~l-~v-~~IP  388 (762)
T TIGR03714       311 LDRITGRLLEGTKLQSGIHQAIEAKEHVELSKETRAMASITYQNLFKMFNKLSGMTGTGKVAEKEFIETYSL-SV-VKIP  388 (762)
T ss_pred             EECCCCcCCCCCCcchHHHHHHHhhcCCCCCCCceeeeeeeHHHHHhhCchhcccCCCChhHHHHHHHHhCC-CE-EEcC
Confidence                                                             02345555543333444333221 11 1111


Q ss_pred             CcccccccceeEEEEEcCcchHHHHHHHHHhh--CCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHH
Q psy1548         320 DEAKLTLHGLQQHYVKLKENEKNKKLFELLDV--LEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKY  397 (448)
Q Consensus       320 ~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~--~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l  397 (448)
                      +. ......-....+.....+|..++...+..  ..+.++||||+|++.++.++..|.+.|+++..+||++.+.+|..+.
T Consensus       389 t~-kp~~r~d~~d~i~~~~~~K~~ai~~~i~~~~~~~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~~~E~~ii~  467 (762)
T TIGR03714       389 TN-KPIIRIDYPDKIYATLPEKLMATLEDVKEYHETGQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNAAKEAQIIA  467 (762)
T ss_pred             CC-CCeeeeeCCCeEEECHHHHHHHHHHHHHHHhhCCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCChHHHHHHHH
Confidence            11 10000111124556677899999888865  3567999999999999999999999999999999999999987777


Q ss_pred             HHHhcCCCceEEEEecC
Q psy1548         398 QEFKDFHKGLAITFASD  414 (448)
Q Consensus       398 ~~F~~g~~g~~I~~~t~  414 (448)
                      +.++.|    .|+++|+
T Consensus       468 ~ag~~g----~VlIATd  480 (762)
T TIGR03714       468 EAGQKG----AVTVATS  480 (762)
T ss_pred             HcCCCC----eEEEEcc
Confidence            666554    4666655

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.

>KOG0352|consensus

Probab=99.91  E-value=4e-24  Score=202.78  Aligned_cols=264  Identities=13%  Similarity=0.165  Sum_probs=188.2

Q ss_pred             CCCCchhhhhhhccccccceeeeeC-cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g-~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      +-+++   |.+      ++..+..+ +||.+++|||+||++||.+|.|..      +..+||+.|..+|..++.+.+.++
T Consensus        20 FKs~L---QE~------A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~------~gITIV~SPLiALIkDQiDHL~~L   84 (641)
T KOG0352|consen   20 FKSRL---QEQ------AINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH------GGITIVISPLIALIKDQIDHLKRL   84 (641)
T ss_pred             hcChH---HHH------HHHHHHhccCcEEEeccCCCchhhhhhchHHHh------CCeEEEehHHHHHHHHHHHHHHhc
Confidence            55678   999      88887776 699999999999999999999874      238999999999999988888876


Q ss_pred             hccCCCceEEEEEcCcccHHhHH---HHhcC--CCcEEEEcHHHHHH-----HHHCCCCcCCCeeEEEecchhHHHhh-h
Q psy1548         204 SKYMSNIKVGVFFGGLPIQKDEE---YLKTH--NPQIVVGTPGRILA-----LVRNKKLNLSLLKHFILDECDKMLEQ-L  272 (448)
Q Consensus       204 ~~~~~~~~v~~~~g~~~~~~~~~---~l~~~--~~~IlV~Tp~~l~~-----~l~~~~~~~~~i~~lViDEah~l~~~-~  272 (448)
                           .+.+..+.+..+..+...   .+...  ...+++-||+....     +|+ ...+-.-+.++|+||||++..| +
T Consensus        85 -----KVp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn-~L~~r~~L~Y~vVDEAHCVSQWGH  158 (641)
T KOG0352|consen   85 -----KVPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLN-GLANRDVLRYIVVDEAHCVSQWGH  158 (641)
T ss_pred             -----CCchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHH-HHhhhceeeeEEechhhhHhhhcc
Confidence                 455555555544333322   23222  35689999987532     222 1222345789999999999999 6


Q ss_pred             hhHHHHHHHHHh--CCCCCeEEEEeccCCccHHHHHHH--hcCCCeEEEEcCcccccccceeEEEEEcC-cchHHHHHHH
Q psy1548         273 EMRRDVQEIFRS--SPHTKQVMMFSATLSKEIRPVCKK--FMHDPMEVYVDDEAKLTLHGLQQHYVKLK-ENEKNKKLFE  347 (448)
Q Consensus       273 ~~~~~~~~i~~~--l~~~~q~i~~SAT~~~~~~~~~~~--~l~~~~~i~~~~~~~~~~~~i~~~~~~~~-~~~k~~~L~~  347 (448)
                      +|++++..+-..  .-+.+..++++||.++.+++.+-.  -+++|+.+.-.+...   .++-......+ -.+-+..|.+
T Consensus       159 DFRPDYL~LG~LRS~~~~vpwvALTATA~~~VqEDi~~qL~L~~PVAiFkTP~FR---~NLFYD~~~K~~I~D~~~~LaD  235 (641)
T KOG0352|consen  159 DFRPDYLTLGSLRSVCPGVPWVALTATANAKVQEDIAFQLKLRNPVAIFKTPTFR---DNLFYDNHMKSFITDCLTVLAD  235 (641)
T ss_pred             ccCcchhhhhhHHhhCCCCceEEeecccChhHHHHHHHHHhhcCcHHhccCcchh---hhhhHHHHHHHHhhhHhHhHHH
Confidence            799999887443  335778999999999998886554  356888776544421   11100000000 0123344444


Q ss_pred             HHhhC-------------CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecC
Q psy1548         348 LLDVL-------------EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASD  414 (448)
Q Consensus       348 ll~~~-------------~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~  414 (448)
                      +....             ..+..||||.|+++|+.++-.|...|+++..||+|+...||.++.+.|-+++  +-|+.+|.
T Consensus       236 F~~~~LG~~~~~~~~~K~~~GCGIVYCRTR~~cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~--~PvI~AT~  313 (641)
T KOG0352|consen  236 FSSSNLGKHEKASQNKKTFTGCGIVYCRTRNECEQVAIMLEIAGIPAMAYHAGLKKKERTEVQEKWMNNE--IPVIAATV  313 (641)
T ss_pred             HHHHhcCChhhhhcCCCCcCcceEEEeccHHHHHHHHHHhhhcCcchHHHhcccccchhHHHHHHHhcCC--CCEEEEEe
Confidence            44332             1246899999999999999999999999999999999999999999999998  34444443

>KOG0947|consensus

Probab=99.90  E-value=5.3e-23  Score=211.29  Aligned_cols=297  Identities=17%  Similarity=0.181  Sum_probs=217.1

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      +..|+.++.||++      ++-.+..|.+|+|.|+|.+|||+++-.++.-.-   ..+.+++|.+|-++|.+|-++.|+.
T Consensus       292 ~~~pFelD~FQk~------Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq---~h~TR~iYTSPIKALSNQKfRDFk~  362 (1248)
T KOG0947|consen  292 LIYPFELDTFQKE------AIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQ---KHMTRTIYTSPIKALSNQKFRDFKE  362 (1248)
T ss_pred             hhCCCCccHHHHH------HHHHHHcCCeEEEEecCCCCcchHHHHHHHHHH---hhccceEecchhhhhccchHHHHHH
Confidence            5678999999999      999999999999999999999998766554321   3466999999999999997777766


Q ss_pred             hhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHH
Q psy1548         203 FSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIF  282 (448)
Q Consensus       203 ~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~  282 (448)
                      -.+     .+++++|+.....+        +.++|+|.+.|.+|+-++.--..++.++|+||+|.+.+. ..+..+++++
T Consensus       363 tF~-----DvgLlTGDvqinPe--------AsCLIMTTEILRsMLYrgadliRDvE~VIFDEVHYiND~-eRGvVWEEVi  428 (1248)
T KOG0947|consen  363 TFG-----DVGLLTGDVQINPE--------ASCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYINDV-ERGVVWEEVI  428 (1248)
T ss_pred             hcc-----ccceeecceeeCCC--------cceEeehHHHHHHHHhcccchhhccceEEEeeeeecccc-cccccceeee
Confidence            443     23489999876554        689999999999999998887899999999999999887 8999999999


Q ss_pred             HhCCCCCeEEEEeccCCccHHHHHHHhcC-CCeEEEEcCcccccccceeEEEEEcC------------------------
Q psy1548         283 RSSPHTKQVMMFSATLSKEIRPVCKKFMH-DPMEVYVDDEAKLTLHGLQQHYVKLK------------------------  337 (448)
Q Consensus       283 ~~l~~~~q~i~~SAT~~~~~~~~~~~~l~-~~~~i~~~~~~~~~~~~i~~~~~~~~------------------------  337 (448)
                      -++|+++++|++|||+|+. .+++.|... ....|++... ...+..+++++..-.                        
T Consensus       429 IMlP~HV~~IlLSATVPN~-~EFA~WIGRtK~K~IyViST-~kRPVPLEh~l~t~~~l~kiidq~g~fl~~~~~~a~~~~  506 (1248)
T KOG0947|consen  429 IMLPRHVNFILLSATVPNT-LEFADWIGRTKQKTIYVIST-SKRPVPLEHYLYTKKSLFKIIDQNGIFLLKGIKDAKDSL  506 (1248)
T ss_pred             eeccccceEEEEeccCCCh-HHHHHHhhhccCceEEEEec-CCCccceEEEEEeccceehhhcccchhhhhcchhhhhhh
Confidence            9999999999999999886 355555432 1111111111 011122222211100                        


Q ss_pred             ---------------------------------------cchHH--HHHHHHH---hhCCCCeEEEEECccHHHHHHHHH
Q psy1548         338 ---------------------------------------ENEKN--KKLFELL---DVLEFNQVVIFVKSVTRCIALSTL  373 (448)
Q Consensus       338 ---------------------------------------~~~k~--~~L~~ll---~~~~~~~~IIF~~s~~~a~~l~~~  373 (448)
                                                             ..++.  ....+++   +...--++|+||-+++.|+..++.
T Consensus       507 ~~~ak~~~~~~~~~~~~rgs~~~ggk~~~~~g~~r~~~~~~nrr~~~~~l~lin~L~k~~lLP~VvFvFSkkrCde~a~~  586 (1248)
T KOG0947|consen  507 KKEAKFVDVEKSDARGGRGSQKRGGKTNYHNGGSRGSGIGKNRRKQPTWLDLINHLRKKNLLPVVVFVFSKKRCDEYADY  586 (1248)
T ss_pred             cccccccccccccccccccccccCCcCCCCCCCcccccccccccccchHHHHHHHHhhcccCceEEEEEccccHHHHHHH
Confidence                                                   00011  1122333   222333799999999999999999


Q ss_pred             HHhCCC---------------------------------------cEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecC
Q psy1548         374 LSEQNF---------------------------------------PAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASD  414 (448)
Q Consensus       374 L~~~g~---------------------------------------~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~  414 (448)
                      |...++                                       .++.+|||+-+--+.-+...|+.|-  +-|+|+|.
T Consensus       587 L~~~nL~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RGiaVHH~GlLPivKE~VE~LFqrGl--VKVLFATE  664 (1248)
T KOG0947|consen  587 LTNLNLTDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRGIAVHHGGLLPIVKEVVELLFQRGL--VKVLFATE  664 (1248)
T ss_pred             HhccCcccchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhhcchhhcccchHHHHHHHHHHHhcCc--eEEEeehh
Confidence            974322                                       1788999999999999999999988  78888887


Q ss_pred             hhhHHH--------HHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         415 ENDAKI--------LNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       415 ~~d~~~--------l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      ..-+++        ...+.++-|....+|-+.  .++||.||
T Consensus       665 TFAMGVNMPARtvVF~Sl~KhDG~efR~L~PG--EytQMAGR  704 (1248)
T KOG0947|consen  665 TFAMGVNMPARTVVFSSLRKHDGNEFRELLPG--EYTQMAGR  704 (1248)
T ss_pred             hhhhhcCCCceeEEeeehhhccCcceeecCCh--hHHhhhcc
Confidence            543332        334667777777776443  58999988

>PRK09694 helicase Cas3; Provisional

Probab=99.89  E-value=6.5e-22  Score=212.04  Aligned_cols=283  Identities=17%  Similarity=0.145  Sum_probs=172.6

Q ss_pred             eeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHH
Q psy1548         121 FNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEY  200 (448)
Q Consensus       121 ~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~  200 (448)
                      ++...|+++   |+.      +......+..+++.+|||+|||.+++..+...+. .....+++|..||+++++|+++.+
T Consensus       282 ~~~~~p~p~---Q~~------~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~~-~~~~~gi~~aLPT~Atan~m~~Rl  351 (878)
T PRK09694        282 DNGYQPRQL---QTL------VDALPLQPGLTIIEAPTGSGKTEAALAYAWRLID-QGLADSIIFALPTQATANAMLSRL  351 (878)
T ss_pred             cCCCCChHH---HHH------HHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHHH-hCCCCeEEEECcHHHHHHHHHHHH
Confidence            334467777   998      4333234677999999999999998776654433 333458999999999999999998


Q ss_pred             HHhhcc-CCCceEEEEEcCcccHHhH---------------------HHHhc-----CCCcEEEEcHHHHHHHH-HCCCC
Q psy1548         201 ERFSKY-MSNIKVGVFFGGLPIQKDE---------------------EYLKT-----HNPQIVVGTPGRILALV-RNKKL  252 (448)
Q Consensus       201 ~~~~~~-~~~~~v~~~~g~~~~~~~~---------------------~~l~~-----~~~~IlV~Tp~~l~~~l-~~~~~  252 (448)
                      ..+... +++..+.+.+|........                     ..+..     .-.+|+|||+.+++..+ ..+..
T Consensus       352 ~~~~~~~f~~~~v~L~Hg~a~l~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~kr~llapi~V~TiDQlL~a~l~~kh~  431 (878)
T PRK09694        352 EALASKLFPSPNLILAHGNSRFNHLFQSLKSRAATEQGQEEAWVQCCEWLSQSNKRVFLGQIGVCTIDQVLISVLPVKHR  431 (878)
T ss_pred             HHHHHHhcCCCceEeecCcchhhhhhhhhhcccccccccchhhhHHHHHHhhhhhhhhcCCEEEcCHHHHHHHHHccchH
Confidence            875542 2245666776654322110                     11110     11589999999887543 22222


Q ss_pred             cCCCe----eEEEecchhHHHhhhhhHHHHHHHHHhCC-CCCeEEEEeccCCccHHHHH-HHhcCC---------CeEEE
Q psy1548         253 NLSLL----KHFILDECDKMLEQLEMRRDVQEIFRSSP-HTKQVMMFSATLSKEIRPVC-KKFMHD---------PMEVY  317 (448)
Q Consensus       253 ~~~~i----~~lViDEah~l~~~~~~~~~~~~i~~~l~-~~~q~i~~SAT~~~~~~~~~-~~~l~~---------~~~i~  317 (448)
                      .+..+    ++|||||+|.+ +. .+...+..+++.+. ....+|+||||+|...++.+ ..+-..         |....
T Consensus       432 ~lR~~~La~svvIiDEVHAy-D~-ym~~lL~~~L~~l~~~g~~vIllSATLP~~~r~~L~~a~~~~~~~~~~~~YPlvt~  509 (878)
T PRK09694        432 FIRGFGLGRSVLIVDEVHAY-DA-YMYGLLEAVLKAQAQAGGSVILLSATLPATLKQKLLDTYGGHDPVELSSAYPLITW  509 (878)
T ss_pred             HHHHHhhccCeEEEechhhC-CH-HHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhccccccccccccccccc
Confidence            22222    47999999966 43 45556666666543 35679999999998866543 333211         10000


Q ss_pred             EcCc--ccc----------cccceeEEEEEcCc-chHHHHHHHHHhh-CCCCeEEEEECccHHHHHHHHHHHhCC---Cc
Q psy1548         318 VDDE--AKL----------TLHGLQQHYVKLKE-NEKNKKLFELLDV-LEFNQVVIFVKSVTRCIALSTLLSEQN---FP  380 (448)
Q Consensus       318 ~~~~--~~~----------~~~~i~~~~~~~~~-~~k~~~L~~ll~~-~~~~~~IIF~~s~~~a~~l~~~L~~~g---~~  380 (448)
                      ....  ...          ....+.-....... ......+..+++. ..+++++|||||++.|+.+++.|++.+   .+
T Consensus       510 ~~~~~~~~~~~~~~~~~~~~~~~v~v~~~~~~~~~~~~~~l~~i~~~~~~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~  589 (878)
T PRK09694        510 RGVNGAQRFDLSAHPEQLPARFTIQLEPICLADMLPDLTLLQRMIAAANAGAQVCLICNLVDDAQKLYQRLKELNNTQVD  589 (878)
T ss_pred             cccccceeeeccccccccCcceEEEEEeeccccccCHHHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhhCCCCce
Confidence            0000  000          00111111111111 1122333444443 246789999999999999999999864   67


Q ss_pred             EEEEeCCCCHHHH----HHHHHHH-hcCCCc-eEEEEecCh
Q psy1548         381 AVSIHRGMTQEER----LKKYQEF-KDFHKG-LAITFASDE  415 (448)
Q Consensus       381 ~~~lh~~~~~~eR----~~~l~~F-~~g~~g-~~I~~~t~~  415 (448)
                      +..+||+++..+|    .++++.| ++|+.. ..|.++|.-
T Consensus       590 v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQV  630 (878)
T PRK09694        590 IDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVATQV  630 (878)
T ss_pred             EEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEECcc
Confidence            9999999999999    4678888 555421 256666653

>KOG0353|consensus

Probab=99.89  E-value=1.5e-22  Score=189.53  Aligned_cols=278  Identities=14%  Similarity=0.189  Sum_probs=206.2

Q ss_pred             ccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChh
Q psy1548          83 RDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGK  162 (448)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGK  162 (448)
                      ++++.+.+....+++..                      |.+...|+   |..      +|...+.|+++++..|||.||
T Consensus        74 d~fpws~e~~~ilk~~f----------------------~lekfrpl---q~~------ain~~ma~ed~~lil~tgggk  122 (695)
T KOG0353|consen   74 DDFPWSDEAKDILKEQF----------------------HLEKFRPL---QLA------AINATMAGEDAFLILPTGGGK  122 (695)
T ss_pred             CCCCCchHHHHHHHHHh----------------------hHHhcChh---HHH------HhhhhhccCceEEEEeCCCcc
Confidence            35666666666665543                      46777888   999      999999999999999999999


Q ss_pred             HHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHH---HH--hcCCCcEEE
Q psy1548         163 TAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE---YL--KTHNPQIVV  237 (448)
Q Consensus       163 T~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~---~l--~~~~~~IlV  237 (448)
                      ++||.+|+|..      ...+|++||...|+.++.-+++.+     ++....+....+.....+   .+  ++....+++
T Consensus       123 slcyqlpal~a------dg~alvi~plislmedqil~lkql-----gi~as~lnansske~~k~v~~~i~nkdse~kliy  191 (695)
T KOG0353|consen  123 SLCYQLPALCA------DGFALVICPLISLMEDQILQLKQL-----GIDASMLNANSSKEEAKRVEAAITNKDSEFKLIY  191 (695)
T ss_pred             chhhhhhHHhc------CCceEeechhHHHHHHHHHHHHHh-----CcchhhccCcccHHHHHHHHHHHcCCCceeEEEE
Confidence            99999999874      347999999999999888888887     455455544444322111   11  222467999


Q ss_pred             EcHHHHHH---HHH--CCCCcCCCeeEEEecchhHHHhh-hhhHHHHHHH--HHhCCCCCeEEEEeccCCccHHHHHHHh
Q psy1548         238 GTPGRILA---LVR--NKKLNLSLLKHFILDECDKMLEQ-LEMRRDVQEI--FRSSPHTKQVMMFSATLSKEIRPVCKKF  309 (448)
Q Consensus       238 ~Tp~~l~~---~l~--~~~~~~~~i~~lViDEah~l~~~-~~~~~~~~~i--~~~l~~~~q~i~~SAT~~~~~~~~~~~~  309 (448)
                      .||+++..   ++.  ++.+....++++.+||+|+...| ++|++++..+  ++.--++..+++++||.++.+.+.++..
T Consensus       192 vtpekiaksk~~mnkleka~~~~~~~~iaidevhccsqwghdfr~dy~~l~ilkrqf~~~~iigltatatn~vl~d~k~i  271 (695)
T KOG0353|consen  192 VTPEKIAKSKKFMNKLEKALEAGFFKLIAIDEVHCCSQWGHDFRPDYKALGILKRQFKGAPIIGLTATATNHVLDDAKDI  271 (695)
T ss_pred             ecHHHHHHHHHHHHHHHHHhhcceeEEEeecceeehhhhCcccCcchHHHHHHHHhCCCCceeeeehhhhcchhhHHHHH
Confidence            99999853   221  24455678899999999999998 6799988864  5555578889999999999887777766


Q ss_pred             cCCCeEEEEcCcccccccceeEEEEEcCcc--hHHHHHHHHHhh-CCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeC
Q psy1548         310 MHDPMEVYVDDEAKLTLHGLQQHYVKLKEN--EKNKKLFELLDV-LEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHR  386 (448)
Q Consensus       310 l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~--~k~~~L~~ll~~-~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~  386 (448)
                      +.-...+.....  ...+++...+...+..  +-.+-+..+++. ..+...||||-+++.|++++..|+.+|+.+..+|+
T Consensus       272 l~ie~~~tf~a~--fnr~nl~yev~qkp~n~dd~~edi~k~i~~~f~gqsgiiyc~sq~d~ekva~alkn~gi~a~~yha  349 (695)
T KOG0353|consen  272 LCIEAAFTFRAG--FNRPNLKYEVRQKPGNEDDCIEDIAKLIKGDFAGQSGIIYCFSQKDCEKVAKALKNHGIHAGAYHA  349 (695)
T ss_pred             HhHHhhheeecc--cCCCCceeEeeeCCCChHHHHHHHHHHhccccCCCcceEEEeccccHHHHHHHHHhcCcccccccc
Confidence            543222222222  3445665555544432  233444555543 35668999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHhcCC
Q psy1548         387 GMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       387 ~~~~~eR~~~l~~F~~g~  404 (448)
                      .|.+++|.-+-+.|-.|+
T Consensus       350 ~lep~dks~~hq~w~a~e  367 (695)
T KOG0353|consen  350 NLEPEDKSGAHQGWIAGE  367 (695)
T ss_pred             ccCccccccccccccccc
Confidence            999999999999999998

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.88  E-value=3e-22  Score=209.16  Aligned_cols=250  Identities=16%  Similarity=0.130  Sum_probs=163.7

Q ss_pred             cCCCCchhhhhhhccccccceeeee-C--cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHH
Q psy1548         124 DMPEDSDTYLHRVARAGRFGTKAVL-G--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEY  200 (448)
Q Consensus       124 ~~p~~~~~yQ~~~~~~~~~~~~~~~-g--~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~  200 (448)
                      .....+++||++      ++..++. |  ++.++++|||+|||++.+..+.. +     +.++|||||+..|+.||.+.+
T Consensus       251 ~~~~~LRpYQ~e------Al~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~-l-----~k~tLILvps~~Lv~QW~~ef  318 (732)
T TIGR00603       251 KPTTQIRPYQEK------SLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACT-V-----KKSCLVLCTSAVSVEQWKQQF  318 (732)
T ss_pred             ccCCCcCHHHHH------HHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHH-h-----CCCEEEEeCcHHHHHHHHHHH
Confidence            344668999999      7766653 4  47899999999999997655433 2     236999999999999999999


Q ss_pred             HHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCC--------CCcCCCeeEEEecchhHHHhhh
Q psy1548         201 ERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNK--------KLNLSLLKHFILDECDKMLEQL  272 (448)
Q Consensus       201 ~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~--------~~~~~~i~~lViDEah~l~~~~  272 (448)
                      .++.... ...+..++|+.....      .....|+|+|++.+.....+.        .+.-..+.++|+||||++... 
T Consensus       319 ~~~~~l~-~~~I~~~tg~~k~~~------~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lpA~-  390 (732)
T TIGR00603       319 KMWSTID-DSQICRFTSDAKERF------HGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPAA-  390 (732)
T ss_pred             HHhcCCC-CceEEEEecCccccc------ccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccccHH-
Confidence            9987543 456677777642111      112579999998875432221        122245779999999988654 


Q ss_pred             hhHHHHHHHHHhCCCCCeEEEEeccCCccHH--HHHHHhcCCCeEEEEcCcc-----cccccceeEEEE-----------
Q psy1548         273 EMRRDVQEIFRSSPHTKQVMMFSATLSKEIR--PVCKKFMHDPMEVYVDDEA-----KLTLHGLQQHYV-----------  334 (448)
Q Consensus       273 ~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~--~~~~~~l~~~~~i~~~~~~-----~~~~~~i~~~~~-----------  334 (448)
                      .|+    .++..++ ....+++|||+..+-.  ..+. ++-.|..+......     ...........+           
T Consensus       391 ~fr----~il~~l~-a~~RLGLTATP~ReD~~~~~L~-~LiGP~vye~~~~eLi~~G~LA~~~~~ev~v~~t~~~~~~yl  464 (732)
T TIGR00603       391 MFR----RVLTIVQ-AHCKLGLTATLVREDDKITDLN-FLIGPKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYL  464 (732)
T ss_pred             HHH----HHHHhcC-cCcEEEEeecCcccCCchhhhh-hhcCCeeeecCHHHHHhCCccccceEEEEEecCCHHHHHHHH
Confidence            433    3444443 3346999999864321  1222 22334443332210     111111100111           


Q ss_pred             ----------EcCcchHHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhc
Q psy1548         335 ----------KLKENEKNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKD  402 (448)
Q Consensus       335 ----------~~~~~~k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~  402 (448)
                                ......|+..+..+++.+  .+.++||||++...++.++..|.     +..+||++++.+|.++++.|++
T Consensus       465 ~~~~~~k~~l~~~np~K~~~~~~Li~~he~~g~kiLVF~~~~~~l~~~a~~L~-----~~~I~G~ts~~ER~~il~~Fr~  539 (732)
T TIGR00603       465 RENSRKRMLLYVMNPNKFRACQFLIRFHEQRGDKIIVFSDNVFALKEYAIKLG-----KPFIYGPTSQQERMQILQNFQH  539 (732)
T ss_pred             HhcchhhhHHhhhChHHHHHHHHHHHHHhhcCCeEEEEeCCHHHHHHHHHHcC-----CceEECCCCHHHHHHHHHHHHh
Confidence                      111224666666777655  66799999999999999998873     4568999999999999999997


Q ss_pred             CC
Q psy1548         403 FH  404 (448)
Q Consensus       403 g~  404 (448)
                      |.
T Consensus       540 ~~  541 (732)
T TIGR00603       540 NP  541 (732)
T ss_pred             CC
Confidence            63

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).

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.88  E-value=3e-21  Score=211.18  Aligned_cols=258  Identities=17%  Similarity=0.209  Sum_probs=166.7

Q ss_pred             CCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeec----cHHHHHHHHHHHH
Q psy1548         126 PEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH----TRELAFQISKEYE  201 (448)
Q Consensus       126 p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~P----t~~L~~q~~~~~~  201 (448)
                      --|+..+-.+      .+..+..+..++++|+||||||.  .+|.+...........+++.-|    +++||.++.+.+.
T Consensus        72 ~LPi~~~r~~------Il~ai~~~~VviI~GeTGSGKTT--qlPq~lle~g~g~~g~I~~TQPRRlAArsLA~RVA~El~  143 (1294)
T PRK11131         72 NLPVSQKKQD------ILEAIRDHQVVIVAGETGSGKTT--QLPKICLELGRGVKGLIGHTQPRRLAARTVANRIAEELE  143 (1294)
T ss_pred             CCCHHHHHHH------HHHHHHhCCeEEEECCCCCCHHH--HHHHHHHHcCCCCCCceeeCCCcHHHHHHHHHHHHHHHh
Confidence            3455555555      55566566778889999999998  4784432211111123344446    5678888877776


Q ss_pred             HhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchh-HHHhhhhhHHH-HH
Q psy1548         202 RFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECD-KMLEQLEMRRD-VQ  279 (448)
Q Consensus       202 ~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah-~l~~~~~~~~~-~~  279 (448)
                      .-.    +-.+++-...   ..+.   .. .++|+|+||++|++.+..+.. ++++++||||||| ++++. +|... +.
T Consensus       144 ~~l----G~~VGY~vrf---~~~~---s~-~t~I~v~TpG~LL~~l~~d~~-Ls~~~~IIIDEAHERsLn~-DfLLg~Lk  210 (1294)
T PRK11131        144 TEL----GGCVGYKVRF---NDQV---SD-NTMVKLMTDGILLAEIQQDRL-LMQYDTIIIDEAHERSLNI-DFILGYLK  210 (1294)
T ss_pred             hhh----cceeceeecC---cccc---CC-CCCEEEEChHHHHHHHhcCCc-cccCcEEEecCcccccccc-chHHHHHH
Confidence            421    2222222111   1111   12 379999999999999886644 8999999999999 46665 66543 33


Q ss_pred             HHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcc------hHHHHHHHHHh---
Q psy1548         280 EIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKEN------EKNKKLFELLD---  350 (448)
Q Consensus       280 ~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~------~k~~~L~~ll~---  350 (448)
                      .++.. .++.|+|+||||++.  ..+.+.|...|. +.+...    ...+..+|......      +....+...+.   
T Consensus       211 ~lL~~-rpdlKvILmSATid~--e~fs~~F~~apv-I~V~Gr----~~pVei~y~p~~~~~~~~~~d~l~~ll~~V~~l~  282 (1294)
T PRK11131        211 ELLPR-RPDLKVIITSATIDP--ERFSRHFNNAPI-IEVSGR----TYPVEVRYRPIVEEADDTERDQLQAIFDAVDELG  282 (1294)
T ss_pred             Hhhhc-CCCceEEEeeCCCCH--HHHHHHcCCCCE-EEEcCc----cccceEEEeecccccchhhHHHHHHHHHHHHHHh
Confidence            33322 246799999999974  466666666664 444332    13355666655332      12233333222   


Q ss_pred             hCCCCeEEEEECccHHHHHHHHHHHhCCCc---EEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChh
Q psy1548         351 VLEFNQVVIFVKSVTRCIALSTLLSEQNFP---AVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDEN  416 (448)
Q Consensus       351 ~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~---~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~  416 (448)
                      ....+.+||||++..+++.+++.|++.+++   +..+||+|++++|.++++.+  |  +..|.++|+-.
T Consensus       283 ~~~~GdILVFLpg~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~Vf~~~--g--~rkIIVATNIA  347 (1294)
T PRK11131        283 REGPGDILIFMSGEREIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQSH--S--GRRIVLATNVA  347 (1294)
T ss_pred             cCCCCCEEEEcCCHHHHHHHHHHHHhcCCCcceEeecccCCCHHHHHHHhccc--C--CeeEEEeccHH
Confidence            234678999999999999999999988764   77899999999999998863  3  34677777643

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

Probab=99.88  E-value=2.2e-21  Score=206.48  Aligned_cols=267  Identities=18%  Similarity=0.204  Sum_probs=201.7

Q ss_pred             cCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         124 DMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       124 ~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      ..|..+++||++      ++..+..|.+|+++||||+|||++...++...+..+   .+++|.+|.++|.+|.++.+...
T Consensus       115 ~~~F~LD~fQ~~------a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~~---qrviYTsPIKALsNQKyrdl~~~  185 (1041)
T COG4581         115 EYPFELDPFQQE------AIAILERGESVLVCAPTSSGKTVVAEYAIALALRDG---QRVIYTSPIKALSNQKYRDLLAK  185 (1041)
T ss_pred             hCCCCcCHHHHH------HHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHcC---CceEeccchhhhhhhHHHHHHHH
Confidence            367788999999      999999999999999999999999888877766443   36999999999999998888776


Q ss_pred             hccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHH
Q psy1548         204 SKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFR  283 (448)
Q Consensus       204 ~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~  283 (448)
                      .+.. .-.+++++|+...+..        +.++|.|.+.|.+++..+...+..+.++|+||+|.|.+. ..+..+++++.
T Consensus       186 fgdv-~~~vGL~TGDv~IN~~--------A~clvMTTEILRnMlyrg~~~~~~i~~ViFDEvHyi~D~-eRG~VWEE~Ii  255 (1041)
T COG4581         186 FGDV-ADMVGLMTGDVSINPD--------APCLVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIGDR-ERGVVWEEVII  255 (1041)
T ss_pred             hhhh-hhhccceecceeeCCC--------CceEEeeHHHHHHHhccCcccccccceEEEEeeeecccc-ccchhHHHHHH
Confidence            5432 2346889999876543        689999999999999999889999999999999999997 88999999999


Q ss_pred             hCCCCCeEEEEeccCCccHHHHHHHhc---CCCeEEEEcCcccccccceeEEEEEc-------CcchH------------
Q psy1548         284 SSPHTKQVMMFSATLSKEIRPVCKKFM---HDPMEVYVDDEAKLTLHGLQQHYVKL-------KENEK------------  341 (448)
Q Consensus       284 ~l~~~~q~i~~SAT~~~~~~~~~~~~l---~~~~~i~~~~~~~~~~~~i~~~~~~~-------~~~~k------------  341 (448)
                      .+|...|+++||||+|+. .++..|+.   ..|..+.....   .+..+.+++..-       +...+            
T Consensus       256 ~lP~~v~~v~LSATv~N~-~EF~~Wi~~~~~~~~~vv~t~~---RpvPL~~~~~~~~~l~~lvde~~~~~~~~~~~a~~~  331 (1041)
T COG4581         256 LLPDHVRFVFLSATVPNA-EEFAEWIQRVHSQPIHVVSTEH---RPVPLEHFVYVGKGLFDLVDEKKKFNAENFPSANRS  331 (1041)
T ss_pred             hcCCCCcEEEEeCCCCCH-HHHHHHHHhccCCCeEEEeecC---CCCCeEEEEecCCceeeeecccccchhhcchhhhhh
Confidence            999999999999999876 34444433   34554443333   233344443221       11110            


Q ss_pred             -----------------------------------HHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhC---------
Q psy1548         342 -----------------------------------NKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQ---------  377 (448)
Q Consensus       342 -----------------------------------~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~---------  377 (448)
                                                         ...+...+.....-++|+|+-++..|+..+..+...         
T Consensus       332 l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~iv~~l~~~~~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e  411 (1041)
T COG4581         332 LSCFSEKVRETDDGDVGRYARRTKALRGSAKGPAGRPEIVNKLDKDNLLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKE  411 (1041)
T ss_pred             hhccchhccccCccccccccccccccCCcccccccchHHHhhhhhhcCCceEEEEEchhhHHHHHHHhcccccccCCcHH
Confidence                                               001122222223447999999999999999877511         


Q ss_pred             -------------------CCc-------------EEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         378 -------------------NFP-------------AVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       378 -------------------g~~-------------~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                                         +++             ..++|+||-+..|..+...|+.|-  +-+.|+|..
T Consensus       412 ~~i~~ii~~~i~~L~~ed~~lp~~~~~~~~~L~RGiavHH~GlLP~~K~~vE~Lfq~GL--vkvvFaTeT  479 (1041)
T COG4581         412 RAIREIIDHAIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLPAIKELVEELFQEGL--VKVVFATET  479 (1041)
T ss_pred             HHHHHHHHHHHhhcChhhhcCcccHHHHHHHHhhhhhhhccccchHHHHHHHHHHhccc--eeEEeehhh
Confidence                               111             458999999999999999999998  566666654

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.88  E-value=6.5e-21  Score=200.73  Aligned_cols=259  Identities=17%  Similarity=0.183  Sum_probs=176.9

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .|..+   |-.      ..-.+..|+  |..++||+|||++|.+|++.....+   ..++|++||+.||.|..+.+..+.
T Consensus        82 ~~ydv---Qli------Gg~~Lh~G~--Iaem~TGeGKTL~a~Lpa~~~al~G---~~V~VvTpn~yLA~qd~e~m~~l~  147 (896)
T PRK13104         82 RHFDV---QLI------GGMVLHEGN--IAEMRTGEGKTLVATLPAYLNAISG---RGVHIVTVNDYLAKRDSQWMKPIY  147 (896)
T ss_pred             CcchH---HHh------hhhhhccCc--cccccCCCCchHHHHHHHHHHHhcC---CCEEEEcCCHHHHHHHHHHHHHHh
Confidence            56677   777      222334444  8899999999999999999776543   359999999999999999999999


Q ss_pred             ccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHH-HHHHHCC-CCcC-----CCeeEEEecchhHHHhh------
Q psy1548         205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRI-LALVRNK-KLNL-----SLLKHFILDECDKMLEQ------  271 (448)
Q Consensus       205 ~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l-~~~l~~~-~~~~-----~~i~~lViDEah~l~~~------  271 (448)
                      ..+ ++++++++|+.+...+...+   .++|+||||+++ .++++.+ .+++     ..+.++|+||||.|+-+      
T Consensus       148 ~~l-GLtv~~i~gg~~~~~r~~~y---~~dIvygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDEaDsiLIDeArtPL  223 (896)
T PRK13104        148 EFL-GLTVGVIYPDMSHKEKQEAY---KADIVYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEVDSILIDEARTPL  223 (896)
T ss_pred             ccc-CceEEEEeCCCCHHHHHHHh---CCCEEEECChhhhHHHHhcCCccchHhhhccccceEEeccHhhhhhhccCCce
Confidence            998 89999999998766655444   389999999999 8888876 3334     58899999999988633      


Q ss_pred             ---------hhhHHHHHHHHHhCCCC--------------CeEEEEec--------------------------------
Q psy1548         272 ---------LEMRRDVQEIFRSSPHT--------------KQVMMFSA--------------------------------  296 (448)
Q Consensus       272 ---------~~~~~~~~~i~~~l~~~--------------~q~i~~SA--------------------------------  296 (448)
                               ......+..+...+...              .+.+.+|-                                
T Consensus       224 IISg~~~~~~~~y~~~~~~v~~l~~~~~~~~~~dy~idek~~~v~Lte~G~~~~e~~~~~~~il~~~~~l~~~~~~~~~~  303 (896)
T PRK13104        224 IISGAAEDSSELYIKINSLIPQLKKQEEEGDEGDYTIDEKQKQAHLTDAGHLHIEELLTKAKLLDPGESLYHASNIMLMH  303 (896)
T ss_pred             eeeCCCccchHHHHHHHHHHHHHHhccccCCCCCEEEEcCCCceEEchHHHHHHHHHHHhCCccCCcccccCchhhhHHH
Confidence                     11222222232222111              11222222                                


Q ss_pred             --------------------------------------------------------------------------------
Q psy1548         297 --------------------------------------------------------------------------------  296 (448)
Q Consensus       297 --------------------------------------------------------------------------------  296 (448)
                                                                                                      
T Consensus       304 ~i~~aL~A~~lf~~d~dYiV~dg~V~iVDe~TGR~m~grr~s~GLHQaiEaKE~v~i~~e~~t~AsIT~Qn~Fr~Y~kLs  383 (896)
T PRK13104        304 HVNAALKAHAMFHRDIDYIVKDNQVVIVDEHTGRTMPGRRWSEGLHQAVEAKEGVPIQNENQTLASITFQNFFRMYNKLS  383 (896)
T ss_pred             HHHHHHHHHHHhcCCCceEEECCEEEEEECCCCCcCCCCCcChHHHHHHHHHcCCCCCCCceeeeeehHHHHHHhcchhc
Confidence                                                                                            


Q ss_pred             ----cCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhC--CCCeEEEEECccHHHHHH
Q psy1548         297 ----TLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVL--EFNQVVIFVKSVTRCIAL  370 (448)
Q Consensus       297 ----T~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l  370 (448)
                          |...+..++...|--+-+  .+.+. ......-....++.....|..++.+.+...  .+.++||||+|++.++.+
T Consensus       384 GMTGTa~te~~Ef~~iY~l~Vv--~IPtn-kp~~R~d~~d~v~~t~~~k~~av~~~i~~~~~~g~PVLVgt~Sie~sE~l  460 (896)
T PRK13104        384 GMTGTADTEAYEFQQIYNLEVV--VIPTN-RSMIRKDEADLVYLTQADKFQAIIEDVRECGVRKQPVLVGTVSIEASEFL  460 (896)
T ss_pred             cCCCCChhHHHHHHHHhCCCEE--ECCCC-CCcceecCCCeEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHH
Confidence                111111111111110000  00000 000000011234455667888887777443  567999999999999999


Q ss_pred             HHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC
Q psy1548         371 STLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       371 ~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~  404 (448)
                      +..|++.|++...+|+.+.+.+|..+.+.|+.|.
T Consensus       461 s~~L~~~gi~h~vLnak~~q~Ea~iia~Ag~~G~  494 (896)
T PRK13104        461 SQLLKKENIKHQVLNAKFHEKEAQIIAEAGRPGA  494 (896)
T ss_pred             HHHHHHcCCCeEeecCCCChHHHHHHHhCCCCCc
Confidence            9999999999999999999999999999999986

>KOG0951|consensus

Probab=99.87  E-value=1.1e-21  Score=206.30  Aligned_cols=262  Identities=21%  Similarity=0.303  Sum_probs=192.5

Q ss_pred             cceeeeeC-cceeeeccCCChhHHHHHHHHHHhhhccC--------CCeEEEEeeccHHHHHHHHHHHHHhhccCCCceE
Q psy1548         142 FGTKAVLG-MDILCQAKSGMGKTAVFVLATLQQLETTD--------SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKV  212 (448)
Q Consensus       142 ~~~~~~~g-~~vli~apTGsGKT~~~~l~~l~~l~~~~--------~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v  212 (448)
                      ..+.++.+ .|+++|||||+|||..+++.+|+.+..+.        ...+++|++|+++|++.+...+.+....+ +++|
T Consensus       317 v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLvqE~VgsfSkRla~~-GI~V  395 (1674)
T KOG0951|consen  317 VYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALVQEMVGSFSKRLAPL-GITV  395 (1674)
T ss_pred             HHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeHHHHHHHHHHHHHhhcccc-CcEE
Confidence            66677765 69999999999999999999999986543        23589999999999999988888877777 9999


Q ss_pred             EEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCC--CcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhC-----
Q psy1548         213 GVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK--LNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSS-----  285 (448)
Q Consensus       213 ~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~--~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l-----  285 (448)
                      .-.+|+.....+.  +.  ..+|+||||++.--.-+++.  ...+-++++|+||.|.+.+  +.++.++.+..+.     
T Consensus       396 ~ElTgD~~l~~~q--ie--eTqVIV~TPEK~DiITRk~gdraY~qlvrLlIIDEIHLLhD--dRGpvLESIVaRt~r~se  469 (1674)
T KOG0951|consen  396 LELTGDSQLGKEQ--IE--ETQVIVTTPEKWDIITRKSGDRAYEQLVRLLIIDEIHLLHD--DRGPVLESIVARTFRRSE  469 (1674)
T ss_pred             EEecccccchhhh--hh--cceeEEeccchhhhhhcccCchhHHHHHHHHhhhhhhhccc--ccchHHHHHHHHHHHHhh
Confidence            9999987644332  11  36899999999755444422  2235678899999996655  5777776665433     


Q ss_pred             --CCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcch---HHHHHHH-----HHhhCCCC
Q psy1548         286 --PHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENE---KNKKLFE-----LLDVLEFN  355 (448)
Q Consensus       286 --~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~---k~~~L~~-----ll~~~~~~  355 (448)
                        ...++++++|||+|+- .+....+..++..+...+. ...+..++|.|+.+...+   +.+++.+     ++.....+
T Consensus       470 s~~e~~RlVGLSATLPNy-~DV~~Fl~v~~~glf~fd~-syRpvPL~qq~Igi~ek~~~~~~qamNe~~yeKVm~~agk~  547 (1674)
T KOG0951|consen  470 STEEGSRLVGLSATLPNY-EDVASFLRVDPEGLFYFDS-SYRPVPLKQQYIGITEKKPLKRFQAMNEACYEKVLEHAGKN  547 (1674)
T ss_pred             hcccCceeeeecccCCch-hhhHHHhccCcccccccCc-ccCcCCccceEeccccCCchHHHHHHHHHHHHHHHHhCCCC
Confidence              3467999999999986 3444333344533433333 467788999999887653   3333333     33444557


Q ss_pred             eEEEEECccHHHHHHHHHHHhC-------------------------------------CCcEEEEeCCCCHHHHHHHHH
Q psy1548         356 QVVIFVKSVTRCIALSTLLSEQ-------------------------------------NFPAVSIHRGMTQEERLKKYQ  398 (448)
Q Consensus       356 ~~IIF~~s~~~a~~l~~~L~~~-------------------------------------g~~~~~lh~~~~~~eR~~~l~  398 (448)
                      ++|||+.+++++-+.|+.++..                                     .+.++.+|+||+..+|..+.+
T Consensus       548 qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkdLLpygfaIHhAGl~R~dR~~~Ed  627 (1674)
T KOG0951|consen  548 QVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKDLLPYGFAIHHAGLNRKDRELVED  627 (1674)
T ss_pred             cEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHHHhhccceeeccCCCcchHHHHHH
Confidence            9999999999999999888721                                     123789999999999999999


Q ss_pred             HHhcCCCceEEEEecC
Q psy1548         399 EFKDFHKGLAITFASD  414 (448)
Q Consensus       399 ~F~~g~~g~~I~~~t~  414 (448)
                      .|..|+  +.+.++|.
T Consensus       628 Lf~~g~--iqvlvsta  641 (1674)
T KOG0951|consen  628 LFADGH--IQVLVSTA  641 (1674)
T ss_pred             HHhcCc--eeEEEeeh
Confidence            999999  44444444

>KOG0948|consensus

Probab=99.87  E-value=6.3e-21  Score=191.85  Aligned_cols=254  Identities=20%  Similarity=0.204  Sum_probs=197.5

Q ss_pred             cCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         124 DMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       124 ~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      .+|..+++||..      ++..+-++.+|+++|.|.+|||.++-.++.+.+...   -|+||..|-++|.+|-++.+..=
T Consensus       125 ~YPF~LDpFQ~~------aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~k---QRVIYTSPIKALSNQKYREl~~E  195 (1041)
T KOG0948|consen  125 TYPFTLDPFQST------AIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLREK---QRVIYTSPIKALSNQKYRELLEE  195 (1041)
T ss_pred             CCCcccCchHhh------hhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHhc---CeEEeeChhhhhcchhHHHHHHH
Confidence            468889999999      999999999999999999999999988888776543   38999999999999988777653


Q ss_pred             hccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHH
Q psy1548         204 SKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFR  283 (448)
Q Consensus       204 ~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~  283 (448)
                      .+     .|++.+|+......        +..+|+|.+.|.+++-++.--+..+.|+|+||+|.|-+. ..+-.+++-+-
T Consensus       196 F~-----DVGLMTGDVTInP~--------ASCLVMTTEILRsMLYRGSEvmrEVaWVIFDEIHYMRDk-ERGVVWEETII  261 (1041)
T KOG0948|consen  196 FK-----DVGLMTGDVTINPD--------ASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDK-ERGVVWEETII  261 (1041)
T ss_pred             hc-----ccceeecceeeCCC--------CceeeeHHHHHHHHHhccchHhheeeeEEeeeehhcccc-ccceeeeeeEE
Confidence            32     56788999876654        679999999999999998888999999999999999886 77788888888


Q ss_pred             hCCCCCeEEEEeccCCccHHHHHHH---hcCCCeEEEEcCcccccccceeEEEEE---------cCcc-----hHHHH--
Q psy1548         284 SSPHTKQVMMFSATLSKEIRPVCKK---FMHDPMEVYVDDEAKLTLHGLQQHYVK---------LKEN-----EKNKK--  344 (448)
Q Consensus       284 ~l~~~~q~i~~SAT~~~~~~~~~~~---~l~~~~~i~~~~~~~~~~~~i~~~~~~---------~~~~-----~k~~~--  344 (448)
                      .+|++.+.+++|||+|+. .+++.|   .-+.|..+...+-   .+..++||.+.         +++.     +.+..  
T Consensus       262 llP~~vr~VFLSATiPNA-~qFAeWI~~ihkQPcHVVYTdy---RPTPLQHyifP~ggdGlylvVDek~~FrednF~~am  337 (1041)
T KOG0948|consen  262 LLPDNVRFVFLSATIPNA-RQFAEWICHIHKQPCHVVYTDY---RPTPLQHYIFPAGGDGLYLVVDEKGKFREDNFQKAM  337 (1041)
T ss_pred             eccccceEEEEeccCCCH-HHHHHHHHHHhcCCceEEeecC---CCCcceeeeecCCCCeeEEEEecccccchHHHHHHH
Confidence            999999999999999986 344444   4456766554333   23445555222         2221     11222  


Q ss_pred             ------------------------------------HHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCc--------
Q psy1548         345 ------------------------------------LFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFP--------  380 (448)
Q Consensus       345 ------------------------------------L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~--------  380 (448)
                                                          +...+-.....++|||+-++++|+.+|-.+.+..++        
T Consensus       338 ~~l~~~~~~~~~~~~~~k~~kG~~~~~~~~~s~i~kiVkmi~~~~~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~V  417 (1041)
T KOG0948|consen  338 SVLRKAGESDGKKKANKKGRKGGTGGKGPGDSDIYKIVKMIMERNYLPVIVFSFSKKECEAYALQMSKLDFNTDEEKELV  417 (1041)
T ss_pred             HHhhccCCCccccccccccccCCcCCCCCCcccHHHHHHHHHhhcCCceEEEEecHhHHHHHHHhhccCcCCChhHHHHH
Confidence                                                222222233458999999999999999988765443        


Q ss_pred             -------------------------------EEEEeCCCCHHHHHHHHHHHhcCC
Q psy1548         381 -------------------------------AVSIHRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       381 -------------------------------~~~lh~~~~~~eR~~~l~~F~~g~  404 (448)
                                                     +..+|+|+-+--+.-+.=.|++|-
T Consensus       418 ~~iF~nAi~~LseeDr~LPqie~iLPLL~RGIGIHHsGLLPIlKE~IEILFqEGL  472 (1041)
T KOG0948|consen  418 ETIFNNAIDQLSEEDRELPQIENILPLLRRGIGIHHSGLLPILKEVIEILFQEGL  472 (1041)
T ss_pred             HHHHHHHHHhcChhhccchHHHHHHHHHHhccccccccchHHHHHHHHHHHhccH
Confidence                                           788999999998888888999987

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.86  E-value=4.2e-20  Score=196.31  Aligned_cols=255  Identities=20%  Similarity=0.188  Sum_probs=170.5

Q ss_pred             CCCCchhhhhhhccccccceeeeeC---cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHH
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLG---MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYE  201 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g---~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  201 (448)
                      .|..+.++|++      +++.+..+   +++++.++||||||.+|+.++...+..   +.++||++|+++|+.|+.+.++
T Consensus       141 ~~~~Lt~~Q~~------ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~---g~~vLvLvPt~~L~~Q~~~~l~  211 (679)
T PRK05580        141 EPPTLNPEQAA------AVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQ---GKQALVLVPEIALTPQMLARFR  211 (679)
T ss_pred             CCCCCCHHHHH------HHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHHHHHHHHH
Confidence            45556777999      88888774   789999999999999998887776643   4589999999999999998888


Q ss_pred             HhhccCCCceEEEEEcCcccHHhH---HHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhh----h
Q psy1548         202 RFSKYMSNIKVGVFFGGLPIQKDE---EYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLE----M  274 (448)
Q Consensus       202 ~~~~~~~~~~v~~~~g~~~~~~~~---~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~----~  274 (448)
                      +..    +.++..++|+.+..+..   ..+..+.++|+|||++.+.       ..+++++++|+||+|...-...    +
T Consensus       212 ~~f----g~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~-------~p~~~l~liVvDEeh~~s~~~~~~p~y  280 (679)
T PRK05580        212 ARF----GAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF-------LPFKNLGLIIVDEEHDSSYKQQEGPRY  280 (679)
T ss_pred             HHh----CCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc-------ccccCCCEEEEECCCccccccCcCCCC
Confidence            754    56788899987755443   3345566899999998763       4478899999999996532201    1


Q ss_pred             -HHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcc-cccccceeEEEEEcCcch-------HHHHH
Q psy1548         275 -RRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEA-KLTLHGLQQHYVKLKENE-------KNKKL  345 (448)
Q Consensus       275 -~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~-~~~~~~i~~~~~~~~~~~-------k~~~L  345 (448)
                       ..++ .+++....+.+++++|||.+.+....+..  +....+...... ....+.+  ..+......       -...+
T Consensus       281 ~~r~v-a~~ra~~~~~~~il~SATps~~s~~~~~~--g~~~~~~l~~r~~~~~~p~v--~~id~~~~~~~~~~~~ls~~l  355 (679)
T PRK05580        281 HARDL-AVVRAKLENIPVVLGSATPSLESLANAQQ--GRYRLLRLTKRAGGARLPEV--EIIDMRELLRGENGSFLSPPL  355 (679)
T ss_pred             cHHHH-HHHHhhccCCCEEEEcCCCCHHHHHHHhc--cceeEEEeccccccCCCCeE--EEEechhhhhhcccCCCCHHH
Confidence             1122 23344457889999999977554443321  122222222210 0111111  111111100       11223


Q ss_pred             HHHHhh-C-CCCeEEEEECcc-----------------------------------------------------------
Q psy1548         346 FELLDV-L-EFNQVVIFVKSV-----------------------------------------------------------  364 (448)
Q Consensus       346 ~~ll~~-~-~~~~~IIF~~s~-----------------------------------------------------------  364 (448)
                      .+.++. . .++++|||+|++                                                           
T Consensus       356 ~~~i~~~l~~g~qvll~~nrrGy~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~l~~~  435 (679)
T PRK05580        356 LEAIKQRLERGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGSTDLVPV  435 (679)
T ss_pred             HHHHHHHHHcCCeEEEEEcCCCCCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCCeeEEe
Confidence            333332 2 355899998753                                                           


Q ss_pred             -HHHHHHHHHHHhC--CCcEEEEeCCCC--HHHHHHHHHHHhcCC
Q psy1548         365 -TRCIALSTLLSEQ--NFPAVSIHRGMT--QEERLKKYQEFKDFH  404 (448)
Q Consensus       365 -~~a~~l~~~L~~~--g~~~~~lh~~~~--~~eR~~~l~~F~~g~  404 (448)
                       ..++++++.|++.  +.++..+|++++  ++++.+++++|++|+
T Consensus       436 g~G~e~~~e~l~~~fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g~  480 (679)
T PRK05580        436 GPGTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGE  480 (679)
T ss_pred             eccHHHHHHHHHHhCCCCcEEEEeccccccchhHHHHHHHHhcCC
Confidence             2567888888886  789999999997  468999999999987

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.86  E-value=1.9e-20  Score=197.01  Aligned_cols=153  Identities=18%  Similarity=0.246  Sum_probs=132.4

Q ss_pred             ccCCCCHHHHHHHh-----hccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeecc
Q psy1548          83 RDFLLKPEILRAIV-----DCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAK  157 (448)
Q Consensus        83 ~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~ap  157 (448)
                      +.+.+..++.+.+.     ..|                       |..|+.+.+||.+      ++|.+..+++++++++
T Consensus        65 eafal~re~~~r~lg~~~~~~G-----------------------~~~p~~~tp~qvQ------~I~~i~l~~gvIAeaq  115 (970)
T PRK12899         65 EAYGVVKNVCRRLAGTPVEVSG-----------------------YHQQWDMVPYDVQ------ILGAIAMHKGFITEMQ  115 (970)
T ss_pred             HHhCCCHHHHHHHhcccccccc-----------------------ccCCCCCChHHHH------HhhhhhcCCCeEEEeC
Confidence            46778888888876     456                       9999777777999      9999999999999999


Q ss_pred             CCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEE
Q psy1548         158 SGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVV  237 (448)
Q Consensus       158 TGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV  237 (448)
                      ||+|||++|++|++..+..+.   .++||+||++||.|+.+.+..+.+.+ ++++++++||.+...+...+   .++|+|
T Consensus       116 TGeGKTLAf~LP~l~~aL~g~---~v~IVTpTrELA~Qdae~m~~L~k~l-GLsV~~i~GG~~~~eq~~~y---~~DIVy  188 (970)
T PRK12899        116 TGEGKTLTAVMPLYLNALTGK---PVHLVTVNDYLAQRDCEWVGSVLRWL-GLTTGVLVSGSPLEKRKEIY---QCDVVY  188 (970)
T ss_pred             CCCChHHHHHHHHHHHHhhcC---CeEEEeCCHHHHHHHHHHHHHHHhhc-CCeEEEEeCCCCHHHHHHHc---CCCEEE
Confidence            999999999999998775432   48899999999999999999999988 89999999999888776554   389999


Q ss_pred             EcHHHH-HHHHHCCCCcCC-------CeeEEEecchhHHHhh
Q psy1548         238 GTPGRI-LALVRNKKLNLS-------LLKHFILDECDKMLEQ  271 (448)
Q Consensus       238 ~Tp~~l-~~~l~~~~~~~~-------~i~~lViDEah~l~~~  271 (448)
                      |||+++ .++++.+.+.++       .+.++|+||||.|+-+
T Consensus       189 gTPgRLgfDyLrd~~~~~~~~~~vqr~~~~~IIDEADsmLiD  230 (970)
T PRK12899        189 GTASEFGFDYLRDNSIATRKEEQVGRGFYFAIIDEVDSILID  230 (970)
T ss_pred             ECCChhHHHHhhCCCCCcCHHHhhcccccEEEEechhhhhhh
Confidence            999999 999998766665       4589999999988654

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

Probab=99.85  E-value=5.9e-20  Score=186.28  Aligned_cols=248  Identities=18%  Similarity=0.154  Sum_probs=160.5

Q ss_pred             Cchhhhhhhccccccceeeee----CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         128 DSDTYLHRVARAGRFGTKAVL----GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       128 ~~~~yQ~~~~~~~~~~~~~~~----g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      .+++||++      ++..+..    ++..++++|||+|||.+++..+...      ...+|||||+++|+.|+.+.+.+.
T Consensus        36 ~lr~yQ~~------al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~------~~~~Lvlv~~~~L~~Qw~~~~~~~  103 (442)
T COG1061          36 ELRPYQEE------ALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAEL------KRSTLVLVPTKELLDQWAEALKKF  103 (442)
T ss_pred             CCcHHHHH------HHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHh------cCCEEEEECcHHHHHHHHHHHHHh
Confidence            46888999      7767666    8999999999999998876655443      123999999999999998777776


Q ss_pred             hccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHH
Q psy1548         204 SKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFR  283 (448)
Q Consensus       204 ~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~  283 (448)
                      ...  +..++.+.|+......        ..|.|+|.+.+........+......+||+||||++... .++.....+  
T Consensus       104 ~~~--~~~~g~~~~~~~~~~~--------~~i~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~~a~-~~~~~~~~~--  170 (442)
T COG1061         104 LLL--NDEIGIYGGGEKELEP--------AKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAP-SYRRILELL--  170 (442)
T ss_pred             cCC--ccccceecCceeccCC--------CcEEEEEhHHHhhhhhhhhhcccccCEEEEEccccCCcH-HHHHHHHhh--
Confidence            532  1234444444321110        259999999887642112233346889999999998775 443333332  


Q ss_pred             hCCCCCeEEEEeccCCccHHH---HHHHhcCCCeEEEEcCcc-----cccccceeEEEE---------------------
Q psy1548         284 SSPHTKQVMMFSATLSKEIRP---VCKKFMHDPMEVYVDDEA-----KLTLHGLQQHYV---------------------  334 (448)
Q Consensus       284 ~l~~~~q~i~~SAT~~~~~~~---~~~~~l~~~~~i~~~~~~-----~~~~~~i~~~~~---------------------  334 (448)
                        .....++++|||++..-..   .+..++ .|..+......     ...+..+.....                     
T Consensus       171 --~~~~~~LGLTATp~R~D~~~~~~l~~~~-g~~vy~~~~~~li~~g~Lap~~~~~i~~~~t~~~~~~~~~~~~~~~~~~  247 (442)
T COG1061         171 --SAAYPRLGLTATPEREDGGRIGDLFDLI-GPIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKESARFRELL  247 (442)
T ss_pred             --hcccceeeeccCceeecCCchhHHHHhc-CCeEeecCHHHHHhCCCccceEEEEEEeccchHHHHHhhhhhhhhhhhh
Confidence              2222289999997643211   111122 23333332110     111111111111                     


Q ss_pred             ---------------EcCcchHHHHHHHHHhhC-CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHH
Q psy1548         335 ---------------KLKENEKNKKLFELLDVL-EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQ  398 (448)
Q Consensus       335 ---------------~~~~~~k~~~L~~ll~~~-~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~  398 (448)
                                     ......+...+..++..+ .+.+++|||.+..+++.++..|...|+ +..+.+..+..+|..+++
T Consensus       248 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~  326 (442)
T COG1061         248 RARGTLRAENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILE  326 (442)
T ss_pred             hhhhhhhHHHHHHHHhhccHHHHHHHHHHHHHhcCCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHH
Confidence                           001112334444455444 366999999999999999999999888 899999999999999999


Q ss_pred             HHhcCC
Q psy1548         399 EFKDFH  404 (448)
Q Consensus       399 ~F~~g~  404 (448)
                      .|+.|.
T Consensus       327 ~fr~g~  332 (442)
T COG1061         327 RFRTGG  332 (442)
T ss_pred             HHHcCC
Confidence            999987

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.84  E-value=2.1e-19  Score=189.26  Aligned_cols=264  Identities=20%  Similarity=0.197  Sum_probs=184.7

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHH-HhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATL-QQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l-~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      .|..+   |-.      ..-.+..|+  |..++||+|||+++.+|++ +.+ .+   ..+-|++||..||.|..+.+..+
T Consensus        81 ~~~dv---Qli------g~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL-~G---~~V~IvTpn~yLA~rd~e~~~~l  145 (830)
T PRK12904         81 RHFDV---QLI------GGMVLHEGK--IAEMKTGEGKTLVATLPAYLNAL-TG---KGVHVVTVNDYLAKRDAEWMGPL  145 (830)
T ss_pred             CCCcc---HHH------hhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHH-cC---CCEEEEecCHHHHHHHHHHHHHH
Confidence            67788   888      443445564  8999999999999999996 544 32   24679999999999999999999


Q ss_pred             hccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHH-HHHHHCCC------CcCCCeeEEEecchhHHHhh-----
Q psy1548         204 SKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRI-LALVRNKK------LNLSLLKHFILDECDKMLEQ-----  271 (448)
Q Consensus       204 ~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l-~~~l~~~~------~~~~~i~~lViDEah~l~~~-----  271 (448)
                      ...+ ++++++++|+.+...+...+   .++|++|||+.+ .++++.+.      .....+.++|+||||.|+=+     
T Consensus       146 ~~~L-Glsv~~i~~~~~~~er~~~y---~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEaDsiLIDeArtp  221 (830)
T PRK12904        146 YEFL-GLSVGVILSGMSPEERREAY---AADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEVDSILIDEARTP  221 (830)
T ss_pred             Hhhc-CCeEEEEcCCCCHHHHHHhc---CCCeEEECCcchhhhhhhcccccchhhhcccccceEEEechhhheeccCCCc
Confidence            9999 99999999998877665554   379999999999 88887654      23678899999999987532     


Q ss_pred             ----------hhhHHHHHHHHHhCCCC--------C--------------------------------------------
Q psy1548         272 ----------LEMRRDVQEIFRSSPHT--------K--------------------------------------------  289 (448)
Q Consensus       272 ----------~~~~~~~~~i~~~l~~~--------~--------------------------------------------  289 (448)
                                ......+..+...+...        .                                            
T Consensus       222 LiiSg~~~~~~~~y~~~~~~v~~l~~~~dy~vde~~~~v~lte~G~~~~e~~~~~~~ly~~~~~~~~~~i~~AL~A~~l~  301 (830)
T PRK12904        222 LIISGPAEDSSELYKRANKIVPTLEKEGDYTVDEKSRTVGLTEEGIEKAEKLLGIENLYDPENIALVHHLNQALRAHELF  301 (830)
T ss_pred             eeeECCCCcccHHHHHHHHHHHhcCCCCCeEEEcCCCeeeECHHHHHHHHHHhCCccccChhhhHHHHHHHHHHHHHHHH
Confidence                      11223333333333110        0                                            


Q ss_pred             -----------------------------------------------------------------eEEEEeccCCccHHH
Q psy1548         290 -----------------------------------------------------------------QVMMFSATLSKEIRP  304 (448)
Q Consensus       290 -----------------------------------------------------------------q~i~~SAT~~~~~~~  304 (448)
                                                                                       ++.+||.|...+..+
T Consensus       302 ~~d~dYiV~dg~V~ivDe~TGR~~~gr~ws~GLHQaiEaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~te~~E  381 (830)
T PRK12904        302 KRDVDYIVKDGEVVIVDEFTGRLMPGRRYSDGLHQAIEAKEGVKIQNENQTLASITFQNYFRMYEKLAGMTGTADTEAEE  381 (830)
T ss_pred             hcCCcEEEECCEEEEEECCCCccCCCCccchHHHHHHHHhcCCCCCCCceeeeeeeHHHHHHhcchhcccCCCcHHHHHH
Confidence                                                                             224444444433333


Q ss_pred             HHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhh--CCCCeEEEEECccHHHHHHHHHHHhCCCcEE
Q psy1548         305 VCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDV--LEFNQVVIFVKSVTRCIALSTLLSEQNFPAV  382 (448)
Q Consensus       305 ~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~--~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~  382 (448)
                      +...|.-+-+.|  ++. ......-....+.....+|..++...+..  ..+.++||||+|++.++.++..|.+.|+++.
T Consensus       382 ~~~iY~l~vv~I--Ptn-kp~~r~d~~d~i~~t~~~K~~aI~~~I~~~~~~grpVLIft~Si~~se~Ls~~L~~~gi~~~  458 (830)
T PRK12904        382 FREIYNLDVVVI--PTN-RPMIRIDHPDLIYKTEKEKFDAVVEDIKERHKKGQPVLVGTVSIEKSELLSKLLKKAGIPHN  458 (830)
T ss_pred             HHHHhCCCEEEc--CCC-CCeeeeeCCCeEEECHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHCCCceE
Confidence            333332221111  111 10000001123444566799999998865  4667999999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHhcCCCceEEEEecC
Q psy1548         383 SIHRGMTQEERLKKYQEFKDFHKGLAITFASD  414 (448)
Q Consensus       383 ~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~  414 (448)
                      .+|+.  +.+|...+..|+.++  ..|+++|+
T Consensus       459 vLnak--q~eREa~Iia~Ag~~--g~VtIATN  486 (830)
T PRK12904        459 VLNAK--NHEREAEIIAQAGRP--GAVTIATN  486 (830)
T ss_pred             eccCc--hHHHHHHHHHhcCCC--ceEEEecc
Confidence            99996  889999999998877  25666655

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

Probab=99.83  E-value=2.6e-19  Score=181.58  Aligned_cols=262  Identities=21%  Similarity=0.221  Sum_probs=185.5

Q ss_pred             CCCCchhhhhhhccccccceeeeeC------cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHH
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLG------MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK  198 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g------~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~  198 (448)
                      .|+.+-..|+.      ++..+...      .+-|++|.-|||||++++++++..+.   .|.++..++||.-||.|-+.
T Consensus       259 LPF~LT~aQ~~------vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~---~G~Q~ALMAPTEILA~QH~~  329 (677)
T COG1200         259 LPFKLTNAQKR------VIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIE---AGYQAALMAPTEILAEQHYE  329 (677)
T ss_pred             CCCCccHHHHH------HHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHH---cCCeeEEeccHHHHHHHHHH
Confidence            45555566888      77766653      57899999999999999999998875   45689999999999999999


Q ss_pred             HHHHhhccCCCceEEEEEcCcccHHh---HHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhH
Q psy1548         199 EYERFSKYMSNIKVGVFFGGLPIQKD---EEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMR  275 (448)
Q Consensus       199 ~~~~~~~~~~~~~v~~~~g~~~~~~~---~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~  275 (448)
                      .+.++...+ ++++..++|.......   ...+.++..+|+|||..     +-.+...++++.++|+||-|+..-     
T Consensus       330 ~~~~~l~~~-~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHA-----LiQd~V~F~~LgLVIiDEQHRFGV-----  398 (677)
T COG1200         330 SLRKWLEPL-GIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHA-----LIQDKVEFHNLGLVIIDEQHRFGV-----  398 (677)
T ss_pred             HHHHHhhhc-CCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcch-----hhhcceeecceeEEEEeccccccH-----
Confidence            999999988 8999999998765443   44567788999999975     334566789999999999996533     


Q ss_pred             HHHHHHHHhCCC-CCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHh-hC-
Q psy1548         276 RDVQEIFRSSPH-TKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLD-VL-  352 (448)
Q Consensus       276 ~~~~~i~~~l~~-~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~-~~-  352 (448)
                       .-+..+..... ...++.||||.-+....+.  ...+-. +.+-++--.-...|..+.+..  +.+ ..+++.++ .. 
T Consensus       399 -~QR~~L~~KG~~~Ph~LvMTATPIPRTLAlt--~fgDld-vS~IdElP~GRkpI~T~~i~~--~~~-~~v~e~i~~ei~  471 (677)
T COG1200         399 -HQRLALREKGEQNPHVLVMTATPIPRTLALT--AFGDLD-VSIIDELPPGRKPITTVVIPH--ERR-PEVYERIREEIA  471 (677)
T ss_pred             -HHHHHHHHhCCCCCcEEEEeCCCchHHHHHH--Hhcccc-chhhccCCCCCCceEEEEecc--ccH-HHHHHHHHHHHH
Confidence             23333444444 5678999999766544433  232221 222222011122344444332  222 22333332 22 


Q ss_pred             CCCeEEEEECccH--------HHHHHHHHHHhC--CCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         353 EFNQVVIFVKSVT--------RCIALSTLLSEQ--NFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       353 ~~~~~IIF~~s~~--------~a~~l~~~L~~~--g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                      .+.++.+.|+-.+        .|+.+++.|+..  ++++..+||.|+.+++.+++++|++|+  +.|+++|+-
T Consensus       472 ~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e--~~ILVaTTV  542 (677)
T COG1200         472 KGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGE--IDILVATTV  542 (677)
T ss_pred             cCCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcCC--CcEEEEeeE
Confidence            5678999998654        456677777754  677999999999999999999999998  577777764

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.82  E-value=1.5e-18  Score=190.86  Aligned_cols=264  Identities=16%  Similarity=0.206  Sum_probs=171.8

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      |...-|+..+..+      .+..+..+..++++|+||||||..  +|.+..-.......++++.-|.|--|..+...+..
T Consensus        62 ~~~~LPi~~~~~~------Il~~l~~~~vvii~g~TGSGKTTq--lPq~lle~~~~~~~~I~~tQPRRlAA~svA~RvA~  133 (1283)
T TIGR01967        62 YPDNLPVSAKRED------IAEAIAENQVVIIAGETGSGKTTQ--LPKICLELGRGSHGLIGHTQPRRLAARTVAQRIAE  133 (1283)
T ss_pred             CCCCCCHHHHHHH------HHHHHHhCceEEEeCCCCCCcHHH--HHHHHHHcCCCCCceEecCCccHHHHHHHHHHHHH
Confidence            5555677555556      555665667889999999999984  56544322212223566667888777766655544


Q ss_pred             hhccCCCceEEEEEcCc-ccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchh-HHHhhhhhHHH-HH
Q psy1548         203 FSKYMSNIKVGVFFGGL-PIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECD-KMLEQLEMRRD-VQ  279 (448)
Q Consensus       203 ~~~~~~~~~v~~~~g~~-~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah-~l~~~~~~~~~-~~  279 (448)
                      -.    +..++...|.. ....+.   . ...+|.|+|+|.|+..+..+. .+.++++||||||| ++++. ++.-. +.
T Consensus       134 el----g~~lG~~VGY~vR~~~~~---s-~~T~I~~~TdGiLLr~l~~d~-~L~~~~~IIIDEaHERsL~~-D~LL~lLk  203 (1283)
T TIGR01967       134 EL----GTPLGEKVGYKVRFHDQV---S-SNTLVKLMTDGILLAETQQDR-FLSRYDTIIIDEAHERSLNI-DFLLGYLK  203 (1283)
T ss_pred             Hh----CCCcceEEeeEEcCCccc---C-CCceeeeccccHHHHHhhhCc-ccccCcEEEEcCcchhhccc-hhHHHHHH
Confidence            33    34444444431 111111   1 237899999999999887654 37899999999999 47775 66554 55


Q ss_pred             HHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCc------chHHHHHHHHHhh--
Q psy1548         280 EIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKE------NEKNKKLFELLDV--  351 (448)
Q Consensus       280 ~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~------~~k~~~L~~ll~~--  351 (448)
                      .++... ++.|+|+||||++.  ..+.+.|...|. +.+...    ...+..+|.....      .++...+...+..  
T Consensus       204 ~il~~r-pdLKlIlmSATld~--~~fa~~F~~apv-I~V~Gr----~~PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~  275 (1283)
T TIGR01967       204 QLLPRR-PDLKIIITSATIDP--ERFSRHFNNAPI-IEVSGR----TYPVEVRYRPLVEEQEDDDLDQLEAILDAVDELF  275 (1283)
T ss_pred             HHHhhC-CCCeEEEEeCCcCH--HHHHHHhcCCCE-EEECCC----cccceeEEecccccccchhhhHHHHHHHHHHHHH
Confidence            554443 57899999999964  466666655554 443322    1234445543322      1233334333332  


Q ss_pred             -CCCCeEEEEECccHHHHHHHHHHHhCC---CcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChh
Q psy1548         352 -LEFNQVVIFVKSVTRCIALSTLLSEQN---FPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDEN  416 (448)
Q Consensus       352 -~~~~~~IIF~~s~~~a~~l~~~L~~~g---~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~  416 (448)
                       ...+.+|||+++..+++.+++.|++.+   +.+..+||+|++++|.++++.+    .+..|.++|+-.
T Consensus       276 ~~~~GdILVFLpg~~EI~~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~----~~rkIVLATNIA  340 (1283)
T TIGR01967       276 AEGPGDILIFLPGEREIRDAAEILRKRNLRHTEILPLYARLSNKEQQRVFQPH----SGRRIVLATNVA  340 (1283)
T ss_pred             hhCCCCEEEeCCCHHHHHHHHHHHHhcCCCCcEEEeccCCCCHHHHHHHhCCC----CCceEEEeccHH
Confidence             245789999999999999999999864   4588999999999999986543    234677777653

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.

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.82  E-value=6.8e-19  Score=190.12  Aligned_cols=304  Identities=17%  Similarity=0.155  Sum_probs=187.6

Q ss_pred             chhhhhhhccccccceeeee--CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhcc
Q psy1548         129 SDTYLHRVARAGRFGTKAVL--GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKY  206 (448)
Q Consensus       129 ~~~yQ~~~~~~~~~~~~~~~--g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  206 (448)
                      +.+||..      ....++.  ...+|+...+|.|||..+.+.+...+..+ ...++|||||. .|..||..++.+..  
T Consensus       153 l~pHQl~------~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g-~~~rvLIVvP~-sL~~QW~~El~~kF--  222 (956)
T PRK04914        153 LIPHQLY------IAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTG-RAERVLILVPE-TLQHQWLVEMLRRF--  222 (956)
T ss_pred             CCHHHHH------HHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcC-CCCcEEEEcCH-HHHHHHHHHHHHHh--
Confidence            3455888      4333332  35789999999999988766555444433 33489999998 79999988886543  


Q ss_pred             CCCceEEEEEcCcccHHh---HHHHhcCCCcEEEEcHHHHHHHHH-CCCCcCCCeeEEEecchhHHHhhh-hhHHHHHHH
Q psy1548         207 MSNIKVGVFFGGLPIQKD---EEYLKTHNPQIVVGTPGRILALVR-NKKLNLSLLKHFILDECDKMLEQL-EMRRDVQEI  281 (448)
Q Consensus       207 ~~~~~v~~~~g~~~~~~~---~~~l~~~~~~IlV~Tp~~l~~~l~-~~~~~~~~i~~lViDEah~l~~~~-~~~~~~~~i  281 (448)
                        ++.+.++.++......   ...+.  ..+++|+|.+.+...-. ...+.-...+++|+||||++-... .-...+..+
T Consensus       223 --~l~~~i~~~~~~~~~~~~~~~pf~--~~~~vI~S~~~l~~~~~~~~~l~~~~wdlvIvDEAH~lk~~~~~~s~~y~~v  298 (956)
T PRK04914        223 --NLRFSLFDEERYAEAQHDADNPFE--TEQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHHLVWSEEAPSREYQVV  298 (956)
T ss_pred             --CCCeEEEcCcchhhhcccccCccc--cCcEEEEEHHHhhhCHHHHHHHhhcCCCEEEEechhhhccCCCCcCHHHHHH
Confidence              4444444333211000   00011  25799999887754110 011222467899999999985210 011112222


Q ss_pred             HHhCCCCCeEEEEeccCCc-c------------------HHHHH------------------------------HHhcCC
Q psy1548         282 FRSSPHTKQVMMFSATLSK-E------------------IRPVC------------------------------KKFMHD  312 (448)
Q Consensus       282 ~~~l~~~~q~i~~SAT~~~-~------------------~~~~~------------------------------~~~l~~  312 (448)
                      .........++++|||+-. .                  ...+.                              ..++++
T Consensus       299 ~~La~~~~~~LLLTATP~q~~~~e~falL~lLdP~~f~~~~~F~~e~~~~~~~a~~v~~l~~~~~~~~~~~~~l~~ll~~  378 (956)
T PRK04914        299 EQLAEVIPGVLLLTATPEQLGQESHFARLRLLDPDRFHDYEAFVEEQQQYRPVADAVQALLAGEKLSDDALNALGELLGE  378 (956)
T ss_pred             HHHhhccCCEEEEEcCcccCCcHHHHHhhhhhCCCcCCCHHHHHHHHHhhHHHHHHHHHHhcCCcCCHHHHHHHHHHhcc
Confidence            2222233468999999421 0                  00110                              011100


Q ss_pred             C---------------------------------eEEEEcCcc----cccccceeEEEE---------------------
Q psy1548         313 P---------------------------------MEVYVDDEA----KLTLHGLQQHYV---------------------  334 (448)
Q Consensus       313 ~---------------------------------~~i~~~~~~----~~~~~~i~~~~~---------------------  334 (448)
                      .                                 ..+......    ......+....+                     
T Consensus       379 ~~~~~l~~~~~~~~~~~~~~~~~~i~~L~d~hg~~rvm~RntR~~v~~fp~R~~~~~~l~~~~~y~~~~~~~~~~~~~~~  458 (956)
T PRK04914        379 QDIEPLLQAANSDSEEAQAARQELISELLDRHGTGRVLFRNTRAAVKGFPKRELHPIPLPLPEQYQTAIKVSLEARARDM  458 (956)
T ss_pred             cchhHHHhhhcccccccHHHHHHHHHHHHhhcCcceEEEeccHHhhcCCCcCceeEeecCCCHHHHHHHHHhHHHHHHhh
Confidence            0                                 000000000    000000000000                     


Q ss_pred             ---------------EcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHH-hCCCcEEEEeCCCCHHHHHHHHH
Q psy1548         335 ---------------KLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLS-EQNFPAVSIHRGMTQEERLKKYQ  398 (448)
Q Consensus       335 ---------------~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~-~~g~~~~~lh~~~~~~eR~~~l~  398 (448)
                                     +...+.|...|.++++.....|+||||+++..+..+++.|+ +.|+++..+||+|++.+|.++++
T Consensus       459 l~pe~~~~~~~~~~~~~~~d~Ki~~L~~~L~~~~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~~eR~~~~~  538 (956)
T PRK04914        459 LYPEQIYQEFEDNATWWNFDPRVEWLIDFLKSHRSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSIIERDRAAA  538 (956)
T ss_pred             cCHHHHHHHHhhhhhccccCHHHHHHHHHHHhcCCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCHHHHHHHHH
Confidence                           11223467788888888778899999999999999999994 56999999999999999999999


Q ss_pred             HHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         399 EFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       399 ~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      .|++++.+..|+++|+..-++.  +++..-.+-..++|.+.+.+++++||
T Consensus       539 ~F~~~~~~~~VLIsTdvgseGl--Nlq~a~~VInfDlP~nP~~~eQRIGR  586 (956)
T PRK04914        539 YFADEEDGAQVLLCSEIGSEGR--NFQFASHLVLFDLPFNPDLLEQRIGR  586 (956)
T ss_pred             HHhcCCCCccEEEechhhccCC--CcccccEEEEecCCCCHHHHHHHhcc
Confidence            9999877788888887644443  56766677888999999999999998

>TIGR00595 priA primosomal protein N'

Probab=99.82  E-value=2.6e-18  Score=176.56  Aligned_cols=233  Identities=19%  Similarity=0.201  Sum_probs=149.8

Q ss_pred             eeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHh---HHHHh
Q psy1548         153 LCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD---EEYLK  229 (448)
Q Consensus       153 li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~---~~~l~  229 (448)
                      |+.||||||||.+|+..+...+..   +.++||++|+++|+.|+.+.+++..    +.++..++|+.+..+.   +..+.
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~---g~~vLvlvP~i~L~~Q~~~~l~~~f----~~~v~vlhs~~~~~er~~~~~~~~   73 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLAL---GKSVLVLVPEIALTPQMIQRFKYRF----GSQVAVLHSGLSDSEKLQAWRKVK   73 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHHHHHHHHHHHh----CCcEEEEECCCCHHHHHHHHHHHH
Confidence            578999999999997665554432   4489999999999999998888754    5667788887765443   33445


Q ss_pred             cCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhh--h--h-HHHHHHHHHhCCCCCeEEEEeccCCccHHH
Q psy1548         230 THNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQL--E--M-RRDVQEIFRSSPHTKQVMMFSATLSKEIRP  304 (448)
Q Consensus       230 ~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~--~--~-~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~  304 (448)
                      .+.++|+|||+..+.       ..++++++|||||.|...-+.  .  + ..++. +++....+.+++++|||.+.+...
T Consensus        74 ~g~~~IVVGTrsalf-------~p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a-~~ra~~~~~~vil~SATPsles~~  145 (505)
T TIGR00595        74 NGEILVVIGTRSALF-------LPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVA-VYRAKKFNCPVVLGSATPSLESYH  145 (505)
T ss_pred             cCCCCEEECChHHHc-------CcccCCCEEEEECCCccccccccCCCCcHHHHH-HHHHHhcCCCEEEEeCCCCHHHHH
Confidence            566899999998663       347889999999999764320  1  1 11222 233334578899999996644333


Q ss_pred             HHHHhcCCCeEEEEcCcc-cccccceeEEEEEcCcch----HHHHHHHHHhh-C-CCCeEEEEECccHH-----------
Q psy1548         305 VCKKFMHDPMEVYVDDEA-KLTLHGLQQHYVKLKENE----KNKKLFELLDV-L-EFNQVVIFVKSVTR-----------  366 (448)
Q Consensus       305 ~~~~~l~~~~~i~~~~~~-~~~~~~i~~~~~~~~~~~----k~~~L~~ll~~-~-~~~~~IIF~~s~~~-----------  366 (448)
                      .+.  .+....+...... ....+.+  .++......    -...+.+.++. . .++++|||+|++..           
T Consensus       146 ~~~--~g~~~~~~l~~r~~~~~~p~v--~vid~~~~~~~~~ls~~l~~~i~~~l~~g~qvLvflnrrGya~~~~C~~Cg~  221 (505)
T TIGR00595       146 NAK--QKAYRLLVLTRRVSGRKPPEV--KLIDMRKEPRQSFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCRSCGY  221 (505)
T ss_pred             HHh--cCCeEEeechhhhcCCCCCeE--EEEecccccccCCccHHHHHHHHHHHHcCCcEEEEEeCCcCCCeeEhhhCcC
Confidence            322  1222222221110 1111111  122222111    11223333322 2 35689999887653           


Q ss_pred             -------------------------------------------------HHHHHHHHHhC--CCcEEEEeCCCCHHHH--
Q psy1548         367 -------------------------------------------------CIALSTLLSEQ--NFPAVSIHRGMTQEER--  393 (448)
Q Consensus       367 -------------------------------------------------a~~l~~~L~~~--g~~~~~lh~~~~~~eR--  393 (448)
                                                                       ++++++.|++.  +.++..+|++++..++  
T Consensus       222 ~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~~l~~~g~Gte~~~e~l~~~fp~~~v~~~d~d~~~~~~~~  301 (505)
T TIGR00595       222 ILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAH  301 (505)
T ss_pred             ccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCCeeEeecccHHHHHHHHHhhCCCCcEEEEecccccCccHH
Confidence                                                             58888888886  7899999999987766  


Q ss_pred             HHHHHHHhcCC
Q psy1548         394 LKKYQEFKDFH  404 (448)
Q Consensus       394 ~~~l~~F~~g~  404 (448)
                      .+++++|++|+
T Consensus       302 ~~~l~~f~~g~  312 (505)
T TIGR00595       302 EALLNQFANGK  312 (505)
T ss_pred             HHHHHHHhcCC
Confidence            89999999987

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).

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.81  E-value=2e-18  Score=155.88  Aligned_cols=186  Identities=28%  Similarity=0.441  Sum_probs=148.9

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeC-cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYE  201 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g-~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  201 (448)
                      +..|++.   |.+      +++.+..+ +++++.+|||+|||.+++.+++..+.... ..++++++|+..++.|+...+.
T Consensus         6 ~~~~~~~---Q~~------~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~-~~~~l~~~p~~~~~~~~~~~~~   75 (201)
T smart00487        6 FEPLRPY---QKE------AIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK-GKRVLVLVPTRELAEQWAEELK   75 (201)
T ss_pred             CCCCCHH---HHH------HHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccC-CCcEEEEeCCHHHHHHHHHHHH
Confidence            4455555   999      99998888 99999999999999999999988776543 3479999999999999999998


Q ss_pred             HhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHH
Q psy1548         202 RFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEI  281 (448)
Q Consensus       202 ~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i  281 (448)
                      .+.... ........++.........+..+..+++++|++.+.+.+.........++++|+||+|.+... .+...+..+
T Consensus        76 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~~~~~~~~~iIiDE~h~~~~~-~~~~~~~~~  153 (201)
T smart00487       76 KLGPSL-GLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLDG-GFGDQLEKL  153 (201)
T ss_pred             HHhccC-CeEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCCcCHhHCCEEEEECHHHHhcC-CcHHHHHHH
Confidence            887654 323444455544344445555553499999999999999887777788999999999999875 678888888


Q ss_pred             HHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcC
Q psy1548         282 FRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDD  320 (448)
Q Consensus       282 ~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~  320 (448)
                      +..+++..+++++|||+++........+..+...+....
T Consensus       154 ~~~~~~~~~~v~~saT~~~~~~~~~~~~~~~~~~~~~~~  192 (201)
T smart00487      154 LKLLPKNVQLLLLSATPPEEIENLLELFLNDPVFIDVGP  192 (201)
T ss_pred             HHhCCccceEEEEecCCchhHHHHHHHhcCCCEEEeCCc
Confidence            888888899999999999998888888888666665443

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.79  E-value=3.9e-18  Score=179.38  Aligned_cols=129  Identities=21%  Similarity=0.225  Sum_probs=101.9

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .|..+   |-.      ..-.+..|  -|..++||.|||+++.+|++.....+.   .+.||+|+..||.+..+++..+.
T Consensus        82 ~~ydV---Qli------Ggl~L~~G--~IaEm~TGEGKTL~a~lp~~l~al~g~---~VhIvT~ndyLA~RD~e~m~~l~  147 (908)
T PRK13107         82 RHFDV---QLL------GGMVLDSN--RIAEMRTGEGKTLTATLPAYLNALTGK---GVHVITVNDYLARRDAENNRPLF  147 (908)
T ss_pred             CcCch---HHh------cchHhcCC--ccccccCCCCchHHHHHHHHHHHhcCC---CEEEEeCCHHHHHHHHHHHHHHH
Confidence            56777   877      22233334  488999999999999999987765443   49999999999999999999999


Q ss_pred             ccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHH-HHHHHCC-CCcC-----CCeeEEEecchhHHHhh
Q psy1548         205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRI-LALVRNK-KLNL-----SLLKHFILDECDKMLEQ  271 (448)
Q Consensus       205 ~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l-~~~l~~~-~~~~-----~~i~~lViDEah~l~~~  271 (448)
                      ..+ +++++++.++.+....   .....++|++|||+.+ .++|+.+ .+..     ..+.++|+||+|.++-+
T Consensus       148 ~~l-Glsv~~i~~~~~~~~r---~~~Y~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEvDsiLiD  217 (908)
T PRK13107        148 EFL-GLTVGINVAGLGQQEK---KAAYNADITYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEVDSILID  217 (908)
T ss_pred             Hhc-CCeEEEecCCCCHHHH---HhcCCCCeEEeCCCcccchhhhccCccchhhhhccccceeeecchhhhccc
Confidence            998 9999999998775332   2333489999999999 8888765 3333     77889999999987644

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.76  E-value=3.8e-18  Score=183.03  Aligned_cols=281  Identities=20%  Similarity=0.219  Sum_probs=170.9

Q ss_pred             ceeeeccCCChhHHHHHHHHHHhhhc-cCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHH--
Q psy1548         151 DILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEY--  227 (448)
Q Consensus       151 ~vli~apTGsGKT~~~~l~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~--  227 (448)
                      .+++.||||+|||.+.+.+++..+.. .....+++++.|++.+++++++.++.+.... .+......|..........  
T Consensus       216 ~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~-~~~~~~~h~~~~~~~~~~~~~  294 (733)
T COG1203         216 LVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGLF-SVIGKSLHSSSKEPLLLEPDQ  294 (733)
T ss_pred             cEEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHHHHHHHHHHHhhhccc-ccccccccccccchhhhcccc
Confidence            88999999999999999999887766 3456799999999999999999999877654 3322212222221110000  


Q ss_pred             -----------HhcCCCcEEEEcHHHHHHHHH-CCCCc-C--CCeeEEEecchhHHHhhhhhHHHHHHHHHhCC-CCCeE
Q psy1548         228 -----------LKTHNPQIVVGTPGRILALVR-NKKLN-L--SLLKHFILDECDKMLEQLEMRRDVQEIFRSSP-HTKQV  291 (448)
Q Consensus       228 -----------l~~~~~~IlV~Tp~~l~~~l~-~~~~~-~--~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~-~~~q~  291 (448)
                                 ....-..+.++||..+..... ..... +  -....+|+||+|.+.+. .....+..++..+. .+..+
T Consensus       295 ~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~~~~-~~~~~l~~~i~~l~~~g~~i  373 (733)
T COG1203         295 DILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLYADE-TMLAALLALLEALAEAGVPV  373 (733)
T ss_pred             ccceeEEecccccceeccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHhhccc-chHHHHHHHHHHHHhCCCCE
Confidence                       000113455556655444211 11111 1  11246999999987664 24555555544443 36789


Q ss_pred             EEEeccCCccHHHHHHHhcCCCeEEEEcCcc--cccccceeEEEEE-cCcchHHHHHHHHH-hhCCCCeEEEEECccHHH
Q psy1548         292 MMFSATLSKEIRPVCKKFMHDPMEVYVDDEA--KLTLHGLQQHYVK-LKENEKNKKLFELL-DVLEFNQVVIFVKSVTRC  367 (448)
Q Consensus       292 i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~--~~~~~~i~~~~~~-~~~~~k~~~L~~ll-~~~~~~~~IIF~~s~~~a  367 (448)
                      +++|||+|+..++.+...+.....+......  ......+.+.... .............. ....+++++|.|||+..|
T Consensus       374 ll~SATlP~~~~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kvlvI~NTV~~A  453 (733)
T COG1203         374 LLMSATLPPFLKEKLKKALGKGREVVENAKFCPKEDEPGLKRKERVDVEDGPQEELIELISEEVKEGKKVLVIVNTVDRA  453 (733)
T ss_pred             EEEecCCCHHHHHHHHHHHhcccceeccccccccccccccccccchhhhhhhhHhhhhcchhhhccCCcEEEEEecHHHH
Confidence            9999999999999888877655544432110  0000111111000 00000001111111 223467999999999999


Q ss_pred             HHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcC--CCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccc
Q psy1548         368 IALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDF--HKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDL  441 (448)
Q Consensus       368 ~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g--~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~  441 (448)
                      ..++..|+..+.++.++||.++..+|.+.++++++-  ..+-.|.++|.        -||..+++...-+.+++.+
T Consensus       454 ie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQ--------VIEagvDidfd~mITe~aP  521 (733)
T COG1203         454 IELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQ--------VIEAGVDIDFDVLITELAP  521 (733)
T ss_pred             HHHHHHHHhcCCCEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEee--------EEEEEeccccCeeeecCCC
Confidence            999999999887899999999999999999977752  22224444443        3444555555555555443

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

Probab=99.76  E-value=1.1e-17  Score=184.45  Aligned_cols=264  Identities=14%  Similarity=0.175  Sum_probs=153.1

Q ss_pred             CCchhhhhhhccccccceeee----eC-cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHH
Q psy1548         127 EDSDTYLHRVARAGRFGTKAV----LG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYE  201 (448)
Q Consensus       127 ~~~~~yQ~~~~~~~~~~~~~~----~g-~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  201 (448)
                      ...++||.+      ++..+.    .| +.++++++||||||.+++ .++..+.......++|+|+|+++|+.|+.+.++
T Consensus       412 ~~lR~YQ~~------AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai-~li~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~  484 (1123)
T PRK11448        412 LGLRYYQED------AIQAVEKAIVEGQREILLAMATGTGKTRTAI-ALMYRLLKAKRFRRILFLVDRSALGEQAEDAFK  484 (1123)
T ss_pred             CCCCHHHHH------HHHHHHHHHHhccCCeEEEeCCCCCHHHHHH-HHHHHHHhcCccCeEEEEecHHHHHHHHHHHHH
Confidence            356889999      665554    33 679999999999998854 344444444445699999999999999999888


Q ss_pred             HhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHC-----CCCcCCCeeEEEecchhHHHhh-----
Q psy1548         202 RFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRN-----KKLNLSLLKHFILDECDKMLEQ-----  271 (448)
Q Consensus       202 ~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~-----~~~~~~~i~~lViDEah~l~~~-----  271 (448)
                      .+.... ......+++.....   ........+|+|+|.+++...+..     ....+.++++||+||||+-...     
T Consensus       485 ~~~~~~-~~~~~~i~~i~~L~---~~~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs~~~d~~~~  560 (1123)
T PRK11448        485 DTKIEG-DQTFASIYDIKGLE---DKFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGYTLDKEMS  560 (1123)
T ss_pred             hccccc-ccchhhhhchhhhh---hhcccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCCCccccccc
Confidence            764221 11111112111101   111122368999999999876532     1245678899999999985310     


Q ss_pred             ---------hhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHH--------------HhcCC---CeEEEEcCccc-c
Q psy1548         272 ---------LEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCK--------------KFMHD---PMEVYVDDEAK-L  324 (448)
Q Consensus       272 ---------~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~--------------~~l~~---~~~i~~~~~~~-~  324 (448)
                               .++...+..++.++.  ...|+||||+......+..              .++.+   |..+...-... .
T Consensus       561 ~~~~~~~~~~~~~~~yr~iL~yFd--A~~IGLTATP~r~t~~~FG~pv~~Ysl~eAI~DG~Lv~~~~p~~i~t~~~~~gi  638 (1123)
T PRK11448        561 EGELQFRDQLDYVSKYRRVLDYFD--AVKIGLTATPALHTTEIFGEPVYTYSYREAVIDGYLIDHEPPIRIETRLSQEGI  638 (1123)
T ss_pred             cchhccchhhhHHHHHHHHHhhcC--ccEEEEecCCccchhHHhCCeeEEeeHHHHHhcCCcccCcCCEEEEEEeccccc
Confidence                     022456777777553  4579999998643322111              11110   12221100000 0


Q ss_pred             cccc------eeE---EE--EEcCcc--------h-------HH----HHHHHHHhhCCCCeEEEEECccHHHHHHHHHH
Q psy1548         325 TLHG------LQQ---HY--VKLKEN--------E-------KN----KKLFELLDVLEFNQVVIFVKSVTRCIALSTLL  374 (448)
Q Consensus       325 ~~~~------i~~---~~--~~~~~~--------~-------k~----~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L  374 (448)
                      ....      +..   .+  ...+..        +       ..    ..+...+....++++||||.++.+|+.+++.|
T Consensus       639 ~~~~~e~~~~~~~~~~~i~~~~l~d~~~~~~~~~~~~vi~~~~~~~i~~~l~~~l~~~~~~KtiIF~~s~~HA~~i~~~L  718 (1123)
T PRK11448        639 HFEKGEEVEVINTQTGEIDLATLEDEVDFEVEDFNRRVITESFNRVVCEELAKYLDPTGEGKTLIFAATDAHADMVVRLL  718 (1123)
T ss_pred             cccccchhhhcchhhhhhhhccCcHHHhhhHHHHHHHHhhHHHHHHHHHHHHHHHhccCCCcEEEEEcCHHHHHHHHHHH
Confidence            0000      000   00  000000        0       00    11122222223479999999999999999887


Q ss_pred             HhC------CC---cEEEEeCCCCHHHHHHHHHHHhcCCC
Q psy1548         375 SEQ------NF---PAVSIHRGMTQEERLKKYQEFKDFHK  405 (448)
Q Consensus       375 ~~~------g~---~~~~lh~~~~~~eR~~~l~~F~~g~~  405 (448)
                      .+.      +.   .+..+||+++  ++.+++++|++++.
T Consensus       719 ~~~f~~~~~~~~~~~v~~itg~~~--~~~~li~~Fk~~~~  756 (1123)
T PRK11448        719 KEAFKKKYGQVEDDAVIKITGSID--KPDQLIRRFKNERL  756 (1123)
T ss_pred             HHHHHhhcCCcCccceEEEeCCcc--chHHHHHHHhCCCC
Confidence            653      22   4567899975  46789999999764

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

Probab=99.75  E-value=1.9e-16  Score=169.20  Aligned_cols=254  Identities=19%  Similarity=0.142  Sum_probs=196.7

Q ss_pred             hhhhccccccceeeee----C--cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhcc
Q psy1548         133 LHRVARAGRFGTKAVL----G--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKY  206 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~----g--~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  206 (448)
                      |..      +|..+..    +  .|-|+||.-|.|||.+++=++...+.   .|.++.+++||.-||+|-++.|+.=...
T Consensus       599 Ql~------AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~---~GKQVAvLVPTTlLA~QHy~tFkeRF~~  669 (1139)
T COG1197         599 QLK------AIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVM---DGKQVAVLVPTTLLAQQHYETFKERFAG  669 (1139)
T ss_pred             HHH------HHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhc---CCCeEEEEcccHHhHHHHHHHHHHHhcC
Confidence            777      7766554    3  58999999999999998888776654   3469999999999999988888877777


Q ss_pred             CCCceEEEEEcCcccHHh---HHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHH
Q psy1548         207 MSNIKVGVFFGGLPIQKD---EEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFR  283 (448)
Q Consensus       207 ~~~~~v~~~~g~~~~~~~---~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~  283 (448)
                      + .+++..+..-.+..++   ...+..|..||+|||..     +-++.+.++++.++||||=|+      |+-.-++-++
T Consensus       670 f-PV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHr-----LL~kdv~FkdLGLlIIDEEqR------FGVk~KEkLK  737 (1139)
T COG1197         670 F-PVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHR-----LLSKDVKFKDLGLLIIDEEQR------FGVKHKEKLK  737 (1139)
T ss_pred             C-CeeEEEecccCCHHHHHHHHHHHhcCCccEEEechH-----hhCCCcEEecCCeEEEechhh------cCccHHHHHH
Confidence            7 6888888766554544   44567889999999973     334567789999999999995      4444566777


Q ss_pred             hCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcch-HHHHHHHHHhhCCCCeEEEEEC
Q psy1548         284 SSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENE-KNKKLFELLDVLEFNQVVIFVK  362 (448)
Q Consensus       284 ~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~-k~~~L~~ll~~~~~~~~IIF~~  362 (448)
                      .+..++-++-+|||.-+....+....+++-..|...+.+.   ..++.++...++.- +...+.++.   ++|++-..+|
T Consensus       738 ~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R---~pV~T~V~~~d~~~ireAI~REl~---RgGQvfYv~N  811 (1139)
T COG1197         738 ELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDR---LPVKTFVSEYDDLLIREAILRELL---RGGQVFYVHN  811 (1139)
T ss_pred             HHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCCC---cceEEEEecCChHHHHHHHHHHHh---cCCEEEEEec
Confidence            7778889999999998888888888888777777666633   23444433333322 233333333   4789999999


Q ss_pred             ccHHHHHHHHHHHhC--CCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         363 SVTRCIALSTLLSEQ--NFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       363 s~~~a~~l~~~L~~~--g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                      .++..+.++..|++.  ...+...||.|+..+-.+++.+|-+|+  -.|++||+-
T Consensus       812 rV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g~--~dVLv~TTI  864 (1139)
T COG1197         812 RVESIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDFYNGE--YDVLVCTTI  864 (1139)
T ss_pred             chhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHHHHHcCC--CCEEEEeee
Confidence            999999999999986  567899999999999999999999998  477777774

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

Probab=99.71  E-value=1.9e-15  Score=157.97  Aligned_cols=262  Identities=19%  Similarity=0.243  Sum_probs=177.9

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .|++.   |..      ....+..|++.-+.||||.|||..-++..+...   ..+.++++++||..|+.|+++.+.++.
T Consensus        82 ~~ws~---QR~------WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a---~kgkr~yii~PT~~Lv~Q~~~kl~~~~  149 (1187)
T COG1110          82 RPWSA---QRV------WAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLA---KKGKRVYIIVPTTTLVRQVYERLKKFA  149 (1187)
T ss_pred             CchHH---HHH------HHHHHHcCCceEEEcCCCCchhHHHHHHHHHHH---hcCCeEEEEecCHHHHHHHHHHHHHHH
Confidence            77777   888      667789999999999999999955443333322   234699999999999999999999998


Q ss_pred             ccCCCceEEE-EEcCcccHH---hHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhh---------
Q psy1548         205 KYMSNIKVGV-FFGGLPIQK---DEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQ---------  271 (448)
Q Consensus       205 ~~~~~~~v~~-~~g~~~~~~---~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~---------  271 (448)
                      .......+.. .++..+...   -...+.++..||+|+|.+-|......  +.-.+++++++|++|.++..         
T Consensus       150 e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~--L~~~kFdfifVDDVDA~LkaskNvDriL~  227 (1187)
T COG1110         150 EDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEE--LSKLKFDFIFVDDVDAILKASKNVDRLLR  227 (1187)
T ss_pred             hhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHH--hcccCCCEEEEccHHHHHhccccHHHHHH
Confidence            7652244444 334333332   34556778899999999877654432  11245788999999977654         


Q ss_pred             -hhhHHH-------HHHHHHhC------------------------CCCCeEEEEeccCCccH--HHHHHHhcCCCeEEE
Q psy1548         272 -LEMRRD-------VQEIFRSS------------------------PHTKQVMMFSATLSKEI--RPVCKKFMHDPMEVY  317 (448)
Q Consensus       272 -~~~~~~-------~~~i~~~l------------------------~~~~q~i~~SAT~~~~~--~~~~~~~l~~~~~i~  317 (448)
                       .||...       +..+...+                        .+..+++..|||..+.-  ..+.+.++.-.    
T Consensus       228 LlGf~eE~i~~a~~~~~lr~~~~~~~~~~~~~e~~~~~e~~~~~~r~k~g~LvvsSATg~~rg~R~~LfReLlgFe----  303 (1187)
T COG1110         228 LLGFSEEVIESAYELIKLRRKLYGEKRAERVREELREVEREREKKRRKLGILVVSSATGKPRGSRLKLFRELLGFE----  303 (1187)
T ss_pred             HcCCCHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhccCCceEEEeeccCCCCCchHHHHHHHhCCc----
Confidence             122211       11111111                        12358899999986542  23455555421    


Q ss_pred             EcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECc---cHHHHHHHHHHHhCCCcEEEEeCCCCHHHHH
Q psy1548         318 VDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKS---VTRCIALSTLLSEQNFPAVSIHRGMTQEERL  394 (448)
Q Consensus       318 ~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s---~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~  394 (448)
                      +... .....||...|...+   -...+.++++.... -.|||++.   ++.|+.+++.|+++|+++..+|+.     ..
T Consensus       304 vG~~-~~~LRNIvD~y~~~~---~~e~~~elvk~lG~-GgLIfV~~d~G~e~aeel~e~Lr~~Gi~a~~~~a~-----~~  373 (1187)
T COG1110         304 VGSG-GEGLRNIVDIYVESE---SLEKVVELVKKLGD-GGLIFVPIDYGREKAEELAEYLRSHGINAELIHAE-----KE  373 (1187)
T ss_pred             cCcc-chhhhheeeeeccCc---cHHHHHHHHHHhCC-CeEEEEEcHHhHHHHHHHHHHHHhcCceEEEeecc-----ch
Confidence            1111 334567777776653   34445666666644 48999999   899999999999999999999994     37


Q ss_pred             HHHHHHhcCCCceEEEEecC
Q psy1548         395 KKYQEFKDFHKGLAITFASD  414 (448)
Q Consensus       395 ~~l~~F~~g~~g~~I~~~t~  414 (448)
                      +.++.|.+|+-.+.|-+++-
T Consensus       374 ~~le~F~~GeidvLVGvAsy  393 (1187)
T COG1110         374 EALEDFEEGEVDVLVGVASY  393 (1187)
T ss_pred             hhhhhhccCceeEEEEeccc
Confidence            89999999996555555554

>KOG0950|consensus

Probab=99.69  E-value=3e-16  Score=163.09  Aligned_cols=260  Identities=17%  Similarity=0.239  Sum_probs=178.2

Q ss_pred             hhhhhhhccccccc--eeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccC
Q psy1548         130 DTYLHRVARAGRFG--TKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYM  207 (448)
Q Consensus       130 ~~yQ~~~~~~~~~~--~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  207 (448)
                      .++|.+      |+  |.++.++|.+..+||+.|||+++-+-++..+....+  .++.+.|..+.++.-...+..+...+
T Consensus       225 fewq~e------cls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~rr--~~llilp~vsiv~Ek~~~l~~~~~~~  296 (1008)
T KOG0950|consen  225 FEWQAE------CLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCRRR--NVLLILPYVSIVQEKISALSPFSIDL  296 (1008)
T ss_pred             HHHHHH------HhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHHhh--ceeEecceeehhHHHHhhhhhhcccc
Confidence            556888      76  677889999999999999999999988887655433  58899999999988888888888887


Q ss_pred             CCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHC--CCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhC
Q psy1548         208 SNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRN--KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSS  285 (448)
Q Consensus       208 ~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~--~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l  285 (448)
                       ++.+...+|..+......     .-++.|+|.++-..+++.  ..-.+..+.++|+||.|.+.+. +....++.++..+
T Consensus       297 -G~~ve~y~g~~~p~~~~k-----~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~-~rg~~lE~~l~k~  369 (1008)
T KOG0950|consen  297 -GFPVEEYAGRFPPEKRRK-----RESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDK-GRGAILELLLAKI  369 (1008)
T ss_pred             -CCcchhhcccCCCCCccc-----ceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeecc-ccchHHHHHHHHH
Confidence             889888887766543321     257999999998766644  2334667889999999988887 7777777776543


Q ss_pred             -----CCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEE----EEcCcchHHHHHHHH--------
Q psy1548         286 -----PHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHY----VKLKENEKNKKLFEL--------  348 (448)
Q Consensus       286 -----~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~----~~~~~~~k~~~L~~l--------  348 (448)
                           ....|+|+||||+++.  .++..|+....  +....   .+..+..+.    ...... +...+..+        
T Consensus       370 ~y~~~~~~~~iIGMSATi~N~--~lL~~~L~A~~--y~t~f---RPv~L~E~ik~G~~i~~~~-r~~~lr~ia~l~~~~~  441 (1008)
T KOG0950|consen  370 LYENLETSVQIIGMSATIPNN--SLLQDWLDAFV--YTTRF---RPVPLKEYIKPGSLIYESS-RNKVLREIANLYSSNL  441 (1008)
T ss_pred             HHhccccceeEeeeecccCCh--HHHHHHhhhhh--eeccc---CcccchhccCCCcccccch-hhHHHHHhhhhhhhhc
Confidence                 2346899999999875  33333332111  11000   011111110    000000 22222222        


Q ss_pred             -----------HhhC--CCCeEEEEECccHHHHHHHHHHHhC--------------------------------------
Q psy1548         349 -----------LDVL--EFNQVVIFVKSVTRCIALSTLLSEQ--------------------------------------  377 (448)
Q Consensus       349 -----------l~~~--~~~~~IIF~~s~~~a~~l~~~L~~~--------------------------------------  377 (448)
                                 +...  .+.++||||++++.|+.+|..+...                                      
T Consensus       442 g~~dpD~~v~L~tet~~e~~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~ld~Vl~~ti  521 (1008)
T KOG0950|consen  442 GDEDPDHLVGLCTETAPEGSSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPVLAKTI  521 (1008)
T ss_pred             ccCCCcceeeehhhhhhcCCeEEEEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcCCcccchHHheec
Confidence                       2111  2446999999999999999665321                                      


Q ss_pred             CCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecC
Q psy1548         378 NFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASD  414 (448)
Q Consensus       378 g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~  414 (448)
                      .+.+.++|+|++.++|..+...|++|.  +.|..+|+
T Consensus       522 ~~GvAyHhaGLT~eER~~iE~afr~g~--i~vl~aTS  556 (1008)
T KOG0950|consen  522 PYGVAYHHAGLTSEEREIIEAAFREGN--IFVLVATS  556 (1008)
T ss_pred             cccceecccccccchHHHHHHHHHhcC--eEEEEecc
Confidence            113889999999999999999999988  45555554

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.69  E-value=1.4e-15  Score=129.15  Aligned_cols=144  Identities=38%  Similarity=0.533  Sum_probs=107.2

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHh
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK  229 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~  229 (448)
                      +++++.+|||+|||.+++..+....... ...++++++|++.++.|+.+.+..+...  ...+..+.+........... 
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~-~~~~~lv~~p~~~l~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~-   76 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSL-KGGQVLVLAPTRELANQVAERLKELFGE--GIKVGYLIGGTSIKQQEKLL-   76 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhcc-cCCCEEEEcCcHHHHHHHHHHHHHHhhC--CcEEEEEecCcchhHHHHHh-
Confidence            4689999999999999888887766542 3458999999999999999988887643  35666666665444333222 


Q ss_pred             cCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccC
Q psy1548         230 THNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATL  298 (448)
Q Consensus       230 ~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~  298 (448)
                      ....+|+++|++.+..............+++|+||+|.+... .................+++++|||+
T Consensus        77 ~~~~~i~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~h~~~~~-~~~~~~~~~~~~~~~~~~~i~~saTp  144 (144)
T cd00046          77 SGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQ-GFGLLGLKILLKLPKDRQVLLLSATP  144 (144)
T ss_pred             cCCCCEEEECcHHHHHHHHcCCcchhcCCEEEEeCHHHHhhc-chHHHHHHHHhhCCccceEEEEeccC
Confidence            335899999999998887766555667889999999988775 33333223344456778899999995

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

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.66  E-value=6.8e-16  Score=162.28  Aligned_cols=299  Identities=16%  Similarity=0.161  Sum_probs=193.8

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .|..+   |..      ..-.+..|+  |....||+|||+++.+|++.....+   ..+-+++|+.-||.|=++.+..+.
T Consensus        80 ~~~dv---Qli------g~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~G---~~v~vvT~neyLA~Rd~e~~~~~~  145 (796)
T PRK12906         80 RPFDV---QII------GGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALTG---KGVHVVTVNEYLSSRDATEMGELY  145 (796)
T ss_pred             CCchh---HHH------HHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHcC---CCeEEEeccHHHHHhhHHHHHHHH
Confidence            67788   888      333445666  9999999999999999988766543   468999999999999999999999


Q ss_pred             ccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHH-HHHHCC------CCcCCCeeEEEecchhHHHhh------
Q psy1548         205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRIL-ALVRNK------KLNLSLLKHFILDECDKMLEQ------  271 (448)
Q Consensus       205 ~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~-~~l~~~------~~~~~~i~~lViDEah~l~~~------  271 (448)
                      ..+ +++++++.++.+.......+   .++|+++|...+- ++|+.+      ......+.+.|+||+|.++=+      
T Consensus       146 ~~L-Gl~vg~i~~~~~~~~r~~~y---~~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~~~aIvDEvDSiLiDeartPL  221 (796)
T PRK12906        146 RWL-GLTVGLNLNSMSPDEKRAAY---NCDITYSTNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEVDSILIDEARTPL  221 (796)
T ss_pred             Hhc-CCeEEEeCCCCCHHHHHHHh---cCCCeecCCccccccchhhccccchhhhhccCcceeeeccchheeeccCCCce
Confidence            999 99999999887655444333   3799999998773 344332      112345678999999966422      


Q ss_pred             ---------hhhHHHHHHHHHhCCC--------------------CC---------------------------------
Q psy1548         272 ---------LEMRRDVQEIFRSSPH--------------------TK---------------------------------  289 (448)
Q Consensus       272 ---------~~~~~~~~~i~~~l~~--------------------~~---------------------------------  289 (448)
                               ......+..+...+..                    .+                                 
T Consensus       222 iisg~~~~~~~~y~~~~~~v~~l~~~~~~~~~~~~~~~dy~id~~~k~v~lte~G~~~~e~~~~i~~l~~~~~~~~~~~i  301 (796)
T PRK12906        222 IISGQAEKATDLYIRADRFVKTLIKDEAEDGDDDEDTGDYKIDEKTKTISLTEQGIRKAEKLFGLDNLYDSENTALAHHI  301 (796)
T ss_pred             ecCCCCCcchHHHHHHHHHHHHHHhhhhccccccCCCCceEEEcccCceeecHHHHHHHHHHcCCccccCchhhhHHHHH
Confidence                     0111111222111110                    00                                 


Q ss_pred             ---------------------------------------------------------------------------eEEEE
Q psy1548         290 ---------------------------------------------------------------------------QVMMF  294 (448)
Q Consensus       290 ---------------------------------------------------------------------------q~i~~  294 (448)
                                                                                                 ++.+|
T Consensus       302 ~~Al~A~~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~ws~GLHQaieaKe~v~i~~e~~t~a~It~qnfFr~Y~kl~Gm  381 (796)
T PRK12906        302 DQALRANYIMLKDIDYVVQDGEVLIVDEFTGRVMEGRRYSDGLHQAIEAKEGVKIQEENQTLATITYQNFFRMYKKLSGM  381 (796)
T ss_pred             HHHHHHHHHHhcCCcEEEECCEEEEEeCCCCCcCCCCccChHHHHHHHHhcCCCcCCCceeeeeehHHHHHHhcchhhcc
Confidence                                                                                       12344


Q ss_pred             eccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhC--CCCeEEEEECccHHHHHHHH
Q psy1548         295 SATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVL--EFNQVVIFVKSVTRCIALST  372 (448)
Q Consensus       295 SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~  372 (448)
                      |.|...+..++...|.- ++. .+++. ......-....+......|...+...+...  .+.++||||+|+..++.++.
T Consensus       382 TGTa~~e~~Ef~~iY~l-~vv-~IPtn-kp~~r~d~~d~i~~t~~~K~~al~~~i~~~~~~g~pvLI~t~si~~se~ls~  458 (796)
T PRK12906        382 TGTAKTEEEEFREIYNM-EVI-TIPTN-RPVIRKDSPDLLYPTLDSKFNAVVKEIKERHAKGQPVLVGTVAIESSERLSH  458 (796)
T ss_pred             CCCCHHHHHHHHHHhCC-CEE-EcCCC-CCeeeeeCCCeEEcCHHHHHHHHHHHHHHHHhCCCCEEEEeCcHHHHHHHHH
Confidence            44443332222222221 111 11111 100000111234445667888888888543  67799999999999999999


Q ss_pred             HHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecC----hhhHHHHHHHHH--HhcCCCCCCCcccccccccc
Q psy1548         373 LLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASD----ENDAKILNNVQD--RFDVSISELPDEIDLSTYIE  446 (448)
Q Consensus       373 ~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~----~~d~~~l~~i~~--~~~~~~~~~p~~~~~~~~~~  446 (448)
                      .|.+.|++...+|+++...++..+.+.++.|.    |+++|+    ..|..+-..+.+  -+.|...++|++.....++.
T Consensus       459 ~L~~~gi~~~~Lna~~~~~Ea~ii~~ag~~g~----VtIATnmAGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~  534 (796)
T PRK12906        459 LLDEAGIPHAVLNAKNHAKEAEIIMNAGQRGA----VTIATNMAGRGTDIKLGPGVKELGGLAVIGTERHESRRIDNQLR  534 (796)
T ss_pred             HHHHCCCCeeEecCCcHHHHHHHHHhcCCCce----EEEEeccccCCCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHh
Confidence            99999999999999999888888888776665    555555    223221112232  25677788888887777877


Q ss_pred             CC
Q psy1548         447 GR  448 (448)
Q Consensus       447 ~~  448 (448)
                      ||
T Consensus       535 GR  536 (796)
T PRK12906        535 GR  536 (796)
T ss_pred             hh
Confidence            77

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

Probab=99.66  E-value=6.9e-15  Score=137.11  Aligned_cols=254  Identities=15%  Similarity=0.162  Sum_probs=164.5

Q ss_pred             hhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCC
Q psy1548         130 DTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  209 (448)
Q Consensus       130 ~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  209 (448)
                      -++|+.++.+  .+..+.+.++.|+.|-||+|||... .+.++....  .|.++.+.+|....+.+++..++.-.   ++
T Consensus        99 s~~Q~~as~~--l~q~i~~k~~~lv~AV~GaGKTEMi-f~~i~~al~--~G~~vciASPRvDVclEl~~Rlk~aF---~~  170 (441)
T COG4098          99 SPGQKKASNQ--LVQYIKQKEDTLVWAVTGAGKTEMI-FQGIEQALN--QGGRVCIASPRVDVCLELYPRLKQAF---SN  170 (441)
T ss_pred             ChhHHHHHHH--HHHHHHhcCcEEEEEecCCCchhhh-HHHHHHHHh--cCCeEEEecCcccchHHHHHHHHHhh---cc
Confidence            3347774443  3344555789999999999999774 444444433  35589999999999999888777654   36


Q ss_pred             ceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCC
Q psy1548         210 IKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTK  289 (448)
Q Consensus       210 ~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~  289 (448)
                      ..+.+++|+.+...+        .+++|+|.-.|++.-       +.+++++|||+|...=. .-......+-+....+.
T Consensus       171 ~~I~~Lyg~S~~~fr--------~plvVaTtHQLlrFk-------~aFD~liIDEVDAFP~~-~d~~L~~Av~~ark~~g  234 (441)
T COG4098         171 CDIDLLYGDSDSYFR--------APLVVATTHQLLRFK-------QAFDLLIIDEVDAFPFS-DDQSLQYAVKKARKKEG  234 (441)
T ss_pred             CCeeeEecCCchhcc--------ccEEEEehHHHHHHH-------hhccEEEEecccccccc-CCHHHHHHHHHhhcccC
Confidence            788899998754322        579999998887653       45678999999965221 11111122233344556


Q ss_pred             eEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcch-HH------HHHHHHHhhC--CCCeEEEE
Q psy1548         290 QVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENE-KN------KKLFELLDVL--EFNQVVIF  360 (448)
Q Consensus       290 q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~-k~------~~L~~ll~~~--~~~~~IIF  360 (448)
                      -.|.+|||.++.++.-+..--  -..+.+....+..+- ....+++...-. ++      ..|...++..  .+.+++||
T Consensus       235 ~~IylTATp~k~l~r~~~~g~--~~~~klp~RfH~~pL-pvPkf~w~~~~~k~l~r~kl~~kl~~~lekq~~~~~P~liF  311 (441)
T COG4098         235 ATIYLTATPTKKLERKILKGN--LRILKLPARFHGKPL-PVPKFVWIGNWNKKLQRNKLPLKLKRWLEKQRKTGRPVLIF  311 (441)
T ss_pred             ceEEEecCChHHHHHHhhhCC--eeEeecchhhcCCCC-CCCceEEeccHHHHhhhccCCHHHHHHHHHHHhcCCcEEEE
Confidence            789999999877665544322  222233222222211 222333443322 21      2456666554  35689999


Q ss_pred             ECccHHHHHHHHHHHhC-C-CcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecC
Q psy1548         361 VKSVTRCIALSTLLSEQ-N-FPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASD  414 (448)
Q Consensus       361 ~~s~~~a~~l~~~L~~~-g-~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~  414 (448)
                      +++....++++..|++. + .....+|+.  ...|.+.++.|++|+  +.+++.|+
T Consensus       312 ~p~I~~~eq~a~~lk~~~~~~~i~~Vhs~--d~~R~EkV~~fR~G~--~~lLiTTT  363 (441)
T COG4098         312 FPEIETMEQVAAALKKKLPKETIASVHSE--DQHRKEKVEAFRDGK--ITLLITTT  363 (441)
T ss_pred             ecchHHHHHHHHHHHhhCCccceeeeecc--CccHHHHHHHHHcCc--eEEEEEee
Confidence            99999999999999653 3 345778876  567999999999999  34444444

>KOG1123|consensus

Probab=99.64  E-value=2.5e-16  Score=152.75  Aligned_cols=253  Identities=17%  Similarity=0.162  Sum_probs=171.7

Q ss_pred             eccCCCCchhhhhhhccccccceeeee-C--cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHH
Q psy1548         122 NYDMPEDSDTYLHRVARAGRFGTKAVL-G--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK  198 (448)
Q Consensus       122 ~~~~p~~~~~yQ~~~~~~~~~~~~~~~-g--~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~  198 (448)
                      +..+.+.+++||..      ++..+.. |  ++.+|+.|.|+|||++-+-++.. +     ..++|++|.+---+.||..
T Consensus       296 dLKPst~iRpYQEk------sL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~t-i-----kK~clvLcts~VSVeQWkq  363 (776)
T KOG1123|consen  296 DLKPSTQIRPYQEK------SLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACT-I-----KKSCLVLCTSAVSVEQWKQ  363 (776)
T ss_pred             CcCcccccCchHHH------HHHHHhCCCcccCceEEEecCCCCceeeeeeeee-e-----cccEEEEecCccCHHHHHH
Confidence            34556678999999      8887774 3  78999999999999886544432 2     2379999999999999999


Q ss_pred             HHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCC--------CCcCCCeeEEEecchhHHHh
Q psy1548         199 EYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNK--------KLNLSLLKHFILDECDKMLE  270 (448)
Q Consensus       199 ~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~--------~~~~~~i~~lViDEah~l~~  270 (448)
                      +++.|+..- +-.++.++++....     . ...+.|+|+|..++..--++.        .+.-....++++||+|.+..
T Consensus       364 Qfk~wsti~-d~~i~rFTsd~Ke~-----~-~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvvPA  436 (776)
T KOG1123|consen  364 QFKQWSTIQ-DDQICRFTSDAKER-----F-PSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVVPA  436 (776)
T ss_pred             HHHhhcccC-ccceEEeecccccc-----C-CCCCcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccchH
Confidence            999998776 56777777765321     1 224789999986653221111        01124456899999998877


Q ss_pred             hhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHH-HhcCCCeEEEEcCccc--------------------------
Q psy1548         271 QLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCK-KFMHDPMEVYVDDEAK--------------------------  323 (448)
Q Consensus       271 ~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~-~~l~~~~~i~~~~~~~--------------------------  323 (448)
                      . -|+..+.-+-..+     -++++||+-.+-.++.. +|+-.|..+..+--+-                          
T Consensus       437 ~-MFRRVlsiv~aHc-----KLGLTATLvREDdKI~DLNFLIGPKlYEAnWmdL~~kGhIA~VqCaEVWCpMt~eFy~eY  510 (776)
T KOG1123|consen  437 K-MFRRVLSIVQAHC-----KLGLTATLVREDDKITDLNFLIGPKLYEANWMDLQKKGHIAKVQCAEVWCPMTPEFYREY  510 (776)
T ss_pred             H-HHHHHHHHHHHHh-----hccceeEEeeccccccccceeecchhhhccHHHHHhCCceeEEeeeeeecCCCHHHHHHH
Confidence            5 6666665554444     38999998554333322 3444444433221100                          


Q ss_pred             ccccceeEEEEEcCcchHHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHh
Q psy1548         324 LTLHGLQQHYVKLKENEKNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFK  401 (448)
Q Consensus       324 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~  401 (448)
                      .....-+...+.+..-.|+....-+++.+  ++.++|||..++-.....|-.|.+     -+++|..++.||.++++.|+
T Consensus       511 L~~~t~kr~lLyvMNP~KFraCqfLI~~HE~RgDKiIVFsDnvfALk~YAikl~K-----pfIYG~Tsq~ERm~ILqnFq  585 (776)
T KOG1123|consen  511 LRENTRKRMLLYVMNPNKFRACQFLIKFHERRGDKIIVFSDNVFALKEYAIKLGK-----PFIYGPTSQNERMKILQNFQ  585 (776)
T ss_pred             HhhhhhhhheeeecCcchhHHHHHHHHHHHhcCCeEEEEeccHHHHHHHHHHcCC-----ceEECCCchhHHHHHHHhcc
Confidence            01111122233334445777766677654  577999999999988888887765     46899999999999999999


Q ss_pred             cCC
Q psy1548         402 DFH  404 (448)
Q Consensus       402 ~g~  404 (448)
                      -+.
T Consensus       586 ~n~  588 (776)
T KOG1123|consen  586 TNP  588 (776)
T ss_pred             cCC
Confidence            887

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.63  E-value=9e-15  Score=158.97  Aligned_cols=269  Identities=15%  Similarity=0.145  Sum_probs=163.8

Q ss_pred             Cchhhhhhhccccccceeee----eCcceeeeccCCChhHHHHHHHHHHhhhc-cCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         128 DSDTYLHRVARAGRFGTKAV----LGMDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       128 ~~~~yQ~~~~~~~~~~~~~~----~g~~vli~apTGsGKT~~~~l~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      .+++||.+      .+..+.    .|.+.|++..+|.|||+..+ .++..+.. ......+|||||.. +..+|.+.+.+
T Consensus       169 ~Lr~YQle------GlnWLi~l~~~g~gGILADEMGLGKTlQaI-alL~~L~~~~~~~gp~LIVvP~S-lL~nW~~Ei~k  240 (1033)
T PLN03142        169 KMRDYQLA------GLNWLIRLYENGINGILADEMGLGKTLQTI-SLLGYLHEYRGITGPHMVVAPKS-TLGNWMNEIRR  240 (1033)
T ss_pred             chHHHHHH------HHHHHHHHHhcCCCEEEEeCCCccHHHHHH-HHHHHHHHhcCCCCCEEEEeChH-HHHHHHHHHHH
Confidence            47999999      665543    57889999999999998754 33333322 22234689999975 56788888998


Q ss_pred             hhccCCCceEEEEEcCcccHHhH--HHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHH
Q psy1548         203 FSKYMSNIKVGVFFGGLPIQKDE--EYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQE  280 (448)
Q Consensus       203 ~~~~~~~~~v~~~~g~~~~~~~~--~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~  280 (448)
                      |+   |.+++..++|........  ..+..+..+|+|+|++.+.....  .+.--..++||+||||++-..   ......
T Consensus       241 w~---p~l~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~~--~L~k~~W~~VIvDEAHrIKN~---~Sklsk  312 (1033)
T PLN03142        241 FC---PVLRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKT--ALKRFSWRYIIIDEAHRIKNE---NSLLSK  312 (1033)
T ss_pred             HC---CCCceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHHH--HhccCCCCEEEEcCccccCCH---HHHHHH
Confidence            87   467777787765422221  11223457999999998865332  122234578999999988553   233444


Q ss_pred             HHHhCCCCCeEEEEeccCC-ccHHHH---HHHhcCC--------------------------------CeEEEE-cCccc
Q psy1548         281 IFRSSPHTKQVMMFSATLS-KEIRPV---CKKFMHD--------------------------------PMEVYV-DDEAK  323 (448)
Q Consensus       281 i~~~l~~~~q~i~~SAT~~-~~~~~~---~~~~l~~--------------------------------~~~i~~-~~~~~  323 (448)
                      .++.+... ..+++|+|+- +.+.++   +..+..+                                |..+.- ...-.
T Consensus       313 alr~L~a~-~RLLLTGTPlqNnl~ELwsLL~FL~P~~f~s~~~F~~~f~~~~~~~~~e~i~~L~~~L~pf~LRR~KsdV~  391 (1033)
T PLN03142        313 TMRLFSTN-YRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISGENDQQEVVQQLHKVLRPFLLRRLKSDVE  391 (1033)
T ss_pred             HHHHhhcC-cEEEEecCCCCCCHHHHHHHHhcCCCCcCCCHHHHHHHHccccccchHHHHHHHHHHhhHHHhhhhHHHHh
Confidence            45555443 3578899942 222221   1111000                                000000 00000


Q ss_pred             ccccceeEEEEEc---------------------------------------------------------------Ccch
Q psy1548         324 LTLHGLQQHYVKL---------------------------------------------------------------KENE  340 (448)
Q Consensus       324 ~~~~~i~~~~~~~---------------------------------------------------------------~~~~  340 (448)
                      ...+......+.+                                                               ....
T Consensus       392 ~~LPpK~e~iv~v~LS~~Qk~lY~~ll~k~~~~l~~g~~~~~LlnilmqLRk~cnHP~L~~~~ep~~~~~~~e~lie~Sg  471 (1033)
T PLN03142        392 KGLPPKKETILKVGMSQMQKQYYKALLQKDLDVVNAGGERKRLLNIAMQLRKCCNHPYLFQGAEPGPPYTTGEHLVENSG  471 (1033)
T ss_pred             hhCCCceeEEEeeCCCHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCHHhhhcccccCcccchhHHhhhhh
Confidence            0000000000000                                                               1123


Q ss_pred             HHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEec
Q psy1548         341 KNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFAS  413 (448)
Q Consensus       341 k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t  413 (448)
                      |...|..++...  .+.++|||+........|...|...|++...+||+++..+|..+++.|+....+..+.+++
T Consensus       472 Kl~lLdkLL~~Lk~~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLS  546 (1033)
T PLN03142        472 KMVLLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLS  546 (1033)
T ss_pred             HHHHHHHHHHHHHhcCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEe
Confidence            455555555443  4569999999999999999999999999999999999999999999998765443333333

>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=99.59  E-value=1.2e-14  Score=130.08  Aligned_cols=153  Identities=18%  Similarity=0.183  Sum_probs=100.6

Q ss_pred             chhhhhhhccccccceeeee-------CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHH
Q psy1548         129 SDTYLHRVARAGRFGTKAVL-------GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYE  201 (448)
Q Consensus       129 ~~~yQ~~~~~~~~~~~~~~~-------g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  201 (448)
                      +++||.+      ++..+..       ++++++.+|||+|||.+++..+.....      ++++++|+..|+.|+.+.+.
T Consensus         4 lr~~Q~~------ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~------~~l~~~p~~~l~~Q~~~~~~   71 (184)
T PF04851_consen    4 LRPYQQE------AIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELAR------KVLIVAPNISLLEQWYDEFD   71 (184)
T ss_dssp             E-HHHHH------HHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHC------EEEEEESSHHHHHHHHHHHH
T ss_pred             CCHHHHH------HHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcccc------ceeEecCHHHHHHHHHHHHH
Confidence            4788999      7777764       589999999999999998765555432      89999999999999999997


Q ss_pred             HhhccCCCce---------EEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCC-----------CcCCCeeEEE
Q psy1548         202 RFSKYMSNIK---------VGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK-----------LNLSLLKHFI  261 (448)
Q Consensus       202 ~~~~~~~~~~---------v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~-----------~~~~~i~~lV  261 (448)
                      .+........         ......................+++++|.+.+........           ......+++|
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI  151 (184)
T PF04851_consen   72 DFGSEKYNFFEKSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVI  151 (184)
T ss_dssp             HHSTTSEEEEE--GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEEE
T ss_pred             HhhhhhhhhcccccccccccccccccccccccccccccccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEEE
Confidence            6654321110         0001111111112222333457899999999988765311           2345678999


Q ss_pred             ecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCC
Q psy1548         262 LDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLS  299 (448)
Q Consensus       262 iDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~  299 (448)
                      +||||++... .-   +..++.  .+...+++||||+.
T Consensus       152 ~DEaH~~~~~-~~---~~~i~~--~~~~~~l~lTATp~  183 (184)
T PF04851_consen  152 IDEAHHYPSD-SS---YREIIE--FKAAFILGLTATPF  183 (184)
T ss_dssp             EETGGCTHHH-HH---HHHHHH--SSCCEEEEEESS-S
T ss_pred             EehhhhcCCH-HH---HHHHHc--CCCCeEEEEEeCcc
Confidence            9999988665 21   444444  55677999999975

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 ....

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

Probab=99.59  E-value=2.3e-13  Score=144.77  Aligned_cols=263  Identities=13%  Similarity=0.138  Sum_probs=169.5

Q ss_pred             CCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhcc
Q psy1548         127 EDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKY  206 (448)
Q Consensus       127 ~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  206 (448)
                      -|+..+..+      .+..+....-++|+||||||||...=.-+++.-.  ..+..+.+.-|.|--|..+.+.+..-.+.
T Consensus        49 LPv~~~~~~------i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~--~~~g~I~~tQPRRlAArsvA~RvAeel~~  120 (845)
T COG1643          49 LPVTAVRDE------ILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGL--GIAGKIGCTQPRRLAARSVAERVAEELGE  120 (845)
T ss_pred             CCcHHHHHH------HHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhc--ccCCeEEecCchHHHHHHHHHHHHHHhCC
Confidence            345444555      5556666788999999999999763332333222  33446777789986666665555443322


Q ss_pred             CCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhH-HHHHHHHHhC
Q psy1548         207 MSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMR-RDVQEIFRSS  285 (448)
Q Consensus       207 ~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~-~~~~~i~~~l  285 (448)
                      .++-.|++-.-..+..       .....|-++|.|.|++.+..+.. ++.++++|+||+|.-.-+.++. ..+..++...
T Consensus       121 ~~G~~VGY~iRfe~~~-------s~~Trik~mTdGiLlrei~~D~~-Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~r  192 (845)
T COG1643         121 KLGETVGYSIRFESKV-------SPRTRIKVMTDGILLREIQNDPL-LSGYSVVIIDEAHERSLNTDILLGLLKDLLARR  192 (845)
T ss_pred             CcCceeeEEEEeeccC-------CCCceeEEeccHHHHHHHhhCcc-cccCCEEEEcchhhhhHHHHHHHHHHHHHHhhc
Confidence            2244454443322211       11267999999999999987655 8899999999999643222433 3344456667


Q ss_pred             CCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcC-cch-HHHHHHHHHhh---CCCCeEEEE
Q psy1548         286 PHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLK-ENE-KNKKLFELLDV---LEFNQVVIF  360 (448)
Q Consensus       286 ~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~-~~~-k~~~L~~ll~~---~~~~~~IIF  360 (448)
                      ++..++|.||||+..+  ++...|..-|+ +.+...    ...++.+|.... .+. -.+.+...+..   ...|.++||
T Consensus       193 r~DLKiIimSATld~~--rfs~~f~~apv-i~i~GR----~fPVei~Y~~~~~~d~~l~~ai~~~v~~~~~~~~GdILvF  265 (845)
T COG1643         193 RDDLKLIIMSATLDAE--RFSAYFGNAPV-IEIEGR----TYPVEIRYLPEAEADYILLDAIVAAVDIHLREGSGSILVF  265 (845)
T ss_pred             CCCceEEEEecccCHH--HHHHHcCCCCE-EEecCC----ccceEEEecCCCCcchhHHHHHHHHHHHhccCCCCCEEEE
Confidence            7778999999998654  55554443444 333222    233455553332 333 33444444433   356799999


Q ss_pred             ECccHHHHHHHHHHHh----CCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecC
Q psy1548         361 VKSVTRCIALSTLLSE----QNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASD  414 (448)
Q Consensus       361 ~~s~~~a~~l~~~L~~----~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~  414 (448)
                      .+...+.+.+++.|.+    ....+..+||.|+.+++.++++--..|+.  .|.++|+
T Consensus       266 LpG~~EI~~~~~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~R--KVVlATN  321 (845)
T COG1643         266 LPGQREIERTAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKR--KVVLATN  321 (845)
T ss_pred             CCcHHHHHHHHHHHHhccccCCcEEeeccccCCHHHHHhhcCCCCCCcc--eEEEEcc
Confidence            9999999999999998    35789999999999999998877766642  2445444

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

Probab=99.58  E-value=2.3e-14  Score=147.80  Aligned_cols=253  Identities=16%  Similarity=0.165  Sum_probs=153.3

Q ss_pred             chhhhhhhccccccceeeeeCc-ceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccC
Q psy1548         129 SDTYLHRVARAGRFGTKAVLGM-DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYM  207 (448)
Q Consensus       129 ~~~yQ~~~~~~~~~~~~~~~g~-~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  207 (448)
                      .+.||+.|-+.  .+.++..|+ .+|+++.||+|||.++ +.++.++.+.....++|+|+-+++|+.|.+..+..+..  
T Consensus       166 ~RyyQ~~AI~r--v~Eaf~~g~~raLlvMATGTGKTrTA-iaii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P--  240 (875)
T COG4096         166 PRYYQIIAIRR--VIEAFSKGQNRALLVMATGTGKTRTA-IAIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLP--  240 (875)
T ss_pred             chHHHHHHHHH--HHHHHhcCCceEEEEEecCCCcceeH-HHHHHHHHhcchhheeeEEechHHHHHHHHHHHHHhCC--
Confidence            48889993221  334455563 5999999999999875 56777777766677999999999999999888777764  


Q ss_pred             CCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCC-----CCcCCCeeEEEecchhHHHhhhhhHHHHHHHH
Q psy1548         208 SNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNK-----KLNLSLLKHFILDECDKMLEQLEMRRDVQEIF  282 (448)
Q Consensus       208 ~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~-----~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~  282 (448)
                       +........+.....        .++|.++|.+.+...+...     .+....+++||+||||+     +.......++
T Consensus       241 -~~~~~n~i~~~~~~~--------s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHR-----gi~~~~~~I~  306 (875)
T COG4096         241 -FGTKMNKIEDKKGDT--------SSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHR-----GIYSEWSSIL  306 (875)
T ss_pred             -CccceeeeecccCCc--------ceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhh-----hHHhhhHHHH
Confidence             333333332222111        3689999999998877654     45567799999999996     4444555676


Q ss_pred             HhCCCCCeEEEEeccCCccHHHHHHHhc-CCCeE------------------EEEcCcc---cccccc-----------e
Q psy1548         283 RSSPHTKQVMMFSATLSKEIRPVCKKFM-HDPME------------------VYVDDEA---KLTLHG-----------L  329 (448)
Q Consensus       283 ~~l~~~~q~i~~SAT~~~~~~~~~~~~l-~~~~~------------------i~~~~~~---~~~~~~-----------i  329 (448)
                      .++..-.  ++++||+......---.|. ..|+.                  +.+....   -..+..           +
T Consensus       307 dYFdA~~--~gLTATP~~~~d~~T~~~F~g~Pt~~YsleeAV~DGfLvpy~vi~i~~~~~~~G~~~~~~serek~~g~~i  384 (875)
T COG4096         307 DYFDAAT--QGLTATPKETIDRSTYGFFNGEPTYAYSLEEAVEDGFLVPYKVIRIDTDFDLDGWKPDAGSEREKLQGEAI  384 (875)
T ss_pred             HHHHHHH--HhhccCcccccccccccccCCCcceeecHHHHhhccccCCCCceEEeeeccccCcCcCccchhhhhhcccc
Confidence            6654333  3448887653222211222 33322                  2211110   000000           0


Q ss_pred             --e-EEEEEcC-------c---chHHHHHHHHHhhC----CCCeEEEEECccHHHHHHHHHHHhC-----CCcEEEEeCC
Q psy1548         330 --Q-QHYVKLK-------E---NEKNKKLFELLDVL----EFNQVVIFVKSVTRCIALSTLLSEQ-----NFPAVSIHRG  387 (448)
Q Consensus       330 --~-~~~~~~~-------~---~~k~~~L~~ll~~~----~~~~~IIF~~s~~~a~~l~~~L~~~-----g~~~~~lh~~  387 (448)
                        . +.+-..+       .   ..-...+.+.+...    ..+|+||||.+..+|+.+...|...     |--+..+.|+
T Consensus       385 ~~dd~~~~~~d~dr~~v~~~~~~~V~r~~~~~l~~~~~g~~~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~~IT~d  464 (875)
T COG4096         385 DEDDQNFEARDFDRTLVIPFRTETVARELTEYLKRGATGDEIGKTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITGD  464 (875)
T ss_pred             CcccccccccccchhccccchHHHHHHHHHHHhccccCCCccCceEEEeeCcHHHHHHHHHHHHhCccccCceEEEEecc
Confidence              0 0000000       0   00122334444441    1458999999999999999999764     3447777777


Q ss_pred             CCHHHHHHHHHHHhcCC
Q psy1548         388 MTQEERLKKYQEFKDFH  404 (448)
Q Consensus       388 ~~~~eR~~~l~~F~~g~  404 (448)
                      -.+.  ...+..|...+
T Consensus       465 ~~~~--q~~Id~f~~ke  479 (875)
T COG4096         465 AEQA--QALIDNFIDKE  479 (875)
T ss_pred             chhh--HHHHHHHHhcC
Confidence            5444  45667776644

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

Probab=99.56  E-value=8.9e-13  Score=144.57  Aligned_cols=84  Identities=18%  Similarity=0.204  Sum_probs=62.2

Q ss_pred             hhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHH-HHHHhhccCC-
Q psy1548         131 TYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK-EYERFSKYMS-  208 (448)
Q Consensus       131 ~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~-~~~~~~~~~~-  208 (448)
                      +.|.++..+  ....+..|+++++.||||+|||++|++|++....   .+.+++|.+||++|..|+.. .+..+.+.++ 
T Consensus       248 ~~Q~~~~~~--i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~---~~~~vvi~t~t~~Lq~Ql~~~~~~~l~~~~~~  322 (850)
T TIGR01407       248 PEQLKLAEL--VLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI---TEKPVVISTNTKVLQSQLLEKDIPLLNEILNF  322 (850)
T ss_pred             HHHHHHHHH--HHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc---CCCeEEEEeCcHHHHHHHHHHHHHHHHHHcCC
Confidence            338873332  2335667899999999999999999999988765   23489999999999999865 5666655442 


Q ss_pred             CceEEEEEcCc
Q psy1548         209 NIKVGVFFGGL  219 (448)
Q Consensus       209 ~~~v~~~~g~~  219 (448)
                      ++++..+.|+.
T Consensus       323 ~~~~~~~kG~~  333 (850)
T TIGR01407       323 KINAALIKGKS  333 (850)
T ss_pred             CceEEEEEcch
Confidence            36777777654

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.

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

Probab=99.53  E-value=4.9e-13  Score=142.42  Aligned_cols=136  Identities=20%  Similarity=0.220  Sum_probs=88.5

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHh
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK  229 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~  229 (448)
                      +..++..+||||||++.+..+...+ .....+++|+|+|+.+|..|+.+.+..+....  .     .+..+...-...+.
T Consensus       264 ~~gli~~~TGsGKT~t~~~la~~l~-~~~~~~~vl~lvdR~~L~~Q~~~~f~~~~~~~--~-----~~~~s~~~L~~~l~  335 (667)
T TIGR00348       264 RGGLIWHTQGSGKTLTMLFAARKAL-ELLKNPKVFFVVDRRELDYQLMKEFQSLQKDC--A-----ERIESIAELKRLLE  335 (667)
T ss_pred             ceeEEEEecCCCccHHHHHHHHHHH-hhcCCCeEEEEECcHHHHHHHHHHHHhhCCCC--C-----cccCCHHHHHHHHh
Confidence            5799999999999988766554433 33456799999999999999999998875321  0     11111122223333


Q ss_pred             cCCCcEEEEcHHHHHHHHHCC--CCcCCCe-eEEEecchhHHHhhhhhHHHHHHHH-HhCCCCCeEEEEeccCC
Q psy1548         230 THNPQIVVGTPGRILALVRNK--KLNLSLL-KHFILDECDKMLEQLEMRRDVQEIF-RSSPHTKQVMMFSATLS  299 (448)
Q Consensus       230 ~~~~~IlV~Tp~~l~~~l~~~--~~~~~~i-~~lViDEah~l~~~~~~~~~~~~i~-~~l~~~~q~i~~SAT~~  299 (448)
                      ....+|+|+|.+++...+...  ......- -+||+||||+.... .    +...+ +.+| +...++||||+-
T Consensus       336 ~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHrs~~~-~----~~~~l~~~~p-~a~~lGfTaTP~  403 (667)
T TIGR00348       336 KDDGGIIITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHRSQYG-E----LAKNLKKALK-NASFFGFTGTPI  403 (667)
T ss_pred             CCCCCEEEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCccccch-H----HHHHHHhhCC-CCcEEEEeCCCc
Confidence            334689999999998654331  1111111 27999999976443 3    33333 3444 567899999974

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

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

Probab=99.49  E-value=1e-14  Score=148.56  Aligned_cols=136  Identities=23%  Similarity=0.280  Sum_probs=112.5

Q ss_pred             ccccccCCCcee--eeecCceeEEeecCCCccccccccC---CCccccccccccccccchhhhhhhhccCceeeeccCCc
Q psy1548           8 QEKLSCGSGNVF--LFFRAFIRFSSSFPHSKMADNDDLL---DYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGF   82 (448)
Q Consensus         8 ~~~~~~~~~~~~--~~~r~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (448)
                      .+.|.++.+++|  ||+|+||+|.+..-.+...+...+.   .......+.|..++...+..+.+....|.....+|.+.
T Consensus       185 ~~~L~l~~~~~~~~sfdRpNi~~~v~~~~~~~~q~~fi~~~~~~~~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~YHaGl  264 (590)
T COG0514         185 REQLGLQDANIFRGSFDRPNLALKVVEKGEPSDQLAFLATVLPQLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGL  264 (590)
T ss_pred             HHHhcCCCcceEEecCCCchhhhhhhhcccHHHHHHHHHhhccccCCCeEEEEeeHHhHHHHHHHHHHCCCceEEecCCC
Confidence            357888888899  9999999999887543333333444   34456679999999988888888888888888888887


Q ss_pred             ccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548          83 RDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      +.-........++.+..+|+|||++||||||+++||+|+||+.|..++.|.|++|||||..
T Consensus       265 ~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfViH~~lP~s~EsYyQE~GRAGRDG  325 (590)
T COG0514         265 SNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDG  325 (590)
T ss_pred             CHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceEEEEecCCCCHHHHHHHHhhccCCC
Confidence            7666666666777788899999999999999999999999999999999999999999954

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=99.46  E-value=1.4e-11  Score=133.74  Aligned_cols=83  Identities=23%  Similarity=0.264  Sum_probs=63.2

Q ss_pred             hhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHH-HHHHHHhhccCCC
Q psy1548         131 TYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI-SKEYERFSKYMSN  209 (448)
Q Consensus       131 ~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~-~~~~~~~~~~~~~  209 (448)
                      +-|.+.+.+  ....+..++.+++.|+||+|||++|++|++...    .+.+++|++||++|++|+ .+.+..+.+.+ +
T Consensus       248 ~~Q~~ma~~--V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~----~~~~vvI~t~T~~Lq~Ql~~~~i~~l~~~~-~  320 (820)
T PRK07246        248 PKQESFAKL--VGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS----DQRQIIVSVPTKILQDQIMAEEVKAIQEVF-H  320 (820)
T ss_pred             HHHHHHHHH--HHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc----CCCcEEEEeCcHHHHHHHHHHHHHHHHHhc-C
Confidence            336664442  333445678999999999999999999988754    245899999999999999 46777777776 6


Q ss_pred             ceEEEEEcCcc
Q psy1548         210 IKVGVFFGGLP  220 (448)
Q Consensus       210 ~~v~~~~g~~~  220 (448)
                      +++..+.|+.+
T Consensus       321 ~~~~~~kg~~~  331 (820)
T PRK07246        321 IDCHSLKGPQN  331 (820)
T ss_pred             CcEEEEECCcc
Confidence            77777776543

>KOG0385|consensus

Probab=99.42  E-value=3.4e-12  Score=130.09  Aligned_cols=271  Identities=17%  Similarity=0.243  Sum_probs=168.8

Q ss_pred             Cchhhhhhhccccccceeee----eCcceeeeccCCChhHHHHHHHHHHhhhc-cCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         128 DSDTYLHRVARAGRFGTKAV----LGMDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       128 ~~~~yQ~~~~~~~~~~~~~~----~g~~vli~apTGsGKT~~~~l~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      .+++||-+      -+.++.    .|-|.|+....|.|||+.. ++++..+.. ..-...-||+||...|.+. .+.+++
T Consensus       167 ~lr~YQve------GlnWLi~l~engingILaDEMGLGKTlQt-Is~l~yl~~~~~~~GPfLVi~P~StL~NW-~~Ef~r  238 (971)
T KOG0385|consen  167 ELRDYQLE------GLNWLISLYENGINGILADEMGLGKTLQT-ISLLGYLKGRKGIPGPFLVIAPKSTLDNW-MNEFKR  238 (971)
T ss_pred             ccchhhhc------cHHHHHHHHhcCcccEeehhcccchHHHH-HHHHHHHHHhcCCCCCeEEEeeHhhHHHH-HHHHHH
Confidence            35888998      555544    4889999999999999774 444444433 2223358999999988654 455666


Q ss_pred             hhccCCCceEEEEEcCcccHHh--HHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHH
Q psy1548         203 FSKYMSNIKVGVFFGGLPIQKD--EEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQE  280 (448)
Q Consensus       203 ~~~~~~~~~v~~~~g~~~~~~~--~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~  280 (448)
                      |+   |++++.+++|+......  ...+..+..+|+|+|.+..+.-  ...+.--..+++||||||++-..   ...+..
T Consensus       239 f~---P~l~~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~d--k~~lk~~~W~ylvIDEaHRiKN~---~s~L~~  310 (971)
T KOG0385|consen  239 FT---PSLNVVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKD--KSFLKKFNWRYLVIDEAHRIKNE---KSKLSK  310 (971)
T ss_pred             hC---CCcceEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhh--HHHHhcCCceEEEechhhhhcch---hhHHHH
Confidence            65   78999999998642221  1223445689999999987653  11222234579999999998554   344556


Q ss_pred             HHHhCCCCCeEEEEecc-CCccHHH---HHHHhcCC--------------------------------------------
Q psy1548         281 IFRSSPHTKQVMMFSAT-LSKEIRP---VCKKFMHD--------------------------------------------  312 (448)
Q Consensus       281 i~~~l~~~~q~i~~SAT-~~~~~~~---~~~~~l~~--------------------------------------------  312 (448)
                      +++.+....+ +++|.| +-+.+.+   ++...+.+                                            
T Consensus       311 ~lr~f~~~nr-LLlTGTPLQNNL~ELWaLLnFllPdiF~~~e~F~swF~~~~~~~~~e~v~~Lh~vL~pFlLRR~K~dVe  389 (971)
T KOG0385|consen  311 ILREFKTDNR-LLLTGTPLQNNLHELWALLNFLLPDIFNSAEDFDSWFDFTNCEGDQELVSRLHKVLRPFLLRRIKSDVE  389 (971)
T ss_pred             HHHHhcccce-eEeeCCcccccHHHHHHHHHhhchhhccCHHHHHHHHcccccccCHHHHHHHHhhhhHHHHHHHHHhHh
Confidence            6666654444 444555 2221111   11111100                                            


Q ss_pred             -----C--eEEEEcCc------------------------cccccc--------ceeEEEEE---------------cCc
Q psy1548         313 -----P--MEVYVDDE------------------------AKLTLH--------GLQQHYVK---------------LKE  338 (448)
Q Consensus       313 -----~--~~i~~~~~------------------------~~~~~~--------~i~~~~~~---------------~~~  338 (448)
                           .  ..+.+.-.                        ....+.        ...|-|+.               +..
T Consensus       390 ~sLppKkE~~iyvgms~mQkk~Y~~iL~kdl~~~n~~~~~~k~kL~NI~mQLRKccnHPYLF~g~ePg~pyttdehLv~n  469 (971)
T KOG0385|consen  390 KSLPPKKELIIYVGMSSMQKKWYKAILMKDLDALNGEGKGEKTKLQNIMMQLRKCCNHPYLFDGAEPGPPYTTDEHLVTN  469 (971)
T ss_pred             hcCCCcceeeEeccchHHHHHHHHHHHHhcchhhcccccchhhHHHHHHHHHHHhcCCccccCCCCCCCCCCcchHHHhc
Confidence                 0  00110000                        000000        01111211               112


Q ss_pred             chHHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC------------
Q psy1548         339 NEKNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH------------  404 (448)
Q Consensus       339 ~~k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~------------  404 (448)
                      ..|...|..+|..+  .+.++|||.....-.+-|-.+.--+|+...-+.|.++-++|...++.|....            
T Consensus       470 SGKm~vLDkLL~~Lk~~GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~FiFlLSTRA  549 (971)
T KOG0385|consen  470 SGKMLVLDKLLPKLKEQGHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFNAPPSEKFIFLLSTRA  549 (971)
T ss_pred             CcceehHHHHHHHHHhCCCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCCcHHHHHHHHhcCCCCcceEEEEEeccc
Confidence            33666676666554  4679999998888888888877778999999999999999999999998876            


Q ss_pred             CceEEEEecCh
Q psy1548         405 KGLAITFASDE  415 (448)
Q Consensus       405 ~g~~I~~~t~~  415 (448)
                      .|+||.+++.+
T Consensus       550 GGLGINL~aAD  560 (971)
T KOG0385|consen  550 GGLGINLTAAD  560 (971)
T ss_pred             ccccccccccc
Confidence            67787777653

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.36  E-value=4.5e-11  Score=123.91  Aligned_cols=127  Identities=17%  Similarity=0.113  Sum_probs=97.1

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .|..+   |..      ..-.++.|+  +....||.|||+++.+|++.....   |..+.+++|+.-||.+=++.+..+.
T Consensus        78 r~ydv---Qli------g~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL~---G~~VhvvT~NdyLA~RDae~m~~ly  143 (764)
T PRK12326         78 RPFDV---QLL------GALRLLAGD--VIEMATGEGKTLAGAIAAAGYALQ---GRRVHVITVNDYLARRDAEWMGPLY  143 (764)
T ss_pred             CcchH---HHH------HHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHc---CCCeEEEcCCHHHHHHHHHHHHHHH
Confidence            67778   888      555556663  779999999999999998876544   3468999999999999999999999


Q ss_pred             ccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHH-HHHHCC------CCcCCCeeEEEecchhHHH
Q psy1548         205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRIL-ALVRNK------KLNLSLLKHFILDECDKML  269 (448)
Q Consensus       205 ~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~-~~l~~~------~~~~~~i~~lViDEah~l~  269 (448)
                      ..+ +++++++.++.+.......+   .++|+++|..-+- ++|+.+      ......+.+.|+||+|.++
T Consensus       144 ~~L-GLsvg~i~~~~~~~err~aY---~~DItYgTn~e~gFDyLRDnm~~~~~~~v~R~~~faIVDEvDSiL  211 (764)
T PRK12326        144 EAL-GLTVGWITEESTPEERRAAY---ACDVTYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEADSVL  211 (764)
T ss_pred             Hhc-CCEEEEECCCCCHHHHHHHH---cCCCEEcCCcccccccchhhhccChHhhcCCccceeeecchhhhe
Confidence            998 99999999887755444444   3799999987762 333322      1223557789999999765

>KOG0922|consensus

Probab=99.34  E-value=1.5e-10  Score=117.33  Aligned_cols=251  Identities=16%  Similarity=0.178  Sum_probs=152.5

Q ss_pred             CchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHH-HHhhhccCCCeEEEEeeccHHHHHHHHHHHH-Hhhc
Q psy1548         128 DSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLAT-LQQLETTDSNVYVLVMCHTRELAFQISKEYE-RFSK  205 (448)
Q Consensus       128 ~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~-l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~-~~~~  205 (448)
                      |+..|-.+      .+..+.+..-+++.|+||||||..  +|= |........| ++-+.-|.|--|..+.+... ....
T Consensus        51 PI~~~r~~------il~~ve~nqvlIviGeTGsGKSTQ--ipQyL~eaG~~~~g-~I~~TQPRRVAavslA~RVAeE~~~  121 (674)
T KOG0922|consen   51 PIYKYRDQ------ILYAVEDNQVLIVIGETGSGKSTQ--IPQYLAEAGFASSG-KIACTQPRRVAAVSLAKRVAEEMGC  121 (674)
T ss_pred             CHHHHHHH------HHHHHHHCCEEEEEcCCCCCcccc--HhHHHHhcccccCC-cEEeecCchHHHHHHHHHHHHHhCC
Confidence            45444555      666666778899999999999965  442 2222222333 46777788876666554433 2333


Q ss_pred             cCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhh-hHHHHHHHHHh
Q psy1548         206 YMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLE-MRRDVQEIFRS  284 (448)
Q Consensus       206 ~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~-~~~~~~~i~~~  284 (448)
                      .+ +-.|+...--.+...       ....|.+.|-|.|++-+..+.. ++..++||+||||.-.-..+ ....++++++.
T Consensus       122 ~l-G~~VGY~IRFed~ts-------~~TrikymTDG~LLRE~l~Dp~-LskYsvIIlDEAHERsl~TDiLlGlLKki~~~  192 (674)
T KOG0922|consen  122 QL-GEEVGYTIRFEDSTS-------KDTRIKYMTDGMLLREILKDPL-LSKYSVIILDEAHERSLHTDILLGLLKKILKK  192 (674)
T ss_pred             Cc-CceeeeEEEecccCC-------CceeEEEecchHHHHHHhcCCc-cccccEEEEechhhhhhHHHHHHHHHHHHHhc
Confidence            33 445544432211111       1267999999999887665443 68899999999995321101 22223333332


Q ss_pred             CCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcch-HHHHHHHHH---hhCCCCeEEEE
Q psy1548         285 SPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENE-KNKKLFELL---DVLEFNQVVIF  360 (448)
Q Consensus       285 l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~-k~~~L~~ll---~~~~~~~~IIF  360 (448)
                       .+..++|++|||+..+  .+...|..-|+... ...    ...++..|..-+..+ -.+.+...+   ...+.+-+|||
T Consensus       193 -R~~LklIimSATlda~--kfS~yF~~a~i~~i-~GR----~fPVei~y~~~p~~dYv~a~~~tv~~Ih~~E~~GDILvF  264 (674)
T KOG0922|consen  193 -RPDLKLIIMSATLDAE--KFSEYFNNAPILTI-PGR----TFPVEILYLKEPTADYVDAALITVIQIHLTEPPGDILVF  264 (674)
T ss_pred             -CCCceEEEEeeeecHH--HHHHHhcCCceEee-cCC----CCceeEEeccCCchhhHHHHHHHHHHHHccCCCCCEEEE
Confidence             3456899999998643  44444444344333 222    234555555433332 223333333   33466789999


Q ss_pred             ECccHHHHHHHHHHHhC----CC----cEEEEeCCCCHHHHHHHHHHHhcCC
Q psy1548         361 VKSVTRCIALSTLLSEQ----NF----PAVSIHRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       361 ~~s~~~a~~l~~~L~~~----g~----~~~~lh~~~~~~eR~~~l~~F~~g~  404 (448)
                      ...+++.+.+++.|.+.    +-    -+..+||.|+.+++.++++.--.|.
T Consensus       265 LtGqeEIe~~~~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~  316 (674)
T KOG0922|consen  265 LTGQEEIEAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGK  316 (674)
T ss_pred             eCCHHHHHHHHHHHHHHhhhccccCcceeeeecccCCHHHhhccccCCCCCc
Confidence            99999999999999874    11    2478999999999999988766554

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

Probab=99.33  E-value=1.2e-10  Score=122.52  Aligned_cols=152  Identities=22%  Similarity=0.230  Sum_probs=107.2

Q ss_pred             hhhhhhhccccccceeeeeC----cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhc
Q psy1548         130 DTYLHRVARAGRFGTKAVLG----MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK  205 (448)
Q Consensus       130 ~~yQ~~~~~~~~~~~~~~~g----~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  205 (448)
                      ..-|+.      +...+...    +..++.+.||||||.+|+-.+-..+..   |.++|+++|-.+|..|+...++... 
T Consensus       200 n~~Q~~------a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~---GkqvLvLVPEI~Ltpq~~~rf~~rF-  269 (730)
T COG1198         200 NQEQQA------AVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQ---GKQVLVLVPEIALTPQLLARFKARF-  269 (730)
T ss_pred             CHHHHH------HHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHc---CCEEEEEeccccchHHHHHHHHHHh-
Confidence            344777      55554433    678999999999999998776666643   3589999999999999888777765 


Q ss_pred             cCCCceEEEEEcCcccHH---hHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHH--hh--hhhHHHH
Q psy1548         206 YMSNIKVGVFFGGLPIQK---DEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKML--EQ--LEMRRDV  278 (448)
Q Consensus       206 ~~~~~~v~~~~g~~~~~~---~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~--~~--~~~~~~~  278 (448)
                         +.++..++++.+..+   .+.....+...|+|||-..+.       ..++++.+||+||=|.-.  ..  ..+...-
T Consensus       270 ---g~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF-------~Pf~~LGLIIvDEEHD~sYKq~~~prYhARd  339 (730)
T COG1198         270 ---GAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALF-------LPFKNLGLIIVDEEHDSSYKQEDGPRYHARD  339 (730)
T ss_pred             ---CCChhhhcccCChHHHHHHHHHHhcCCceEEEEechhhc-------CchhhccEEEEeccccccccCCcCCCcCHHH
Confidence               577888887766543   344556788999999965442       357899999999999431  10  0122222


Q ss_pred             HHHHHhCCCCCeEEEEeccCCcc
Q psy1548         279 QEIFRSSPHTKQVMMFSATLSKE  301 (448)
Q Consensus       279 ~~i~~~l~~~~q~i~~SAT~~~~  301 (448)
                      -.+++.-..++++|+-|||.+-+
T Consensus       340 vA~~Ra~~~~~pvvLgSATPSLE  362 (730)
T COG1198         340 VAVLRAKKENAPVVLGSATPSLE  362 (730)
T ss_pred             HHHHHHHHhCCCEEEecCCCCHH
Confidence            23444445688999999996544

>KOG0920|consensus

Probab=99.32  E-value=1e-10  Score=124.38  Aligned_cols=252  Identities=14%  Similarity=0.143  Sum_probs=160.8

Q ss_pred             cceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCccc
Q psy1548         142 FGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPI  221 (448)
Q Consensus       142 ~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~  221 (448)
                      .+..+.+..-++|+|.||+|||...---+|+.....+...++++.-|.|--|..+.+++..=.....+-.|+.-.+....
T Consensus       181 Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsvAeRVa~ER~~~~g~~VGYqvrl~~~  260 (924)
T KOG0920|consen  181 ILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISVAERVAKERGESLGEEVGYQVRLESK  260 (924)
T ss_pred             HHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcCCCCeEEecCCchHHHHHHHHHHHHHhccccCCeeeEEEeeecc
Confidence            55566667789999999999998755556665544445667777779988887777766553333224444444333221


Q ss_pred             HHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCcc
Q psy1548         222 QKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKE  301 (448)
Q Consensus       222 ~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~  301 (448)
                      ..      . ...+++||.|.|++.+.. .-.+..+.++|+||+|.-.-..+|.-.+.+.+-...++.++|+||||+..+
T Consensus       261 ~s------~-~t~L~fcTtGvLLr~L~~-~~~l~~vthiivDEVHER~i~~DflLi~lk~lL~~~p~LkvILMSAT~dae  332 (924)
T KOG0920|consen  261 RS------R-ETRLLFCTTGVLLRRLQS-DPTLSGVTHIIVDEVHERSINTDFLLILLKDLLPRNPDLKVILMSATLDAE  332 (924)
T ss_pred             cC------C-ceeEEEecHHHHHHHhcc-CcccccCceeeeeeEEEccCCcccHHHHHHHHhhhCCCceEEEeeeecchH
Confidence            11      1 257999999999999987 445788999999999965433355555555555556889999999998733


Q ss_pred             HHHHHHHhcCCCeEEEEcCc-ccc--------------cccceeEE------------EEEcCcchHHHHHHHHHhh---
Q psy1548         302 IRPVCKKFMHDPMEVYVDDE-AKL--------------TLHGLQQH------------YVKLKENEKNKKLFELLDV---  351 (448)
Q Consensus       302 ~~~~~~~~l~~~~~i~~~~~-~~~--------------~~~~i~~~------------~~~~~~~~k~~~L~~ll~~---  351 (448)
                        .+..-|...|+ +.+... ...              ......++            ......+-....+..++..   
T Consensus       333 --~fs~YF~~~pv-i~i~grtfpV~~~fLEDil~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~id~~Li~~li~~I~~  409 (924)
T KOG0920|consen  333 --LFSDYFGGCPV-ITIPGRTFPVKEYFLEDILSKTGYVSEDDSARSGPERSQLRLARLKLWEPEIDYDLIEDLIEYIDE  409 (924)
T ss_pred             --HHHHHhCCCce-EeecCCCcchHHHHHHHHHHHhcccccccccccccccCccccccchhccccccHHHHHHHHHhccc
Confidence              33333333333 322111 000              00000000            0000111233444444433   


Q ss_pred             -CCCCeEEEEECccHHHHHHHHHHHhC-------CCcEEEEeCCCCHHHHHHHHHHHhcCC
Q psy1548         352 -LEFNQVVIFVKSVTRCIALSTLLSEQ-------NFPAVSIHRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       352 -~~~~~~IIF~~s~~~a~~l~~~L~~~-------g~~~~~lh~~~~~~eR~~~l~~F~~g~  404 (448)
                       ...+.+|||.+...++..+.+.|...       .+-+..+|+.|+..++..+...--.|.
T Consensus       410 ~~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~  470 (924)
T KOG0920|consen  410 REFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGT  470 (924)
T ss_pred             CCCCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCCc
Confidence             34678999999999999999999752       256889999999999999988877764

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.30  E-value=1.1e-10  Score=123.74  Aligned_cols=127  Identities=19%  Similarity=0.165  Sum_probs=96.2

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .|..+   |-..|.      .+.  .--|....||.|||+++.+|++.....   |..+.+++|+.-||.+-++.+..+.
T Consensus        82 ~~ydV---QliGg~------~Lh--~G~iaEM~TGEGKTLvA~l~a~l~al~---G~~VhvvT~ndyLA~RD~e~m~~l~  147 (913)
T PRK13103         82 RHFDV---QLIGGM------TLH--EGKIAEMRTGEGKTLVGTLAVYLNALS---GKGVHVVTVNDYLARRDANWMRPLY  147 (913)
T ss_pred             Ccchh---HHHhhh------Hhc--cCccccccCCCCChHHHHHHHHHHHHc---CCCEEEEeCCHHHHHHHHHHHHHHh
Confidence            56677   777322      222  345788999999999999998865544   3468999999999999999999999


Q ss_pred             ccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHH-HHHHHCCC------CcCCCeeEEEecchhHHH
Q psy1548         205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRI-LALVRNKK------LNLSLLKHFILDECDKML  269 (448)
Q Consensus       205 ~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l-~~~l~~~~------~~~~~i~~lViDEah~l~  269 (448)
                      ..+ +++++++.++.+.......+.   ++|++||..-+ .++|+.+.      .....+.+.||||+|.++
T Consensus       148 ~~l-Gl~v~~i~~~~~~~err~~Y~---~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDsiL  215 (913)
T PRK13103        148 EFL-GLSVGIVTPFQPPEEKRAAYA---ADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDSIL  215 (913)
T ss_pred             ccc-CCEEEEECCCCCHHHHHHHhc---CCEEEEcccccccchhhccceechhhhcccccceeEechhhhee
Confidence            998 999999988876555444442   79999999876 33333321      123778899999999764

>KOG0951|consensus

Probab=99.30  E-value=1.8e-10  Score=122.99  Aligned_cols=267  Identities=15%  Similarity=0.177  Sum_probs=166.2

Q ss_pred             CCcccccceeEeeccCCCCchhhhhhhccccccceeeee-CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeec
Q psy1548         110 RGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVL-GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH  188 (448)
Q Consensus       110 ~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~-g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~P  188 (448)
                      .+++-++...+|...  .++   |.+      .++.+-+ ..++++.+|+|||||+|+-++++.    .....+++++.|
T Consensus      1130 ~~l~N~~~~~lf~~~--n~i---qtq------Vf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~----~~~~~~~vyi~p 1194 (1674)
T KOG0951|consen 1130 SALRNPSFETLFQDF--NPI---QTQ------VFTSLYNTNDNVLVGAPNGSGKTACAELALLR----PDTIGRAVYIAP 1194 (1674)
T ss_pred             hccCCcchhhhcccc--CCc---eEE------EEeeeecccceEEEecCCCCchhHHHHHHhcC----CccceEEEEecc
Confidence            344444444444322  677   888      8888776 578999999999999999888876    234569999999


Q ss_pred             cHHHHHHHHHHHH-HhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhH
Q psy1548         189 TRELAFQISKEYE-RFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDK  267 (448)
Q Consensus       189 t~~L~~q~~~~~~-~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~  267 (448)
                      ..+.+..+++.+. +|.... +..+..++|......  ..+..  .+|+|+||+++..+ +    ....++++|.||+|.
T Consensus      1195 ~~~i~~~~~~~w~~~f~~~~-G~~~~~l~ge~s~~l--kl~~~--~~vii~tpe~~d~l-q----~iQ~v~l~i~d~lh~ 1264 (1674)
T KOG0951|consen 1195 LEEIADEQYRDWEKKFSKLL-GLRIVKLTGETSLDL--KLLQK--GQVIISTPEQWDLL-Q----SIQQVDLFIVDELHL 1264 (1674)
T ss_pred             hHHHHHHHHHHHHHhhcccc-CceEEecCCccccch--HHhhh--cceEEechhHHHHH-h----hhhhcceEeeehhhh
Confidence            9999977666544 455444 788888888775443  23333  48999999998665 2    567889999999997


Q ss_pred             HHhhhh----hHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCc-chHH
Q psy1548         268 MLEQLE----MRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKE-NEKN  342 (448)
Q Consensus       268 l~~~~~----~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~-~~k~  342 (448)
                      +.+..+    ....+..+-..+-++.+++++|..+.+. +++  ..+.....+...+.....+-.+.-.-+.... ....
T Consensus      1265 igg~~g~v~evi~S~r~ia~q~~k~ir~v~ls~~lana-~d~--ig~s~~~v~Nf~p~~R~~Pl~i~i~~~~~~~~~~~~ 1341 (1674)
T KOG0951|consen 1265 IGGVYGAVYEVICSMRYIASQLEKKIRVVALSSSLANA-RDL--IGASSSGVFNFSPSVRPVPLEIHIQSVDISHFESRM 1341 (1674)
T ss_pred             hcccCCceEEEEeeHHHHHHHHHhheeEEEeehhhccc-hhh--ccccccceeecCcccCCCceeEEEEEeccchhHHHH
Confidence            764311    0111445555566677899999988654 333  1222222233333322222222211111111 1111


Q ss_pred             H-----HHHHHHhh-CCCCeEEEEECccHHHHHHHHHHHh----------------------CCCcEEEEeCCCCHHHHH
Q psy1548         343 K-----KLFELLDV-LEFNQVVIFVKSVTRCIALSTLLSE----------------------QNFPAVSIHRGMTQEERL  394 (448)
Q Consensus       343 ~-----~L~~ll~~-~~~~~~IIF~~s~~~a~~l~~~L~~----------------------~g~~~~~lh~~~~~~eR~  394 (448)
                      .     ....+.+. ..+++++||++++++|..++..|-.                      ...+...=|.+|+..+..
T Consensus      1342 ~am~~~~~~ai~~~a~~~k~~~vf~p~rk~~~~~a~~~~~~s~~~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~ 1421 (1674)
T KOG0951|consen 1342 LAMTKPTYTAIVRHAGNRKPAIVFLPTRKHARLVAVDLVTFSHADEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQE 1421 (1674)
T ss_pred             HHhhhhHHHHHHHHhcCCCCeEEEeccchhhhhhhhccchhhccCcHHHHHHHHhcchHhhhhcccccccccccCcchHH
Confidence            1     11112211 2466899999999999988865421                      011112228899999988


Q ss_pred             HHHHHHhcCC
Q psy1548         395 KKYQEFKDFH  404 (448)
Q Consensus       395 ~~l~~F~~g~  404 (448)
                      -+-.-|..|.
T Consensus      1422 iv~~l~e~g~ 1431 (1674)
T KOG0951|consen 1422 IVQQLFEAGA 1431 (1674)
T ss_pred             HHHHHHhcCc
Confidence            8888888887

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=99.23  E-value=4.7e-10  Score=118.56  Aligned_cols=127  Identities=20%  Similarity=0.206  Sum_probs=94.2

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .|..+   |-.      ..  +...+.-|..+.||.|||+++.+|++-....   |..+.|++++..||.+-.+++..+.
T Consensus        76 r~ydv---Qli------g~--l~L~~G~IaEm~TGEGKTL~a~l~ayl~aL~---G~~VhVvT~NdyLA~RD~e~m~pvy  141 (870)
T CHL00122         76 RHFDV---QLI------GG--LVLNDGKIAEMKTGEGKTLVATLPAYLNALT---GKGVHIVTVNDYLAKRDQEWMGQIY  141 (870)
T ss_pred             CCCch---Hhh------hh--HhhcCCccccccCCCCchHHHHHHHHHHHhc---CCceEEEeCCHHHHHHHHHHHHHHH
Confidence            46777   777      22  2224567999999999999999998643332   4468999999999999999999999


Q ss_pred             ccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHH-HHHHCCC------CcCCCeeEEEecchhHHH
Q psy1548         205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRIL-ALVRNKK------LNLSLLKHFILDECDKML  269 (448)
Q Consensus       205 ~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~-~~l~~~~------~~~~~i~~lViDEah~l~  269 (448)
                      ..+ ++.++++.++.+.......+   .++|+++|..-+- ++|+.+.      .....+.+.|+||+|.++
T Consensus       142 ~~L-GLsvg~i~~~~~~~err~aY---~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvDSiL  209 (870)
T CHL00122        142 RFL-GLTVGLIQEGMSSEERKKNY---LKDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVDSIL  209 (870)
T ss_pred             HHc-CCceeeeCCCCChHHHHHhc---CCCCEecCCccccccchhhccCcChHHhhccccceeeeecchhhe
Confidence            999 99999998887765544433   3799999997653 3333221      123567899999999764

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

Probab=99.22  E-value=8.2e-11  Score=122.67  Aligned_cols=75  Identities=24%  Similarity=0.300  Sum_probs=58.0

Q ss_pred             ceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh-ccCC-CceEEEEEcC
Q psy1548         143 GTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS-KYMS-NIKVGVFFGG  218 (448)
Q Consensus       143 ~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~-~~~~-~~~v~~~~g~  218 (448)
                      ...+..++.+++.||||+|||++|++|++..+... .+.++||++||++|+.|+.+.+..+. +.++ .+++..+.|.
T Consensus        10 ~~al~~~~~lliEA~TGtGKTlAYLlpal~~~~~~-~~~rvlIstpT~~Lq~Ql~~~l~~l~~~~l~~~i~~~~lkGr   86 (636)
T TIGR03117        10 LTSLRQKRIGMLEASTGVGKTLAMIMAALTMLKER-PDQKIAIAVPTLALMGQLWSELERLTAEGLAGPVQAGFFPGS   86 (636)
T ss_pred             HHHHhcCCeEEEEcCCCCcHHHHHHHHHHHHHHhc-cCceEEEECCcHHHHHHHHHHHHHHHHhhcCCCeeEEEEECC
Confidence            34455688999999999999999999999876532 24589999999999999999988887 3321 4555555543

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.

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.21  E-value=2.8e-09  Score=112.78  Aligned_cols=73  Identities=11%  Similarity=0.145  Sum_probs=60.6

Q ss_pred             hHHHHHHHHHhh--CCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecC
Q psy1548         340 EKNKKLFELLDV--LEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASD  414 (448)
Q Consensus       340 ~k~~~L~~ll~~--~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~  414 (448)
                      .+...|...++.  ..+.++||||+|++.|+.+++.|.+.|+++..+||++++.+|.++++.|+.|+  +.|+++++
T Consensus       426 ~qi~~Ll~eI~~~~~~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~--i~VLV~t~  500 (655)
T TIGR00631       426 GQVDDLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGE--FDVLVGIN  500 (655)
T ss_pred             chHHHHHHHHHHHHcCCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCC--ceEEEEcC
Confidence            345555555543  24678999999999999999999999999999999999999999999999987  45555554

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

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=99.21  E-value=1.2e-09  Score=115.38  Aligned_cols=127  Identities=17%  Similarity=0.180  Sum_probs=93.6

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .|..+   |-..|.      .+  ..--|..+.||-|||+++.+|++-....+   ..+-||+++--||..=.+++..+.
T Consensus        85 r~ydV---QliGgl------~L--h~G~IAEM~TGEGKTL~atlpaylnAL~G---kgVhVVTvNdYLA~RDae~m~~vy  150 (939)
T PRK12902         85 RHFDV---QLIGGM------VL--HEGQIAEMKTGEGKTLVATLPSYLNALTG---KGVHVVTVNDYLARRDAEWMGQVH  150 (939)
T ss_pred             Ccchh---HHHhhh------hh--cCCceeeecCCCChhHHHHHHHHHHhhcC---CCeEEEeCCHHHHHhHHHHHHHHH
Confidence            57777   777222      22  34458899999999999999987654443   358999999999999899999999


Q ss_pred             ccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHH-HHHHHC------CCCcCCCeeEEEecchhHHH
Q psy1548         205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRI-LALVRN------KKLNLSLLKHFILDECDKML  269 (448)
Q Consensus       205 ~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l-~~~l~~------~~~~~~~i~~lViDEah~l~  269 (448)
                      ..+ ++.|+++.++.+........   .+||++||+..+ .++|+.      .......+.+.||||+|.++
T Consensus       151 ~~L-GLtvg~i~~~~~~~err~aY---~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEvDSIL  218 (939)
T PRK12902        151 RFL-GLSVGLIQQDMSPEERKKNY---ACDITYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEVDSIL  218 (939)
T ss_pred             HHh-CCeEEEECCCCChHHHHHhc---CCCeEEecCCcccccchhhhhcccccccccCccceEEEeccccee
Confidence            888 99999998877654443333   489999999887 222221      22334677889999999764

>KOG0949|consensus

Probab=99.18  E-value=5.7e-11  Score=123.93  Aligned_cols=158  Identities=14%  Similarity=0.134  Sum_probs=109.4

Q ss_pred             hhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCc
Q psy1548         131 TYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI  210 (448)
Q Consensus       131 ~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~  210 (448)
                      .+|.+      .+...-.+++++|+|||.+|||.+--. ++..+.+......+|+++|+++|++|+...+..-....--.
T Consensus       514 ~WQ~e------lLDsvDr~eSavIVAPTSaGKTfisfY-~iEKVLResD~~VVIyvaPtKaLVnQvsa~VyaRF~~~t~~  586 (1330)
T KOG0949|consen  514 EWQRE------LLDSVDRNESAVIVAPTSAGKTFISFY-AIEKVLRESDSDVVIYVAPTKALVNQVSANVYARFDTKTFL  586 (1330)
T ss_pred             HHHHH------HhhhhhcccceEEEeeccCCceeccHH-HHHHHHhhcCCCEEEEecchHHHhhhhhHHHHHhhccCccc
Confidence            44888      777777899999999999999977443 33444444445589999999999999877666543211012


Q ss_pred             eEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHC---CCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCC
Q psy1548         211 KVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRN---KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPH  287 (448)
Q Consensus       211 ~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~---~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~  287 (448)
                      +...+.|......+..   .-.|+|+|+-|+.+.+++..   ...+.++++++|+||+|.+... .-.-.++.++-.  -
T Consensus       587 rg~sl~g~ltqEYsin---p~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~-ed~l~~Eqll~l--i  660 (1330)
T KOG0949|consen  587 RGVSLLGDLTQEYSIN---PWNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNE-EDGLLWEQLLLL--I  660 (1330)
T ss_pred             cchhhHhhhhHHhcCC---chhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhcccc-ccchHHHHHHHh--c
Confidence            2333444443333322   11489999999999998877   4566799999999999988654 333334444333  3


Q ss_pred             CCeEEEEeccCCcc
Q psy1548         288 TKQVMMFSATLSKE  301 (448)
Q Consensus       288 ~~q~i~~SAT~~~~  301 (448)
                      .|.++++|||+.+.
T Consensus       661 ~CP~L~LSATigN~  674 (1330)
T KOG0949|consen  661 PCPFLVLSATIGNP  674 (1330)
T ss_pred             CCCeeEEecccCCH
Confidence            56799999999664

>KOG0387|consensus

Probab=99.17  E-value=2.3e-10  Score=117.40  Aligned_cols=257  Identities=18%  Similarity=0.226  Sum_probs=152.1

Q ss_pred             chhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhcc-CCCeEEEEeeccHHHHHHHHHHHHHhhccC
Q psy1548         129 SDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-DSNVYVLVMCHTRELAFQISKEYERFSKYM  207 (448)
Q Consensus       129 ~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  207 (448)
                      +.+||++..+  +.|.....+.--|+....|.|||... +..|..+... .-...+|||||.. +..||.+++..|.   
T Consensus       206 Lf~yQreGV~--WL~~L~~q~~GGILgDeMGLGKTIQi-isFLaaL~~S~k~~~paLIVCP~T-ii~qW~~E~~~w~---  278 (923)
T KOG0387|consen  206 LFPYQREGVQ--WLWELYCQRAGGILGDEMGLGKTIQI-ISFLAALHHSGKLTKPALIVCPAT-IIHQWMKEFQTWW---  278 (923)
T ss_pred             hhHHHHHHHH--HHHHHHhccCCCeecccccCccchhH-HHHHHHHhhcccccCceEEEccHH-HHHHHHHHHHHhC---
Confidence            4788999221  12233344677899999999999542 2222222222 2224799999986 6678888888887   


Q ss_pred             CCceEEEEEcCcccHH---------hHHHH---hcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhH
Q psy1548         208 SNIKVGVFFGGLPIQK---------DEEYL---KTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMR  275 (448)
Q Consensus       208 ~~~~v~~~~g~~~~~~---------~~~~l---~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~  275 (448)
                      |..++..++|......         ....+   .....+|+|+|.+.+.-  ....+.-...+++|+||.|++-..   .
T Consensus       279 p~~rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~--~~d~l~~~~W~y~ILDEGH~IrNp---n  353 (923)
T KOG0387|consen  279 PPFRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRI--QGDDLLGILWDYVILDEGHRIRNP---N  353 (923)
T ss_pred             cceEEEEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhcc--cCcccccccccEEEecCcccccCC---c
Confidence            4678888877655210         01111   11124799999876532  223333445679999999987543   2


Q ss_pred             HHHHHHHHhCCCCCeEEEEecc-CCccHHHHH------------------------------------------------
Q psy1548         276 RDVQEIFRSSPHTKQVMMFSAT-LSKEIRPVC------------------------------------------------  306 (448)
Q Consensus       276 ~~~~~i~~~l~~~~q~i~~SAT-~~~~~~~~~------------------------------------------------  306 (448)
                      ..+...++.++...+ |++|.| +-+.+.++-                                                
T Consensus       354 s~islackki~T~~R-iILSGTPiQNnL~ELwsLfDFv~PG~Lgt~~~F~~~f~~pI~~GgyaNAs~~qv~~aykca~~L  432 (923)
T KOG0387|consen  354 SKISLACKKIRTVHR-IILSGTPIQNNLTELWSLFDFVFPGKLGTLPVFQQNFEHPINRGGYANASPRQVQTAYKCAVAL  432 (923)
T ss_pred             cHHHHHHHhccccce-EEeeCccccchHHHHHHHhhhccCCcccchHHHHhhhhhheeccccCCCCHHHHHHHHHHHHHH
Confidence            333334444443333 344444 222211111                                                


Q ss_pred             -----------------------------------------HHhcC--------------------------CCeEEEEc
Q psy1548         307 -----------------------------------------KKFMH--------------------------DPMEVYVD  319 (448)
Q Consensus       307 -----------------------------------------~~~l~--------------------------~~~~i~~~  319 (448)
                                                               ..|+.                          +|..+.-.
T Consensus       433 r~lI~PylLRR~K~dv~~~~Lp~K~E~VlfC~LT~~QR~~Y~~fl~s~~v~~i~ng~~~~l~Gi~iLrkICnHPdll~~~  512 (923)
T KOG0387|consen  433 RDLISPYLLRRMKSDVKGLKLPKKEEIVLFCRLTKLQRRLYQRFLNSSEVNKILNGKRNCLSGIDILRKICNHPDLLDRR  512 (923)
T ss_pred             HHHhHHHHHHHHHHHhhhccCCCccceEEEEeccHHHHHHHHHHhhhHHHHHHHcCCccceechHHHHhhcCCcccccCc
Confidence                                                     11100                          00000000


Q ss_pred             CcccccccceeE--EE-EEcCcchHHHHHHHHHhh--CCCCeEEEEECccHHHHHHHHHHH-hCCCcEEEEeCCCCHHHH
Q psy1548         320 DEAKLTLHGLQQ--HY-VKLKENEKNKKLFELLDV--LEFNQVVIFVKSVTRCIALSTLLS-EQNFPAVSIHRGMTQEER  393 (448)
Q Consensus       320 ~~~~~~~~~i~~--~~-~~~~~~~k~~~L~~ll~~--~~~~~~IIF~~s~~~a~~l~~~L~-~~g~~~~~lh~~~~~~eR  393 (448)
                      ++      ...+  .+ -.++...|...+..++..  ..+.++|+|..++....-+-..|. ..|+.+.-+.|..+...|
T Consensus       513 ~~------~~~~~~D~~g~~k~sGKm~vl~~ll~~W~kqg~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~~~~R  586 (923)
T KOG0387|consen  513 DE------DEKQGPDYEGDPKRSGKMKVLAKLLKDWKKQGDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTPAALR  586 (923)
T ss_pred             cc------ccccCCCcCCChhhcchHHHHHHHHHHHhhCCCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCccchh
Confidence            00      0000  00 111223367777777643  256699999999999999999998 579999999999999999


Q ss_pred             HHHHHHHhcCC
Q psy1548         394 LKKYQEFKDFH  404 (448)
Q Consensus       394 ~~~l~~F~~g~  404 (448)
                      ..++++|.++.
T Consensus       587 ~~lVd~Fne~~  597 (923)
T KOG0387|consen  587 QKLVDRFNEDE  597 (923)
T ss_pred             hHHHHhhcCCC
Confidence            99999999988

>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=99.11  E-value=1.7e-08  Score=100.56  Aligned_cols=258  Identities=16%  Similarity=0.185  Sum_probs=171.3

Q ss_pred             CCeEEEEeeccHHHHHHHHHHHHHhhccCCCc----eEEEEEc--------------CcccHHhHHHHhc----------
Q psy1548         179 SNVYVLVMCHTRELAFQISKEYERFSKYMSNI----KVGVFFG--------------GLPIQKDEEYLKT----------  230 (448)
Q Consensus       179 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~----~v~~~~g--------------~~~~~~~~~~l~~----------  230 (448)
                      ..+++|||+|+|..|.++.+.+..+......+    +...-+|              ......+...+..          
T Consensus        36 tRPkVLIL~P~R~~A~~~V~~Li~l~~~~~~~~nk~RF~~efg~~~~~~~~~~~~~~~~~kP~D~~~~F~GN~DD~FrlG  115 (442)
T PF06862_consen   36 TRPKVLILLPFRNSALRIVETLISLLPPGKQVENKKRFEEEFGLPEDEDDDEEPPEFKKSKPEDFKALFSGNNDDCFRLG  115 (442)
T ss_pred             CCceEEEEcccHHHHHHHHHHHHHHcCccchHHHHHHHHHHcCCCccccchhhhccccCCCchhHHHhcCCCccceEEEe
Confidence            45899999999999999888888776541000    0000011              0001111111111          


Q ss_pred             --------------CCCcEEEEcHHHHHHHHHC------CCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCC---C
Q psy1548         231 --------------HNPQIVVGTPGRILALVRN------KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSP---H  287 (448)
Q Consensus       231 --------------~~~~IlV~Tp~~l~~~l~~------~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~---~  287 (448)
                                    ...||+|++|=-|...+..      ....+++|.++|+|.||.++.  ..+..+..++..+.   .
T Consensus       116 ik~trk~ikLys~Fy~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~M--QNW~Hv~~v~~~lN~~P~  193 (442)
T PF06862_consen  116 IKFTRKSIKLYSDFYSSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLLM--QNWEHVLHVFEHLNLQPK  193 (442)
T ss_pred             EEEecCeeeeecccccCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHHH--hhHHHHHHHHHHhccCCC
Confidence                          1368999999888877763      234579999999999998776  46677777766553   2


Q ss_pred             C---------------------CeEEEEeccCCccHHHHHHHhcCCCe---EEEEcCc----ccccccceeEEEEEcCcc
Q psy1548         288 T---------------------KQVMMFSATLSKEIRPVCKKFMHDPM---EVYVDDE----AKLTLHGLQQHYVKLKEN  339 (448)
Q Consensus       288 ~---------------------~q~i~~SAT~~~~~~~~~~~~l~~~~---~i~~~~~----~~~~~~~i~~~~~~~~~~  339 (448)
                      .                     +|+|++|+...+++..+....+.+..   .+.....    .......+.|.+...+..
T Consensus       194 ~~~~~DfsRVR~w~Ldg~a~~~RQtii~S~~~~pe~~slf~~~~~N~~G~v~~~~~~~~~g~i~~v~~~v~Q~F~r~~~~  273 (442)
T PF06862_consen  194 KSHDTDFSRVRPWYLDGQAKYYRQTIIFSSFQTPEINSLFNRHCQNYAGKVRLKPPYEASGVISQVVVQVRQVFQRFDCS  273 (442)
T ss_pred             CCCCCCHHHHHHHHHcCcchheeEeEEecCCCCHHHHHHHHhhCcCccceEEEeeccccceeeeccccCCceEEEEecCC
Confidence            1                     39999999999999999888665432   2221111    023445677887765432


Q ss_pred             -------hHHHHHHH----HHh-hCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCce
Q psy1548         340 -------EKNKKLFE----LLD-VLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGL  407 (448)
Q Consensus       340 -------~k~~~L~~----ll~-~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~  407 (448)
                             .+++....    -+. ....+.+|||++|--.=-.+.++|++.++....+|.-.+..+-.++-..|.+|+  .
T Consensus       274 s~~~~~d~Rf~yF~~~iLP~l~~~~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G~--~  351 (442)
T PF06862_consen  274 SPADDPDARFKYFTKKILPQLKRDSKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSDISRARSQFFHGR--K  351 (442)
T ss_pred             CcchhhhHHHHHHHHHHHHHhhhccCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcCC--c
Confidence                   23333333    222 334568999999999999999999999999999999999999999999999998  5


Q ss_pred             EEEEecChhhHHHHHHHHHHhcCCCCCCCcccc
Q psy1548         408 AITFASDENDAKILNNVQDRFDVSISELPDEID  440 (448)
Q Consensus       408 ~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~  440 (448)
                      .|+++|.....-.--.|...-++-+..+|+...
T Consensus       352 ~iLL~TER~HFfrRy~irGi~~viFY~~P~~p~  384 (442)
T PF06862_consen  352 PILLYTERFHFFRRYRIRGIRHVIFYGPPENPQ  384 (442)
T ss_pred             eEEEEEhHHhhhhhceecCCcEEEEECCCCChh
Confidence            777777753222222344444455666666644

; GO: 0005634 nucleus

>KOG4150|consensus

Probab=99.11  E-value=1.5e-10  Score=114.52  Aligned_cols=300  Identities=14%  Similarity=0.003  Sum_probs=193.4

Q ss_pred             hhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceE
Q psy1548         133 LHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKV  212 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v  212 (448)
                      |.+      ++..+..|+++++...|.+||+++|.+.....+...+ ....+++.|+.++++...+.+.-.....|..+.
T Consensus       291 ~~~------~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~-~s~~~~~~~~~~~~~~~~~~~~V~~~~I~~~K~  363 (1034)
T KOG4150|consen  291 SLE------LLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLCH-ATNSLLPSEMVEHLRNGSKGQVVHVEVIKARKS  363 (1034)
T ss_pred             hHH------HHhhhhhcccccccchhhcCCccCcccchhhhhhcCc-ccceecchhHHHHhhccCCceEEEEEehhhhhc
Confidence            888      8889999999999999999999999988877655443 346889999999998765544333322222322


Q ss_pred             EEE-EcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCC----cCCCeeEEEecchhHHHhhhhhHHHHH----HHHH
Q psy1548         213 GVF-FGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKL----NLSLLKHFILDECDKMLEQLEMRRDVQ----EIFR  283 (448)
Q Consensus       213 ~~~-~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~----~~~~i~~lViDEah~l~~~~~~~~~~~----~i~~  283 (448)
                      .++ +.+........++.+.+.+++++.|..+...+.-+..    .+-...+.+.||+|.....  +.....    .+.+
T Consensus       364 A~V~~~D~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~~--~~~~~~~~~R~L~~  441 (1034)
T KOG4150|consen  364 AYVEMSDKLSETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLFP--TKALAQDQLRALSD  441 (1034)
T ss_pred             ceeecccCCCchhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeeecc--hhhHHHHHHHHHHH
Confidence            222 2222234445556555689999999988765533222    2344567999999976542  333333    3333


Q ss_pred             hC-----CCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcc------hHHHHHH---HHH
Q psy1548         284 SS-----PHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKEN------EKNKKLF---ELL  349 (448)
Q Consensus       284 ~l-----~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~------~k~~~L~---~ll  349 (448)
                      .+     ..+.|++-.+||+...++....-+.-+...+...+.   .+..-++.+++.++.      +|...+.   .++
T Consensus       442 L~~~F~~~~~~~~~~~~~~~K~~~~~~~~~~~~~E~~Li~~DG---SPs~~K~~V~WNP~~~P~~~~~~~~~i~E~s~~~  518 (1034)
T KOG4150|consen  442 LIKGFEASINMGVYDGDTPYKDRTRLRSELANLSELELVTIDG---SPSSEKLFVLWNPSAPPTSKSEKSSKVVEVSHLF  518 (1034)
T ss_pred             HHHHHHhhcCcceEeCCCCcCCHHHHHHHhcCCcceEEEEecC---CCCccceEEEeCCCCCCcchhhhhhHHHHHHHHH
Confidence            22     347799999999988876655544444444333333   355667777776531      2222222   222


Q ss_pred             hh--CCCCeEEEEECccHHHHHHHHHHHhC----CC----cEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHH
Q psy1548         350 DV--LEFNQVVIFVKSVTRCIALSTLLSEQ----NF----PAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAK  419 (448)
Q Consensus       350 ~~--~~~~~~IIF~~s~~~a~~l~~~L~~~----g~----~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~  419 (448)
                      ..  ..+-++|.||.+++-|+.+...-++.    |-    .+..+.||.+.++|.++..+.-.|+  +.=.++|..-+.+
T Consensus       519 ~~~i~~~~R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~--L~giIaTNALELG  596 (1034)
T KOG4150|consen  519 AEMVQHGLRCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGK--LCGIIATNALELG  596 (1034)
T ss_pred             HHHHHcCCcEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCCe--eeEEEecchhhhc
Confidence            21  13458999999999999887655432    22    3677899999999999999999888  3344455543333


Q ss_pred             HHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         420 ILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       420 ~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      .  +|...-.+-...+|.++.+.++-.||
T Consensus       597 I--DIG~LDAVl~~GFP~S~aNl~QQ~GR  623 (1034)
T KOG4150|consen  597 I--DIGHLDAVLHLGFPGSIANLWQQAGR  623 (1034)
T ss_pred             c--ccccceeEEEccCchhHHHHHHHhcc
Confidence            2  55555556667778887777766655

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.09  E-value=2.1e-09  Score=114.71  Aligned_cols=111  Identities=20%  Similarity=0.183  Sum_probs=83.5

Q ss_pred             EEcCcchHHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEE
Q psy1548         334 VKLKENEKNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITF  411 (448)
Q Consensus       334 ~~~~~~~k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~  411 (448)
                      ++....+|...+...+...  .+.++||||+|++.++.|+..|++.|++...+|+  .+.+|...+-.|..+.  ..|++
T Consensus       576 vy~t~~eK~~Ali~~I~~~~~~grpVLIft~Sve~sE~Ls~~L~~~gI~h~vLna--kq~~REa~Iia~AG~~--g~VtI  651 (1025)
T PRK12900        576 VYKTRREKYNAIVLKVEELQKKGQPVLVGTASVEVSETLSRMLRAKRIAHNVLNA--KQHDREAEIVAEAGQK--GAVTI  651 (1025)
T ss_pred             EecCHHHHHHHHHHHHHHHhhCCCCEEEEeCcHHHHHHHHHHHHHcCCCceeecC--CHHHhHHHHHHhcCCC--CeEEE
Confidence            3445567999999988654  5779999999999999999999999999999997  6889999999998876  37777


Q ss_pred             ecCh----hhHHHHHHHHHH--hcCCCCCCCccccccccccCC
Q psy1548         412 ASDE----NDAKILNNVQDR--FDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       412 ~t~~----~d~~~l~~i~~~--~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      +|+-    .|......+...  +.+...+.|++.....++.||
T Consensus       652 ATNMAGRGtDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~GR  694 (1025)
T PRK12900        652 ATNMAGRGTDIKLGEGVRELGGLFILGSERHESRRIDRQLRGR  694 (1025)
T ss_pred             eccCcCCCCCcCCccchhhhCCceeeCCCCCchHHHHHHHhhh
Confidence            7763    233332233332  344566777776666777776

>KOG0351|consensus

Probab=99.08  E-value=8.6e-11  Score=126.82  Aligned_cols=133  Identities=22%  Similarity=0.270  Sum_probs=106.5

Q ss_pred             cccccCCCcee--eeecCceeEEeecCCCcccccc---ccCC-CccccccccccccccchhhhhhhhccCceeeeccCCc
Q psy1548           9 EKLSCGSGNVF--LFFRAFIRFSSSFPHSKMADND---DLLD-YEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGF   82 (448)
Q Consensus         9 ~~~~~~~~~~~--~~~r~~~~~~~~~~~~~~~~~~---~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (448)
                      ..|.++.+.+|  ||.|+||.|+|.....+....+   .... ..++..+.|...+...+.........+.....+|.|.
T Consensus       440 ~~L~l~~~~~~~~sfnR~NL~yeV~~k~~~~~~~~~~~~~~~~~~~~s~IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl  519 (941)
T KOG0351|consen  440 RSLGLRNPELFKSSFNRPNLKYEVSPKTDKDALLDILEESKLRHPDQSGIIYCLSRKECEQVSAVLRSLGKSAAFYHAGL  519 (941)
T ss_pred             HHhCCCCcceecccCCCCCceEEEEeccCccchHHHHHHhhhcCCCCCeEEEeCCcchHHHHHHHHHHhchhhHhhhcCC
Confidence            45788889999  9999999999999885432222   2222 2456778898888777766666666666677778877


Q ss_pred             ccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccc
Q psy1548          83 RDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR  141 (448)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~  141 (448)
                      .......-+..|+...-+|.|||-+||||||++|||.|+||..|..++.|.|++|||||
T Consensus       520 ~~~~R~~Vq~~w~~~~~~VivATVAFGMGIdK~DVR~ViH~~lPks~E~YYQE~GRAGR  578 (941)
T KOG0351|consen  520 PPKERETVQKAWMSDKIRVIVATVAFGMGIDKPDVRFVIHYSLPKSFEGYYQEAGRAGR  578 (941)
T ss_pred             CHHHHHHHHHHHhcCCCeEEEEEeeccCCCCCCceeEEEECCCchhHHHHHHhccccCc
Confidence            77666666677777778999999999999999999999999999999999999999999

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

Probab=99.07  E-value=7e-10  Score=92.84  Aligned_cols=136  Identities=18%  Similarity=0.193  Sum_probs=79.5

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL  228 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l  228 (448)
                      |+--++...+|+|||--.+.-++..-..  .+.++|+|.|||.++..+.+.++..     .+++..  .-.. .   .  
T Consensus         4 g~~~~~d~hpGaGKTr~vlp~~~~~~i~--~~~rvLvL~PTRvva~em~~aL~~~-----~~~~~t--~~~~-~---~--   68 (148)
T PF07652_consen    4 GELTVLDLHPGAGKTRRVLPEIVREAIK--RRLRVLVLAPTRVVAEEMYEALKGL-----PVRFHT--NARM-R---T--   68 (148)
T ss_dssp             TEEEEEE--TTSSTTTTHHHHHHHHHHH--TT--EEEEESSHHHHHHHHHHTTTS-----SEEEES--TTSS--------
T ss_pred             CceeEEecCCCCCCcccccHHHHHHHHH--ccCeEEEecccHHHHHHHHHHHhcC-----CcccCc--eeee-c---c--
Confidence            5556788999999998755545543322  3458999999999999988777643     222211  1100 0   0  


Q ss_pred             hcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhh-hhhHHHHHHHHHhCCCCCeEEEEeccCCccH
Q psy1548         229 KTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQ-LEMRRDVQEIFRSSPHTKQVMMFSATLSKEI  302 (448)
Q Consensus       229 ~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~-~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~  302 (448)
                      ..+..-|-++|...+...+.+ .....+.+++|+||||..-.. ..++..+...-. . ..+.+|++|||.|...
T Consensus        69 ~~g~~~i~vMc~at~~~~~~~-p~~~~~yd~II~DEcH~~Dp~sIA~rg~l~~~~~-~-g~~~~i~mTATPPG~~  140 (148)
T PF07652_consen   69 HFGSSIIDVMCHATYGHFLLN-PCRLKNYDVIIMDECHFTDPTSIAARGYLRELAE-S-GEAKVIFMTATPPGSE  140 (148)
T ss_dssp             --SSSSEEEEEHHHHHHHHHT-SSCTTS-SEEEECTTT--SHHHHHHHHHHHHHHH-T-TS-EEEEEESS-TT--
T ss_pred             ccCCCcccccccHHHHHHhcC-cccccCccEEEEeccccCCHHHHhhheeHHHhhh-c-cCeeEEEEeCCCCCCC
Confidence            112356888999998887766 555789999999999964221 123333333322 1 3467999999998664

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 ....

>KOG1000|consensus

Probab=99.07  E-value=4.9e-09  Score=102.61  Aligned_cols=254  Identities=13%  Similarity=0.114  Sum_probs=154.9

Q ss_pred             hhhhhhhccccccce-eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCC
Q psy1548         130 DTYLHRVARAGRFGT-KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS  208 (448)
Q Consensus       130 ~~yQ~~~~~~~~~~~-~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  208 (448)
                      -+||.+      -.. ++..|..+++....|.|||..++.-+... ..   ..-.||+||.. +-..|.+.+.+|.... 
T Consensus       200 lPFQre------Gv~faL~RgGR~llADeMGLGKTiQAlaIA~yy-ra---EwplliVcPAs-vrftWa~al~r~lps~-  267 (689)
T KOG1000|consen  200 LPFQRE------GVIFALERGGRILLADEMGLGKTIQALAIARYY-RA---EWPLLIVCPAS-VRFTWAKALNRFLPSI-  267 (689)
T ss_pred             Cchhhh------hHHHHHhcCCeEEEecccccchHHHHHHHHHHH-hh---cCcEEEEecHH-HhHHHHHHHHHhcccc-
Confidence            445877      332 44568899999999999998865333322 11   22589999986 5567788888887543 


Q ss_pred             CceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCC
Q psy1548         209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHT  288 (448)
Q Consensus       209 ~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~  288 (448)
                       ..+.++.++.+.....   -. ...|.|.+.+.+..+-.  .+.-...+.+|+||+|.+-+  +-......++..+...
T Consensus       268 -~pi~vv~~~~D~~~~~---~t-~~~v~ivSye~ls~l~~--~l~~~~~~vvI~DEsH~Lk~--sktkr~Ka~~dllk~a  338 (689)
T KOG1000|consen  268 -HPIFVVDKSSDPLPDV---CT-SNTVAIVSYEQLSLLHD--ILKKEKYRVVIFDESHMLKD--SKTKRTKAATDLLKVA  338 (689)
T ss_pred             -cceEEEecccCCcccc---cc-CCeEEEEEHHHHHHHHH--HHhcccceEEEEechhhhhc--cchhhhhhhhhHHHHh
Confidence             2355555554432211   11 24688989887754322  12223467899999997755  3344456666666666


Q ss_pred             CeEEEEeccCC-------------------ccHHHHHHHhcCCC-eEEEEcCcc-------------------------c
Q psy1548         289 KQVMMFSATLS-------------------KEIRPVCKKFMHDP-MEVYVDDEA-------------------------K  323 (448)
Q Consensus       289 ~q~i~~SAT~~-------------------~~~~~~~~~~l~~~-~~i~~~~~~-------------------------~  323 (448)
                      .++|++|.|..                   +...++...|.... +.+..+...                         .
T Consensus       339 khvILLSGTPavSRP~elytqi~avd~tlfp~f~efa~rYCd~k~vr~~~Dykg~tnl~EL~~lL~k~lMIRRlK~dvL~  418 (689)
T KOG1000|consen  339 KHVILLSGTPAVSRPSELYTQIRAVDHTLFPNFHEFAIRYCDGKQVRFCFDYKGCTNLEELAALLFKRLMIRRLKADVLK  418 (689)
T ss_pred             hheEEecCCcccCCchhhhhhhhhhcccccccHHHHHHHhcCccccceeeecCCCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            77899999931                   11222333332211 111111000                         0


Q ss_pred             ccccceeEEEEEcCc-------------------------------------chHHHHHHHHHhh------CCCCeEEEE
Q psy1548         324 LTLHGLQQHYVKLKE-------------------------------------NEKNKKLFELLDV------LEFNQVVIF  360 (448)
Q Consensus       324 ~~~~~i~~~~~~~~~-------------------------------------~~k~~~L~~ll~~------~~~~~~IIF  360 (448)
                      ..+..-.+..+.+..                                     .-|...+.+.+..      .++.+.+||
T Consensus       419 qLPpKrr~Vv~~~~gr~da~~~~lv~~a~~~t~~~~~e~~~~~l~l~y~~tgiaK~~av~eyi~~~~~l~d~~~~KflVF  498 (689)
T KOG1000|consen  419 QLPPKRREVVYVSGGRIDARMDDLVKAAADYTKVNSMERKHESLLLFYSLTGIAKAAAVCEYILENYFLPDAPPRKFLVF  498 (689)
T ss_pred             hCCccceEEEEEcCCccchHHHHHHHHhhhcchhhhhhhhhHHHHHHHHHhcccccHHHHHHHHhCcccccCCCceEEEE
Confidence            001111111111110                                     0133333333333      135589999


Q ss_pred             ECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC
Q psy1548         361 VKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       361 ~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~  404 (448)
                      |....-.+.+...+.+.++..+-+.|..+..+|....+.|+..+
T Consensus       499 aHH~~vLd~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~se  542 (689)
T KOG1000|consen  499 AHHQIVLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSE  542 (689)
T ss_pred             ehhHHHHHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhcccc
Confidence            99999999999999999999999999999999999999999987

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

Probab=99.06  E-value=6.4e-08  Score=96.01  Aligned_cols=52  Identities=13%  Similarity=0.167  Sum_probs=50.4

Q ss_pred             CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC
Q psy1548         353 EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       353 ~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~  404 (448)
                      .+.+++|-+-|++-|+.|.++|.+.|+++.++|++...-+|.+++.+.+.|.
T Consensus       445 ~~eRvLVTtLTKkmAEdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~  496 (663)
T COG0556         445 KNERVLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGE  496 (663)
T ss_pred             cCCeEEEEeehHHHHHHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCC
Confidence            4679999999999999999999999999999999999999999999999999

>KOG0392|consensus

Probab=99.06  E-value=4.6e-09  Score=112.20  Aligned_cols=158  Identities=16%  Similarity=0.178  Sum_probs=95.1

Q ss_pred             ccCCCC----chhhhhhhccccccceeee--e--CcceeeeccCCChhHHHHHHHHHH-hhhccC-----CCeEEEEeec
Q psy1548         123 YDMPED----SDTYLHRVARAGRFGTKAV--L--GMDILCQAKSGMGKTAVFVLATLQ-QLETTD-----SNVYVLVMCH  188 (448)
Q Consensus       123 ~~~p~~----~~~yQ~~~~~~~~~~~~~~--~--g~~vli~apTGsGKT~~~~l~~l~-~l~~~~-----~~~~~lil~P  188 (448)
                      |.-|.+    +|.||++      -+.++.  .  +-+.|++...|-|||+..+--+.. ....+.     ...-.|||||
T Consensus       966 y~Ip~pI~a~LRkYQqE------GVnWLaFLnky~LHGILcDDMGLGKTLQticilAsd~y~r~s~~~e~~~~PSLIVCP 1039 (1549)
T KOG0392|consen  966 YKIPVPISAKLRKYQQE------GVNWLAFLNKYKLHGILCDDMGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCP 1039 (1549)
T ss_pred             cccccchhHHHHHHHHh------ccHHHHHHHHhcccceeeccccccHHHHHHHHHHHHHHhhcccchhhccCCeEEECC
Confidence            445555    4999999      554443  2  468999999999999876433332 222211     2234899999


Q ss_pred             cHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHH
Q psy1548         189 TRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM  268 (448)
Q Consensus       189 t~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l  268 (448)
                      .. |+--|..++.+|..   -+++....|+.......+.-.+ ..+|+|++.+.+.+-+..  +.-....|+|+||-|.+
T Consensus      1040 sT-LtGHW~~E~~kf~p---fL~v~~yvg~p~~r~~lR~q~~-~~~iiVtSYDv~RnD~d~--l~~~~wNYcVLDEGHVi 1112 (1549)
T KOG0392|consen 1040 ST-LTGHWKSEVKKFFP---FLKVLQYVGPPAERRELRDQYK-NANIIVTSYDVVRNDVDY--LIKIDWNYCVLDEGHVI 1112 (1549)
T ss_pred             ch-hhhHHHHHHHHhcc---hhhhhhhcCChHHHHHHHhhcc-ccceEEeeHHHHHHHHHH--HHhcccceEEecCccee
Confidence            86 77777777777764   4577667766433222222222 369999999887643321  11123458999999976


Q ss_pred             HhhhhhHHHHHHHHHhCCCCCeEEEEecc
Q psy1548         269 LEQLEMRRDVQEIFRSSPHTKQVMMFSAT  297 (448)
Q Consensus       269 ~~~~~~~~~~~~i~~~l~~~~q~i~~SAT  297 (448)
                      -+.   ...+.+..+.+..+.+ +++|.|
T Consensus      1113 kN~---ktkl~kavkqL~a~hR-LILSGT 1137 (1549)
T KOG0392|consen 1113 KNS---KTKLTKAVKQLRANHR-LILSGT 1137 (1549)
T ss_pred             cch---HHHHHHHHHHHhhcce-EEeeCC
Confidence            442   3334444444444444 455666

>KOG0389|consensus

Probab=99.04  E-value=3.8e-09  Score=108.54  Aligned_cols=131  Identities=17%  Similarity=0.170  Sum_probs=86.7

Q ss_pred             chhhhhhhccccccceeee----eCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         129 SDTYLHRVARAGRFGTKAV----LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       129 ~~~yQ~~~~~~~~~~~~~~----~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      +.+||.-      -+.++.    .+-+.|+....|-|||.. .++.+..+........-|||||+..|-++ .+++.+|+
T Consensus       400 LkdYQlv------GvNWL~Llyk~~l~gILADEMGLGKTiQ-vIaFlayLkq~g~~gpHLVVvPsSTleNW-lrEf~kwC  471 (941)
T KOG0389|consen  400 LKDYQLV------GVNWLLLLYKKKLNGILADEMGLGKTIQ-VIAFLAYLKQIGNPGPHLVVVPSSTLENW-LREFAKWC  471 (941)
T ss_pred             ccchhhh------hHHHHHHHHHccccceehhhccCcchhH-HHHHHHHHHHcCCCCCcEEEecchhHHHH-HHHHHHhC
Confidence            5788888      555443    356789999999999955 44555555444444568999999987554 44566666


Q ss_pred             ccCCCceEEEEEcCcccHHhHHHH-hcC--CCcEEEEcHHHHHHHHH-CCCCcCCCeeEEEecchhHHHh
Q psy1548         205 KYMSNIKVGVFFGGLPIQKDEEYL-KTH--NPQIVVGTPGRILALVR-NKKLNLSLLKHFILDECDKMLE  270 (448)
Q Consensus       205 ~~~~~~~v~~~~g~~~~~~~~~~l-~~~--~~~IlV~Tp~~l~~~l~-~~~~~~~~i~~lViDEah~l~~  270 (448)
                         |.+++..++|......+.+.. ..+  ..+|+++|......--. +.-+.-.++.++|+||+|.+-+
T Consensus       472 ---Psl~Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmLKN  538 (941)
T KOG0389|consen  472 ---PSLKVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLKN  538 (941)
T ss_pred             ---CceEEEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHHHHHHHhccccEEEecchhhhhc
Confidence               788999999998655444433 222  58999999865531100 0112235567899999996644

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.04  E-value=1.9e-07  Score=99.54  Aligned_cols=99  Identities=14%  Similarity=0.191  Sum_probs=85.1

Q ss_pred             HHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC--------------
Q psy1548         341 KNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH--------------  404 (448)
Q Consensus       341 k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~--------------  404 (448)
                      +...+...+...  .+.++||||+|.+.|+.+++.|.+.|+++..+||++++.+|..+++.|+.|+              
T Consensus       431 q~~~L~~~L~~~~~~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~~L~rGf  510 (652)
T PRK05298        431 QVDDLLSEIRKRVAKGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGL  510 (652)
T ss_pred             cHHHHHHHHHHHHhCCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeCHHhCCc
Confidence            344555555432  4678999999999999999999999999999999999999999999999988              


Q ss_pred             ------------------------------------CceEEEEecC--------hhhHHHHHHHHHHhcCCCCCCCccc
Q psy1548         405 ------------------------------------KGLAITFASD--------ENDAKILNNVQDRFDVSISELPDEI  439 (448)
Q Consensus       405 ------------------------------------~g~~I~~~t~--------~~d~~~l~~i~~~~~~~~~~~p~~~  439 (448)
                                                          .|.+|++++.        ..+...+++||..++.++..+|..+
T Consensus       511 dlp~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~~~G~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~  589 (652)
T PRK05298        511 DIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQKAIDETERRREIQIAYNEEHGITPKTI  589 (652)
T ss_pred             cccCCcEEEEeCCcccccCCCHHHHHHHhccccCCCCCEEEEEecCCCHHHHHHHHHHHHHHHHHHHhhhccCCCChhH
Confidence                                                7888999984        2478889999999999999999885

>KOG0390|consensus

Probab=99.03  E-value=2e-08  Score=105.58  Aligned_cols=160  Identities=14%  Similarity=0.092  Sum_probs=95.8

Q ss_pred             CCchhhhhhhccc------cccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCC-----eEEEEeeccHHHHHH
Q psy1548         127 EDSDTYLHRVARA------GRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSN-----VYVLVMCHTRELAFQ  195 (448)
Q Consensus       127 ~~~~~yQ~~~~~~------~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~-----~~~lil~Pt~~L~~q  195 (448)
                      ..++++|+++.+.      |...|  ....-+|++-..|+|||+..+ +.+..+......     .+.|||+|.. |+..
T Consensus       237 ~~LrPHQ~EG~~FL~knl~g~~~~--~~~~GCImAd~~GlGKTlq~I-sflwtlLrq~P~~~~~~~k~lVV~P~s-Lv~n  312 (776)
T KOG0390|consen  237 KILRPHQREGFEFLYKNLAGLIRP--KNSGGCIMADEPGLGKTLQCI-SFIWTLLRQFPQAKPLINKPLVVAPSS-LVNN  312 (776)
T ss_pred             hhcCchHHHHHHHHHhhhhccccc--CCCCceEeeCCCCcchHHHHH-HHHHHHHHhCcCccccccccEEEccHH-HHHH
Confidence            3357779996552      22222  122346777788999998754 444444333333     5899999986 7888


Q ss_pred             HHHHHHHhhccCCCceEEEEEcCccc--HHhHHHH----hcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHH
Q psy1548         196 ISKEYERFSKYMSNIKVGVFFGGLPI--QKDEEYL----KTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKML  269 (448)
Q Consensus       196 ~~~~~~~~~~~~~~~~v~~~~g~~~~--~~~~~~l----~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~  269 (448)
                      |.+++.+|.... .+....++|....  ......+    ......|++-+.+.+.+....  +....++++|+||.|++-
T Consensus       313 WkkEF~KWl~~~-~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~~--il~~~~glLVcDEGHrlk  389 (776)
T KOG0390|consen  313 WKKEFGKWLGNH-RINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYCRK--ILLIRPGLLVCDEGHRLK  389 (776)
T ss_pred             HHHHHHHhcccc-ccceeeeecccchhhhhhHHHHHhhhhheeEEEEeccHHHHHHHHHH--HhcCCCCeEEECCCCCcc
Confidence            999999998753 5677777777652  1111111    111245788888888655442  335677899999999764


Q ss_pred             hhhhhHHHHHHHHHhCCCCCeEEEEecc
Q psy1548         270 EQLEMRRDVQEIFRSSPHTKQVMMFSAT  297 (448)
Q Consensus       270 ~~~~~~~~~~~i~~~l~~~~q~i~~SAT  297 (448)
                      ..   ...+...+..+.-. +-|++|.|
T Consensus       390 N~---~s~~~kaL~~l~t~-rRVLLSGT  413 (776)
T KOG0390|consen  390 NS---DSLTLKALSSLKTP-RRVLLTGT  413 (776)
T ss_pred             ch---hhHHHHHHHhcCCC-ceEEeeCC
Confidence            42   12222233333222 34566777

>KOG0924|consensus

Probab=99.02  E-value=9.9e-09  Score=103.89  Aligned_cols=239  Identities=13%  Similarity=0.129  Sum_probs=134.3

Q ss_pred             eCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH-hhccCCCceEEEEEcCcccHHhHH
Q psy1548         148 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER-FSKYMSNIKVGVFFGGLPIQKDEE  226 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~-~~~~~~~~~v~~~~g~~~~~~~~~  226 (448)
                      ...-++|.+.||||||....--++.  ..-.....+-+.-|.|.-|..+.+.+.. +...+ +-.|+....-.+..    
T Consensus       370 ~n~vvvivgETGSGKTTQl~QyL~e--dGY~~~GmIGcTQPRRvAAiSVAkrVa~EM~~~l-G~~VGYsIRFEdvT----  442 (1042)
T KOG0924|consen  370 ENQVVVIVGETGSGKTTQLAQYLYE--DGYADNGMIGCTQPRRVAAISVAKRVAEEMGVTL-GDTVGYSIRFEDVT----  442 (1042)
T ss_pred             hCcEEEEEecCCCCchhhhHHHHHh--cccccCCeeeecCchHHHHHHHHHHHHHHhCCcc-ccccceEEEeeecC----
Confidence            3456889999999999763211111  1111222444555888877776555443 22222 33333222111111    


Q ss_pred             HHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHH
Q psy1548         227 YLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVC  306 (448)
Q Consensus       227 ~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~  306 (448)
                         .....|-+.|-+.|++-.... -.+.+...+|+||||.-.-+.+..-.+.+..-.-..+.++|.+||||..  +++.
T Consensus       443 ---~~~T~IkymTDGiLLrEsL~d-~~L~kYSviImDEAHERslNtDilfGllk~~larRrdlKliVtSATm~a--~kf~  516 (1042)
T KOG0924|consen  443 ---SEDTKIKYMTDGILLRESLKD-RDLDKYSVIIMDEAHERSLNTDILFGLLKKVLARRRDLKLIVTSATMDA--QKFS  516 (1042)
T ss_pred             ---CCceeEEEeccchHHHHHhhh-hhhhheeEEEechhhhcccchHHHHHHHHHHHHhhccceEEEeeccccH--HHHH
Confidence               112568899999987643322 2367788999999996432212111111111122346789999999864  4777


Q ss_pred             HHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHH-HHHHHHhhC---CCCeEEEEECccHHHHHHHHHHHhC-----
Q psy1548         307 KKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNK-KLFELLDVL---EFNQVVIFVKSVTRCIALSTLLSEQ-----  377 (448)
Q Consensus       307 ~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~-~L~~ll~~~---~~~~~IIF~~s~~~a~~l~~~L~~~-----  377 (448)
                      ..|..-|....-...     ..+.-.|...+.++-.+ ++-..+.-+   ..|-++||....+..+..+..++..     
T Consensus       517 nfFgn~p~f~IpGRT-----yPV~~~~~k~p~eDYVeaavkq~v~Ihl~~~~GdilIfmtGqediE~t~~~i~~~l~ql~  591 (1042)
T KOG0924|consen  517 NFFGNCPQFTIPGRT-----YPVEIMYTKTPVEDYVEAAVKQAVQIHLSGPPGDILIFMTGQEDIECTCDIIKEKLEQLD  591 (1042)
T ss_pred             HHhCCCceeeecCCc-----cceEEEeccCchHHHHHHHHhhheEeeccCCCCCEEEecCCCcchhHHHHHHHHHHHhhh
Confidence            766656654332222     22333444444433222 233333222   4568999999887766666555431     


Q ss_pred             -----CCcEEEEeCCCCHHHHHHHHHHHhcCC
Q psy1548         378 -----NFPAVSIHRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       378 -----g~~~~~lh~~~~~~eR~~~l~~F~~g~  404 (448)
                           ++.+..+++.|+.+-+.++++.--.|.
T Consensus       592 ~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~v  623 (1042)
T KOG0924|consen  592 SAPTTDLAVLPIYSQLPADLQAKIFQKAEGGV  623 (1042)
T ss_pred             cCCCCceEEEeehhhCchhhhhhhcccCCCCc
Confidence                 677999999999998888766544443

>KOG0384|consensus

Probab=99.01  E-value=7.3e-10  Score=118.44  Aligned_cols=270  Identities=18%  Similarity=0.243  Sum_probs=164.1

Q ss_pred             CCchhhhhhhccccccceeee----eCcceeeeccCCChhHHHHHHHHHHhhhccC-CCeEEEEeeccHHHHHHHHHHHH
Q psy1548         127 EDSDTYLHRVARAGRFGTKAV----LGMDILCQAKSGMGKTAVFVLATLQQLETTD-SNVYVLVMCHTRELAFQISKEYE  201 (448)
Q Consensus       127 ~~~~~yQ~~~~~~~~~~~~~~----~g~~vli~apTGsGKT~~~~l~~l~~l~~~~-~~~~~lil~Pt~~L~~q~~~~~~  201 (448)
                      ..+++||.+      -+..++    .+.|+|+.-..|.|||..- +..|..+.... -.+-.|||+|...+. .+.+.+.
T Consensus       369 ~~LRdyQLe------GlNWl~~~W~~~~n~ILADEmgLgktvqt-i~fl~~l~~~~~~~gpflvvvplst~~-~W~~ef~  440 (1373)
T KOG0384|consen  369 NELRDYQLE------GLNWLLYSWYKRNNCILADEMGLGKTVQT-ITFLSYLFHSLQIHGPFLVVVPLSTIT-AWEREFE  440 (1373)
T ss_pred             chhhhhhcc------cchhHHHHHHhcccceehhhcCCCcchHH-HHHHHHHHHhhhccCCeEEEeehhhhH-HHHHHHH
Confidence            457999999      776655    4789999999999999652 33333332211 122478888987665 4566788


Q ss_pred             HhhccCCCceEEEEEcCcccHHhHHHHh---cC-----CCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhh
Q psy1548         202 RFSKYMSNIKVGVFFGGLPIQKDEEYLK---TH-----NPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLE  273 (448)
Q Consensus       202 ~~~~~~~~~~v~~~~g~~~~~~~~~~l~---~~-----~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~  273 (448)
                      .|.    +.++.+++|.......+....   ..     .++++++|.+.++.--.  .+.--...++++||||++-..  
T Consensus       441 ~w~----~mn~i~y~g~~~sr~~i~~ye~~~~~~~~~lkf~~lltTye~~LkDk~--~L~~i~w~~~~vDeahrLkN~--  512 (1373)
T KOG0384|consen  441 TWT----DMNVIVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVLKDKA--ELSKIPWRYLLVDEAHRLKND--  512 (1373)
T ss_pred             HHh----hhceeeeecchhHHHHHHHHHheecCCccccccceeehhhHHHhccHh--hhccCCcceeeecHHhhcCch--
Confidence            887    678888888876444333221   11     37899999988754221  111223457999999998643  


Q ss_pred             hHHHHHHHHHhCCCCCeEEEEecc-CCccHHHHHH--HhcCCCeE-----------------------------------
Q psy1548         274 MRRDVQEIFRSSPHTKQVMMFSAT-LSKEIRPVCK--KFMHDPME-----------------------------------  315 (448)
Q Consensus       274 ~~~~~~~i~~~l~~~~q~i~~SAT-~~~~~~~~~~--~~l~~~~~-----------------------------------  315 (448)
                       ...+-..+..+.-+.++++ |.| +-+.++++..  .|+ .|..                                   
T Consensus       513 -~~~l~~~l~~f~~~~rlli-tgTPlQNsikEL~sLl~Fl-~P~kf~~~~~f~~~~~~~~e~~~~~L~~~L~P~~lRr~k  589 (1373)
T KOG0384|consen  513 -ESKLYESLNQFKMNHRLLI-TGTPLQNSLKELWSLLHFL-MPGKFDSWDEFLEEFDEETEEQVRKLQQILKPFLLRRLK  589 (1373)
T ss_pred             -HHHHHHHHHHhcccceeee-cCCCccccHHHHHHHhccc-CCCCCCcHHHHHHhhcchhHHHHHHHHHHhhHHHHHHHH
Confidence             2223333444444444444 455 3344433321  111 0100                                   


Q ss_pred             --------------EEEcCc------------------------cccccc--------ceeEEEEEcCcchH--------
Q psy1548         316 --------------VYVDDE------------------------AKLTLH--------GLQQHYVKLKENEK--------  341 (448)
Q Consensus       316 --------------i~~~~~------------------------~~~~~~--------~i~~~~~~~~~~~k--------  341 (448)
                                    +.+.-.                        .....-        .-.|-|+.-..+++        
T Consensus       590 kdvekslp~k~E~IlrVels~lQk~yYk~ILtkN~~~LtKG~~g~~~~lLNimmELkKccNHpyLi~gaee~~~~~~~~~  669 (1373)
T KOG0384|consen  590 KDVEKSLPPKEETILRVELSDLQKQYYKAILTKNFSALTKGAKGSTPSLLNIMMELKKCCNHPYLIKGAEEKILGDFRDK  669 (1373)
T ss_pred             hhhccCCCCCcceEEEeehhHHHHHHHHHHHHhhHHHHhccCCCCCchHHHHHHHHHHhcCCccccCcHHHHHHHhhhhc
Confidence                          000000                        000000        00222333222221        


Q ss_pred             --HHHHHHHHhh-------------C--CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC
Q psy1548         342 --NKKLFELLDV-------------L--EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       342 --~~~L~~ll~~-------------~--~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~  404 (448)
                        ...|..+|..             +  .++++|||...+.-.+-|+++|...+++.--+.|.+.-+-|..++..|....
T Consensus       670 ~~d~~L~~lI~sSGKlVLLDKLL~rLk~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~  749 (1373)
T KOG0384|consen  670 MRDEALQALIQSSGKLVLLDKLLPRLKEGGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPD  749 (1373)
T ss_pred             chHHHHHHHHHhcCcEEeHHHHHHHHhcCCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCC
Confidence              1234343322             1  4579999999999999999999999999999999999999999999998876


Q ss_pred             ------------CceEEEEecCh
Q psy1548         405 ------------KGLAITFASDE  415 (448)
Q Consensus       405 ------------~g~~I~~~t~~  415 (448)
                                  .|+||++.|.+
T Consensus       750 SddFvFLLSTRAGGLGINLatAD  772 (1373)
T KOG0384|consen  750 SDDFVFLLSTRAGGLGINLATAD  772 (1373)
T ss_pred             CCceEEEEecccCcccccccccc
Confidence                        78888887764

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.00  E-value=2.5e-09  Score=102.74  Aligned_cols=77  Identities=14%  Similarity=0.133  Sum_probs=59.1

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCC---CeEEEEeeccHHHHHHHHHHHH
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDS---NVYVLVMCHTRELAFQISKEYE  201 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~---~~~~lil~Pt~~L~~q~~~~~~  201 (448)
                      +|...++.|.+.+++  ....+..|+++++.+|||+|||++|++|++..+...+.   +.+++|.++|..+..|....++
T Consensus         5 FPy~~r~~Q~~~m~~--v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~   82 (289)
T smart00488        5 FPYEPYPIQYEFMEE--LKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELR   82 (289)
T ss_pred             CCCCCCHHHHHHHHH--HHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHH
Confidence            344445669996654  44555678999999999999999999999876654332   2489999999999998877777


Q ss_pred             Hh
Q psy1548         202 RF  203 (448)
Q Consensus       202 ~~  203 (448)
                      ++
T Consensus        83 ~~   84 (289)
T smart00488       83 KL   84 (289)
T ss_pred             hc
Confidence            65

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.00  E-value=2.5e-09  Score=102.74  Aligned_cols=77  Identities=14%  Similarity=0.133  Sum_probs=59.1

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCC---CeEEEEeeccHHHHHHHHHHHH
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDS---NVYVLVMCHTRELAFQISKEYE  201 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~---~~~~lil~Pt~~L~~q~~~~~~  201 (448)
                      +|...++.|.+.+++  ....+..|+++++.+|||+|||++|++|++..+...+.   +.+++|.++|..+..|....++
T Consensus         5 FPy~~r~~Q~~~m~~--v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~   82 (289)
T smart00489        5 FPYEPYPIQYEFMEE--LKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELR   82 (289)
T ss_pred             CCCCCCHHHHHHHHH--HHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHH
Confidence            344445669996654  44555678999999999999999999999876654332   2489999999999998877777


Q ss_pred             Hh
Q psy1548         202 RF  203 (448)
Q Consensus       202 ~~  203 (448)
                      ++
T Consensus        83 ~~   84 (289)
T smart00489       83 KL   84 (289)
T ss_pred             hc
Confidence            65

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.99  E-value=7.3e-09  Score=109.26  Aligned_cols=127  Identities=20%  Similarity=0.214  Sum_probs=91.3

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .|..+   |..      ..-.+..|+  |....||-|||+++.+|++-....   |..+-|++..--||..=.+++..+.
T Consensus        78 r~ydV---Qli------GglvLh~G~--IAEMkTGEGKTLvAtLpayLnAL~---GkgVhVVTvNdYLA~RDae~mg~vy  143 (925)
T PRK12903         78 RPYDV---QII------GGIILDLGS--VAEMKTGEGKTITSIAPVYLNALT---GKGVIVSTVNEYLAERDAEEMGKVF  143 (925)
T ss_pred             CcCch---HHH------HHHHHhcCC--eeeecCCCCccHHHHHHHHHHHhc---CCceEEEecchhhhhhhHHHHHHHH
Confidence            67788   888      333344553  799999999999999998654333   2347777888889887777888888


Q ss_pred             ccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHH-HHHHHCCC------CcCCCeeEEEecchhHHH
Q psy1548         205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRI-LALVRNKK------LNLSLLKHFILDECDKML  269 (448)
Q Consensus       205 ~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l-~~~l~~~~------~~~~~i~~lViDEah~l~  269 (448)
                      ..+ +++|++...+.+.......+   .++|++||..-+ .++|+.+-      .-...+.+.|+||+|.++
T Consensus       144 ~fL-GLsvG~i~~~~~~~~rr~aY---~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEVDSIL  211 (925)
T PRK12903        144 NFL-GLSVGINKANMDPNLKREAY---ACDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEVDSIL  211 (925)
T ss_pred             HHh-CCceeeeCCCCChHHHHHhc---cCCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccchhee
Confidence            888 99999998876655444433   379999998876 34444321      123567789999999764

>KOG0926|consensus

Probab=98.99  E-value=4.1e-09  Score=108.33  Aligned_cols=271  Identities=17%  Similarity=0.209  Sum_probs=150.1

Q ss_pred             eEeeccCCCCchhhhhhhc------cccccceeeeeCcceeeeccCCChhHHHHHHHH-HHhhhc----cCCCeEEEEee
Q psy1548         119 IVFNYDMPEDSDTYLHRVA------RAGRFGTKAVLGMDILCQAKSGMGKTAVFVLAT-LQQLET----TDSNVYVLVMC  187 (448)
Q Consensus       119 ~v~~~~~p~~~~~yQ~~~~------~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~-l~~l~~----~~~~~~~lil~  187 (448)
                      +++....|..+   |..--      +-.+.+.++...--+||+|.||||||..  +|- |.....    ...+.-+=|.-
T Consensus       238 ~yV~V~R~~EI---Q~sR~~LPI~aeEq~IMEaIn~n~vvIIcGeTGsGKTTQ--vPQFLYEAGf~s~~~~~~gmIGITq  312 (1172)
T KOG0926|consen  238 FYVIVSRPAEI---QESRLDLPIVAEEQRIMEAINENPVVIICGETGSGKTTQ--VPQFLYEAGFASEQSSSPGMIGITQ  312 (1172)
T ss_pred             EEEEecCcHHH---HHHHhcCchhHHHHHHHHHhhcCCeEEEecCCCCCcccc--chHHHHHcccCCccCCCCCeeeecC
Confidence            45667788888   76510      0112444455556689999999999975  342 221111    11233566677


Q ss_pred             ccHHHHHHHHHHHH-HhhccC-CCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecch
Q psy1548         188 HTRELAFQISKEYE-RFSKYM-SNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDEC  265 (448)
Q Consensus       188 Pt~~L~~q~~~~~~-~~~~~~-~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEa  265 (448)
                      |.|--|..+.+... .++. + ..+...+-+.++-..         ...|.++|-|.|+.-+.++ +.+.....||+|||
T Consensus       313 PRRVAaiamAkRVa~EL~~-~~~eVsYqIRfd~ti~e---------~T~IkFMTDGVLLrEi~~D-flL~kYSvIIlDEA  381 (1172)
T KOG0926|consen  313 PRRVAAIAMAKRVAFELGV-LGSEVSYQIRFDGTIGE---------DTSIKFMTDGVLLREIEND-FLLTKYSVIILDEA  381 (1172)
T ss_pred             chHHHHHHHHHHHHHHhcc-CccceeEEEEeccccCC---------CceeEEecchHHHHHHHHh-HhhhhceeEEechh
Confidence            88876665554433 3333 3 123333334443211         2579999999998877654 34788889999999


Q ss_pred             hHHHhh----hhhHHHHHHHHHhCCC------CCeEEEEeccCCccHHHHH--HHhcC-CCeEEEEcCcccccccceeEE
Q psy1548         266 DKMLEQ----LEMRRDVQEIFRSSPH------TKQVMMFSATLSKEIRPVC--KKFMH-DPMEVYVDDEAKLTLHGLQQH  332 (448)
Q Consensus       266 h~l~~~----~~~~~~~~~i~~~l~~------~~q~i~~SAT~~~~~~~~~--~~~l~-~~~~i~~~~~~~~~~~~i~~~  332 (448)
                      |.-.-.    .|+...+-.+-..+.+      ..++|+||||+.-.  ++.  +.++. -|-.+.++.. + -+..| |+
T Consensus       382 HERSvnTDILiGmLSRiV~LR~k~~ke~~~~kpLKLIIMSATLRVs--DFtenk~LFpi~pPlikVdAR-Q-fPVsI-HF  456 (1172)
T KOG0926|consen  382 HERSVNTDILIGMLSRIVPLRQKYYKEQCQIKPLKLIIMSATLRVS--DFTENKRLFPIPPPLIKVDAR-Q-FPVSI-HF  456 (1172)
T ss_pred             hhccchHHHHHHHHHHHHHHHHHHhhhhcccCceeEEEEeeeEEec--ccccCceecCCCCceeeeecc-c-CceEE-Ee
Confidence            964221    1333333333333322      44789999997422  332  11222 2334444433 1 11222 22


Q ss_pred             EEEcCcch---HHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEE
Q psy1548         333 YVKLKENE---KNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAI  409 (448)
Q Consensus       333 ~~~~~~~~---k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I  409 (448)
                      --..+.+.   -+...+.+=+.++.|-+|||+-...++..|++.|++. ++.  .|++..-+.--+..+++++....+++
T Consensus       457 ~krT~~DYi~eAfrKtc~IH~kLP~G~ILVFvTGQqEV~qL~~kLRK~-~p~--~f~~~k~~k~~k~~~e~k~~~s~~~~  533 (1172)
T KOG0926|consen  457 NKRTPDDYIAEAFRKTCKIHKKLPPGGILVFVTGQQEVDQLCEKLRKR-FPE--SFGGVKMKKNVKAFKELKENPSDIGD  533 (1172)
T ss_pred             ccCCCchHHHHHHHHHHHHhhcCCCCcEEEEEeChHHHHHHHHHHHhh-Ccc--ccccchhhhhhhhccccccchhhhcc
Confidence            12222222   2333344445568889999999999999999999885 222  45655544445555666654433444


Q ss_pred             EEec
Q psy1548         410 TFAS  413 (448)
Q Consensus       410 ~~~t  413 (448)
                      +--+
T Consensus       534 ~~k~  537 (1172)
T KOG0926|consen  534 SNKT  537 (1172)
T ss_pred             Cccc
Confidence            4333

>KOG0923|consensus

Probab=98.98  E-value=1.3e-08  Score=102.93  Aligned_cols=246  Identities=14%  Similarity=0.134  Sum_probs=147.0

Q ss_pred             cceeeeeCcceeeeccCCChhHHHHHHHHH-HhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcc
Q psy1548         142 FGTKAVLGMDILCQAKSGMGKTAVFVLATL-QQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLP  220 (448)
Q Consensus       142 ~~~~~~~g~~vli~apTGsGKT~~~~l~~l-~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~  220 (448)
                      .+.++....-++|.|.||||||..  +|-. ......+++.++-+.-|.|--|..+...+..   .+ +++.+--+|-.-
T Consensus       273 ll~av~e~QVLiI~GeTGSGKTTQ--iPQyL~EaGytk~gk~IgcTQPRRVAAmSVAaRVA~---EM-gvkLG~eVGYsI  346 (902)
T KOG0923|consen  273 LLKAVKEHQVLIIVGETGSGKTTQ--IPQYLYEAGYTKGGKKIGCTQPRRVAAMSVAARVAE---EM-GVKLGHEVGYSI  346 (902)
T ss_pred             HHHHHHhCcEEEEEcCCCCCcccc--ccHHHHhcccccCCceEeecCcchHHHHHHHHHHHH---Hh-CcccccccceEE
Confidence            444455566788999999999975  5532 2212223444566777998877776554432   22 333222222110


Q ss_pred             cHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCc
Q psy1548         221 IQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSK  300 (448)
Q Consensus       221 ~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~  300 (448)
                      .-++.   -....-|-++|-|+|++-+.. ..++.+..+++|||||.-.-..+..-.+..-+....+.-++++.|||+..
T Consensus       347 RFEdc---TSekTvlKYMTDGmLlREfL~-epdLasYSViiiDEAHERTL~TDILfgLvKDIar~RpdLKllIsSAT~DA  422 (902)
T KOG0923|consen  347 RFEDC---TSEKTVLKYMTDGMLLREFLS-EPDLASYSVIIVDEAHERTLHTDILFGLVKDIARFRPDLKLLISSATMDA  422 (902)
T ss_pred             Eeccc---cCcceeeeeecchhHHHHHhc-cccccceeEEEeehhhhhhhhhhHHHHHHHHHHhhCCcceEEeeccccCH
Confidence            00000   001245889999999875543 33478899999999995422112211122222334577889999999864


Q ss_pred             cHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHH-HHHHHhhC---CCCeEEEEECccHHHHHHHHHHHh
Q psy1548         301 EIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKK-LFELLDVL---EFNQVVIFVKSVTRCIALSTLLSE  376 (448)
Q Consensus       301 ~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~-L~~ll~~~---~~~~~IIF~~s~~~a~~l~~~L~~  376 (448)
                      +  ++...|-.-|+......     ...+.-+|...++.+=.++ +..++.-+   +.+-+|||....++.+...+.|.+
T Consensus       423 e--kFS~fFDdapIF~iPGR-----RyPVdi~Yt~~PEAdYldAai~tVlqIH~tqp~GDILVFltGQeEIEt~~e~l~~  495 (902)
T KOG0923|consen  423 E--KFSAFFDDAPIFRIPGR-----RYPVDIFYTKAPEADYLDAAIVTVLQIHLTQPLGDILVFLTGQEEIETVKENLKE  495 (902)
T ss_pred             H--HHHHhccCCcEEeccCc-----ccceeeecccCCchhHHHHHHhhheeeEeccCCccEEEEeccHHHHHHHHHHHHH
Confidence            4  55554444444333222     2345556666666554443 33444332   567899999999998888887765


Q ss_pred             C---------CCcEEEEeCCCCHHHHHHHHHHHhcCC
Q psy1548         377 Q---------NFPAVSIHRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       377 ~---------g~~~~~lh~~~~~~eR~~~l~~F~~g~  404 (448)
                      .         .+-+..+|++++.+.+.++++--=.|.
T Consensus       496 ~~~~LGski~eliv~PiYaNLPselQakIFePtP~ga  532 (902)
T KOG0923|consen  496 RCRRLGSKIRELIVLPIYANLPSELQAKIFEPTPPGA  532 (902)
T ss_pred             HHHHhccccceEEEeeccccCChHHHHhhcCCCCCCc
Confidence            3         234789999999999999887655543

>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=98.96  E-value=2.4e-09  Score=103.50  Aligned_cols=143  Identities=15%  Similarity=0.157  Sum_probs=81.3

Q ss_pred             eCcceeeeccCCChhHHHHHHHHHHhhhccCC---CeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHh
Q psy1548         148 LGMDILCQAKSGMGKTAVFVLATLQQLETTDS---NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD  224 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~---~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~  224 (448)
                      ..+.+++...+|+|||...+..+. .+.....   ...+|||||. .+..|+..++.++.... ..++..+.|.......
T Consensus        24 ~~~g~lL~de~GlGKT~~~i~~~~-~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~~~~~~-~~~v~~~~~~~~~~~~  100 (299)
T PF00176_consen   24 PPRGGLLADEMGLGKTITAIALIS-YLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEKWFDPD-SLRVIIYDGDSERRRL  100 (299)
T ss_dssp             TT-EEEE---TTSSHHHHHHHHHH-HHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHHHSGT--TS-EEEESSSCHHHHT
T ss_pred             CCCCEEEEECCCCCchhhhhhhhh-hhhhccccccccceeEeecc-chhhhhhhhhccccccc-cccccccccccccccc
Confidence            346889999999999987654443 3322221   1259999999 77889999999998643 5666666665511111


Q ss_pred             HHHHhcCCCcEEEEcHHHHHHHHHC---CCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccC
Q psy1548         225 EEYLKTHNPQIVVGTPGRILALVRN---KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATL  298 (448)
Q Consensus       225 ~~~l~~~~~~IlV~Tp~~l~~~l~~---~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~  298 (448)
                      ... .....+++|+|.+.+......   ..+..-+.+++|+||+|.+-+.   .......+..+. ....+++|||+
T Consensus       101 ~~~-~~~~~~vvi~ty~~~~~~~~~~~~~~l~~~~~~~vIvDEaH~~k~~---~s~~~~~l~~l~-~~~~~lLSgTP  172 (299)
T PF00176_consen  101 SKN-QLPKYDVVITTYETLRKARKKKDKEDLKQIKWDRVIVDEAHRLKNK---DSKRYKALRKLR-ARYRWLLSGTP  172 (299)
T ss_dssp             TSS-SCCCSSEEEEEHHHHH--TSTHTTHHHHTSEEEEEEETTGGGGTTT---TSHHHHHHHCCC-ECEEEEE-SS-
T ss_pred             ccc-ccccceeeeccccccccccccccccccccccceeEEEecccccccc---cccccccccccc-cceEEeecccc
Confidence            111 112478999999998811000   1111234789999999988432   222333333354 56678899995

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.

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

Probab=98.94  E-value=4.8e-10  Score=121.62  Aligned_cols=135  Identities=21%  Similarity=0.207  Sum_probs=96.4

Q ss_pred             cccccCCCcee--eeecCceeEEeecCCCcc-ccccccCC--CccccccccccccccchhhhhhhhccCceeeeccCCcc
Q psy1548           9 EKLSCGSGNVF--LFFRAFIRFSSSFPHSKM-ADNDDLLD--YEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFR   83 (448)
Q Consensus         9 ~~~~~~~~~~~--~~~r~~~~~~~~~~~~~~-~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (448)
                      ..|.+....+|  +|.|+|+.|.+.....+. .+...+..  ..++..+.|...+...+.........+.....+|.+..
T Consensus       636 ~~L~l~~~~vfr~Sf~RpNL~y~Vv~k~kk~le~L~~~I~~~~~~esgIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs  715 (1195)
T PLN03137        636 QALGLVNCVVFRQSFNRPNLWYSVVPKTKKCLEDIDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMD  715 (1195)
T ss_pred             HHcCCCCcEEeecccCccceEEEEeccchhHHHHHHHHHHhcccCCCceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCC
Confidence            35666677777  999999999887654331 11111211  12456678887777666666666666766777776654


Q ss_pred             cCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548          84 DFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      .-....-+..+.....+|+|||+++|||||+++|++|+||..|..++.|.|++|||||..
T Consensus       716 ~eeR~~vqe~F~~Gei~VLVATdAFGMGIDkPDVR~VIHydlPkSiEsYyQriGRAGRDG  775 (1195)
T PLN03137        716 PAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDG  775 (1195)
T ss_pred             HHHHHHHHHHHhcCCCcEEEEechhhcCCCccCCcEEEEcCCCCCHHHHHhhhcccCCCC
Confidence            433333333444455699999999999999999999999999999999999999999943

>KOG0953|consensus

Probab=98.89  E-value=5.8e-09  Score=103.49  Aligned_cols=223  Identities=17%  Similarity=0.141  Sum_probs=147.4

Q ss_pred             ceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhc
Q psy1548         151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKT  230 (448)
Q Consensus       151 ~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~  230 (448)
                      =++-+|||.||||.-    +|+++...+   ..++--|.|-||.++++.+...     ++.|-+++|.........   .
T Consensus       193 Ii~H~GPTNSGKTy~----ALqrl~~ak---sGvycGPLrLLA~EV~~r~na~-----gipCdL~TGeE~~~~~~~---~  257 (700)
T KOG0953|consen  193 IIMHVGPTNSGKTYR----ALQRLKSAK---SGVYCGPLRLLAHEVYDRLNAL-----GIPCDLLTGEERRFVLDN---G  257 (700)
T ss_pred             EEEEeCCCCCchhHH----HHHHHhhhc---cceecchHHHHHHHHHHHhhhc-----CCCccccccceeeecCCC---C
Confidence            355679999999965    567765544   4678899999999999988876     677778887643222211   1


Q ss_pred             CCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhc
Q psy1548         231 HNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFM  310 (448)
Q Consensus       231 ~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l  310 (448)
                      +.++.+-||-++..-        -..+++.||||+++|-+...-+...+.++.....+..+++=     +.+.++.++.+
T Consensus       258 ~~a~hvScTVEM~sv--------~~~yeVAViDEIQmm~Dp~RGwAWTrALLGl~AdEiHLCGe-----psvldlV~~i~  324 (700)
T KOG0953|consen  258 NPAQHVSCTVEMVSV--------NTPYEVAVIDEIQMMRDPSRGWAWTRALLGLAADEIHLCGE-----PSVLDLVRKIL  324 (700)
T ss_pred             CcccceEEEEEEeec--------CCceEEEEehhHHhhcCcccchHHHHHHHhhhhhhhhccCC-----chHHHHHHHHH
Confidence            235677777664321        23467899999999877622233444555554445444442     44556666655


Q ss_pred             C---CCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCc-EEEEeC
Q psy1548         311 H---DPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFP-AVSIHR  386 (448)
Q Consensus       311 ~---~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~-~~~lh~  386 (448)
                      .   +.+.+              +.|....+-.-.+.+..-++....|-+|| |-|++..-.+...+.+.|.. ++.++|
T Consensus       325 k~TGd~vev--------------~~YeRl~pL~v~~~~~~sl~nlk~GDCvV-~FSkk~I~~~k~kIE~~g~~k~aVIYG  389 (700)
T KOG0953|consen  325 KMTGDDVEV--------------REYERLSPLVVEETALGSLSNLKPGDCVV-AFSKKDIFTVKKKIEKAGNHKCAVIYG  389 (700)
T ss_pred             hhcCCeeEE--------------EeecccCcceehhhhhhhhccCCCCCeEE-EeehhhHHHHHHHHHHhcCcceEEEec
Confidence            3   22221              12222222222234555566666665554 55788889999999988766 999999


Q ss_pred             CCCHHHHHHHHHHHhcCCCceEEEEecChh
Q psy1548         387 GMTQEERLKKYQEFKDFHKGLAITFASDEN  416 (448)
Q Consensus       387 ~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~  416 (448)
                      +++++.|...-..|.+......|.++|+.-
T Consensus       390 sLPPeTr~aQA~~FNd~~~e~dvlVAsDAI  419 (700)
T KOG0953|consen  390 SLPPETRLAQAALFNDPSNECDVLVASDAI  419 (700)
T ss_pred             CCCCchhHHHHHHhCCCCCccceEEeeccc
Confidence            999999999999999977667888887753

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=98.85  E-value=1.6e-08  Score=111.80  Aligned_cols=79  Identities=15%  Similarity=0.212  Sum_probs=54.5

Q ss_pred             hhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHH----HHHhhccCC
Q psy1548         133 LHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKE----YERFSKYMS  208 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~----~~~~~~~~~  208 (448)
                      |.+.+.+  ....+..++.+++.||||+|||++|++|++.....  .+.+++|-++|+.|-+|+...    ++++...  
T Consensus       262 Q~~m~~~--v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~--~~~~vvIsT~T~~LQ~Ql~~kDiP~L~~~~~~--  335 (928)
T PRK08074        262 QQEMMKE--VYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKK--KEEPVVISTYTIQLQQQLLEKDIPLLQKIFPF--  335 (928)
T ss_pred             HHHHHHH--HHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhc--cCCeEEEEcCCHHHHHHHHHhhHHHHHHHcCC--
Confidence            6663331  22344457889999999999999999999875432  245899999999999997652    3433321  


Q ss_pred             CceEEEEEc
Q psy1548         209 NIKVGVFFG  217 (448)
Q Consensus       209 ~~~v~~~~g  217 (448)
                      ++++.++-|
T Consensus       336 ~~~~~~lKG  344 (928)
T PRK08074        336 PVEAALLKG  344 (928)
T ss_pred             CceEEEEEc
Confidence            455555554

>KOG1002|consensus

Probab=98.84  E-value=1e-07  Score=93.48  Aligned_cols=126  Identities=22%  Similarity=0.231  Sum_probs=84.9

Q ss_pred             chhhhhhhccccccceeeeeC-----cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         129 SDTYLHRVARAGRFGTKAVLG-----MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       129 ~~~yQ~~~~~~~~~~~~~~~g-----~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      +-+||.+      .+.++...     .-.++....|+|||...+..++..+    .+..+||++|+.+|. |+.+.+.++
T Consensus       185 LL~fQkE------~l~Wl~~QE~Ss~~GGiLADEMGMGKTIQtIaLllae~----~ra~tLVvaP~VAlm-QW~nEI~~~  253 (791)
T KOG1002|consen  185 LLPFQKE------GLAWLTSQEESSVAGGILADEMGMGKTIQTIALLLAEV----DRAPTLVVAPTVALM-QWKNEIERH  253 (791)
T ss_pred             chhhhHH------HHHHHHHhhhhhhccceehhhhccchHHHHHHHHHhcc----ccCCeeEEccHHHHH-HHHHHHHHh
Confidence            4567888      44444332     3457788999999988665555532    334599999999985 677888888


Q ss_pred             hccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCC-------------cCCCee--EEEecchhHH
Q psy1548         204 SKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKL-------------NLSLLK--HFILDECDKM  268 (448)
Q Consensus       204 ~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~-------------~~~~i~--~lViDEah~l  268 (448)
                      ...  ..++...+|. ........+.+  ++++.+|...+.+..++...             .+.+++  .+|+||||.+
T Consensus       254 T~g--slkv~~YhG~-~R~~nikel~~--YDvVLTty~vvEs~yRk~~~GfrrKngv~ke~SlLHsi~~~RiIlDEAH~I  328 (791)
T KOG1002|consen  254 TSG--SLKVYIYHGA-KRDKNIKELMN--YDVVLTTYAVVESVYRKQDYGFRRKNGVDKEKSLLHSIKFYRIILDEAHNI  328 (791)
T ss_pred             ccC--ceEEEEEecc-cccCCHHHhhc--CcEEEEecHHHHHHHHhccccccccCCcccccchhhhceeeeeehhhhccc
Confidence            763  5666665554 44556666665  79999999988776654211             133344  4999999966


Q ss_pred             Hh
Q psy1548         269 LE  270 (448)
Q Consensus       269 ~~  270 (448)
                      -+
T Consensus       329 K~  330 (791)
T KOG1002|consen  329 KD  330 (791)
T ss_pred             cc
Confidence            43

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

Probab=98.83  E-value=4.5e-07  Score=95.37  Aligned_cols=233  Identities=15%  Similarity=0.182  Sum_probs=139.5

Q ss_pred             eeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcC
Q psy1548         152 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTH  231 (448)
Q Consensus       152 vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~  231 (448)
                      .++.+|.|||||.+..-++-+.+.  ....++|+|+..+.|+.+....++...-.  +.....-.++..       +...
T Consensus        52 ~vVRSpMGTGKTtaLi~wLk~~l~--~~~~~VLvVShRrSL~~sL~~rf~~~~l~--gFv~Y~d~~~~~-------i~~~  120 (824)
T PF02399_consen   52 LVVRSPMGTGKTTALIRWLKDALK--NPDKSVLVVSHRRSLTKSLAERFKKAGLS--GFVNYLDSDDYI-------IDGR  120 (824)
T ss_pred             EEEECCCCCCcHHHHHHHHHHhcc--CCCCeEEEEEhHHHHHHHHHHHHhhcCCC--cceeeecccccc-------cccc
Confidence            578899999999765443333322  23458999999999999988887754210  222111111111       1111


Q ss_pred             CCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHH------H-HHHhCCCCCeEEEEeccCCccHHH
Q psy1548         232 NPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQ------E-IFRSSPHTKQVMMFSATLSKEIRP  304 (448)
Q Consensus       232 ~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~------~-i~~~l~~~~q~i~~SAT~~~~~~~  304 (448)
                      +.+-++++.++|.++..   -.+.+.++|||||+-..+.. -+.+.++      . +...+.....+|++-|+++...-+
T Consensus       121 ~~~rLivqIdSL~R~~~---~~l~~yDvVIIDEv~svL~q-L~S~Tm~~~~~v~~~L~~lI~~ak~VI~~DA~ln~~tvd  196 (824)
T PF02399_consen  121 PYDRLIVQIDSLHRLDG---SLLDRYDVVIIDEVMSVLNQ-LFSPTMRQREEVDNLLKELIRNAKTVIVMDADLNDQTVD  196 (824)
T ss_pred             ccCeEEEEehhhhhccc---ccccccCEEEEehHHHHHHH-HhHHHHhhHHHHHHHHHHHHHhCCeEEEecCCCCHHHHH
Confidence            24677778777765532   23567899999999988775 3322222      2 233445667899999999999999


Q ss_pred             HHHHhcCCCe-EEEEcCccccc-ccceeEEEEE----------------------------------cCcchHHHHHHHH
Q psy1548         305 VCKKFMHDPM-EVYVDDEAKLT-LHGLQQHYVK----------------------------------LKENEKNKKLFEL  348 (448)
Q Consensus       305 ~~~~~l~~~~-~i~~~~~~~~~-~~~i~~~~~~----------------------------------~~~~~k~~~L~~l  348 (448)
                      ++..+.++.. .+....- ... ..+-...++.                                  ....+.......+
T Consensus       197 Fl~~~Rp~~~i~vI~n~y-~~~~fs~R~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tF~~~L  275 (824)
T PF02399_consen  197 FLASCRPDENIHVIVNTY-ASPGFSNRRCTFLRSLGTDTLAAALNPEDENADTSPTPKHSPDPTATAAISNDETTFFSEL  275 (824)
T ss_pred             HHHHhCCCCcEEEEEeee-ecCCcccceEEEecccCcHHHHHHhCCcccccccCCCcCCCCccccccccccchhhHHHHH
Confidence            9888765433 3322211 100 0000000000                                  0001123334444


Q ss_pred             HhhC-CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC
Q psy1548         349 LDVL-EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       349 l~~~-~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~  404 (448)
                      +... .++++-||++|...++.+++.....+..+..++|.-+..+.    +.|++-.
T Consensus       276 ~~~L~~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~dv----~~W~~~~  328 (824)
T PF02399_consen  276 LARLNAGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLEDV----ESWKKYD  328 (824)
T ss_pred             HHHHhCCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCcccc----cccccee
Confidence            4443 35678899999999999999888888888888887666522    4576654

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

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=98.80  E-value=3.3e-07  Score=98.82  Aligned_cols=153  Identities=18%  Similarity=0.177  Sum_probs=93.1

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhH---
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---  225 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~---  225 (448)
                      |-=++-.|.||+|||++= .-+++.+.....+.|..|-.-.|.|-.|.-+.+++-.+.. +-...++.|+....+--   
T Consensus       431 GfF~vNMASTGcGKT~aN-ARImyaLsd~~~g~RfsiALGLRTLTLQTGda~r~rL~L~-~ddLAVlIGs~Av~~L~e~~  508 (1110)
T TIGR02562       431 GAFGVNMASTGCGKTLAN-ARAMYALRDDKQGARFAIALGLRSLTLQTGHALKTRLNLS-DDDLAVLIGGTAVQTLFDLS  508 (1110)
T ss_pred             CeEEEEecCCCcchHHHH-HHHHHHhCCCCCCceEEEEccccceeccchHHHHHhcCCC-ccceEEEECHHHHHHHHHHH
Confidence            334566799999999874 4455566666677788888888888888888877654332 44445555543211000   


Q ss_pred             ----------------------------------------HHHhc-------CCCcEEEEcHHHHHHHHHC---CCCcCC
Q psy1548         226 ----------------------------------------EYLKT-------HNPQIVVGTPGRILALVRN---KKLNLS  255 (448)
Q Consensus       226 ----------------------------------------~~l~~-------~~~~IlV~Tp~~l~~~l~~---~~~~~~  255 (448)
                                                              ..+..       -...++|||++.++.....   +...+.
T Consensus       509 ~~~~~~~~~~GSeS~e~l~~e~~~~~~~~~~g~l~~~~l~~~l~~~~k~~rll~apv~V~TIDQlL~a~~~~r~~~~~l~  588 (1110)
T TIGR02562       509 KEKIEQVDEDGSESAPIFLAEGQDCNLPDWDGPLDTIELLGRLSLDDKEKTLLAAPVLVCTIDHLIPATESHRGGHHIAP  588 (1110)
T ss_pred             hhhccccccCCCccchhhhcccCcCCeeeccCCccchhhhhhhccChhhhhhhcCCeEEecHHHHHHHhhhcccchhHHH
Confidence                                                    00000       0246999999999877622   122111


Q ss_pred             C----eeEEEecchhHHHhhhhhHHHHHHHHHhCC-CCCeEEEEeccCCccHHHH
Q psy1548         256 L----LKHFILDECDKMLEQLEMRRDVQEIFRSSP-HTKQVMMFSATLSKEIRPV  305 (448)
Q Consensus       256 ~----i~~lViDEah~l~~~~~~~~~~~~i~~~l~-~~~q~i~~SAT~~~~~~~~  305 (448)
                      .    =+.|||||+|.+-.  .....+..++..+. -..+++++|||+|+.+...
T Consensus       589 ll~La~svlVlDEVHaYD~--~~~~~L~rlL~w~~~lG~~VlLmSATLP~~l~~~  641 (1110)
T TIGR02562       589 MLRLMSSDLILDEPDDYEP--EDLPALLRLVQLAGLLGSRVLLSSATLPPALVKT  641 (1110)
T ss_pred             HHHhcCCCEEEECCccCCH--HHHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHH
Confidence            1    13699999995433  33334444444322 2567999999999975443

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.

>KOG0925|consensus

Probab=98.71  E-value=2.3e-07  Score=90.94  Aligned_cols=256  Identities=16%  Similarity=0.139  Sum_probs=144.1

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      ...|...+.++.-.+-+.+..                        ..  |+..|+.+      .+..+....-++++|.|
T Consensus        24 ~Npf~~~p~s~rY~~ilk~R~------------------------~L--Pvw~~k~~------F~~~l~~nQ~~v~vGet   71 (699)
T KOG0925|consen   24 INPFNGKPYSQRYYDILKKRR------------------------EL--PVWEQKEE------FLKLLLNNQIIVLVGET   71 (699)
T ss_pred             cCCCCCCcCcHHHHHHHHHHh------------------------cC--chHHhHHH------HHHHHhcCceEEEEecC
Confidence            345788888888777776643                        22  45555666      66677778889999999


Q ss_pred             CChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEE
Q psy1548         159 GMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVG  238 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~  238 (448)
                      |||||...--..+.......  ..+...-|.|--|.++...   .+..+ ++..+--.|-.-..++..   ....-+-++
T Consensus        72 gsGKttQiPq~~~~~~~~~~--~~v~CTQprrvaamsva~R---VadEM-Dv~lG~EVGysIrfEdC~---~~~T~Lky~  142 (699)
T KOG0925|consen   72 GSGKTTQIPQFVLEYELSHL--TGVACTQPRRVAAMSVAQR---VADEM-DVTLGEEVGYSIRFEDCT---SPNTLLKYC  142 (699)
T ss_pred             CCCccccCcHHHHHHHHhhc--cceeecCchHHHHHHHHHH---HHHHh-ccccchhccccccccccC---ChhHHHHHh
Confidence            99999652212222222211  2455566888777775443   33344 555544444321111100   000012234


Q ss_pred             cHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhh-hhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEE
Q psy1548         239 TPGRILALVRNKKLNLSLLKHFILDECDKMLEQL-EMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVY  317 (448)
Q Consensus       239 Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~-~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~  317 (448)
                      |-+.|++-.-+.. .+.+..++|+||||.-.-.. -....++.+...- ++.++|.+|||+...  ++ +.|..++-.+.
T Consensus       143 tDgmLlrEams~p-~l~~y~viiLDeahERtlATDiLmGllk~v~~~r-pdLk~vvmSatl~a~--Kf-q~yf~n~Pll~  217 (699)
T KOG0925|consen  143 TDGMLLREAMSDP-LLGRYGVIILDEAHERTLATDILMGLLKEVVRNR-PDLKLVVMSATLDAE--KF-QRYFGNAPLLA  217 (699)
T ss_pred             cchHHHHHHhhCc-ccccccEEEechhhhhhHHHHHHHHHHHHHHhhC-CCceEEEeecccchH--HH-HHHhCCCCeee
Confidence            5555544333222 36788999999999642110 2233344444444 488999999997533  44 44555555554


Q ss_pred             EcCcccccccceeEEEEEcCcchHH-HHHHHHHhh---CCCCeEEEEECccHHHHHHHHHHHhC---------CCcEEEE
Q psy1548         318 VDDEAKLTLHGLQQHYVKLKENEKN-KKLFELLDV---LEFNQVVIFVKSVTRCIALSTLLSEQ---------NFPAVSI  384 (448)
Q Consensus       318 ~~~~~~~~~~~i~~~~~~~~~~~k~-~~L~~ll~~---~~~~~~IIF~~s~~~a~~l~~~L~~~---------g~~~~~l  384 (448)
                      +...     +.++.+|..-.+.+-+ .++...+.-   ...|-+++|....++.+..++.+.+.         ...|..+
T Consensus       218 vpg~-----~PvEi~Yt~e~erDylEaairtV~qih~~ee~GDilvFLtgeeeIe~aC~~i~re~~~L~~~~g~l~v~PL  292 (699)
T KOG0925|consen  218 VPGT-----HPVEIFYTPEPERDYLEAAIRTVLQIHMCEEPGDILVFLTGEEEIEDACRKISREVDNLGPQVGPLKVVPL  292 (699)
T ss_pred             cCCC-----CceEEEecCCCChhHHHHHHHHHHHHHhccCCCCEEEEecCHHHHHHHHHHHHHHHHhhccccCCceEEec
Confidence            4322     2333344333333333 333333333   35678999999999999999888743         2457888


Q ss_pred             e
Q psy1548         385 H  385 (448)
Q Consensus       385 h  385 (448)
                      |
T Consensus       293 y  293 (699)
T KOG0925|consen  293 Y  293 (699)
T ss_pred             C
Confidence            8

>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=98.68  E-value=1.4e-07  Score=79.14  Aligned_cols=114  Identities=25%  Similarity=0.255  Sum_probs=86.1

Q ss_pred             eEEEEEcCcchHHHHHHHHHhhCC--CCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCce
Q psy1548         330 QQHYVKLKENEKNKKLFELLDVLE--FNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGL  407 (448)
Q Consensus       330 ~~~~~~~~~~~k~~~L~~ll~~~~--~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~  407 (448)
                      .+.+...+ +.|...+..++....  ++++||||++...++.+++.|.+.+.++..+||+++..+|..+++.|+++.  .
T Consensus         3 ~~~~~~~~-~~k~~~i~~~i~~~~~~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~--~   79 (131)
T cd00079           3 KQYVLPVE-DEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGE--I   79 (131)
T ss_pred             EEEEEECC-HHHHHHHHHHHHhcccCCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCC--C
Confidence            34444433 368888888887663  779999999999999999999998999999999999999999999999987  5


Q ss_pred             EEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         408 AITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       408 ~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      .|+++|.....++  ++...-.+-+...|.+...+.++.||
T Consensus        80 ~ili~t~~~~~G~--d~~~~~~vi~~~~~~~~~~~~Q~~GR  118 (131)
T cd00079          80 VVLVATDVIARGI--DLPNVSVVINYDLPWSPSSYLQRIGR  118 (131)
T ss_pred             cEEEEcChhhcCc--ChhhCCEEEEeCCCCCHHHheecccc
Confidence            6666666432222  34433334445556667777788887

>KOG0353|consensus

Probab=98.62  E-value=2.7e-08  Score=94.44  Aligned_cols=116  Identities=17%  Similarity=0.215  Sum_probs=85.9

Q ss_pred             eeecCceeEEeec-CCCcccccccc-----CCCccccccccccccccchhhhhhhhccCceeeeccCCcccCCCCHHHHH
Q psy1548          20 LFFRAFIRFSSSF-PHSKMADNDDL-----LDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILR   93 (448)
Q Consensus        20 ~~~r~~~~~~~~~-~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (448)
                      +|.|+||+|.+.. |.+..+-.+++     -+|...+.+.|....+..+.........|.....++...+-...+.--..
T Consensus       283 ~fnr~nl~yev~qkp~n~dd~~edi~k~i~~~f~gqsgiiyc~sq~d~ekva~alkn~gi~a~~yha~lep~dks~~hq~  362 (695)
T KOG0353|consen  283 GFNRPNLKYEVRQKPGNEDDCIEDIAKLIKGDFAGQSGIIYCFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQG  362 (695)
T ss_pred             ccCCCCceeEeeeCCCChHHHHHHHHHHhccccCCCcceEEEeccccHHHHHHHHHhcCccccccccccCcccccccccc
Confidence            8999999998765 55542222222     23455677888887777777666666666666556665554444444566


Q ss_pred             HHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhh
Q psy1548          94 AIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHR  135 (448)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~  135 (448)
                      |+...-+|.|+|-+||||||+|+||+|+|-..|.+++.|.+.
T Consensus       363 w~a~eiqvivatvafgmgidkpdvrfvihhsl~ksienyyqa  404 (695)
T KOG0353|consen  363 WIAGEIQVIVATVAFGMGIDKPDVRFVIHHSLPKSIENYYQA  404 (695)
T ss_pred             ccccceEEEEEEeeecccCCCCCeeEEEecccchhHHHHHHH
Confidence            777777999999999999999999999999999999998885

>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=98.59  E-value=3.3e-07  Score=86.10  Aligned_cols=130  Identities=23%  Similarity=0.239  Sum_probs=92.3

Q ss_pred             cCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         124 DMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       124 ~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      ..|..+   |..      ++-.+..|+  |++..||-|||++..+|+.-....   |..+-|++.+.-||..=.+.+..+
T Consensus        76 ~~p~~v---Qll------~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~---G~~V~vvT~NdyLA~RD~~~~~~~  141 (266)
T PF07517_consen   76 LRPYDV---QLL------GALALHKGR--LAEMKTGEGKTLIAALPAALNALQ---GKGVHVVTSNDYLAKRDAEEMRPF  141 (266)
T ss_dssp             ----HH---HHH------HHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTT---SS-EEEEESSHHHHHHHHHHHHHH
T ss_pred             CcccHH---HHh------hhhhcccce--eEEecCCCCcHHHHHHHHHHHHHh---cCCcEEEeccHHHhhccHHHHHHH
Confidence            367777   888      444444444  999999999999998887665543   346888999999999988899999


Q ss_pred             hccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHH-HHHCC----C--CcCCCeeEEEecchhHHHhh
Q psy1548         204 SKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILA-LVRNK----K--LNLSLLKHFILDECDKMLEQ  271 (448)
Q Consensus       204 ~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~-~l~~~----~--~~~~~i~~lViDEah~l~~~  271 (448)
                      ...+ +++++..+++.+.........   ++|+++|...+.- .++..    .  .....+.++|+||+|.++=+
T Consensus       142 y~~L-Glsv~~~~~~~~~~~r~~~Y~---~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~LiD  212 (266)
T PF07517_consen  142 YEFL-GLSVGIITSDMSSEERREAYA---ADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSILID  212 (266)
T ss_dssp             HHHT-T--EEEEETTTEHHHHHHHHH---SSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHTTT
T ss_pred             HHHh-hhccccCccccCHHHHHHHHh---CcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEEEe
Confidence            9998 999999999987554433343   5899999998853 44321    1  11467889999999987643

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 ....

>PRK14873 primosome assembly protein PriA; Provisional

Probab=98.57  E-value=8.5e-07  Score=93.97  Aligned_cols=140  Identities=16%  Similarity=0.127  Sum_probs=94.4

Q ss_pred             eeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHh---HHHH
Q psy1548         152 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD---EEYL  228 (448)
Q Consensus       152 vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~---~~~l  228 (448)
                      .+..+.+|||||.+|+-.+-..+..   |.++|+++|...|..|+.+.++...+   +..+..++++.+..+.   +...
T Consensus       163 ~i~~~~~GSGKTevyl~~i~~~l~~---Gk~vLvLvPEi~lt~q~~~rl~~~f~---~~~v~~lhS~l~~~~R~~~w~~~  236 (665)
T PRK14873        163 AVWQALPGEDWARRLAAAAAATLRA---GRGALVVVPDQRDVDRLEAALRALLG---AGDVAVLSAGLGPADRYRRWLAV  236 (665)
T ss_pred             HHhhcCCCCcHHHHHHHHHHHHHHc---CCeEEEEecchhhHHHHHHHHHHHcC---CCcEEEECCCCCHHHHHHHHHHH
Confidence            3444446999999998776665543   44799999999999999888887653   2567778877665543   3445


Q ss_pred             hcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHH-hh-hhhH---HHHHHHHHhCCCCCeEEEEeccCCccHH
Q psy1548         229 KTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKML-EQ-LEMR---RDVQEIFRSSPHTKQVMMFSATLSKEIR  303 (448)
Q Consensus       229 ~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~-~~-~~~~---~~~~~i~~~l~~~~q~i~~SAT~~~~~~  303 (448)
                      ..+..+|+|||-.-+.       ..++++.+||+||=|.-. .. ...+   .++ .+++....+..+|+.|||.+-+..
T Consensus       237 ~~G~~~IViGtRSAvF-------aP~~~LgLIIvdEEhd~sykq~~~p~yhaRdv-A~~Ra~~~~~~lvLgSaTPSles~  308 (665)
T PRK14873        237 LRGQARVVVGTRSAVF-------APVEDLGLVAIWDDGDDLLAEPRAPYPHAREV-ALLRAHQHGCALLIGGHARTAEAQ  308 (665)
T ss_pred             hCCCCcEEEEcceeEE-------eccCCCCEEEEEcCCchhhcCCCCCCccHHHH-HHHHHHHcCCcEEEECCCCCHHHH
Confidence            6777899999964432       347889999999998431 11 0111   122 223333467789999999775544


Q ss_pred             HH
Q psy1548         304 PV  305 (448)
Q Consensus       304 ~~  305 (448)
                      ..
T Consensus       309 ~~  310 (665)
T PRK14873        309 AL  310 (665)
T ss_pred             HH
Confidence            33

>KOG4439|consensus

Probab=98.56  E-value=1.3e-06  Score=89.31  Aligned_cols=116  Identities=20%  Similarity=0.249  Sum_probs=74.3

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhc-----c--CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCccc
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLET-----T--DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPI  221 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~-----~--~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~  221 (448)
                      +.-.|+....|-|||+..+-.++.+-..     .  .....+|||||.. |..||..++.+-.... .++|.+++|....
T Consensus       345 ~~GGILaddmGLGKTlsmislil~qK~~~~~~~~~~~~a~~TLII~PaS-li~qW~~Ev~~rl~~n-~LsV~~~HG~n~r  422 (901)
T KOG4439|consen  345 PSGGILADDMGLGKTLSMISLILHQKAARKAREKKGESASKTLIICPAS-LIHQWEAEVARRLEQN-ALSVYLYHGPNKR  422 (901)
T ss_pred             CCCcccccccccccchHHHHHHHHHHHHHHhhcccccccCCeEEeCcHH-HHHHHHHHHHHHHhhc-ceEEEEecCCccc
Confidence            4567889999999999765555543211     1  1112599999987 6677777766544433 5788888887754


Q ss_pred             HHhHHHHhcCCCcEEEEcHHHHHH----HHHCC--CCcCCCe--eEEEecchhHH
Q psy1548         222 QKDEEYLKTHNPQIVVGTPGRILA----LVRNK--KLNLSLL--KHFILDECDKM  268 (448)
Q Consensus       222 ~~~~~~l~~~~~~IlV~Tp~~l~~----~l~~~--~~~~~~i--~~lViDEah~l  268 (448)
                      .-....+..  +||||+|..-+..    -+...  .-.+-+|  ..||+||||.+
T Consensus       423 ~i~~~~L~~--YDvViTTY~lva~~~~~e~~~~~~~spL~~I~W~RVILDEAH~I  475 (901)
T KOG4439|consen  423 EISAKELRK--YDVVITTYNLVANKPDDELEEGKNSSPLARIAWSRVILDEAHNI  475 (901)
T ss_pred             cCCHHHHhh--cceEEEeeeccccCCchhhhcccCccHHHHhhHHHhhhhhhhhh
Confidence            445555655  7999999876544    11111  1112233  35999999965

>KOG0952|consensus

Probab=98.54  E-value=3.3e-08  Score=104.69  Aligned_cols=240  Identities=18%  Similarity=0.208  Sum_probs=144.7

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL  228 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l  228 (448)
                      ..++++-+|||+|||++|.+.+...+...+. .++++++|..+|+..-.+........ +++++.-+.|+....  ...+
T Consensus       943 d~~~~~g~ptgsgkt~~ae~a~~~~~~~~p~-~kvvyIap~kalvker~~Dw~~r~~~-~g~k~ie~tgd~~pd--~~~v 1018 (1230)
T KOG0952|consen  943 DLNFLLGAPTGSGKTVVAELAIFRALSYYPG-SKVVYIAPDKALVKERSDDWSKRDEL-PGIKVIELTGDVTPD--VKAV 1018 (1230)
T ss_pred             chhhhhcCCccCcchhHHHHHHHHHhccCCC-ccEEEEcCCchhhcccccchhhhccc-CCceeEeccCccCCC--hhhe
Confidence            5789999999999999999998877655544 69999999999988755555544333 378888888887544  2233


Q ss_pred             hcCCCcEEEEcHHHHHHHHHC--CCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHh-------CCCCCeEEEEeccCC
Q psy1548         229 KTHNPQIVVGTPGRILALVRN--KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRS-------SPHTKQVMMFSATLS  299 (448)
Q Consensus       229 ~~~~~~IlV~Tp~~l~~~l~~--~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~-------l~~~~q~i~~SAT~~  299 (448)
                      .  .++++|+||+++-...++  ..-.+.++..+|+||.|++.+  +..+.++.+...       +++.++.+++|.-+ 
T Consensus      1019 ~--~~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg~--~rgPVle~ivsr~n~~s~~t~~~vr~~glsta~- 1093 (1230)
T KOG0952|consen 1019 R--EADIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLGE--DRGPVLEVIVSRMNYISSQTEEPVRYLGLSTAL- 1093 (1230)
T ss_pred             e--cCceEEcccccccCccccccchhhhccccceeecccccccC--CCcceEEEEeeccccCccccCcchhhhhHhhhh-
Confidence            3  278999999998777663  334578899999999997766  555544443322       22344666664433 


Q ss_pred             ccHHHHHHHhcCCCeEEEEcCcccccccce---------eEEEEEcCcchHHHHHHHHHhh-CCCCeEEEEECccHHHHH
Q psy1548         300 KEIRPVCKKFMHDPMEVYVDDEAKLTLHGL---------QQHYVKLKENEKNKKLFELLDV-LEFNQVVIFVKSVTRCIA  369 (448)
Q Consensus       300 ~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i---------~~~~~~~~~~~k~~~L~~ll~~-~~~~~~IIF~~s~~~a~~  369 (448)
                      ....++.++....+. ....+.  ..+..+         .+++....+.+|.  ....++. .+..+++||+.++.+...
T Consensus      1094 ~na~dla~wl~~~~~-~nf~~s--vrpvp~~~~i~gfp~~~~cprm~smnkp--a~qaik~~sp~~p~lifv~srrqtrl 1168 (1230)
T KOG0952|consen 1094 ANANDLADWLNIKDM-YNFRPS--VRPVPLEVHIDGFPGQHYCPRMMSMNKP--AFQAIKTHSPIKPVLIFVSSRRQTRL 1168 (1230)
T ss_pred             hccHHHHHHhCCCCc-CCCCcc--cccCCceEeecCCCchhcchhhhhcccH--HHHHHhcCCCCCceEEEeeccccccc
Confidence            334555555443332 111000  011111         2233333333332  2333444 456789999999877655


Q ss_pred             HHHHHHh----CCCcEEEEeCCCCHHHHHHHHHHHhcCC
Q psy1548         370 LSTLLSE----QNFPAVSIHRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       370 l~~~L~~----~g~~~~~lh~~~~~~eR~~~l~~F~~g~  404 (448)
                      -+..|-.    ..-+--+++.+  ..+-+-++..-++..
T Consensus      1169 ta~~li~~~~~~~~p~~fl~~d--e~e~e~~~~~~~d~~ 1205 (1230)
T KOG0952|consen 1169 TALDLIASCATEDNPKQFLNMD--ELELEIIMSKVRDTN 1205 (1230)
T ss_pred             chHhHHhhccCCCCchhccCCC--HHHHHHHHHHhcccc
Confidence            5544432    22233344333  555555665555543

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=98.53  E-value=5.7e-08  Score=103.09  Aligned_cols=134  Identities=29%  Similarity=0.385  Sum_probs=86.6

Q ss_pred             cccccCCCcee--eeecCceeEEeecCCCccccccccC-CCccccccccccccccchhhhhhhhccCceeeeccCCcccC
Q psy1548           9 EKLSCGSGNVF--LFFRAFIRFSSSFPHSKMADNDDLL-DYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDF   85 (448)
Q Consensus         9 ~~~~~~~~~~~--~~~r~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (448)
                      +.|.++.+.+|  +|.|+|+.|.+....++.....+.+ .........+.......+.........+.....+|.+...-
T Consensus       182 ~~l~~~~~~~~~~~~~r~nl~~~v~~~~~~~~~l~~~l~~~~~~~~IIf~~sr~~~e~la~~L~~~g~~~~~~H~~l~~~  261 (591)
T TIGR01389       182 ELLRLADANEFITSFDRPNLRFSVVKKNNKQKFLLDYLKKHRGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNK  261 (591)
T ss_pred             HHcCCCCCCeEecCCCCCCcEEEEEeCCCHHHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHhCCCCEEEEECCCCHH
Confidence            35666667666  8999999998876554422221221 11234455666655555544444444444444444433321


Q ss_pred             CCCHHHHHHH-hhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548          86 LLKPEILRAI-VDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        86 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      . ...+++.+ ....+|+|||++++||||++++++|+|+..|..++.|.|++|||||..
T Consensus       262 ~-R~~i~~~F~~g~~~vlVaT~a~~~GID~p~v~~VI~~~~p~s~~~y~Q~~GRaGR~G  319 (591)
T TIGR01389       262 V-RAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDG  319 (591)
T ss_pred             H-HHHHHHHHHcCCCcEEEEechhhccCcCCCCCEEEEcCCCCCHHHHhhhhccccCCC
Confidence            1 12222222 234589999999999999999999999999999999999999999943

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.

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=98.51  E-value=7.3e-08  Score=102.23  Aligned_cols=142  Identities=22%  Similarity=0.321  Sum_probs=91.9

Q ss_pred             cccccCCCcee--eeecCceeEEeecCCCccccccccCCC----ccccccccccccccchhhhhhhhccCceeeeccCCc
Q psy1548           9 EKLSCGSGNVF--LFFRAFIRFSSSFPHSKMADNDDLLDY----EDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGF   82 (448)
Q Consensus         9 ~~~~~~~~~~~--~~~r~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (448)
                      +.+.+..+.++  +|.|+|+.|.+......   .+.+..+    .......+.......+.........+..+...+.+.
T Consensus       194 ~~l~l~~~~~~~~~~~r~nl~~~v~~~~~~---~~~l~~~l~~~~~~~~IIFc~tr~~~e~la~~L~~~g~~v~~~Ha~l  270 (607)
T PRK11057        194 RLLGLNDPLIQISSFDRPNIRYTLVEKFKP---LDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGL  270 (607)
T ss_pred             HHhCCCCeEEEECCCCCCcceeeeeeccch---HHHHHHHHHhcCCCCEEEEECcHHHHHHHHHHHHhCCCCEEEecCCC
Confidence            45566666666  89999999876543322   2222222    223445666555545554545545555555555544


Q ss_pred             ccCCCCHHHHHHH-hhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeecc
Q psy1548          83 RDFLLKPEILRAI-VDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAK  157 (448)
Q Consensus        83 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~ap  157 (448)
                      ..-.. ..+++.+ ....+|+|||++++||||+++++.|+||+.|..++.|.|++|||||..   ..|..+++..|
T Consensus       271 ~~~~R-~~i~~~F~~g~~~VLVaT~a~~~GIDip~V~~VI~~d~P~s~~~y~Qr~GRaGR~G---~~~~~ill~~~  342 (607)
T PRK11057        271 DNDVR-ADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDG---LPAEAMLFYDP  342 (607)
T ss_pred             CHHHH-HHHHHHHHCCCCCEEEEechhhccCCCCCcCEEEEeCCCCCHHHHHHHhhhccCCC---CCceEEEEeCH
Confidence            33221 2233333 233489999999999999999999999999999999999999999944   23455555554

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.47  E-value=8.3e-07  Score=95.43  Aligned_cols=47  Identities=23%  Similarity=0.327  Sum_probs=39.3

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQIS  197 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~  197 (448)
                      ++.++|.||||+|||++|++|++......  +.+++|-++|+.|-+|+.
T Consensus        49 ~~~lviEAgTGtGKTlaYLlPai~~A~~~--~k~vVIST~T~~LQeQL~   95 (697)
T PRK11747         49 GRILVIEAGTGVGKTLSYLLAGIPIARAE--KKKLVISTATVALQEQLV   95 (697)
T ss_pred             cceEEEECCCCcchhHHHHHHHHHHHHHc--CCeEEEEcCCHHHHHHHH
Confidence            36789999999999999999998754433  347999999999998875

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=98.45  E-value=1.4e-07  Score=97.26  Aligned_cols=131  Identities=20%  Similarity=0.293  Sum_probs=85.7

Q ss_pred             ccccCCCcee--eeecCceeEEeecCCCccccccccCC-----CccccccccccccccchhhhhhhhccCceeeeccCCc
Q psy1548          10 KLSCGSGNVF--LFFRAFIRFSSSFPHSKMADNDDLLD-----YEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGF   82 (448)
Q Consensus        10 ~~~~~~~~~~--~~~r~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (448)
                      .+.+..+.++  +|.|+|+.|.+.....+.  .+++.+     ........+.......+.........+..+...+.+.
T Consensus       183 ~l~l~~~~~~~~s~~r~nl~~~v~~~~~~~--~~~l~~~l~~~~~~~~~IIF~~s~~~~e~la~~L~~~g~~~~~~H~~l  260 (470)
T TIGR00614       183 QLNLKNPQIFCTSFDRPNLYYEVRRKTPKI--LEDLLRFIRKEFKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGL  260 (470)
T ss_pred             HcCCCCCcEEeCCCCCCCcEEEEEeCCccH--HHHHHHHHHHhcCCCceEEEECcHHHHHHHHHHHHhcCCCeeEeeCCC
Confidence            4556666666  899999999876544221  112221     1222335666555555555545544455455555544


Q ss_pred             ccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          83 RDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ..-....-+..+.....+|+|||++++||||+++++.|+||..|..+..|.|++|||||.
T Consensus       261 ~~~eR~~i~~~F~~g~~~vLVaT~~~~~GID~p~V~~VI~~~~P~s~~~y~Qr~GRaGR~  320 (470)
T TIGR00614       261 EISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRD  320 (470)
T ss_pred             CHHHHHHHHHHHHcCCCcEEEEechhhccCCcccceEEEEeCCCCCHHHHHhhhcCcCCC
Confidence            332222222233334458999999999999999999999999999999999999999993

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

>COG4889 Predicted helicase [General function prediction only]

Probab=98.40  E-value=3.2e-07  Score=95.52  Aligned_cols=136  Identities=15%  Similarity=0.141  Sum_probs=89.0

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeC----cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLG----MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK  198 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g----~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~  198 (448)
                      ...|...++||++      ++..+..|    ...=+.+.+|+|||+..+ -+...+..    .++|+++|+.+|..|..+
T Consensus       156 l~~~kk~R~hQq~------Aid~a~~~F~~n~RGkLIMAcGTGKTfTsL-kisEala~----~~iL~LvPSIsLLsQTlr  224 (1518)
T COG4889         156 LKKPKKPRPHQQT------AIDAAKEGFSDNDRGKLIMACGTGKTFTSL-KISEALAA----ARILFLVPSISLLSQTLR  224 (1518)
T ss_pred             cCCCCCCChhHHH------HHHHHHhhcccccCCcEEEecCCCccchHH-HHHHHHhh----hheEeecchHHHHHHHHH
Confidence            4466777889999      88777765    223344668999998854 33343332    589999999999999766


Q ss_pred             HHHHhhccCCCceEEEEEcCcccHHh-----------------------HHH-HhcCCCcEEEEcHHHHHHHHHCCCCcC
Q psy1548         199 EYERFSKYMSNIKVGVFFGGLPIQKD-----------------------EEY-LKTHNPQIVVGTPGRILALVRNKKLNL  254 (448)
Q Consensus       199 ~~~~~~~~~~~~~v~~~~g~~~~~~~-----------------------~~~-l~~~~~~IlV~Tp~~l~~~l~~~~~~~  254 (448)
                      .+..-.. + +++...++++......                       ... -+...--|+++|.+.+...-......+
T Consensus       225 ew~~~~~-l-~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTYQSl~~i~eAQe~G~  302 (1518)
T COG4889         225 EWTAQKE-L-DFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTYQSLPRIKEAQEAGL  302 (1518)
T ss_pred             HHhhccC-c-cceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEEcccchHHHHHHHHcCC
Confidence            6554322 2 4555555554332111                       000 111234689999999877665555567


Q ss_pred             CCeeEEEecchhHHHhh
Q psy1548         255 SLLKHFILDECDKMLEQ  271 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~  271 (448)
                      ..++++|.||||+-...
T Consensus       303 ~~fDliicDEAHRTtGa  319 (1518)
T COG4889         303 DEFDLIICDEAHRTTGA  319 (1518)
T ss_pred             CCccEEEecchhccccc
Confidence            88999999999986543

>KOG0352|consensus

Probab=98.36  E-value=6.3e-08  Score=93.40  Aligned_cols=133  Identities=17%  Similarity=0.170  Sum_probs=98.3

Q ss_pred             ccccCC-Ccee--eeecCceeEEeecCCCccccccccCCC-----------------ccccccccccccccchhhhhhhh
Q psy1548          10 KLSCGS-GNVF--LFFRAFIRFSSSFPHSKMADNDDLLDY-----------------EDEENTEQIVADGAGDALAKQKE   69 (448)
Q Consensus        10 ~~~~~~-~~~~--~~~r~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~~~   69 (448)
                      .|.+.. .++|  -=+|.||.|++.+.....++...|-|+                 -..-.++|.+++.+.+..+-...
T Consensus       197 qL~L~~PVAiFkTP~FR~NLFYD~~~K~~I~D~~~~LaDF~~~~LG~~~~~~~~~K~~~GCGIVYCRTR~~cEq~AI~l~  276 (641)
T KOG0352|consen  197 QLKLRNPVAIFKTPTFRDNLFYDNHMKSFITDCLTVLADFSSSNLGKHEKASQNKKTFTGCGIVYCRTRNECEQVAIMLE  276 (641)
T ss_pred             HHhhcCcHHhccCcchhhhhhHHHHHHHHhhhHhHhHHHHHHHhcCChhhhhcCCCCcCcceEEEeccHHHHHHHHHHhh
Confidence            344533 3666  446899999988877654443333222                 12345778877776665554444


Q ss_pred             ccCceeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          70 VKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ..|...-.++.|++.-....-+-.|+.....|.++|+.||||.|+++||+|+||+.|..+--|.|+-|||||.
T Consensus       277 ~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~PvI~AT~SFGMGVDKp~VRFViHW~~~qn~AgYYQESGRAGRD  349 (641)
T KOG0352|consen  277 IAGIPAMAYHAGLKKKERTEVQEKWMNNEIPVIAATVSFGMGVDKPDVRFVIHWSPSQNLAGYYQESGRAGRD  349 (641)
T ss_pred             hcCcchHHHhcccccchhHHHHHHHhcCCCCEEEEEeccccccCCcceeEEEecCchhhhHHHHHhccccccC
Confidence            5566566677888877776777777888889999999999999999999999999999999999999999983

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=98.32  E-value=2.9e-06  Score=91.83  Aligned_cols=146  Identities=16%  Similarity=0.181  Sum_probs=87.1

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHH------HhhccCCC--ceEEEEEcCc-
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYE------RFSKYMSN--IKVGVFFGGL-  219 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~------~~~~~~~~--~~v~~~~g~~-  219 (448)
                      ..++.+.++||+|||.+|+-.++..... -+..+.||+||+.++...+...+.      .|...+.+  +....+.++. 
T Consensus        59 ~~n~~~~M~TGtGKT~~~~~~i~~l~~~-~~~~~fii~vp~~aI~egv~~~l~s~~~k~hF~~~y~~~~~~~~~~~S~k~  137 (986)
T PRK15483         59 KANIDIKMETGTGKTYVYTRLMYELHQK-YGLFKFIIVVPTPAIKEGTRNFIQSDYAKQHFSQFYENTRIELYVINAGDK  137 (986)
T ss_pred             cceEEEEeCCCCCHHHHHHHHHHHHHHH-cCCcEEEEEeCCHHHHHHHHHHhhHHHHHHHHHHHcCCceeEEEEEecCcc
Confidence            4689999999999999998877765433 234589999999998877765544      12211212  3333333332 


Q ss_pred             ------ccHHhHHHHhcC------CCcEEEEcHHHHHHHHH-CC---------C-CcCCCe----eEEEecchhHHHhhh
Q psy1548         220 ------PIQKDEEYLKTH------NPQIVVGTPGRILALVR-NK---------K-LNLSLL----KHFILDECDKMLEQL  272 (448)
Q Consensus       220 ------~~~~~~~~l~~~------~~~IlV~Tp~~l~~~l~-~~---------~-~~~~~i----~~lViDEah~l~~~~  272 (448)
                            ........+...      ..+|+|.|.+.+..-.. ..         . ..+..+    -.+|+||+|++... 
T Consensus       138 ~k~gr~~~~~~i~~Fa~~~~~~~~~I~Ilv~niqa~n~~~~~~~~~D~~l~~g~~~p~~~i~~~~PivIiDEPh~~~~~-  216 (986)
T PRK15483        138 KKSGRKNFPAQLSNFVKASRQNSNTIHVLLINAGMLNSASMTRDDYDQTLLGGFTSPVDALAATRPVVIIDEPHRFPRD-  216 (986)
T ss_pred             cccccccChHHHHHHHhccccCCCceEEEEEehHHhcccccccchhhhhhccCCCChHHHHHhCCCEEEEECCCCCCcc-
Confidence                  112333333221      37899999998855211 10         0 111111    26999999988542 


Q ss_pred             hhHHHHHHHHHhCCCCCeEEEEeccCCc
Q psy1548         273 EMRRDVQEIFRSSPHTKQVMMFSATLSK  300 (448)
Q Consensus       273 ~~~~~~~~i~~~l~~~~q~i~~SAT~~~  300 (448)
                        ...+..+ ..+.+.+ ++.+|||.+.
T Consensus       217 --~k~~~~i-~~lnpl~-~lrysAT~~~  240 (986)
T PRK15483        217 --NKFYQAI-EALKPQM-IIRFGATFPD  240 (986)
T ss_pred             --hHHHHHH-HhcCccc-EEEEeeecCC
Confidence              1233444 3343333 5679999986

>KOG2340|consensus

Probab=98.31  E-value=5.9e-06  Score=82.09  Aligned_cols=294  Identities=15%  Similarity=0.155  Sum_probs=174.5

Q ss_pred             cceeeeeCcceeeeccC-CChh--HHHHHHHHHHhhhc----------------------------cCCCeEEEEeeccH
Q psy1548         142 FGTKAVLGMDILCQAKS-GMGK--TAVFVLATLQQLET----------------------------TDSNVYVLVMCHTR  190 (448)
Q Consensus       142 ~~~~~~~g~~vli~apT-GsGK--T~~~~l~~l~~l~~----------------------------~~~~~~~lil~Pt~  190 (448)
                      .+..+.+.+|++.--.| +.|+  +-.|++-+++++..                            +-..+++|||||+|
T Consensus       224 L~~~m~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~tRpkVLivvpfR  303 (698)
T KOG2340|consen  224 LFKIMFNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFTRPKVLIVVPFR  303 (698)
T ss_pred             HHHHHHhhhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCCCceEEEEecch
Confidence            55556667887754322 3344  45678888877621                            01247999999999


Q ss_pred             HHHHHHHHHHHHhhccCCCce--------EEEEEcC----------------------cccH--------HhHHHHh--c
Q psy1548         191 ELAFQISKEYERFSKYMSNIK--------VGVFFGG----------------------LPIQ--------KDEEYLK--T  230 (448)
Q Consensus       191 ~L~~q~~~~~~~~~~~~~~~~--------v~~~~g~----------------------~~~~--------~~~~~l~--~  230 (448)
                      +-|..+.+.+..+......-+        ..--+++                      ++..        .....+.  -
T Consensus       304 e~A~riVn~lis~l~G~~q~k~~V~Nk~RF~~eys~~te~~~~~~~kP~D~~~lf~GNtDD~FriGl~ftkKtikLys~f  383 (698)
T KOG2340|consen  304 ESAYRIVNLLISLLSGDDQGKSEVWNKKRFEGEYSGPTELPPPRAKKPEDFEELFSGNTDDAFRIGLAFTKKTIKLYSKF  383 (698)
T ss_pred             HHHHHHHHHHHHHhcCccccchhhhhhhhhchhcCCCcccCCCCCCCchhHHHHhcCCCcchhhhhHHHHHHHHHHHhhh
Confidence            999999988888733221101        1111121                      1100        0000110  1


Q ss_pred             CCCcEEEEcHHHHHHHHHCC------CCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCC---CC-------------
Q psy1548         231 HNPQIVVGTPGRILALVRNK------KLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSP---HT-------------  288 (448)
Q Consensus       231 ~~~~IlV~Tp~~l~~~l~~~------~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~---~~-------------  288 (448)
                      ...||+||+|--|.-++.+.      .-.+++|.++|||-||.|+.  ..+..+..++..+.   ..             
T Consensus       384 y~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l~--QNwEhl~~ifdHLn~~P~k~h~~DfSRVR~wy  461 (698)
T KOG2340|consen  384 YKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIMLM--QNWEHLLHIFDHLNLQPSKQHDVDFSRVRMWY  461 (698)
T ss_pred             cccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHHH--hhHHHHHHHHHHhhcCcccccCCChhheehhe
Confidence            24689999998877666521      12368899999999998877  46777787877653   21             


Q ss_pred             --------CeEEEEeccCCccHHHHHHHhcCCCeE-EEEcCc--c---cccccceeEEEEE--cC-----cchHHHHHHH
Q psy1548         289 --------KQVMMFSATLSKEIRPVCKKFMHDPME-VYVDDE--A---KLTLHGLQQHYVK--LK-----ENEKNKKLFE  347 (448)
Q Consensus       289 --------~q~i~~SAT~~~~~~~~~~~~l~~~~~-i~~~~~--~---~~~~~~i~~~~~~--~~-----~~~k~~~L~~  347 (448)
                              +|+++||+--.+....+...++.+-.- +.....  .   ......+.|.+..  ++     .+.++.....
T Consensus       462 L~~qsr~~rQtl~Fs~y~~~~~nS~fn~~c~N~~Gkv~~~~~~~~gsi~~v~~~l~Qvf~ri~~~si~~~~D~RFkyFv~  541 (698)
T KOG2340|consen  462 LDGQSRYFRQTLLFSRYSHPLFNSLFNQYCQNMAGKVKARNLQSGGSISNVGIPLCQVFQRIEVKSIIETPDARFKYFVD  541 (698)
T ss_pred             eccHHHHHHHHHHHHhhccHHHHHHHHHhhhhhcceeeeccccCCCchhhccchhhhhhhheeccCcccCchHHHHHHHH
Confidence                    277888887777666666665543211 111100  0   0111112222211  21     2334444433


Q ss_pred             HHh-hC---CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHH
Q psy1548         348 LLD-VL---EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNN  423 (448)
Q Consensus       348 ll~-~~---~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~  423 (448)
                      -+- ..   ...-++||.++--.--++.+++++.++....+|.-.++..-.++-+-|..|.  ..++++|.....-.-..
T Consensus       542 ~ImPq~~k~t~s~~LiyIPSYfDFVRvRNy~K~e~i~F~~i~EYssk~~vsRAR~lF~qgr--~~vlLyTER~hffrR~~  619 (698)
T KOG2340|consen  542 KIMPQLIKRTESGILIYIPSYFDFVRVRNYMKKEEISFVMINEYSSKSKVSRARELFFQGR--KSVLLYTERAHFFRRYH  619 (698)
T ss_pred             hhchhhcccccCceEEEecchhhHHHHHHHhhhhhcchHHHhhhhhHhhhhHHHHHHHhcC--ceEEEEehhhhhhhhhe
Confidence            321 11   1234799999999999999999999999888888888888888888999877  47777776532222223


Q ss_pred             HHHHhcCCCCCCCccc
Q psy1548         424 VQDRFDVSISELPDEI  439 (448)
Q Consensus       424 i~~~~~~~~~~~p~~~  439 (448)
                      |...-++.++++|...
T Consensus       620 ikGVk~vVfYqpP~~P  635 (698)
T KOG2340|consen  620 IKGVKNVVFYQPPNNP  635 (698)
T ss_pred             ecceeeEEEecCCCCc
Confidence            4444445556666553

>KOG0391|consensus

Probab=98.25  E-value=6e-06  Score=88.51  Aligned_cols=152  Identities=13%  Similarity=0.191  Sum_probs=99.7

Q ss_pred             chhhhhhhccccccceeeee----CcceeeeccCCChhHHHHHHHHHHhhhc--cCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         129 SDTYLHRVARAGRFGTKAVL----GMDILCQAKSGMGKTAVFVLATLQQLET--TDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       129 ~~~yQ~~~~~~~~~~~~~~~----g~~vli~apTGsGKT~~~~l~~l~~l~~--~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      +++||..      -+.++..    .-|.|+....|.|||.. .|.+|.++.-  +.-| --|||+||..+.++ .-.+++
T Consensus       616 LReYQki------GLdWLatLYeknlNGILADEmGLGKTIQ-tISllAhLACeegnWG-PHLIVVpTsviLnW-EMElKR  686 (1958)
T KOG0391|consen  616 LREYQKI------GLDWLATLYEKNLNGILADEMGLGKTIQ-TISLLAHLACEEGNWG-PHLIVVPTSVILNW-EMELKR  686 (1958)
T ss_pred             HHHHHHh------hHHHHHHHHHhcccceehhhhcccchhH-HHHHHHHHHhcccCCC-CceEEeechhhhhh-hHHHhh
Confidence            4899998      5555432    45889999999999966 3555555532  2334 36888899876654 557888


Q ss_pred             hhccCCCceEEEEEcCcccHHhHH--HHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHH
Q psy1548         203 FSKYMSNIKVGVFFGGLPIQKDEE--YLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQE  280 (448)
Q Consensus       203 ~~~~~~~~~v~~~~g~~~~~~~~~--~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~  280 (448)
                      |+   |++++..++|.....+...  ..+.+..||.|++...+.+-+..  +.-++.+|+|+||||.+-++  -...++.
T Consensus       687 wc---PglKILTYyGs~kErkeKRqgW~kPnaFHVCItSYklv~qd~~A--FkrkrWqyLvLDEaqnIKnf--ksqrWQA  759 (1958)
T KOG0391|consen  687 WC---PGLKILTYYGSHKERKEKRQGWAKPNAFHVCITSYKLVFQDLTA--FKRKRWQYLVLDEAQNIKNF--KSQRWQA  759 (1958)
T ss_pred             hC---CcceEeeecCCHHHHHHHhhcccCCCeeEEeehhhHHHHhHHHH--HHhhccceeehhhhhhhcch--hHHHHHH
Confidence            88   5889999999864322221  12334579999998877665432  23356789999999998664  2344555


Q ss_pred             HHHhCCCCCeEEEEeccC
Q psy1548         281 IFRSSPHTKQVMMFSATL  298 (448)
Q Consensus       281 i~~~l~~~~q~i~~SAT~  298 (448)
                      ++.. ... +.++++.|.
T Consensus       760 llnf-nsq-rRLLLtgTP  775 (1958)
T KOG0391|consen  760 LLNF-NSQ-RRLLLTGTP  775 (1958)
T ss_pred             Hhcc-chh-heeeecCCc
Confidence            5543 233 345666663

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

Probab=98.24  E-value=8.4e-06  Score=90.26  Aligned_cols=141  Identities=20%  Similarity=0.150  Sum_probs=93.5

Q ss_pred             eCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEY  227 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~  227 (448)
                      .++..+|.--+|||||++....+-..+ .....+.+++|+-.++|-.|+.+.+..+.....  ...   ...+...-...
T Consensus       272 ~~~~G~IWHtqGSGKTlTm~~~A~~l~-~~~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~--~~~---~~~s~~~Lk~~  345 (962)
T COG0610         272 DGKGGYIWHTQGSGKTLTMFKLARLLL-ELPKNPKVLFVVDRKDLDDQTSDEFQSFGKVAF--NDP---KAESTSELKEL  345 (962)
T ss_pred             cCCceEEEeecCCchHHHHHHHHHHHH-hccCCCeEEEEechHHHHHHHHHHHHHHHHhhh--hcc---cccCHHHHHHH
Confidence            356799999999999998665544333 336778999999999999999999999875431  111   22333333444


Q ss_pred             HhcCCCcEEEEcHHHHHHHHHCC-CCcCCC-eeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCC
Q psy1548         228 LKTHNPQIVVGTPGRILALVRNK-KLNLSL-LKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLS  299 (448)
Q Consensus       228 l~~~~~~IlV~Tp~~l~~~l~~~-~~~~~~-i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~  299 (448)
                      +..+.-.|+|+|.+++....... .....+ =-.+|+||||+--.. .....+   -..+ ++...++||.|+-
T Consensus       346 l~~~~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHRSQ~G-~~~~~~---~~~~-~~a~~~gFTGTPi  414 (962)
T COG0610         346 LEDGKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRSQYG-ELAKLL---KKAL-KKAIFIGFTGTPI  414 (962)
T ss_pred             HhcCCCcEEEEEecccchhhhcccccccCCCcEEEEEechhhcccc-HHHHHH---HHHh-ccceEEEeeCCcc
Confidence            55444489999999998877654 111222 126899999975332 222222   3333 3377899999963

>KOG0386|consensus

Probab=98.17  E-value=4.5e-06  Score=88.56  Aligned_cols=65  Identities=18%  Similarity=0.158  Sum_probs=54.8

Q ss_pred             hHHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC
Q psy1548         340 EKNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       340 ~k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~  404 (448)
                      -|+..|-.++-++  .+++++.||....-..-+-.+|.-.++....+.|....++|-..++.|....
T Consensus       710 GKfELLDRiLPKLkatgHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~TK~~eRg~ll~~FN~Pd  776 (1157)
T KOG0386|consen  710 GKFELLDRILPKLKATGHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQTKVEERGDLLEIFNAPD  776 (1157)
T ss_pred             cHHHHHHhhhHHHHhcCcchhhHHHHHHHHHHHHHHHhhhhhheeeecCCcchhhHHHHHHHhcCCC
Confidence            3666666666554  4779999998888888888888888999999999999999999999999887

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=98.12  E-value=2.4e-05  Score=72.42  Aligned_cols=66  Identities=20%  Similarity=0.246  Sum_probs=48.2

Q ss_pred             hhhhhhhccccccceeeeeCcc-eeeeccCCChhHHHHHHHHHHhh------hccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         130 DTYLHRVARAGRFGTKAVLGMD-ILCQAKSGMGKTAVFVLATLQQL------ETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       130 ~~yQ~~~~~~~~~~~~~~~g~~-vli~apTGsGKT~~~~l~~l~~l------~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      ...|.+      ++..++.... .+|+||.|+|||.+.. .++..+      .....+.++|+++|+..-+.++.+.+.+
T Consensus         3 n~~Q~~------Ai~~~~~~~~~~~i~GpPGTGKT~~l~-~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    3 NESQRE------AIQSALSSNGITLIQGPPGTGKTTTLA-SIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             -HHHHH------HHHHHCTSSE-EEEE-STTSSHHHHHH-HHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CHHHHH------HHHHHHcCCCCEEEECCCCCChHHHHH-HHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            345888      8888888888 9999999999995433 333333      1234566899999999999998888777

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=98.02  E-value=4.7e-05  Score=82.30  Aligned_cols=114  Identities=22%  Similarity=0.206  Sum_probs=77.4

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHh
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK  229 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~  229 (448)
                      .--|..+.||-|||+++.+|++-....++   .+-||+..-=||..=.+++..+...+ ++.|+++..............
T Consensus       183 ~G~IAEM~TGEGKTLvAtlp~yLnAL~Gk---gVHvVTVNDYLA~RDaewmgply~fL-GLsvg~i~~~~~~~~~rr~aY  258 (1112)
T PRK12901        183 QGKIAEMATGEGKTLVATLPVYLNALTGN---GVHVVTVNDYLAKRDSEWMGPLYEFH-GLSVDCIDKHQPNSEARRKAY  258 (1112)
T ss_pred             CCceeeecCCCCchhHHHHHHHHHHHcCC---CcEEEEechhhhhccHHHHHHHHHHh-CCceeecCCCCCCHHHHHHhC
Confidence            44578899999999999999876655443   35666666678876667777777777 999998866332233322222


Q ss_pred             cCCCcEEEEcHHHH-HHHHHCC------CCcCCCeeEEEecchhHHH
Q psy1548         230 THNPQIVVGTPGRI-LALVRNK------KLNLSLLKHFILDECDKML  269 (448)
Q Consensus       230 ~~~~~IlV~Tp~~l-~~~l~~~------~~~~~~i~~lViDEah~l~  269 (448)
                        .+||.++|..-+ .++|+.+      ......+.+.|+||+|.++
T Consensus       259 --~~DItYgTn~EfGFDYLRDnm~~~~~~~vqR~~~fAIVDEvDSIL  303 (1112)
T PRK12901        259 --NADITYGTNNEFGFDYLRDNMAHSPEDLVQRKHNYAIVDEVDSVL  303 (1112)
T ss_pred             --CCcceecCCCccccccchhccccchHhhhCcCCceeEeechhhhh
Confidence              379999998765 2333321      1223557789999999765

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

Probab=97.97  E-value=4.1e-05  Score=75.99  Aligned_cols=109  Identities=16%  Similarity=0.252  Sum_probs=67.5

Q ss_pred             ceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhc
Q psy1548         151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKT  230 (448)
Q Consensus       151 ~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~  230 (448)
                      -++|.|..|||||+.++ -++..+.....+..++++++..+|...+.+.+..-...           .            
T Consensus         3 v~~I~G~aGTGKTvla~-~l~~~l~~~~~~~~~~~l~~n~~l~~~l~~~l~~~~~~-----------~------------   58 (352)
T PF09848_consen    3 VILITGGAGTGKTVLAL-NLAKELQNSEEGKKVLYLCGNHPLRNKLREQLAKKYNP-----------K------------   58 (352)
T ss_pred             EEEEEecCCcCHHHHHH-HHHHHhhccccCCceEEEEecchHHHHHHHHHhhhccc-----------c------------
Confidence            36899999999998754 34444422334568999999999998877766553200           0            


Q ss_pred             CCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhh------hhhHHHHHHHHHh
Q psy1548         231 HNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQ------LEMRRDVQEIFRS  284 (448)
Q Consensus       231 ~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~------~~~~~~~~~i~~~  284 (448)
                       .....+..|..+...+..........+++|+||||++...      ......+..+++.
T Consensus        59 -~~~~~~~~~~~~i~~~~~~~~~~~~~DviivDEAqrl~~~~~~~~~~~~~~~L~~i~~~  117 (352)
T PF09848_consen   59 -LKKSDFRKPTSFINNYSESDKEKNKYDVIIVDEAQRLRTKGDQYNNFSEPNQLDEIIKR  117 (352)
T ss_pred             -hhhhhhhhhHHHHhhcccccccCCcCCEEEEehhHhhhhccccccccccHHHHHHHHhc
Confidence             0122333444443333222344577899999999999772      0124566666665

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

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

Probab=97.95  E-value=0.00019  Score=79.87  Aligned_cols=133  Identities=17%  Similarity=0.155  Sum_probs=84.9

Q ss_pred             Cchhhhhhhccccccceeee-----eCcceeeeccCCChhHHHHHHHHHHhhhccCC-CeEEEEeeccHHHHHHHHHHHH
Q psy1548         128 DSDTYLHRVARAGRFGTKAV-----LGMDILCQAKSGMGKTAVFVLATLQQLETTDS-NVYVLVMCHTRELAFQISKEYE  201 (448)
Q Consensus       128 ~~~~yQ~~~~~~~~~~~~~~-----~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~-~~~~lil~Pt~~L~~q~~~~~~  201 (448)
                      .+++||..      .+..+.     .+.+.++....|.|||+..+..+......... .+.++++||+.. +.++.+.+.
T Consensus       338 ~lr~yq~~------g~~wl~~~l~~~~~~~ilaD~mglGKTiq~i~~l~~~~~~~~~~~~~~liv~p~s~-~~nw~~e~~  410 (866)
T COG0553         338 ELRPYQLE------GVNWLSELLRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVPASL-LSNWKREFE  410 (866)
T ss_pred             hhHHHHHH------HHHHHHHHHHhccCCCcccccccchhHHHHHHHHHhhhhcccCCCCCeEEEecHHH-HHHHHHHHh
Confidence            35888988      554433     26788888999999997765544442222222 357999999974 556666777


Q ss_pred             HhhccCCCce-EEEEEcCccc----HHhHHHHhcC----CCcEEEEcHHHHHHHH-HCCCCcCCCeeEEEecchhHHHh
Q psy1548         202 RFSKYMSNIK-VGVFFGGLPI----QKDEEYLKTH----NPQIVVGTPGRILALV-RNKKLNLSLLKHFILDECDKMLE  270 (448)
Q Consensus       202 ~~~~~~~~~~-v~~~~g~~~~----~~~~~~l~~~----~~~IlV~Tp~~l~~~l-~~~~~~~~~i~~lViDEah~l~~  270 (448)
                      ++..   .++ +....|....    ......+...    ..+++++|.+.+.... ....+.-....++|+||+|.+-+
T Consensus       411 k~~~---~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~v~itty~~l~~~~~~~~~l~~~~~~~~v~DEa~~ikn  486 (866)
T COG0553         411 KFAP---DLRLVLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGLKKIEWDRVVLDEAHRIKN  486 (866)
T ss_pred             hhCc---cccceeeeeCCcccccHHHHHHHHHhhhcccceeeEEechHHHHHHhhhhHHHHhhceeeeeehhhHHHHhh
Confidence            7764   445 6666666541    2222222221    1689999999887632 11233345567899999998644

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=97.86  E-value=1.7e-05  Score=85.95  Aligned_cols=79  Identities=16%  Similarity=0.170  Sum_probs=64.1

Q ss_pred             eeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHH
Q psy1548         121 FNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEY  200 (448)
Q Consensus       121 ~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~  200 (448)
                      |+|..+.+.   |.+.+++  ++..+..|+++++.+|||+|||++.+.|+|......+...+++|.+.|..-..|+.+++
T Consensus         6 FPy~~~y~~---Q~~~m~~--v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~sRThsQl~q~i~El   80 (705)
T TIGR00604         6 FPYEKIYPE---QRSYMRD--LKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEEL   80 (705)
T ss_pred             cCCCCCCHH---HHHHHHH--HHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhccccccEEEEcccchHHHHHHHHH
Confidence            445555555   9886664  55666679999999999999999999999987765554568999999999999999999


Q ss_pred             HHhh
Q psy1548         201 ERFS  204 (448)
Q Consensus       201 ~~~~  204 (448)
                      +++.
T Consensus        81 k~~~   84 (705)
T TIGR00604        81 RKLM   84 (705)
T ss_pred             Hhhh
Confidence            9854

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).

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

Probab=97.82  E-value=4.6e-05  Score=70.87  Aligned_cols=87  Identities=30%  Similarity=0.407  Sum_probs=71.3

Q ss_pred             CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCc-ccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCC
Q psy1548         178 DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGL-PIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSL  256 (448)
Q Consensus       178 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~-~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~  256 (448)
                      .+.|.+||||.+---|..+.+.++.|...  +..+.-+++.. ...++...+..+..+|.||||+++..++..+.+.+++
T Consensus       124 ~gsP~~lvvs~SalRa~dl~R~l~~~~~k--~~~v~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~~~L~l~~  201 (252)
T PF14617_consen  124 KGSPHVLVVSSSALRAADLIRALRSFKGK--DCKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLENGALSLSN  201 (252)
T ss_pred             CCCCEEEEEcchHHHHHHHHHHHHhhccC--CchHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHcCCCCccc
Confidence            45789999999988888888888887532  34444444443 6678888888878999999999999999999999999


Q ss_pred             eeEEEecchh
Q psy1548         257 LKHFILDECD  266 (448)
Q Consensus       257 i~~lViDEah  266 (448)
                      +++||||--|
T Consensus       202 l~~ivlD~s~  211 (252)
T PF14617_consen  202 LKRIVLDWSY  211 (252)
T ss_pred             CeEEEEcCCc
Confidence            9999999865

>KOG0333|consensus

Probab=97.81  E-value=1.6e-05  Score=79.01  Aligned_cols=95  Identities=36%  Similarity=0.509  Sum_probs=68.6

Q ss_pred             cccccccccccccchhhhhhhhccCceeeeccCCcccCCCCHHHHHHHhh-ccceeEeeccccCCcccccceeEeeccCC
Q psy1548          48 DEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIVD-CWRILVATNLFGRGMDIERVNIVFNYDMP  126 (448)
Q Consensus        48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~d~~~~~~v~~~~~p  126 (448)
                      +...+......+..+..++..+..+-.+.-.|.+ +...-....+..+.. .+.|+|||++++||||.++|..|+||+++
T Consensus       517 ~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~-k~qeQRe~aL~~fr~~t~dIlVaTDvAgRGIDIpnVSlVinydma  595 (673)
T KOG0333|consen  517 DPPIIIFVNTKKGADALAKILEKAGYKVTTLHGG-KSQEQRENALADFREGTGDILVATDVAGRGIDIPNVSLVINYDMA  595 (673)
T ss_pred             CCCEEEEEechhhHHHHHHHHhhccceEEEeeCC-ccHHHHHHHHHHHHhcCCCEEEEecccccCCCCCccceeeecchh
Confidence            4444555555566666676666655433333321 222233455666666 67999999999999999999999999999


Q ss_pred             CCchhhhhhhccccccc
Q psy1548         127 EDSDTYLHRVARAGRFG  143 (448)
Q Consensus       127 ~~~~~yQ~~~~~~~~~~  143 (448)
                      ..+++|=+.+||+|||.
T Consensus       596 ksieDYtHRIGRTgRAG  612 (673)
T KOG0333|consen  596 KSIEDYTHRIGRTGRAG  612 (673)
T ss_pred             hhHHHHHHHhccccccc
Confidence            99999999999999943

>KOG0388|consensus

Probab=97.73  E-value=0.00014  Score=74.75  Aligned_cols=151  Identities=17%  Similarity=0.201  Sum_probs=96.2

Q ss_pred             chhhhhhhccccccceeee----eCcceeeeccCCChhHHHHHHHHHHhhhccC-CCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         129 SDTYLHRVARAGRFGTKAV----LGMDILCQAKSGMGKTAVFVLATLQQLETTD-SNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       129 ~~~yQ~~~~~~~~~~~~~~----~g~~vli~apTGsGKT~~~~l~~l~~l~~~~-~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      +..||..      .+.++.    .|-|.|+....|.|||... +.++.++.... --+--|||+|...|-+. .+.+.+ 
T Consensus       568 LKEYQlk------GLnWLvnlYdqGiNGILADeMGLGKTVQs-isvlAhLaE~~nIwGPFLVVtpaStL~NW-aqEisr-  638 (1185)
T KOG0388|consen  568 LKEYQLK------GLNWLVNLYDQGINGILADEMGLGKTVQS-ISVLAHLAETHNIWGPFLVVTPASTLHNW-AQEISR-  638 (1185)
T ss_pred             hHHHhhc------cHHHHHHHHHccccceehhhhccchhHHH-HHHHHHHHHhccCCCceEEeehHHHHhHH-HHHHHH-
Confidence            4778888      555544    4889999999999999775 45555553332 12247889998877544 334444 


Q ss_pred             hccCCCceEEEEEcCcccHHhHHHH--------hcCCCcEEEEcHHHHHH---HHHCCCCcCCCeeEEEecchhHHHhhh
Q psy1548         204 SKYMSNIKVGVFFGGLPIQKDEEYL--------KTHNPQIVVGTPGRILA---LVRNKKLNLSLLKHFILDECDKMLEQL  272 (448)
Q Consensus       204 ~~~~~~~~v~~~~g~~~~~~~~~~l--------~~~~~~IlV~Tp~~l~~---~l~~~~~~~~~i~~lViDEah~l~~~~  272 (448)
                        ++|.+++..++|+.........+        .+.+.||+|+|.+.+..   ++++     -...+.|+|||+.+-+  
T Consensus       639 --FlP~~k~lpywGs~~eRkiLrKfw~rKnmY~rna~fhVviTSYQlvVtDeky~qk-----vKWQYMILDEAQAIKS--  709 (1185)
T KOG0388|consen  639 --FLPSFKVLPYWGSPSERKILRKFWNRKNMYRRNAPFHVVITSYQLVVTDEKYLQK-----VKWQYMILDEAQAIKS--  709 (1185)
T ss_pred             --hCccceeecCcCChhhhHHHHHhcchhhhhccCCCceEEEEeeeeeechHHHHHh-----hhhhheehhHHHHhhh--
Confidence              45789999999997654433331        23357999998876532   2221     2235799999998866  


Q ss_pred             hhHHHHHHHHHhCCCCCeEEEEeccCC
Q psy1548         273 EMRRDVQEIFRSSPHTKQVMMFSATLS  299 (448)
Q Consensus       273 ~~~~~~~~i~~~l~~~~q~i~~SAT~~  299 (448)
                      .....+..++...-  +-.++++.|.-
T Consensus       710 SsS~RWKtLLsF~c--RNRLLLTGTPI  734 (1185)
T KOG0388|consen  710 SSSSRWKTLLSFKC--RNRLLLTGTPI  734 (1185)
T ss_pred             hhhhHHHHHhhhhc--cceeeecCCcc
Confidence            34445555554321  22467777753

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=97.67  E-value=0.00063  Score=72.60  Aligned_cols=114  Identities=21%  Similarity=0.288  Sum_probs=82.0

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL  228 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l  228 (448)
                      ...-+.-..||-|||+++.+|+.-....++   .+.+++..-=||.--..++..+...+ ++.+++...+.+.......+
T Consensus        93 h~g~iaEM~TGEGKTL~atlp~ylnaL~gk---gVhvVTvNdYLA~RDae~m~~l~~~L-GlsvG~~~~~m~~~ek~~aY  168 (822)
T COG0653          93 HLGDIAEMRTGEGKTLVATLPAYLNALAGK---GVHVVTVNDYLARRDAEWMGPLYEFL-GLSVGVILAGMSPEEKRAAY  168 (822)
T ss_pred             cCCceeeeecCCchHHHHHHHHHHHhcCCC---CcEEeeehHHhhhhCHHHHHHHHHHc-CCceeeccCCCChHHHHHHH
Confidence            345577889999999999999865444433   46777777778887788888888888 99999999988766555554


Q ss_pred             hcCCCcEEEEcHHHH-HHHHHC------CCCcCCCeeEEEecchhHHH
Q psy1548         229 KTHNPQIVVGTPGRI-LALVRN------KKLNLSLLKHFILDECDKML  269 (448)
Q Consensus       229 ~~~~~~IlV~Tp~~l-~~~l~~------~~~~~~~i~~lViDEah~l~  269 (448)
                         .+||.++|-..+ .+.++.      .......+.+.|+||+|.++
T Consensus       169 ---~~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDEvDSIL  213 (822)
T COG0653         169 ---ACDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDEVDSIL  213 (822)
T ss_pred             ---hcCceeccccccCcchhhhhhhccHHHhhhccCCeEEEcchhhee
Confidence               379999998776 222221      11223457788999999664

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=97.62  E-value=0.00012  Score=66.23  Aligned_cols=139  Identities=13%  Similarity=0.152  Sum_probs=68.7

Q ss_pred             hhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCc
Q psy1548         131 TYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI  210 (448)
Q Consensus       131 ~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~  210 (448)
                      ..|..      ++..++...-+++.||.|+|||+.++..+++.+..+. ..+++++-|..+....    +    +++|+-
T Consensus         7 ~~Q~~------~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~-~~kiii~Rp~v~~~~~----l----GflpG~   71 (205)
T PF02562_consen    7 EEQKF------ALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEGE-YDKIIITRPPVEAGED----L----GFLPGD   71 (205)
T ss_dssp             HHHHH------HHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS--SEEEEEE-S--TT------------SS---
T ss_pred             HHHHH------HHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhCC-CcEEEEEecCCCCccc----c----ccCCCC
Confidence            34888      7778887788999999999999999999988887633 3477888787753111    1    111110


Q ss_pred             ---eEEEEEc-------CcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHH
Q psy1548         211 ---KVGVFFG-------GLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQE  280 (448)
Q Consensus       211 ---~v~~~~g-------~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~  280 (448)
                         +...+..       ..-.......+... ..|-+..+..+    +-.  .+.+ .++|+|||+.+.     ..++..
T Consensus        72 ~~eK~~p~~~p~~d~l~~~~~~~~~~~~~~~-~~Ie~~~~~~i----RGr--t~~~-~~iIvDEaQN~t-----~~~~k~  138 (205)
T PF02562_consen   72 LEEKMEPYLRPIYDALEELFGKEKLEELIQN-GKIEIEPLAFI----RGR--TFDN-AFIIVDEAQNLT-----PEELKM  138 (205)
T ss_dssp             ------TTTHHHHHHHTTTS-TTCHHHHHHT-TSEEEEEGGGG----TT----B-S-EEEEE-SGGG-------HHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhChHhHHHHhhc-CeEEEEehhhh----cCc--cccc-eEEEEecccCCC-----HHHHHH
Confidence               0000000       00000111111111 23444443321    111  2222 689999999653     456778


Q ss_pred             HHHhCCCCCeEEEEecc
Q psy1548         281 IFRSSPHTKQVMMFSAT  297 (448)
Q Consensus       281 i~~~l~~~~q~i~~SAT  297 (448)
                      ++.+...+++++++.-.
T Consensus       139 ilTR~g~~skii~~GD~  155 (205)
T PF02562_consen  139 ILTRIGEGSKIIITGDP  155 (205)
T ss_dssp             HHTTB-TT-EEEEEE--
T ss_pred             HHcccCCCcEEEEecCc
Confidence            88888888888887543

; GO: 0005524 ATP binding; PDB: 3B85_A.

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=97.61  E-value=0.00025  Score=67.22  Aligned_cols=146  Identities=17%  Similarity=0.169  Sum_probs=90.8

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL  228 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l  228 (448)
                      ..-.++--.||.||--...--+++....+  ..+.|+++.+..|..+..+.++.++..  .+.+..+..-.. . ....+
T Consensus        62 R~Gf~lGDGtGvGKGR~iAgiI~~n~l~G--r~r~vwvS~s~dL~~Da~RDl~DIG~~--~i~v~~l~~~~~-~-~~~~~  135 (303)
T PF13872_consen   62 RAGFFLGDGTGVGKGRQIAGIILENWLRG--RKRAVWVSVSNDLKYDAERDLRDIGAD--NIPVHPLNKFKY-G-DIIRL  135 (303)
T ss_pred             CcEEEeccCCCcCccchhHHHHHHHHHcC--CCceEEEECChhhhhHHHHHHHHhCCC--cccceechhhcc-C-cCCCC
Confidence            34567778899999876655566665543  337999999999999999999988754  333333322110 0 00112


Q ss_pred             hcCCCcEEEEcHHHHHHHHHCC---CCcC---------CCeeEEEecchhHHHhhh-------hhHHHHHHHHHhCCCCC
Q psy1548         229 KTHNPQIVVGTPGRILALVRNK---KLNL---------SLLKHFILDECDKMLEQL-------EMRRDVQEIFRSSPHTK  289 (448)
Q Consensus       229 ~~~~~~IlV~Tp~~l~~~l~~~---~~~~---------~~i~~lViDEah~l~~~~-------~~~~~~~~i~~~l~~~~  289 (448)
                         .-.|+++|...|..--..+   ...+         ..=.+||+||||.+.+..       .....+..+-+.+|. .
T Consensus       136 ---~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~sk~g~avl~LQ~~LP~-A  211 (303)
T PF13872_consen  136 ---KEGVLFSTYSTLISESQSGGKYRSRLDQLVDWCGEDFDGVIVFDECHKAKNLSSGSKKPSKTGIAVLELQNRLPN-A  211 (303)
T ss_pred             ---CCCccchhHHHHHhHHhccCCccchHHHHHHHHhcCCCceEEeccchhcCCCCccCccccHHHHHHHHHHHhCCC-C
Confidence               2359999998876654211   1100         112379999999886541       122445556666754 4


Q ss_pred             eEEEEeccCCccHHH
Q psy1548         290 QVMMFSATLSKEIRP  304 (448)
Q Consensus       290 q~i~~SAT~~~~~~~  304 (448)
                      +++.+|||--.+.+.
T Consensus       212 RvvY~SATgasep~N  226 (303)
T PF13872_consen  212 RVVYASATGASEPRN  226 (303)
T ss_pred             cEEEecccccCCCce
Confidence            599999997655433

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=97.59  E-value=0.0002  Score=75.38  Aligned_cols=147  Identities=13%  Similarity=0.224  Sum_probs=79.1

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH----h-hccCCCceEEEEEcCcccHHh
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER----F-SKYMSNIKVGVFFGGLPIQKD  224 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~----~-~~~~~~~~v~~~~g~~~~~~~  224 (448)
                      -++=|.+.||+|||.||+-.+...- ..-+-.+-|||+||.+.-.-+....+.    | .+.+.+.+...+.-+......
T Consensus        75 lNiDI~METGTGKTy~YlrtmfeLh-k~YG~~KFIivVPs~AIkeGv~~~s~~~~ehF~k~~Yent~~e~~i~~~~~~~~  153 (985)
T COG3587          75 LNIDILMETGTGKTYTYLRTMFELH-KKYGLFKFIIVVPSLAIKEGVFLTSKETTEHFFKSEYENTRLESYIYDEDIEKF  153 (985)
T ss_pred             ceeeEEEecCCCceeeHHHHHHHHH-HHhCceeEEEEeccHHHHhhhHHHHHHHHHHHhhhhccCcceeEEeechHHHHH
Confidence            4778899999999999987665432 222335789999999976543333222    2 222223344333332211111


Q ss_pred             HHHHhcCCCcEEEEcHHHHHH------HHHCCCCcC--------------CCe-eEEEecchhHHHhhhhhHHHHHHHHH
Q psy1548         225 EEYLKTHNPQIVVGTPGRILA------LVRNKKLNL--------------SLL-KHFILDECDKMLEQLEMRRDVQEIFR  283 (448)
Q Consensus       225 ~~~l~~~~~~IlV~Tp~~l~~------~l~~~~~~~--------------~~i-~~lViDEah~l~~~~~~~~~~~~i~~  283 (448)
                       ..-.++.|.+++.|...+..      ++.+.....              ..+ -.+|+||-|+|.........+..+  
T Consensus       154 -~~~~~~~~~vLl~~~~Afnk~~inan~iN~~s~~~~~~~~~~~spvd~la~~rPIvIvDEPh~f~~~~k~~~~i~~l--  230 (985)
T COG3587         154 -KFKSNNKPCVLLIFVSAFNKEEINANMINSESMENTNLFNGATSPVDALASMRPIVIVDEPHRFLGDDKTYGAIKQL--  230 (985)
T ss_pred             -hhccCCCceEEEEehhhhccccccccccchhhhcccCccccccCHHHHHHhcCCEEEecChhhcccchHHHHHHHhh--
Confidence             11123347777777654421      222211111              111 269999999997731233333322  


Q ss_pred             hCCCCCeEEEEeccCCccHH
Q psy1548         284 SSPHTKQVMMFSATLSKEIR  303 (448)
Q Consensus       284 ~l~~~~q~i~~SAT~~~~~~  303 (448)
                       .|  .-++=++||+++...
T Consensus       231 -~p--l~ilRfgATfkd~y~  247 (985)
T COG3587         231 -NP--LLILRFGATFKDEYN  247 (985)
T ss_pred             -Cc--eEEEEecccchhhhc
Confidence             21  236779999987643

>PF13245 AAA_19: Part of AAA domain

Probab=97.55  E-value=0.00016  Score=54.57  Aligned_cols=52  Identities=27%  Similarity=0.367  Sum_probs=37.1

Q ss_pred             Ccc-eeeeccCCChhHHHHHHHHHHhhh-ccCCCeEEEEeeccHHHHHHHHHHH
Q psy1548         149 GMD-ILCQAKSGMGKTAVFVLATLQQLE-TTDSNVYVLVMCHTRELAFQISKEY  200 (448)
Q Consensus       149 g~~-vli~apTGsGKT~~~~l~~l~~l~-~~~~~~~~lil~Pt~~L~~q~~~~~  200 (448)
                      +.+ ++|.+|.|||||...+-.+...+. ....+.++++++|++..+..+.+.+
T Consensus         9 ~~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen    9 GSPLFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             hCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCHHHHHHHHHHH
Confidence            444 556999999999665544444442 1222568999999999999987777

>PRK10536 hypothetical protein; Provisional

Probab=97.53  E-value=0.00058  Score=63.60  Aligned_cols=145  Identities=11%  Similarity=0.086  Sum_probs=78.2

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHH---------
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELA---------  193 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~---------  193 (448)
                      +....+....|..      .+..+..+..+++.||+|+|||+.....+++.+... .-.++++.-|+.+..         
T Consensus        54 ~~~i~p~n~~Q~~------~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~-~~~kIiI~RP~v~~ge~LGfLPG~  126 (262)
T PRK10536         54 TSPILARNEAQAH------YLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHK-DVDRIIVTRPVLQADEDLGFLPGD  126 (262)
T ss_pred             CccccCCCHHHHH------HHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcC-CeeEEEEeCCCCCchhhhCcCCCC
Confidence            3344455555888      777777788899999999999988777777655432 233455555665421         


Q ss_pred             --HHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHH-hcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHh
Q psy1548         194 --FQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL-KTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLE  270 (448)
Q Consensus       194 --~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l-~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~  270 (448)
                        +.+.-.+..+...+ ..    +.|.    .....+ ....-.|-|...    .+++...+  . -.++|+|||+.+. 
T Consensus       127 ~~eK~~p~~~pi~D~L-~~----~~~~----~~~~~~~~~~~~~Iei~~l----~ymRGrtl--~-~~~vIvDEaqn~~-  189 (262)
T PRK10536        127 IAEKFAPYFRPVYDVL-VR----RLGA----SFMQYCLRPEIGKVEIAPF----AYMRGRTF--E-NAVVILDEAQNVT-  189 (262)
T ss_pred             HHHHHHHHHHHHHHHH-HH----HhCh----HHHHHHHHhccCcEEEecH----HHhcCCcc--c-CCEEEEechhcCC-
Confidence              11111111111111 00    0011    111111 111123444432    23333332  2 2689999999652 


Q ss_pred             hhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         271 QLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       271 ~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                          ...+..++..++.+.++|+..
T Consensus       190 ----~~~~k~~ltR~g~~sk~v~~G  210 (262)
T PRK10536        190 ----AAQMKMFLTRLGENVTVIVNG  210 (262)
T ss_pred             ----HHHHHHHHhhcCCCCEEEEeC
Confidence                266778888888888887764

>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

Probab=97.46  E-value=0.00011  Score=79.22  Aligned_cols=72  Identities=22%  Similarity=0.265  Sum_probs=54.6

Q ss_pred             CchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         128 DSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       128 ~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      ..++.|.+++.+  ....+..|+.+++.||||+|||++|++|++......+  .+++|.++|+.|-.|+.+....+
T Consensus        15 ~~r~~Q~~~~~~--v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~~--~~viist~t~~lq~q~~~~~~~~   86 (654)
T COG1199          15 EPRPEQREMAEA--VAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEG--KKVIISTRTKALQEQLLEEDLPI   86 (654)
T ss_pred             CCCHHHHHHHHH--HHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHcC--CcEEEECCCHHHHHHHHHhhcch
Confidence            334449885553  2234445667999999999999999999998765543  57999999999999988776554

>PF12340 DUF3638: Protein of unknown function (DUF3638); InterPro: IPR022099 This domain family is found in eukaryotes, and is approximately 230 amino acids in length

Probab=97.44  E-value=0.00067  Score=61.98  Aligned_cols=110  Identities=20%  Similarity=0.193  Sum_probs=65.4

Q ss_pred             hhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCC
Q psy1548         130 DTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  209 (448)
Q Consensus       130 ~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  209 (448)
                      |+-|.+++++  .+ .-.+|+|.+.+.-+|.|||.+ ++|++..+..++.. -+.+++| ++|..|..+.+..-.+..-+
T Consensus        25 R~~Q~~ia~~--mi-~~~~~~n~v~QlnMGeGKTsV-I~Pmla~~LAdg~~-LvrviVp-k~Ll~q~~~~L~~~lg~l~~   98 (229)
T PF12340_consen   25 RPVQVEIARE--MI-SPPSGKNSVMQLNMGEGKTSV-IVPMLALALADGSR-LVRVIVP-KALLEQMRQMLRSRLGGLLN   98 (229)
T ss_pred             eHHHHHHHHH--Hh-CCCCCCCeEeeecccCCccch-HHHHHHHHHcCCCc-EEEEEcC-HHHHHHHHHHHHHHHHHHhC
Confidence            4447774442  12 223689999999999999966 68888877765543 4455555 46888888877754332214


Q ss_pred             ceEEEE--EcCcccHH-h---HH----HHhcCCCcEEEEcHHHHHHH
Q psy1548         210 IKVGVF--FGGLPIQK-D---EE----YLKTHNPQIVVGTPGRILAL  246 (448)
Q Consensus       210 ~~v~~~--~g~~~~~~-~---~~----~l~~~~~~IlV~Tp~~l~~~  246 (448)
                      -++..+  .-..+... .   ..    ..... -.|+++||+.++++
T Consensus        99 r~i~~lpFsR~~~~~~~~~~~~~~l~~~~~~~-~gill~~PEhilSf  144 (229)
T PF12340_consen   99 RRIYHLPFSRSTPLTPETLEKIRQLLEECMRS-GGILLATPEHILSF  144 (229)
T ss_pred             CeeEEecccCCCCCCHHHHHHHHHHHHHHHHc-CCEEEeChHHHHHH
Confidence            344333  22222111 1   11    11122 46999999998764

There are two conserved sequence motifs: LLE and NMG.

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=97.40  E-value=0.00084  Score=70.70  Aligned_cols=140  Identities=14%  Similarity=0.190  Sum_probs=82.3

Q ss_pred             hhhhhhccccccceeeeeCcceeeeccCCChhHHHH--HHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCC
Q psy1548         131 TYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVF--VLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS  208 (448)
Q Consensus       131 ~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~--~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  208 (448)
                      +.|+.      ++..++..+-.++.|+.|+|||.+.  ++..+..........++++.+||-.-+..+.+.+......+ 
T Consensus       148 ~~Qk~------A~~~al~~~~~vitGgpGTGKTt~v~~ll~~l~~~~~~~~~~~I~l~APTGkAA~rL~e~~~~~~~~l-  220 (586)
T TIGR01447       148 NWQKV------AVALALKSNFSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPTGKAAARLAESLRKAVKNL-  220 (586)
T ss_pred             HHHHH------HHHHHhhCCeEEEEcCCCCCHHHHHHHHHHHHHHhccccCCCcEEEECCcHHHHHHHHHHHHhhhccc-
Confidence            45988      8888888899999999999999763  22223222211123579999999987777666555432221 


Q ss_pred             CceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHC------CCCcCCCeeEEEecchhHHHhhhhhHHHHHHHH
Q psy1548         209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRN------KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIF  282 (448)
Q Consensus       209 ~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~------~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~  282 (448)
                      ...           ..   .... ..+-..|-.+++.....      ..-+...+++||||||-++ +.    ..+..++
T Consensus       221 ~~~-----------~~---~~~~-~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIiDEaSMv-d~----~l~~~ll  280 (586)
T TIGR01447       221 AAA-----------EA---LIAA-LPSEAVTIHRLLGIKPDTKRFRHHERNPLPLDVLVVDEASMV-DL----PLMAKLL  280 (586)
T ss_pred             ccc-----------hh---hhhc-cccccchhhhhhcccCCcchhhhcccCCCcccEEEEcccccC-CH----HHHHHHH
Confidence            100           00   0000 11123343333322110      1112345789999999844 32    3466678


Q ss_pred             HhCCCCCeEEEEecc
Q psy1548         283 RSSPHTKQVMMFSAT  297 (448)
Q Consensus       283 ~~l~~~~q~i~~SAT  297 (448)
                      +.+++..++|++.=.
T Consensus       281 ~al~~~~rlIlvGD~  295 (586)
T TIGR01447       281 KALPPNTKLILLGDK  295 (586)
T ss_pred             HhcCCCCEEEEECCh
Confidence            888888998887654

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

>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=97.38  E-value=3.6e-05  Score=58.36  Aligned_cols=73  Identities=22%  Similarity=0.246  Sum_probs=52.5

Q ss_pred             HHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         372 TLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       372 ~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      +.|++.|+++..+||++++++|..++++|++++.  .|+++|.....++  ++...-.+-+.+.|.+...+.|+.||
T Consensus         1 ~~L~~~~~~~~~i~~~~~~~~r~~~~~~f~~~~~--~vli~t~~~~~Gi--d~~~~~~vi~~~~~~~~~~~~Q~~GR   73 (78)
T PF00271_consen    1 KFLEKKGIKVAIIHGDMSQKERQEILKKFNSGEI--RVLIATDILGEGI--DLPDASHVIFYDPPWSPEEYIQRIGR   73 (78)
T ss_dssp             HHHHHTTSSEEEESTTSHHHHHHHHHHHHHTTSS--SEEEESCGGTTSS--TSTTESEEEESSSESSHHHHHHHHTT
T ss_pred             CChHHCCCcEEEEECCCCHHHHHHHHHHhhccCc--eEEEeeccccccc--cccccccccccccCCCHHHHHHHhhc
Confidence            4688899999999999999999999999999985  6777776533332  23322333444556666667777776

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 ....

>KOG0331|consensus

Probab=97.37  E-value=0.00012  Score=74.31  Aligned_cols=43  Identities=44%  Similarity=0.915  Sum_probs=41.8

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR  141 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~  141 (448)
                      ..|+|||+.++||+|.++|+.|+||++|..+++|=+..||+||
T Consensus       392 ~~vLVATdVAaRGLDi~dV~lVInydfP~~vEdYVHRiGRTGR  434 (519)
T KOG0331|consen  392 SPVLVATDVAARGLDVPDVDLVINYDFPNNVEDYVHRIGRTGR  434 (519)
T ss_pred             cceEEEcccccccCCCccccEEEeCCCCCCHHHHHhhcCcccc
Confidence            4899999999999999999999999999999999999999998

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=97.37  E-value=0.00037  Score=63.11  Aligned_cols=118  Identities=18%  Similarity=0.204  Sum_probs=66.0

Q ss_pred             hhhhccccccceeeeeCc--ceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCc
Q psy1548         133 LHRVARAGRFGTKAVLGM--DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI  210 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~g~--~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~  210 (448)
                      |.+      ++..++...  -.+++||.|+|||.+ +-.+...+...  +.++++++||...+..+.+..        +.
T Consensus         6 Q~~------a~~~~l~~~~~~~~l~G~aGtGKT~~-l~~~~~~~~~~--g~~v~~~apT~~Aa~~L~~~~--------~~   68 (196)
T PF13604_consen    6 QRE------AVRAILTSGDRVSVLQGPAGTGKTTL-LKALAEALEAA--GKRVIGLAPTNKAAKELREKT--------GI   68 (196)
T ss_dssp             HHH------HHHHHHHCTCSEEEEEESTTSTHHHH-HHHHHHHHHHT--T--EEEEESSHHHHHHHHHHH--------TS
T ss_pred             HHH------HHHHHHhcCCeEEEEEECCCCCHHHH-HHHHHHHHHhC--CCeEEEECCcHHHHHHHHHhh--------Cc
Confidence            888      777776543  477889999999975 33444444433  468999999998877754431        11


Q ss_pred             eEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCC----CcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCC
Q psy1548         211 KVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK----LNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSP  286 (448)
Q Consensus       211 ~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~----~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~  286 (448)
                      .+                         .|-.+++.......    ..+...+++||||+-.+..     ..+..++...+
T Consensus        69 ~a-------------------------~Ti~~~l~~~~~~~~~~~~~~~~~~vliVDEasmv~~-----~~~~~ll~~~~  118 (196)
T PF13604_consen   69 EA-------------------------QTIHSFLYRIPNGDDEGRPELPKKDVLIVDEASMVDS-----RQLARLLRLAK  118 (196)
T ss_dssp             -E-------------------------EEHHHHTTEECCEECCSSCC-TSTSEEEESSGGG-BH-----HHHHHHHHHS-
T ss_pred             ch-------------------------hhHHHHHhcCCcccccccccCCcccEEEEecccccCH-----HHHHHHHHHHH
Confidence            11                         12111111111100    0144556899999996533     34566666666


Q ss_pred             C-CCeEEEEecc
Q psy1548         287 H-TKQVMMFSAT  297 (448)
Q Consensus       287 ~-~~q~i~~SAT  297 (448)
                      . ..+++++.=+
T Consensus       119 ~~~~klilvGD~  130 (196)
T PF13604_consen  119 KSGAKLILVGDP  130 (196)
T ss_dssp             T-T-EEEEEE-T
T ss_pred             hcCCEEEEECCc
Confidence            5 6777777654

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=97.33  E-value=0.0028  Score=67.02  Aligned_cols=139  Identities=14%  Similarity=0.160  Sum_probs=82.2

Q ss_pred             hhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhc--cCCCeEEEEeeccHHHHHHHHHHHHHhhccCC
Q psy1548         131 TYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLET--TDSNVYVLVMCHTRELAFQISKEYERFSKYMS  208 (448)
Q Consensus       131 ~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~--~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  208 (448)
                      +.|+.      ++...+..+-.+|.|+.|+|||.+. ..++..+..  .....++.+.+||..-|..+.+.+......+ 
T Consensus       155 d~Qk~------Av~~a~~~~~~vItGgpGTGKTt~v-~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~~~~~~~-  226 (615)
T PRK10875        155 DWQKV------AAAVALTRRISVISGGPGTGKTTTV-AKLLAALIQLADGERCRIRLAAPTGKAAARLTESLGKALRQL-  226 (615)
T ss_pred             HHHHH------HHHHHhcCCeEEEEeCCCCCHHHHH-HHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHHhhhhcc-
Confidence            56999      8888888889999999999999663 223322222  1223578889999988877766555433222 


Q ss_pred             CceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHC------CCCcCCCeeEEEecchhHHHhhhhhHHHHHHHH
Q psy1548         209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRN------KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIF  282 (448)
Q Consensus       209 ~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~------~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~  282 (448)
                      +.           ....   ... ...-..|-.+++.....      ...+.-..+++|+||+-++ +    ...+..++
T Consensus       227 ~~-----------~~~~---~~~-~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIvDEaSMv-d----~~lm~~ll  286 (615)
T PRK10875        227 PL-----------TDEQ---KKR-IPEEASTLHRLLGAQPGSQRLRYHAGNPLHLDVLVVDEASMV-D----LPMMARLI  286 (615)
T ss_pred             cc-----------chhh---hhc-CCCchHHHHHHhCcCCCccchhhccccCCCCCeEEEChHhcc-c----HHHHHHHH
Confidence            11           0000   000 01112233333222111      1112344689999999944 4    24566778


Q ss_pred             HhCCCCCeEEEEecc
Q psy1548         283 RSSPHTKQVMMFSAT  297 (448)
Q Consensus       283 ~~l~~~~q~i~~SAT  297 (448)
                      +.+++..++|++.=.
T Consensus       287 ~al~~~~rlIlvGD~  301 (615)
T PRK10875        287 DALPPHARVIFLGDR  301 (615)
T ss_pred             HhcccCCEEEEecch
Confidence            888999999888655

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=97.32  E-value=0.00016  Score=73.61  Aligned_cols=45  Identities=51%  Similarity=0.953  Sum_probs=42.5

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      .+|+|||+++++|||+++++.|++|+.|.....|-+.+||+||..
T Consensus       306 ~~vLVaTdv~~rGiDip~v~~VI~~d~P~s~~~yiqR~GR~gR~G  350 (423)
T PRK04837        306 LDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAG  350 (423)
T ss_pred             CcEEEEechhhcCCCccccCEEEEeCCCCchhheEeccccccCCC
Confidence            489999999999999999999999999999999999999999943

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=97.31  E-value=0.00026  Score=53.60  Aligned_cols=76  Identities=25%  Similarity=0.295  Sum_probs=54.9

Q ss_pred             HHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         369 ALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       369 ~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      .++..|++.++.+..+||+++.++|..+++.|+++..  .|.++|.....+.  ++...-.+-+...|.+...+.++.||
T Consensus         2 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~--~vli~t~~~~~Gi--~~~~~~~vi~~~~~~~~~~~~Q~~gR   77 (82)
T smart00490        2 ELAELLKELGIKVARLHGGLSQEEREEILEKFNNGKI--KVLVATDVAERGL--DLPGVDLVIIYDLPWSPASYIQRIGR   77 (82)
T ss_pred             HHHHHHHHCCCeEEEEECCCCHHHHHHHHHHHHcCCC--eEEEECChhhCCc--ChhcCCEEEEeCCCCCHHHHHHhhcc
Confidence            5678888889999999999999999999999999874  6666665322222  34433344445556666677788777

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.28  E-value=0.0059  Score=60.94  Aligned_cols=132  Identities=12%  Similarity=0.177  Sum_probs=73.5

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhc-cCCCeEEEEee--ccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE  225 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~-~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~  225 (448)
                      ++.+++.||||+|||.+..--+...... ...+.++.+++  +.|.-+..   +++.++..+ ++.+.            
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~e---QL~~~a~~l-gvpv~------------  237 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKK---QIQTYGDIM-GIPVK------------  237 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHH---HHHHHhhcC-CcceE------------
Confidence            4678999999999997764333222111 11233444443  44444443   355555544 44331            


Q ss_pred             HHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCC-CeEEEEeccCCc-cHH
Q psy1548         226 EYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHT-KQVMMFSATLSK-EIR  303 (448)
Q Consensus       226 ~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~-~q~i~~SAT~~~-~~~  303 (448)
                                .+-++..+...+..    +.+.+++++|++.+..........+..++...... ..++.+|||... .+.
T Consensus       238 ----------~~~~~~~l~~~L~~----~~~~DlVLIDTaGr~~~~~~~l~el~~~l~~~~~~~e~~LVlsat~~~~~~~  303 (388)
T PRK12723        238 ----------AIESFKDLKEEITQ----SKDFDLVLVDTIGKSPKDFMKLAEMKELLNACGRDAEFHLAVSSTTKTSDVK  303 (388)
T ss_pred             ----------eeCcHHHHHHHHHH----hCCCCEEEEcCCCCCccCHHHHHHHHHHHHhcCCCCeEEEEEcCCCCHHHHH
Confidence                      11234444444432    35678999999997754312345556666655433 467889999864 355


Q ss_pred             HHHHHhc
Q psy1548         304 PVCKKFM  310 (448)
Q Consensus       304 ~~~~~~l  310 (448)
                      +....|.
T Consensus       304 ~~~~~~~  310 (388)
T PRK12723        304 EIFHQFS  310 (388)
T ss_pred             HHHHHhc
Confidence            5556553

>KOG1802|consensus

Probab=97.25  E-value=0.00061  Score=69.92  Aligned_cols=83  Identities=18%  Similarity=0.060  Sum_probs=61.0

Q ss_pred             eEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHH
Q psy1548         119 IVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK  198 (448)
Q Consensus       119 ~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~  198 (448)
                      .++++...+.-   |..      |..+++...=.||++|.|+|||.+..--+++.+..  ....+|+.+|+.--+.|+.+
T Consensus       404 s~~~lpkLN~S---Q~~------AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~--~~~~VLvcApSNiAVDqLae  472 (935)
T KOG1802|consen  404 SVPNLPKLNAS---QSN------AVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ--HAGPVLVCAPSNIAVDQLAE  472 (935)
T ss_pred             cCCCchhhchH---HHH------HHHHHHcCCceeeecCCCCCceehhHHHHHHHHHh--cCCceEEEcccchhHHHHHH
Confidence            34444444555   888      77788888888999999999998865555554443  34479999999998899888


Q ss_pred             HHHHhhccCCCceEEEEEc
Q psy1548         199 EYERFSKYMSNIKVGVFFG  217 (448)
Q Consensus       199 ~~~~~~~~~~~~~v~~~~g  217 (448)
                      .+.+.     ++++..++.
T Consensus       473 KIh~t-----gLKVvRl~a  486 (935)
T KOG1802|consen  473 KIHKT-----GLKVVRLCA  486 (935)
T ss_pred             HHHhc-----CceEeeeeh
Confidence            77764     567766654

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=97.20  E-value=0.0009  Score=55.96  Aligned_cols=19  Identities=21%  Similarity=0.295  Sum_probs=12.9

Q ss_pred             CcceeeeccCCChhHHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVFV  167 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~  167 (448)
                      ++.++|.||+|+|||.+..
T Consensus         4 ~~~~~i~G~~G~GKT~~~~   22 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIK   22 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHH
Confidence            4678999999999997643

>KOG0989|consensus

Probab=97.19  E-value=0.0021  Score=60.60  Aligned_cols=58  Identities=24%  Similarity=0.451  Sum_probs=41.5

Q ss_pred             CCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCc---cHHHHHHHhc
Q psy1548         251 KLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSK---EIRPVCKKFM  310 (448)
Q Consensus       251 ~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~---~~~~~~~~~l  310 (448)
                      ....+.++.||+||||.|..  +-+..+...+...+....+++.+.-+..   .+..-+.+|.
T Consensus       124 ~~~~~~fKiiIlDEcdsmts--daq~aLrr~mE~~s~~trFiLIcnylsrii~pi~SRC~Kfr  184 (346)
T KOG0989|consen  124 GYPCPPFKIIILDECDSMTS--DAQAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQKFR  184 (346)
T ss_pred             CCCCCcceEEEEechhhhhH--HHHHHHHHHHhccccceEEEEEcCChhhCChHHHhhHHHhc
Confidence            34456678999999999877  5777788888888888888888776543   3333344443

>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=97.17  E-value=0.00035  Score=52.87  Aligned_cols=46  Identities=37%  Similarity=0.720  Sum_probs=42.6

Q ss_pred             hhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccc
Q psy1548          96 VDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR  141 (448)
Q Consensus        96 ~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~  141 (448)
                      .....|+++|+++++|+|.+.+..|+.+..|.....|.|.+||++|
T Consensus        31 ~~~~~vli~t~~~~~Gid~~~~~~vi~~~~~~~~~~~~Q~~GR~~R   76 (78)
T PF00271_consen   31 SGEIRVLIATDILGEGIDLPDASHVIFYDPPWSPEEYIQRIGRAGR   76 (78)
T ss_dssp             TTSSSEEEESCGGTTSSTSTTESEEEESSSESSHHHHHHHHTTSST
T ss_pred             ccCceEEEeeccccccccccccccccccccCCCHHHHHHHhhcCCC
Confidence            3356999999999999999999999999999999999999999887

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 ....

>KOG1803|consensus

Probab=97.13  E-value=0.00055  Score=69.75  Aligned_cols=68  Identities=16%  Similarity=0.123  Sum_probs=49.8

Q ss_pred             CCCCchhhhhhhccccccceeeeeCc-ceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHH
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGM-DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYE  201 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~-~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  201 (448)
                      .|..+++-|..      ++..+.+.+ -.+++||.|+|||.+...-+.+.+..+   .++|+.+||..-+..+.+.+.
T Consensus       182 ~~~~ln~SQk~------Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk~~---k~VLVcaPSn~AVdNiverl~  250 (649)
T KOG1803|consen  182 FNKNLNSSQKA------AVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQK---KRVLVCAPSNVAVDNIVERLT  250 (649)
T ss_pred             CCccccHHHHH------HHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHHcC---CeEEEEcCchHHHHHHHHHhc
Confidence            34455666888      777766664 468899999999988666555555433   489999999998888777543

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

Probab=97.06  E-value=0.00053  Score=71.43  Aligned_cols=56  Identities=45%  Similarity=0.784  Sum_probs=47.7

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeecc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAK  157 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~ap  157 (448)
                      ..|+|||++++||||++++..|+||+.|...+.|=+.+||+||+.   ..|..+.+..|
T Consensus       324 ~~vLVaTDvaaRGiDi~~v~~VinyD~p~~~e~yvHRiGRTgRaG---~~G~ai~fv~~  379 (513)
T COG0513         324 LRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAG---RKGVAISFVTE  379 (513)
T ss_pred             CCEEEEechhhccCCccccceeEEccCCCCHHHheeccCccccCC---CCCeEEEEeCc
Confidence            499999999999999999999999999999999999999999955   34444444444

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=97.03  E-value=0.00042  Score=71.32  Aligned_cols=44  Identities=45%  Similarity=0.867  Sum_probs=41.9

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      .+|+|||+++++|+|+++++.|++|..|.....|-+.+||+||+
T Consensus       296 ~~iLVaTdv~~rGiDip~v~~VI~~~~P~~~~~yvqR~GRaGR~  339 (456)
T PRK10590        296 IRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRA  339 (456)
T ss_pred             CcEEEEccHHhcCCCcccCCEEEEeCCCCCHHHhhhhccccccC
Confidence            47999999999999999999999999999999999999999994

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=97.03  E-value=0.00052  Score=70.15  Aligned_cols=45  Identities=51%  Similarity=0.885  Sum_probs=42.2

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ...|+|||+++++|+|.+++..|++|+.|.....|.+.+||+||.
T Consensus       295 ~~~vLVaTd~~~~GiDip~v~~VI~~d~p~s~~~yiqr~GR~gR~  339 (434)
T PRK11192        295 RVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRA  339 (434)
T ss_pred             CCcEEEEccccccCccCCCCCEEEEECCCCCHHHHhhcccccccC
Confidence            348999999999999999999999999999999999999999993

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

Probab=97.01  E-value=0.00043  Score=72.34  Aligned_cols=45  Identities=42%  Similarity=0.818  Sum_probs=42.4

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      ..|+|||++++||+|+++++.|++|+.|..+..|-+.+|||||..
T Consensus       419 ~~ILVaTdvl~rGiDip~v~~VI~~d~P~s~~~yihRiGRaGR~g  463 (518)
T PLN00206        419 VPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMG  463 (518)
T ss_pred             CCEEEEecHhhccCCcccCCEEEEeCCCCCHHHHHHhccccccCC
Confidence            389999999999999999999999999999999999999999943

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=96.97  E-value=0.017  Score=57.07  Aligned_cols=138  Identities=17%  Similarity=0.247  Sum_probs=75.7

Q ss_pred             eeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHH
Q psy1548         147 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE  226 (448)
Q Consensus       147 ~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~  226 (448)
                      ..++-+.+.||||-|||.+.+--+.......+.....||-+-|--..  ..++++.++..+ ++.+.++...........
T Consensus       201 ~~~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIG--A~EQLk~Ya~im-~vp~~vv~~~~el~~ai~  277 (407)
T COG1419         201 EQKRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIG--AVEQLKTYADIM-GVPLEVVYSPKELAEAIE  277 (407)
T ss_pred             ccCcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhh--HHHHHHHHHHHh-CCceEEecCHHHHHHHHH
Confidence            44788999999999999775432222221222333455555444332  234566776666 666666555554444444


Q ss_pred             HHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCc-cHHHH
Q psy1548         227 YLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSK-EIRPV  305 (448)
Q Consensus       227 ~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~-~~~~~  305 (448)
                      .+.+. -.|+|-|.|                         +-..+......+..++.......-.+.+|||... ++++.
T Consensus       278 ~l~~~-d~ILVDTaG-------------------------rs~~D~~~i~el~~~~~~~~~i~~~Lvlsat~K~~dlkei  331 (407)
T COG1419         278 ALRDC-DVILVDTAG-------------------------RSQYDKEKIEELKELIDVSHSIEVYLVLSATTKYEDLKEI  331 (407)
T ss_pred             HhhcC-CEEEEeCCC-------------------------CCccCHHHHHHHHHHHhccccceEEEEEecCcchHHHHHH
Confidence            44432 334444443                         2111113344555555555444556788888754 46667


Q ss_pred             HHHhcCCC
Q psy1548         306 CKKFMHDP  313 (448)
Q Consensus       306 ~~~~l~~~  313 (448)
                      +..|-.-|
T Consensus       332 ~~~f~~~~  339 (407)
T COG1419         332 IKQFSLFP  339 (407)
T ss_pred             HHHhccCC
Confidence            77665433

>KOG0336|consensus

Probab=96.95  E-value=0.0005  Score=66.66  Aligned_cols=43  Identities=51%  Similarity=0.958  Sum_probs=41.1

Q ss_pred             ceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548         100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus       100 ~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      +|+|+|++++||+|.+++..|+||++|..++.|-+..||+||+
T Consensus       517 rILvaTDlaSRGlDv~DiTHV~NyDFP~nIeeYVHRvGrtGRa  559 (629)
T KOG0336|consen  517 RILVATDLASRGLDVPDITHVYNYDFPRNIEEYVHRVGRTGRA  559 (629)
T ss_pred             EEEEEechhhcCCCchhcceeeccCCCccHHHHHHHhcccccC
Confidence            8899999999999999999999999999999999999998884

>PTZ00110 helicase; Provisional

Probab=96.94  E-value=0.00067  Score=71.26  Aligned_cols=64  Identities=31%  Similarity=0.616  Sum_probs=50.0

Q ss_pred             HHHHHhh-ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeecc
Q psy1548          91 ILRAIVD-CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAK  157 (448)
Q Consensus        91 ~~~~~~~-~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~ap  157 (448)
                      +++.+.+ ...|+|||+++++|+|+++++.|++|+.|..+.+|-|.+||+||+-.   .|..+.+..+
T Consensus       419 il~~F~~G~~~ILVaTdv~~rGIDi~~v~~VI~~d~P~s~~~yvqRiGRtGR~G~---~G~ai~~~~~  483 (545)
T PTZ00110        419 VLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGA---KGASYTFLTP  483 (545)
T ss_pred             HHHHHhcCCCcEEEEcchhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCC---CceEEEEECc
Confidence            3444433 34799999999999999999999999999999999999999999532   3444444433

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=96.94  E-value=0.0032  Score=68.20  Aligned_cols=124  Identities=15%  Similarity=0.126  Sum_probs=73.1

Q ss_pred             chhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCC
Q psy1548         129 SDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS  208 (448)
Q Consensus       129 ~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  208 (448)
                      +.+-|.+      ++..+..++-+++.|+.|+|||.+. -.++..+....+...+++++||..-+..+.+.    .    
T Consensus       324 l~~~Q~~------Ai~~~~~~~~~iitGgpGTGKTt~l-~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e~----~----  388 (720)
T TIGR01448       324 LSEEQKQ------ALDTAIQHKVVILTGGPGTGKTTIT-RAIIELAEELGGLLPVGLAAPTGRAAKRLGEV----T----  388 (720)
T ss_pred             CCHHHHH------HHHHHHhCCeEEEECCCCCCHHHHH-HHHHHHHHHcCCCceEEEEeCchHHHHHHHHh----c----
Confidence            3444999      7777777888999999999999653 34444443322224688889998766543221    1    


Q ss_pred             CceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHC-----CCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHH
Q psy1548         209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRN-----KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFR  283 (448)
Q Consensus       209 ~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~-----~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~  283 (448)
                      +...                         .|..+++.....     ..-.....+++|+|||+++-.     ..+..+++
T Consensus       389 g~~a-------------------------~Tih~lL~~~~~~~~~~~~~~~~~~~llIvDEaSMvd~-----~~~~~Ll~  438 (720)
T TIGR01448       389 GLTA-------------------------STIHRLLGYGPDTFRHNHLEDPIDCDLLIVDESSMMDT-----WLALSLLA  438 (720)
T ss_pred             CCcc-------------------------ccHHHHhhccCCccchhhhhccccCCEEEEeccccCCH-----HHHHHHHH
Confidence            1110                         011111110000     001123567999999996533     23466677


Q ss_pred             hCCCCCeEEEEecc
Q psy1548         284 SSPHTKQVMMFSAT  297 (448)
Q Consensus       284 ~l~~~~q~i~~SAT  297 (448)
                      .++...+++++.-+
T Consensus       439 ~~~~~~rlilvGD~  452 (720)
T TIGR01448       439 ALPDHARLLLVGDT  452 (720)
T ss_pred             hCCCCCEEEEECcc
Confidence            78888888887654

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=96.91  E-value=0.00073  Score=69.64  Aligned_cols=44  Identities=39%  Similarity=0.757  Sum_probs=41.9

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      .+|+|||+.+++|+|.+++..|++|..|...+.|.+.+||+||+
T Consensus       293 ~~vLVaTdv~~rGiDi~~v~~VI~~d~p~~~~~yiqR~GRtGR~  336 (460)
T PRK11776        293 CSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRA  336 (460)
T ss_pred             CcEEEEecccccccchhcCCeEEEecCCCCHhHhhhhcccccCC
Confidence            48999999999999999999999999999999999999999994

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=96.89  E-value=0.012  Score=49.42  Aligned_cols=17  Identities=29%  Similarity=0.467  Sum_probs=15.3

Q ss_pred             CcceeeeccCCChhHHH
Q psy1548         149 GMDILCQAKSGMGKTAV  165 (448)
Q Consensus       149 g~~vli~apTGsGKT~~  165 (448)
                      ++.+++.||+|+|||..
T Consensus        19 ~~~v~i~G~~G~GKT~l   35 (151)
T cd00009          19 PKNLLLYGPPGTGKTTL   35 (151)
T ss_pred             CCeEEEECCCCCCHHHH
Confidence            67899999999999964

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=96.89  E-value=0.0051  Score=55.61  Aligned_cols=131  Identities=14%  Similarity=0.168  Sum_probs=67.2

Q ss_pred             ceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee--ccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHH
Q psy1548         151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL  228 (448)
Q Consensus       151 ~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l  228 (448)
                      -+++.||||+|||.+..--+......   +.++.+++  ..|.=+.+   +++.++..+ ++.+.......         
T Consensus         3 vi~lvGptGvGKTTt~aKLAa~~~~~---~~~v~lis~D~~R~ga~e---QL~~~a~~l-~vp~~~~~~~~---------   66 (196)
T PF00448_consen    3 VIALVGPTGVGKTTTIAKLAARLKLK---GKKVALISADTYRIGAVE---QLKTYAEIL-GVPFYVARTES---------   66 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHT---T--EEEEEESTSSTHHHH---HHHHHHHHH-TEEEEESSTTS---------
T ss_pred             EEEEECCCCCchHhHHHHHHHHHhhc---cccceeecCCCCCccHHH---HHHHHHHHh-ccccchhhcch---------
Confidence            36789999999997754333332222   22444444  34544443   455555544 55443322111         


Q ss_pred             hcCCCcEEEEcHHHH-HHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHH
Q psy1548         229 KTHNPQIVVGTPGRI-LALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCK  307 (448)
Q Consensus       229 ~~~~~~IlV~Tp~~l-~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~  307 (448)
                                .|..+ .+.+..  ...++.++++||-+-+..........+..++....+..-++.+|||...+......
T Consensus        67 ----------~~~~~~~~~l~~--~~~~~~D~vlIDT~Gr~~~d~~~~~el~~~~~~~~~~~~~LVlsa~~~~~~~~~~~  134 (196)
T PF00448_consen   67 ----------DPAEIAREALEK--FRKKGYDLVLIDTAGRSPRDEELLEELKKLLEALNPDEVHLVLSATMGQEDLEQAL  134 (196)
T ss_dssp             ----------CHHHHHHHHHHH--HHHTTSSEEEEEE-SSSSTHHHHHHHHHHHHHHHSSSEEEEEEEGGGGGHHHHHHH
T ss_pred             ----------hhHHHHHHHHHH--HhhcCCCEEEEecCCcchhhHHHHHHHHHHhhhcCCccceEEEecccChHHHHHHH
Confidence                      11111 111111  11234566778877544332245566777777766666678899998766444444


Q ss_pred             Hh
Q psy1548         308 KF  309 (448)
Q Consensus       308 ~~  309 (448)
                      .+
T Consensus       135 ~~  136 (196)
T PF00448_consen  135 AF  136 (196)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>PRK06526 transposase; Provisional

Probab=96.86  E-value=0.0083  Score=56.54  Aligned_cols=24  Identities=17%  Similarity=0.202  Sum_probs=19.1

Q ss_pred             eeeeeCcceeeeccCCChhHHHHH
Q psy1548         144 TKAVLGMDILCQAKSGMGKTAVFV  167 (448)
Q Consensus       144 ~~~~~g~~vli~apTGsGKT~~~~  167 (448)
                      ..+..+.++++.||+|+|||....
T Consensus        93 ~fi~~~~nlll~Gp~GtGKThLa~  116 (254)
T PRK06526         93 DFVTGKENVVFLGPPGTGKTHLAI  116 (254)
T ss_pred             chhhcCceEEEEeCCCCchHHHHH
Confidence            334467899999999999996654

>KOG0342|consensus

Probab=96.85  E-value=0.0015  Score=64.86  Aligned_cols=64  Identities=36%  Similarity=0.554  Sum_probs=51.2

Q ss_pred             HHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeecc
Q psy1548          91 ILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAK  157 (448)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~ap  157 (448)
                      ..+.......|+|||+.+.||+|+|+|.+|+.|..|...++|=+.+||+||   .--.|+.+|+.+|
T Consensus       373 ~~~F~kaesgIL~cTDVaARGlD~P~V~~VvQ~~~P~d~~~YIHRvGRTaR---~gk~G~alL~l~p  436 (543)
T KOG0342|consen  373 FFEFCKAESGILVCTDVAARGLDIPDVDWVVQYDPPSDPEQYIHRVGRTAR---EGKEGKALLLLAP  436 (543)
T ss_pred             HHHHhhcccceEEecchhhccCCCCCceEEEEeCCCCCHHHHHHHhccccc---cCCCceEEEEeCh
Confidence            344455666899999999999999999999999999999999999999888   3233444444444

>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=96.83  E-value=0.01  Score=54.69  Aligned_cols=108  Identities=16%  Similarity=0.245  Sum_probs=60.3

Q ss_pred             ceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhc
Q psy1548         151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKT  230 (448)
Q Consensus       151 ~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~  230 (448)
                      .+++.||+|+|||-. +-++.+.+.....+.+++++... +........++.                            
T Consensus        36 ~l~l~G~~G~GKTHL-L~Ai~~~~~~~~~~~~v~y~~~~-~f~~~~~~~~~~----------------------------   85 (219)
T PF00308_consen   36 PLFLYGPSGLGKTHL-LQAIANEAQKQHPGKRVVYLSAE-EFIREFADALRD----------------------------   85 (219)
T ss_dssp             EEEEEESTTSSHHHH-HHHHHHHHHHHCTTS-EEEEEHH-HHHHHHHHHHHT----------------------------
T ss_pred             ceEEECCCCCCHHHH-HHHHHHHHHhccccccceeecHH-HHHHHHHHHHHc----------------------------
Confidence            478999999999963 45555555444345566666432 343333222221                            


Q ss_pred             CCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhC-CCCCeEEEEeccCCccH
Q psy1548         231 HNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSS-PHTKQVMMFSATLSKEI  302 (448)
Q Consensus       231 ~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l-~~~~q~i~~SAT~~~~~  302 (448)
                             .....+.+.       +...++++||++|.+.........+-.++..+ ..+.++|+.|...|..+
T Consensus        86 -------~~~~~~~~~-------~~~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l  144 (219)
T PF00308_consen   86 -------GEIEEFKDR-------LRSADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSEL  144 (219)
T ss_dssp             -------TSHHHHHHH-------HCTSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTT
T ss_pred             -------ccchhhhhh-------hhcCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccc
Confidence                   011222222       34678899999998865422334444444443 34668887777776654

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.

>KOG0341|consensus

Probab=96.81  E-value=0.00091  Score=64.48  Aligned_cols=44  Identities=43%  Similarity=0.835  Sum_probs=42.1

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ..|+|+|+.+++|+|++++..|+||++|..+++|-+.+||+||+
T Consensus       472 KDVLVATDVASKGLDFp~iqHVINyDMP~eIENYVHRIGRTGRs  515 (610)
T KOG0341|consen  472 KDVLVATDVASKGLDFPDIQHVINYDMPEEIENYVHRIGRTGRS  515 (610)
T ss_pred             CceEEEecchhccCCCccchhhccCCChHHHHHHHHHhcccCCC
Confidence            47999999999999999999999999999999999999999993

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=96.80  E-value=0.001  Score=70.87  Aligned_cols=62  Identities=44%  Similarity=0.820  Sum_probs=49.1

Q ss_pred             HHHHHhh-ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeee
Q psy1548          91 ILRAIVD-CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQ  155 (448)
Q Consensus        91 ~~~~~~~-~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~  155 (448)
                      +++.+.. ...|+|||+++++|+|.+++..|++|+.|...+.|.|.+||+||+-.   .|..+++.
T Consensus       287 il~~Fr~G~~~ILVATdv~arGIDip~V~~VI~~d~P~~~e~yvqRiGRtGRaGr---~G~ai~~v  349 (629)
T PRK11634        287 TLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGR---AGRALLFV  349 (629)
T ss_pred             HHHHHhCCCCCEEEEcchHhcCCCcccCCEEEEeCCCCCHHHHHHHhccccCCCC---cceEEEEe
Confidence            3344433 34799999999999999999999999999999999999999999432   24444444

>PRK08181 transposase; Validated

Probab=96.79  E-value=0.0075  Score=57.24  Aligned_cols=46  Identities=24%  Similarity=0.250  Sum_probs=27.9

Q ss_pred             eeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHH
Q psy1548         147 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI  196 (448)
Q Consensus       147 ~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~  196 (448)
                      ..++++++.||+|+|||.... ++...+..  .+..++++ +..+|+.++
T Consensus       104 ~~~~nlll~Gp~GtGKTHLa~-Aia~~a~~--~g~~v~f~-~~~~L~~~l  149 (269)
T PRK08181        104 AKGANLLLFGPPGGGKSHLAA-AIGLALIE--NGWRVLFT-RTTDLVQKL  149 (269)
T ss_pred             hcCceEEEEecCCCcHHHHHH-HHHHHHHH--cCCceeee-eHHHHHHHH
Confidence            367899999999999995543 23332222  23345444 455666554

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=96.77  E-value=0.0011  Score=70.02  Aligned_cols=52  Identities=40%  Similarity=0.783  Sum_probs=44.9

Q ss_pred             HHHHHhh-ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          91 ILRAIVD-CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        91 ~~~~~~~-~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      +++.+.. ...|+|||+++++|||+++++.|++|+.|.....|-+.+||+||.
T Consensus       299 il~~Fr~G~~~VLVaTdv~arGIDip~V~~VInyd~P~s~~~yvqRiGRaGR~  351 (572)
T PRK04537        299 LLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARL  351 (572)
T ss_pred             HHHHHHcCCCeEEEEehhhhcCCCccCCCEEEEcCCCCCHHHHhhhhcccccC
Confidence            3444433 348999999999999999999999999999999999999999983

>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA

Probab=96.77  E-value=0.0026  Score=61.65  Aligned_cols=63  Identities=17%  Similarity=0.132  Sum_probs=48.1

Q ss_pred             cceeeeeCcceeeeccCCChhHHHHHHHHHHhhhcc-CCCeEEEEeeccHHHHHHHHHHHHHhhcc
Q psy1548         142 FGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-DSNVYVLVMCHTRELAFQISKEYERFSKY  206 (448)
Q Consensus       142 ~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  206 (448)
                      ++..  ...+++|.|+.|||||.+.+--++..+... -...++|++++|+..+..+...+......
T Consensus         8 ~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~aa~e~~~ri~~~l~~   71 (315)
T PF00580_consen    8 IIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNAAAQEMRERIRELLEE   71 (315)
T ss_dssp             HHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             HHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHHHHHHHHHHHHHhcCc
Confidence            5555  678999999999999998766666655444 34458999999999999999988886543

THe family includes both Rep and UvrD helcases. The Rep family helicases are composed of four structural domains []. The Rep proteins function as dimers.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 1UAA_B 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A 1QHG_A 1PJR_A ....

>PRK04296 thymidine kinase; Provisional

Probab=96.76  E-value=0.0033  Score=56.55  Aligned_cols=37  Identities=19%  Similarity=0.132  Sum_probs=23.7

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeec
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH  188 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~P  188 (448)
                      |.=.++.||+|+|||... +-++......  +.+++++-|
T Consensus         2 g~i~litG~~GsGKTT~~-l~~~~~~~~~--g~~v~i~k~   38 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTEL-LQRAYNYEER--GMKVLVFKP   38 (190)
T ss_pred             cEEEEEECCCCCHHHHHH-HHHHHHHHHc--CCeEEEEec
Confidence            344688999999999654 3444443322  446777766

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.76  E-value=0.0062  Score=63.77  Aligned_cols=109  Identities=13%  Similarity=0.168  Sum_probs=57.4

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHh
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK  229 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~  229 (448)
                      ..+++.|++|+|||.. +-++.+.+.....+.+++++. ..+++.+....+..      +                    
T Consensus       315 NpL~LyG~sGsGKTHL-L~AIa~~a~~~~~g~~V~Yit-aeef~~el~~al~~------~--------------------  366 (617)
T PRK14086        315 NPLFIYGESGLGKTHL-LHAIGHYARRLYPGTRVRYVS-SEEFTNEFINSIRD------G--------------------  366 (617)
T ss_pred             CcEEEECCCCCCHHHH-HHHHHHHHHHhCCCCeEEEee-HHHHHHHHHHHHHh------c--------------------
Confidence            3489999999999954 334444443333344566554 44455443222211      0                    


Q ss_pred             cCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCC-CCCeEEEEeccCCccH
Q psy1548         230 THNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSP-HTKQVMMFSATLSKEI  302 (448)
Q Consensus       230 ~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~-~~~q~i~~SAT~~~~~  302 (448)
                               ..+.+...       +.++++||||++|.+.........+-.++..+. .++++|+.|-..|..+
T Consensus       367 ---------~~~~f~~~-------y~~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL  424 (617)
T PRK14086        367 ---------KGDSFRRR-------YREMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQL  424 (617)
T ss_pred             ---------cHHHHHHH-------hhcCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhh
Confidence                     00111111       345688999999987553122333444554443 3567776555555443

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=96.73  E-value=0.0013  Score=68.13  Aligned_cols=44  Identities=48%  Similarity=0.936  Sum_probs=42.1

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      .+++|||+++++|||.++++.|++|..|..+..|-|++|||||.
T Consensus       386 ~~vLvaT~~l~~GIDi~~v~~VI~~~~P~s~~~y~Qr~GRaGR~  429 (475)
T PRK01297        386 IRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRA  429 (475)
T ss_pred             CcEEEEccccccCCcccCCCEEEEeCCCCCHHHHHHhhCccCCC
Confidence            48999999999999999999999999999999999999999994

>KOG0348|consensus

Probab=96.71  E-value=0.0012  Score=66.28  Aligned_cols=44  Identities=39%  Similarity=0.716  Sum_probs=41.0

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ..|++||+.++||+|.|.|++|+.|+.|....+|=+.+||+.|+
T Consensus       498 ~~VLLcTDVAaRGLDlP~V~~vVQYd~P~s~adylHRvGRTARa  541 (708)
T KOG0348|consen  498 RAVLLCTDVAARGLDLPHVGLVVQYDPPFSTADYLHRVGRTARA  541 (708)
T ss_pred             ceEEEehhhhhccCCCCCcCeEEEeCCCCCHHHHHHHhhhhhhc
Confidence            36999999999999999999999999999999999999887773

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=96.70  E-value=0.0058  Score=59.07  Aligned_cols=136  Identities=15%  Similarity=0.203  Sum_probs=79.8

Q ss_pred             cceeeeeC--cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCc---eEEEEE
Q psy1548         142 FGTKAVLG--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI---KVGVFF  216 (448)
Q Consensus       142 ~~~~~~~g--~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~---~v~~~~  216 (448)
                      ++..++..  .=|.+.++.|||||+.++.+.+.+....+...++|+.=|+..+.+++        +++|+.   +...+.
T Consensus       236 ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~dI--------GfLPG~eEeKm~PWm  307 (436)
T COG1875         236 ALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGEDI--------GFLPGTEEEKMGPWM  307 (436)
T ss_pred             HHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCccccc--------CcCCCchhhhccchH
Confidence            66666654  34677899999999999988888877666666788887887765332        122221   111111


Q ss_pred             cCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCe----------eEEEecchhHHHhhhhhHHHHHHHHHhCC
Q psy1548         217 GGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLL----------KHFILDECDKMLEQLEMRRDVQEIFRSSP  286 (448)
Q Consensus       217 g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i----------~~lViDEah~l~~~~~~~~~~~~i~~~l~  286 (448)
                      +.  ..+..+.+...    ==++-+.+...+.++.+.+..+          .++|||||+.+-     ..++..++.+..
T Consensus       308 q~--i~DnLE~L~~~----~~~~~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQNLT-----pheikTiltR~G  376 (436)
T COG1875         308 QA--IFDNLEVLFSP----NEPGDRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQNLT-----PHELKTILTRAG  376 (436)
T ss_pred             HH--HHhHHHHHhcc----cccchHHHHHHHhccceeeeeeeeecccccccceEEEehhhccC-----HHHHHHHHHhcc
Confidence            11  11122222211    0012344555554444332222          369999999653     456788888888


Q ss_pred             CCCeEEEEec
Q psy1548         287 HTKQVMMFSA  296 (448)
Q Consensus       287 ~~~q~i~~SA  296 (448)
                      +..+++++.-
T Consensus       377 ~GsKIVl~gd  386 (436)
T COG1875         377 EGSKIVLTGD  386 (436)
T ss_pred             CCCEEEEcCC
Confidence            8888887643

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=96.68  E-value=0.0051  Score=51.24  Aligned_cols=41  Identities=24%  Similarity=0.186  Sum_probs=25.2

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTREL  192 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L  192 (448)
                      +..+++.||+|+|||..... ++..+....  ..++++.+....
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~-l~~~~~~~~--~~~~~~~~~~~~   42 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARA-LARELGPPG--GGVIYIDGEDIL   42 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHH-HHhccCCCC--CCEEEECCEEcc
Confidence            56789999999999976432 333322211  246666666543

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

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.62  E-value=0.025  Score=56.03  Aligned_cols=136  Identities=13%  Similarity=0.168  Sum_probs=66.9

Q ss_pred             eeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhH
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE  225 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~  225 (448)
                      +..|..+++.||||+|||.....-+....... +..++.++. +-..-.--.+.++.|+..+ ++.+..           
T Consensus       134 ~~~g~ii~lvGptGvGKTTtiakLA~~~~~~~-G~~~V~lit-~D~~R~ga~EqL~~~a~~~-gv~~~~-----------  199 (374)
T PRK14722        134 MERGGVFALMGPTGVGKTTTTAKLAARCVMRF-GASKVALLT-TDSYRIGGHEQLRIFGKIL-GVPVHA-----------  199 (374)
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHHHHHhc-CCCeEEEEe-cccccccHHHHHHHHHHHc-CCceEe-----------
Confidence            34578999999999999977543332222221 112343333 2111111123455555444 433322           


Q ss_pred             HHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCcc-HHH
Q psy1548         226 EYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKE-IRP  304 (448)
Q Consensus       226 ~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~-~~~  304 (448)
                                 +-+++.+...+..    +.+.++++||.+-...........+..+.....+...++.+|||...+ +.+
T Consensus       200 -----------~~~~~~l~~~l~~----l~~~DlVLIDTaG~~~~d~~l~e~La~L~~~~~~~~~lLVLsAts~~~~l~e  264 (374)
T PRK14722        200 -----------VKDGGDLQLALAE----LRNKHMVLIDTIGMSQRDRTVSDQIAMLHGADTPVQRLLLLNATSHGDTLNE  264 (374)
T ss_pred             -----------cCCcccHHHHHHH----hcCCCEEEEcCCCCCcccHHHHHHHHHHhccCCCCeEEEEecCccChHHHHH
Confidence                       2333333333321    344577889988644222122333333322223334578889998654 344


Q ss_pred             HHHHhc
Q psy1548         305 VCKKFM  310 (448)
Q Consensus       305 ~~~~~l  310 (448)
                      .+..|.
T Consensus       265 vi~~f~  270 (374)
T PRK14722        265 VVQAYR  270 (374)
T ss_pred             HHHHHH
Confidence            555554

>KOG0335|consensus

Probab=96.59  E-value=0.0013  Score=65.95  Aligned_cols=43  Identities=56%  Similarity=0.958  Sum_probs=41.3

Q ss_pred             ceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548         100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus       100 ~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      .++|||+++.||+|.+.|+.|++|+.|..+++|=+.+||+||+
T Consensus       389 pvlVaT~VaaRGlDi~~V~hVInyDmP~d~d~YvHRIGRTGR~  431 (482)
T KOG0335|consen  389 PVLVATNVAARGLDIPNVKHVINYDMPADIDDYVHRIGRTGRV  431 (482)
T ss_pred             ceEEEehhhhcCCCCCCCceeEEeecCcchhhHHHhccccccC
Confidence            8999999999999999999999999999999999999998883

>PRK14974 cell division protein FtsY; Provisional

Probab=96.57  E-value=0.024  Score=55.47  Aligned_cols=55  Identities=11%  Similarity=0.215  Sum_probs=41.8

Q ss_pred             CeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhc
Q psy1548         256 LLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFM  310 (448)
Q Consensus       256 ~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l  310 (448)
                      ..+++++|.+.++.........+..+.+...+..-++.++|+...+....++.|.
T Consensus       222 ~~DvVLIDTaGr~~~~~~lm~eL~~i~~~~~pd~~iLVl~a~~g~d~~~~a~~f~  276 (336)
T PRK14974        222 GIDVVLIDTAGRMHTDANLMDELKKIVRVTKPDLVIFVGDALAGNDAVEQAREFN  276 (336)
T ss_pred             CCCEEEEECCCccCCcHHHHHHHHHHHHhhCCceEEEeeccccchhHHHHHHHHH
Confidence            4568999999988643367777888877777777788999998777666666654

>PTZ00424 helicase 45; Provisional

Probab=96.53  E-value=0.002  Score=65.02  Aligned_cols=43  Identities=44%  Similarity=1.025  Sum_probs=41.2

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR  141 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~  141 (448)
                      ..|+|||+.+++|+|.++++.|++++.|.....|-|.+|||||
T Consensus       318 ~~vLvaT~~l~~GiDip~v~~VI~~~~p~s~~~y~qr~GRagR  360 (401)
T PTZ00424        318 TRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGR  360 (401)
T ss_pred             CCEEEEcccccCCcCcccCCEEEEECCCCCHHHEeeccccccc
Confidence            4899999999999999999999999999999999999999998

>KOG0330|consensus

Probab=96.52  E-value=0.0024  Score=61.75  Aligned_cols=65  Identities=38%  Similarity=0.707  Sum_probs=51.2

Q ss_pred             cCCcccCCCCHHHHHHH---------hhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548          79 SSGFRDFLLKPEILRAI---------VDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      ..+|...+++-++....         .....|+|||++++||+|.+-|+.|+||+.|....+|=+..||++|+.
T Consensus       322 ~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TDVaSRGLDip~Vd~VVNyDiP~~skDYIHRvGRtaRaG  395 (476)
T KOG0330|consen  322 NLGFQAIPLHGQMSQSKRLGALNKFKAGARSILVCTDVASRGLDIPHVDVVVNYDIPTHSKDYIHRVGRTARAG  395 (476)
T ss_pred             hcCcceecccchhhHHHHHHHHHHHhccCCcEEEecchhcccCCCCCceEEEecCCCCcHHHHHHHcccccccC
Confidence            34666666665543321         122389999999999999999999999999999999999988888744

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.51  E-value=0.044  Score=55.65  Aligned_cols=132  Identities=17%  Similarity=0.224  Sum_probs=68.3

Q ss_pred             eCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee--ccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhH
Q psy1548         148 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE  225 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~  225 (448)
                      .|+.+++.+|||+|||.+..--+....... .+.++.++.  |.+.-+.   +.++.+.... ++.+             
T Consensus       220 ~~~~i~~vGptGvGKTTt~~kLA~~~~~~~-~g~~V~li~~D~~r~~a~---eqL~~~a~~~-~vp~-------------  281 (424)
T PRK05703        220 QGGVVALVGPTGVGKTTTLAKLAARYALLY-GKKKVALITLDTYRIGAV---EQLKTYAKIM-GIPV-------------  281 (424)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhc-CCCeEEEEECCccHHHHH---HHHHHHHHHh-CCce-------------
Confidence            467899999999999976543222221011 223444444  3333222   2344444333 3322             


Q ss_pred             HHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHh-CCCCCeEEEEeccCCc-cHH
Q psy1548         226 EYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRS-SPHTKQVMMFSATLSK-EIR  303 (448)
Q Consensus       226 ~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~-l~~~~q~i~~SAT~~~-~~~  303 (448)
                               ..+.++..+...+..    +.+.++++||.+-+..........+..++.. ..+....+.+|||... .+.
T Consensus       282 ---------~~~~~~~~l~~~l~~----~~~~DlVlIDt~G~~~~d~~~~~~L~~ll~~~~~~~~~~LVl~a~~~~~~l~  348 (424)
T PRK05703        282 ---------EVVYDPKELAKALEQ----LRDCDVILIDTAGRSQRDKRLIEELKALIEFSGEPIDVYLVLSATTKYEDLK  348 (424)
T ss_pred             ---------EccCCHHhHHHHHHH----hCCCCEEEEeCCCCCCCCHHHHHHHHHHHhccCCCCeEEEEEECCCCHHHHH
Confidence                     222344445554442    2356889999885432221334455555552 2233457888998764 455


Q ss_pred             HHHHHhc
Q psy1548         304 PVCKKFM  310 (448)
Q Consensus       304 ~~~~~~l  310 (448)
                      +....|-
T Consensus       349 ~~~~~f~  355 (424)
T PRK05703        349 DIYKHFS  355 (424)
T ss_pred             HHHHHhC
Confidence            5555553

>KOG0921|consensus

Probab=96.40  E-value=0.011  Score=62.91  Aligned_cols=247  Identities=16%  Similarity=0.150  Sum_probs=128.2

Q ss_pred             eCcceeeeccCCChhHHHHHHHHHHhhhccCCC--eEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhH
Q psy1548         148 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSN--VYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE  225 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~--~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~  225 (448)
                      ...-++|.+.||+|||.-+.--+|..+..+..+  .-+.+--|++-.+..+.+.+-+-.    ...++-.+|-.......
T Consensus       392 dn~v~~I~getgcgk~tq~aq~iLe~~~~ns~g~~~na~v~qprrisaisiaerva~er----~e~~g~tvgy~vRf~Sa  467 (1282)
T KOG0921|consen  392 ENRVVIIKGETGCGKSTQVAQFLLESFLENSNGASFNAVVSQPRRISAISLAERVANER----GEEVGETCGYNVRFDSA  467 (1282)
T ss_pred             cCceeeEeecccccchhHHHHHHHHHHhhccccccccceeccccccchHHHHHHHHHhh----HHhhccccccccccccc
Confidence            345678899999999998888888776555432  234444577776666555444321    11222222222111111


Q ss_pred             HHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCcc----
Q psy1548         226 EYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKE----  301 (448)
Q Consensus       226 ~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~----  301 (448)
                      .....  --|+.+|-+-+++++....   ..+.++++||.|..--..+|...+..=+....+...++++|||+..+    
T Consensus       468 ~prpy--g~i~fctvgvllr~~e~gl---rg~sh~i~deiherdv~~dfll~~lr~m~~ty~dl~v~lmsatIdTd~f~~  542 (1282)
T KOG0921|consen  468 TPRPY--GSIMFCTVGVLLRMMENGL---RGISHVIIDEIHERDVDTDFVLIVLREMISTYRDLRVVLMSATIDTDLFTN  542 (1282)
T ss_pred             ccccc--cceeeeccchhhhhhhhcc---cccccccchhhhhhccchHHHHHHHHhhhccchhhhhhhhhcccchhhhhh
Confidence            00111  2599999999999887654   34567999999964322234333333333333344445555554321    


Q ss_pred             ----------------HHHHHHHhcCCCeEEE-----------EcCcccccccc--eeEEEEEcC---------------
Q psy1548         302 ----------------IRPVCKKFMHDPMEVY-----------VDDEAKLTLHG--LQQHYVKLK---------------  337 (448)
Q Consensus       302 ----------------~~~~~~~~l~~~~~i~-----------~~~~~~~~~~~--i~~~~~~~~---------------  337 (448)
                                      +..++......+....           .++. ......  -+..-..+.               
T Consensus       543 ~f~~~p~~~~~grt~pvq~F~led~~~~~~~vp~~~~~~k~k~~~~~-~~~~~ddK~~n~n~~~dd~~~~~~~~am~~~s  621 (1282)
T KOG0921|consen  543 FFSSIPDVTVHGRTFPVQSFFLEDIIQMTQFVPSEPSQKKRKKDDDE-EDEEVDDKGRNMNILCDPSYNESTRTAMSRLS  621 (1282)
T ss_pred             hhccccceeeccccccHHHHHHHHhhhhhhccCCCcCccchhhcccc-cCchhhhcccccccccChhhcchhhhhhhcch
Confidence                            1122221111111000           0000 000000  000000000               


Q ss_pred             cch----HHHHHHHHHhh-CCCCeEEEEECccHHHHHHHHHHHhC-------CCcEEEEeCCCCHHHHHHHHHHHhcCC
Q psy1548         338 ENE----KNKKLFELLDV-LEFNQVVIFVKSVTRCIALSTLLSEQ-------NFPAVSIHRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       338 ~~~----k~~~L~~ll~~-~~~~~~IIF~~s~~~a~~l~~~L~~~-------g~~~~~lh~~~~~~eR~~~l~~F~~g~  404 (448)
                      +.+    -.+++...+.. .-.+-+++|.+-=...-.|...|...       -.+...+|+.++..+..++.+....|.
T Consensus       622 e~d~~f~l~Eal~~~i~s~~i~gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~ilp~Hsq~~~~eqrkvf~~~p~gv  700 (1282)
T KOG0921|consen  622 EKDIPFGLIEALLNDIASRNIDGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHSQLTSQEQRKVFEPVPEGV  700 (1282)
T ss_pred             hhcchhHHHHHHHhhhcccCCccceeeecCchHHhhhhhhhhhhhhhhccchhcccccchhhcccHhhhhccCcccccc
Confidence            000    11222222211 12456888988888888888877653       346888999999999999999888877

>KOG0298|consensus

Probab=96.39  E-value=0.013  Score=64.72  Aligned_cols=154  Identities=17%  Similarity=0.151  Sum_probs=92.0

Q ss_pred             cceeeeeCcceeeeccCCChhHHHHHHHHHHhhhc---------------cCCCeEEEEeeccHHHHHHHHHHHHHhhcc
Q psy1548         142 FGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLET---------------TDSNVYVLVMCHTRELAFQISKEYERFSKY  206 (448)
Q Consensus       142 ~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~---------------~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  206 (448)
                      +......|+++++.-..|+|||.+-+...+.....               ....+-+|||||.- +..||..++..-...
T Consensus       367 ~~~~~~~g~~~~~ade~~~qk~~~~l~~~l~~~~k~~~~~cS~~~~e~~n~~~tgaTLII~P~a-Il~QW~~EI~kH~~~  445 (1394)
T KOG0298|consen  367 CSGDKKHGKRVQCADEMGWQKTSEKLILELSDLPKLCPSCCSELVKEGENLVETGATLIICPNA-ILMQWFEEIHKHISS  445 (1394)
T ss_pred             hcCCccCCcceeehhhhhccchHHHHHHHHhcccccchhhhhHHHhcccceeecCceEEECcHH-HHHHHHHHHHHhccc
Confidence            44555668899999999999998866555443211               01234689999985 567877777665532


Q ss_pred             CCCceEEEEEcCcccHHh-HHHHhcCCCcEEEEcHHHHHHHHHCC--------------CCcC----CCee--EEEecch
Q psy1548         207 MSNIKVGVFFGGLPIQKD-EEYLKTHNPQIVVGTPGRILALVRNK--------------KLNL----SLLK--HFILDEC  265 (448)
Q Consensus       207 ~~~~~v~~~~g~~~~~~~-~~~l~~~~~~IlV~Tp~~l~~~l~~~--------------~~~~----~~i~--~lViDEa  265 (448)
                        .+++....|-...... ...+-  ++||++||...|..-+...              ...+    -.+.  .|++|||
T Consensus       446 --~lKv~~Y~Girk~~~~~~~el~--~yDIVlTtYdiLr~El~hte~~~~~R~lR~qsr~~~~~SPL~~v~wWRIclDEa  521 (1394)
T KOG0298|consen  446 --LLKVLLYFGIRKTFWLSPFELL--QYDIVLTTYDILRNELYHTEDFGSDRQLRHQSRYMRPNSPLLMVNWWRICLDEA  521 (1394)
T ss_pred             --cceEEEEechhhhcccCchhhh--ccCEEEeehHHHHhHhhcccccCChhhhhcccCCCCCCCchHHHHHHHHhhhHH
Confidence              4577776664321111 11121  4899999999986544221              1111    1111  2899999


Q ss_pred             hHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHH
Q psy1548         266 DKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRP  304 (448)
Q Consensus       266 h~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~  304 (448)
                      +++-.   ......++..+++.. -..+.|.|+-..+.+
T Consensus       522 QMves---ssS~~a~M~~rL~~i-n~W~VTGTPiq~Idd  556 (1394)
T KOG0298|consen  522 QMVES---SSSAAAEMVRRLHAI-NRWCVTGTPIQKIDD  556 (1394)
T ss_pred             Hhhcc---hHHHHHHHHHHhhhh-ceeeecCCchhhhhh
Confidence            95533   344555566666543 357788885433333

>KOG0345|consensus

Probab=96.39  E-value=0.0028  Score=62.76  Aligned_cols=53  Identities=30%  Similarity=0.640  Sum_probs=44.5

Q ss_pred             HHHHHHhh-ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          90 EILRAIVD-CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        90 ~~~~~~~~-~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ..++...+ ...|+.||+.+.||||++++++|++|+.|.....|-+..||++|+
T Consensus       298 k~~~~F~~~~~~vl~~TDVaARGlDip~iD~VvQ~DpP~~~~~FvHR~GRTaR~  351 (567)
T KOG0345|consen  298 KVLEAFRKLSNGVLFCTDVAARGLDIPGIDLVVQFDPPKDPSSFVHRCGRTARA  351 (567)
T ss_pred             HHHHHHHhccCceEEeehhhhccCCCCCceEEEecCCCCChhHHHhhcchhhhc
Confidence            34444444 457999999999999999999999999999998888888887773

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.37  E-value=0.15  Score=43.79  Aligned_cols=38  Identities=26%  Similarity=0.318  Sum_probs=23.2

Q ss_pred             eeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHH
Q psy1548         152 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTREL  192 (448)
Q Consensus       152 vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L  192 (448)
                      +++.||+|+|||.....-+.. ...  .+..++++.....+
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~-~~~--~~~~v~~~~~e~~~   39 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALN-IAT--KGGKVVYVDIEEEI   39 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHH-HHh--cCCEEEEEECCcch
Confidence            578999999999764333322 222  34467777655443

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.37  E-value=0.0081  Score=61.36  Aligned_cols=152  Identities=16%  Similarity=0.220  Sum_probs=77.9

Q ss_pred             eeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH-hhccCCCceEEEEEcCcccHH-hHHHH--h
Q psy1548         154 CQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER-FSKYMSNIKVGVFFGGLPIQK-DEEYL--K  229 (448)
Q Consensus       154 i~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~-~~~~~~~~~v~~~~g~~~~~~-~~~~l--~  229 (448)
                      ..+.||||||++.+-.+|.....+  ...-|+.+............+.. ++..+ -..-.+.+++....- ....+  .
T Consensus         2 f~matgsgkt~~ma~lil~~y~kg--yr~flffvnq~nilekt~~nftd~~s~ky-lf~e~i~~~d~~i~ikkvn~fseh   78 (812)
T COG3421           2 FEMATGSGKTLVMAGLILECYKKG--YRNFLFFVNQANILEKTKLNFTDSVSSKY-LFSENININDENIEIKKVNNFSEH   78 (812)
T ss_pred             cccccCCChhhHHHHHHHHHHHhc--hhhEEEEecchhHHHHHHhhcccchhhhH-hhhhhhhcCCceeeeeeecccCcc
Confidence            467899999999877777766443  23466666665555443322221 00000 000011112211110 00111  1


Q ss_pred             cCCCcEEEEcHHHHHHHHHC---CCCc---CCCee-EEEecchhHHHhh--------hhhHHHHHHHHH-h--CCCCCeE
Q psy1548         230 THNPQIVVGTPGRILALVRN---KKLN---LSLLK-HFILDECDKMLEQ--------LEMRRDVQEIFR-S--SPHTKQV  291 (448)
Q Consensus       230 ~~~~~IlV~Tp~~l~~~l~~---~~~~---~~~i~-~lViDEah~l~~~--------~~~~~~~~~i~~-~--l~~~~q~  291 (448)
                      +....|.++|.+.|...+.+   ..+.   +.+.+ .++-||||++...        ......++..+. .  -.+..-+
T Consensus        79 nd~iei~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln~~tkkk~~de~~~~~~we~~v~la~~~nkd~~~  158 (812)
T COG3421          79 NDAIEIYFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLNTETKKKLNDEASEKRNWESVVKLALEQNKDNLL  158 (812)
T ss_pred             CCceEEEEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhhhhhhhhcccHHHHHhhHHHHHHHHHhcCCCcee
Confidence            22367999999999887744   3333   34444 3667999998654        112222222221 1  1234457


Q ss_pred             EEEeccCCccHHHHHHHh
Q psy1548         292 MMFSATLSKEIRPVCKKF  309 (448)
Q Consensus       292 i~~SAT~~~~~~~~~~~~  309 (448)
                      +.+|||.|.+ .....+|
T Consensus       159 lef~at~~k~-k~v~~ky  175 (812)
T COG3421         159 LEFSATIPKE-KSVEDKY  175 (812)
T ss_pred             ehhhhcCCcc-ccHHHHh
Confidence            8899999843 4444444

>KOG1132|consensus

Probab=96.36  E-value=0.014  Score=62.28  Aligned_cols=68  Identities=18%  Similarity=0.165  Sum_probs=45.4

Q ss_pred             hhhhccccccceeeee----CcceeeeccCCChhHHHHHHHHHHhh---h-----------c--------c---------
Q psy1548         133 LHRVARAGRFGTKAVL----GMDILCQAKSGMGKTAVFVLATLQQL---E-----------T--------T---------  177 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~----g~~vli~apTGsGKT~~~~l~~l~~l---~-----------~--------~---------  177 (448)
                      |..      .+..++.    +.+.++.+|||+|||++.+-..|...   .           .        .         
T Consensus        26 Q~a------~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~k~~~~~~~~s~~~~~~~p~~~s~~~g~~s~e   99 (945)
T KOG1132|consen   26 QLA------FMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHLKSRKPKGKISERKAGFIPTQPSDSGGEKSEE   99 (945)
T ss_pred             HHH------HHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHhhccccccchhhhhccccCCCCccCCCCchhh
Confidence            777      5555444    57899999999999988665554332   1           0        0         


Q ss_pred             ---C-----CCeEEEEeeccHHHHHHHHHHHHHhhcc
Q psy1548         178 ---D-----SNVYVLVMCHTRELAFQISKEYERFSKY  206 (448)
Q Consensus       178 ---~-----~~~~~lil~Pt~~L~~q~~~~~~~~~~~  206 (448)
                         .     +.+++.|-.-|..-..|+.+++++..-.
T Consensus       100 ~~e~~~~~~~ipkIyyaSRTHsQltQvvrElrrT~Y~  136 (945)
T KOG1132|consen  100 AGEPIACYTGIPKIYYASRTHSQLTQVVRELRRTGYR  136 (945)
T ss_pred             hcCccccccCCceEEEecchHHHHHHHHHHHhhcCCC
Confidence               0     1356677777777778888888876543

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.34  E-value=0.062  Score=53.40  Aligned_cols=132  Identities=17%  Similarity=0.198  Sum_probs=69.5

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee--ccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE  226 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~  226 (448)
                      ++.+.+.||||+|||.....-+.. +...  +.++.++.  |.|.-+.+   +++.+.... ++.               
T Consensus       241 ~~vI~LVGptGvGKTTTiaKLA~~-L~~~--GkkVglI~aDt~RiaAvE---QLk~yae~l-gip---------------  298 (436)
T PRK11889        241 VQTIALIGPTGVGKTTTLAKMAWQ-FHGK--KKTVGFITTDHSRIGTVQ---QLQDYVKTI-GFE---------------  298 (436)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHH-HHHc--CCcEEEEecCCcchHHHH---HHHHHhhhc-CCc---------------
Confidence            367899999999999765443332 2222  23444443  34422222   233333222 222               


Q ss_pred             HHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCC-ccHHHH
Q psy1548         227 YLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLS-KEIRPV  305 (448)
Q Consensus       227 ~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~-~~~~~~  305 (448)
                             -+.+.+|..+.+.+..-.- -.+.++++||-+=+..........+..+++...+..-++.+|||.. .++...
T Consensus       299 -------v~v~~d~~~L~~aL~~lk~-~~~~DvVLIDTaGRs~kd~~lm~EL~~~lk~~~PdevlLVLsATtk~~d~~~i  370 (436)
T PRK11889        299 -------VIAVRDEAAMTRALTYFKE-EARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIEI  370 (436)
T ss_pred             -------EEecCCHHHHHHHHHHHHh-ccCCCEEEEeCccccCcCHHHHHHHHHHHhhcCCCeEEEEECCccChHHHHHH
Confidence                   2223466666555432110 1146788888886654332334455555554444444677898765 455677


Q ss_pred             HHHhc
Q psy1548         306 CKKFM  310 (448)
Q Consensus       306 ~~~~l  310 (448)
                      ++.|-
T Consensus       371 ~~~F~  375 (436)
T PRK11889        371 ITNFK  375 (436)
T ss_pred             HHHhc
Confidence            76664

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=96.31  E-value=0.017  Score=59.38  Aligned_cols=44  Identities=16%  Similarity=0.229  Sum_probs=27.2

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHH
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ  195 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q  195 (448)
                      ..+++.||+|+|||... -++.+.+.....+.+++++ +...+..+
T Consensus       149 ~~l~l~G~~G~GKThL~-~ai~~~~~~~~~~~~v~yi-~~~~~~~~  192 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLL-HAIGNYILEKNPNAKVVYV-TSEKFTND  192 (450)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHHHhCCCCeEEEE-EHHHHHHH
Confidence            56899999999999653 3444444433334456666 44445444

>KOG1001|consensus

Probab=96.27  E-value=0.022  Score=60.78  Aligned_cols=110  Identities=20%  Similarity=0.234  Sum_probs=69.0

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccC------CCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHH
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTD------SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQK  223 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~------~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~  223 (448)
                      +-.|+.-..|-|||...+..++..-...+      .....|++||+.. ..|+..++.+..... .+.+.+++|   ...
T Consensus       153 ~ggIladd~glgkt~~ti~l~l~~~~~~~~~~~~~~~kttLivcp~s~-~~qW~~elek~~~~~-~l~v~v~~g---r~k  227 (674)
T KOG1001|consen  153 RGGILADDMGLGKTVKTIALILKQKLKSKEEDRQKEFKTTLIVCPTSL-LTQWKTELEKVTEED-KLSIYVYHG---RTK  227 (674)
T ss_pred             ccceEeeccccchHHHHHHHHHhcccCCcchhhccccCceeEecchHH-HHHHHHHHhccCCcc-ceEEEEecc---ccc
Confidence            34677888999999876555443322222      3456899999864 456666666665543 667777776   122


Q ss_pred             hHHHHhcCCCcEEEEcHHHHHH-HHHCCCCcCCCeeEEEecchhHHHhh
Q psy1548         224 DEEYLKTHNPQIVVGTPGRILA-LVRNKKLNLSLLKHFILDECDKMLEQ  271 (448)
Q Consensus       224 ~~~~l~~~~~~IlV~Tp~~l~~-~l~~~~~~~~~i~~lViDEah~l~~~  271 (448)
                      ....+.  .++|+++|++.+.. .+..     -..-.+|+||+|.+...
T Consensus       228 d~~el~--~~dVVltTy~il~~~~l~~-----i~w~Riildea~~ikn~  269 (674)
T KOG1001|consen  228 DKSELN--SYDVVLTTYDILKNSPLVK-----IKWLRIVLDEAHTIKNK  269 (674)
T ss_pred             ccchhc--CCceEEeeHHHhhcccccc-----eeEEEEEeccccccCCc
Confidence            222222  37899999998764 1111     12235999999987664

>KOG0328|consensus

Probab=96.24  E-value=0.0053  Score=57.00  Aligned_cols=44  Identities=41%  Similarity=0.979  Sum_probs=41.3

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR  141 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~  141 (448)
                      ..+|+++|+...||||.+.|..|+||+.|...+.|=+.+||+||
T Consensus       316 ~SrvLitTDVwaRGiDv~qVslviNYDLP~nre~YIHRIGRSGR  359 (400)
T KOG0328|consen  316 KSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGR  359 (400)
T ss_pred             CceEEEEechhhccCCcceeEEEEecCCCccHHHHhhhhccccc
Confidence            35999999999999999999999999999999899999999888

>PRK05642 DNA replication initiation factor; Validated

Probab=96.21  E-value=0.015  Score=54.22  Aligned_cols=45  Identities=13%  Similarity=0.235  Sum_probs=26.3

Q ss_pred             CeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCc
Q psy1548         256 LLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSK  300 (448)
Q Consensus       256 ~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~  300 (448)
                      +.+++|+|++|.+.........+-.++..+......++++++.++
T Consensus        97 ~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p  141 (234)
T PRK05642         97 QYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSP  141 (234)
T ss_pred             hCCEEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCH
Confidence            456899999997743213344466666555443334555666543

>KOG1015|consensus

Probab=96.16  E-value=0.2  Score=54.20  Aligned_cols=149  Identities=13%  Similarity=0.181  Sum_probs=79.1

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhh-cc-CCCeEEEEeeccHHHHHHHHHHHHHhhccCC---CceEEEEEcCcccHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLE-TT-DSNVYVLVMCHTRELAFQISKEYERFSKYMS---NIKVGVFFGGLPIQK  223 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~-~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~---~~~v~~~~g~~~~~~  223 (448)
                      |--+|+.-=.|.|||+.. +..++.+. .. -+-.++|||||...+ ..|...|.+|...+.   .+.|..+..-.....
T Consensus       696 GsGcILAHcMGLGKTlQV-vtflhTvL~c~klg~ktaLvV~PlNt~-~NW~~EFekWm~~~e~~~~leV~eL~~vkr~e~  773 (1567)
T KOG1015|consen  696 GSGCILAHCMGLGKTLQV-VTFLHTVLLCDKLGFKTALVVCPLNTA-LNWMNEFEKWMEGLEDDEKLEVSELATVKRPEE  773 (1567)
T ss_pred             CcchHHHHhhcccceehh-hHHHHHHHHhhccCCceEEEEcchHHH-HHHHHHHHHhcccccccccceeehhhhccChHH
Confidence            445666667899999763 33333321 11 234589999998865 456778888876431   234443333222233


Q ss_pred             hHHHH---hcCCCcEEEEcHHHHHHHHHCCCC-------------cCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCC
Q psy1548         224 DEEYL---KTHNPQIVVGTPGRILALVRNKKL-------------NLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPH  287 (448)
Q Consensus       224 ~~~~l---~~~~~~IlV~Tp~~l~~~l~~~~~-------------~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~  287 (448)
                      ....|   ... -.|.|.-...+..+...+..             --..-+++|+||+|.+-..   ...+...+.....
T Consensus       774 R~~~L~~W~~~-ggVmIiGYdmyRnLa~gr~vk~rk~ke~f~k~lvdpGPD~vVCDE~HiLKNe---ksa~Skam~~irt  849 (1567)
T KOG1015|consen  774 RSYMLQRWQED-GGVMIIGYDMYRNLAQGRNVKSRKLKEIFNKALVDPGPDFVVCDEGHILKNE---KSAVSKAMNSIRT  849 (1567)
T ss_pred             HHHHHHHHHhc-CCEEEEehHHHHHHhcccchhhhHHHHHHHHhccCCCCCeEEecchhhhccc---hHHHHHHHHHHHh
Confidence            32222   222 25766666665554432211             1134578999999976443   3333333443333


Q ss_pred             CCeEEEEecc-CCccHHH
Q psy1548         288 TKQVMMFSAT-LSKEIRP  304 (448)
Q Consensus       288 ~~q~i~~SAT-~~~~~~~  304 (448)
                      .++ |++|.| +-+++.+
T Consensus       850 kRR-I~LTGTPLQNNLmE  866 (1567)
T KOG1015|consen  850 KRR-IILTGTPLQNNLME  866 (1567)
T ss_pred             hee-EEeecCchhhhhHH
Confidence            444 555555 4444333

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=96.15  E-value=0.087  Score=53.36  Aligned_cols=37  Identities=19%  Similarity=0.278  Sum_probs=24.4

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC  187 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~  187 (448)
                      ..+++.||+|+|||... ..+.+.+.....+..++++.
T Consensus       137 n~l~l~G~~G~GKThL~-~ai~~~l~~~~~~~~v~yi~  173 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLL-HAIGNEILENNPNAKVVYVS  173 (405)
T ss_pred             CeEEEECCCCCcHHHHH-HHHHHHHHHhCCCCcEEEEE
Confidence            46899999999999654 44555544433345666664

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).

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

Probab=96.15  E-value=0.012  Score=64.13  Aligned_cols=44  Identities=27%  Similarity=0.392  Sum_probs=41.8

Q ss_pred             ceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548         100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus       100 ~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      +++|||+++++|||.++++.|++|..|..+..|-|++|||||..
T Consensus       331 ~vLVaTd~lerGIDI~~vd~VI~~~~P~s~~~y~qRiGRaGR~G  374 (742)
T TIGR03817       331 LGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRG  374 (742)
T ss_pred             eEEEECchHhccCCcccccEEEEeCCCCCHHHHHHhccccCCCC
Confidence            78999999999999999999999999999999999999999953

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.

>PRK06893 DNA replication initiation factor; Validated

Probab=96.07  E-value=0.02  Score=53.16  Aligned_cols=47  Identities=17%  Similarity=0.246  Sum_probs=28.7

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCC-CCCeEEEEeccCCcc
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSP-HTKQVMMFSATLSKE  301 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~-~~~q~i~~SAT~~~~  301 (448)
                      .+.+++|+||+|.+.........+..++.... ...+++++|++.++.
T Consensus        90 ~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~  137 (229)
T PRK06893         90 EQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPH  137 (229)
T ss_pred             ccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChH
Confidence            45678999999987543123334445554443 345677777876544

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=95.99  E-value=0.046  Score=56.03  Aligned_cols=48  Identities=27%  Similarity=0.279  Sum_probs=30.3

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHH
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKE  199 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~  199 (448)
                      ..+++.|++|+|||.. +-++.+.+.....+.+++++.+ .++..++...
T Consensus       142 npl~i~G~~G~GKTHL-l~Ai~~~l~~~~~~~~v~yv~~-~~f~~~~~~~  189 (450)
T PRK14087        142 NPLFIYGESGMGKTHL-LKAAKNYIESNFSDLKVSYMSG-DEFARKAVDI  189 (450)
T ss_pred             CceEEECCCCCcHHHH-HHHHHHHHHHhCCCCeEEEEEH-HHHHHHHHHH
Confidence            4689999999999954 3455555544444556766654 4555554433

>PHA02533 17 large terminase protein; Provisional

Probab=95.96  E-value=0.031  Score=58.30  Aligned_cols=151  Identities=13%  Similarity=0.119  Sum_probs=86.5

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .|..++++|..      .+..+..++-.++..+-..|||.+....++...... .+..+++++|+..-|..+.+.++.+.
T Consensus        56 ~Pf~L~p~Q~~------i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~~-~~~~v~i~A~~~~QA~~vF~~ik~~i  128 (534)
T PHA02533         56 IKVQMRDYQKD------MLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCFN-KDKNVGILAHKASMAAEVLDRTKQAI  128 (534)
T ss_pred             eecCCcHHHHH------HHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHhC-CCCEEEEEeCCHHHHHHHHHHHHHHH
Confidence            47778888999      555444456668999999999988765454433333 34589999999999999988888776


Q ss_pred             ccCCCc-eEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHH
Q psy1548         205 KYMSNI-KVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFR  283 (448)
Q Consensus       205 ~~~~~~-~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~  283 (448)
                      ...|.. +.......    .....+.++ ..|.+.|.+       .+...-.+..++++||+|.+.+.   ...+..+..
T Consensus       129 e~~P~l~~~~i~~~~----~~~I~l~NG-S~I~~lss~-------~~t~rG~~~~~liiDE~a~~~~~---~e~~~ai~p  193 (534)
T PHA02533        129 ELLPDFLQPGIVEWN----KGSIELENG-SKIGAYASS-------PDAVRGNSFAMIYIDECAFIPNF---IDFWLAIQP  193 (534)
T ss_pred             HhCHHHhhcceeecC----ccEEEeCCC-CEEEEEeCC-------CCccCCCCCceEEEeccccCCCH---HHHHHHHHH
Confidence            655432 11111100    011111233 445444422       11122235568999999976432   222333333


Q ss_pred             hCCC--CCeEEEEecc
Q psy1548         284 SSPH--TKQVMMFSAT  297 (448)
Q Consensus       284 ~l~~--~~q~i~~SAT  297 (448)
                      .+..  ..+++.+|++
T Consensus       194 ~lasg~~~r~iiiSTp  209 (534)
T PHA02533        194 VISSGRSSKIIITSTP  209 (534)
T ss_pred             HHHcCCCceEEEEECC
Confidence            2222  2356666655

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=95.92  E-value=0.097  Score=46.52  Aligned_cols=48  Identities=19%  Similarity=0.129  Sum_probs=30.7

Q ss_pred             eeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         152 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       152 vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      +++.||+|+|||...+--+...+.   .+..++|++. .+-..++.+.+..+
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~---~g~~v~~~s~-e~~~~~~~~~~~~~   49 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLA---RGEPGLYVTL-EESPEELIENAESL   49 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHH---CCCcEEEEEC-CCCHHHHHHHHHHc
Confidence            689999999999764433333332   2346777764 44566766666665

A related protein is found in archaea.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=95.92  E-value=0.046  Score=55.03  Aligned_cols=36  Identities=22%  Similarity=0.393  Sum_probs=23.0

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEe
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVM  186 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil  186 (448)
                      .++++.||+|+|||.+. --++..+.....+..++++
T Consensus        56 ~~~lI~G~~GtGKT~l~-~~v~~~l~~~~~~~~~v~i   91 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTV-KKVFEELEEIAVKVVYVYI   91 (394)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHHHhcCCcEEEEE
Confidence            67999999999999763 3444444333223445555

>KOG0343|consensus

Probab=95.90  E-value=0.0061  Score=61.62  Aligned_cols=61  Identities=36%  Similarity=0.543  Sum_probs=49.1

Q ss_pred             HhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          95 IVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      .....-|+.||++++||+|+|.|.+|+.++-|..+++|=+.+||+.|   .--.|+++++..|.
T Consensus       362 ~~~~~~vLF~TDv~aRGLDFpaVdwViQ~DCPedv~tYIHRvGRtAR---~~~~G~sll~L~ps  422 (758)
T KOG0343|consen  362 VRKRAVVLFCTDVAARGLDFPAVDWVIQVDCPEDVDTYIHRVGRTAR---YKERGESLLMLTPS  422 (758)
T ss_pred             HHhcceEEEeehhhhccCCCcccceEEEecCchhHHHHHHHhhhhhc---ccCCCceEEEEcch
Confidence            34455799999999999999999999999999999999988887655   44456666665554

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=95.88  E-value=0.048  Score=55.07  Aligned_cols=147  Identities=13%  Similarity=0.172  Sum_probs=78.6

Q ss_pred             eeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHH-HHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhc
Q psy1548         152 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE-LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKT  230 (448)
Q Consensus       152 vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~-L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~  230 (448)
                      .++.|+.|||||.+..+-++..+...+.+.+++++-|+.. |...+...+......+ ++....-....+.  .. .+..
T Consensus         4 ~i~~GgrgSGKS~~~~~~~~~~~~~~~~~~~~~~~r~~~~sl~~sv~~~l~~~i~~~-g~~~~~~~~~~~~--~i-~~~~   79 (396)
T TIGR01547         4 IIAKGGRRSGKTFAIALKLVEKLAINKKQQNILAARKVQNSIRDSVFKDIENLLSIE-GINYEFKKSKSSM--EI-KILN   79 (396)
T ss_pred             EEEeCCCCcccHHHHHHHHHHHHHhcCCCcEEEEEehhhhHHHHHHHHHHHHHHHHc-CChhheeecCCcc--EE-EecC
Confidence            5778999999999988887777666423468899989887 6666777777655544 3321111111110  00 0111


Q ss_pred             CCCcEEEEcH-HHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHh
Q psy1548         231 HNPQIVVGTP-GRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKF  309 (448)
Q Consensus       231 ~~~~IlV~Tp-~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~  309 (448)
                      .+..|++..- +...+ ++    ....+.++.+|||..+..  .....+..-++. +...+.+++|.+++....-+.+.|
T Consensus        80 ~g~~i~f~g~~d~~~~-ik----~~~~~~~~~idEa~~~~~--~~~~~l~~rlr~-~~~~~~i~~t~NP~~~~~w~~~~f  151 (396)
T TIGR01547        80 TGKKFIFKGLNDKPNK-LK----SGAGIAIIWFEEASQLTF--EDIKELIPRLRE-TGGKKFIIFSSNPESPLHWVKKRF  151 (396)
T ss_pred             CCeEEEeecccCChhH-hh----CcceeeeehhhhhhhcCH--HHHHHHHHHhhc-cCCccEEEEEcCcCCCccHHHHHH
Confidence            0134555433 21111 11    123368899999998744  322333222322 122224677777655433444444


Q ss_pred             c
Q psy1548         310 M  310 (448)
Q Consensus       310 l  310 (448)
                      .
T Consensus       152 ~  152 (396)
T TIGR01547       152 I  152 (396)
T ss_pred             H
Confidence            4

This model detects members of a highly divergent family of the large subunit of phage terminase. All members are encoded by phage genomes or within prophage regions of bacterial genomes. This is a distinct family from pfam03354.

>PF05127 Helicase_RecD: Helicase; InterPro: IPR007807 This domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase

Probab=95.88  E-value=0.0021  Score=56.63  Aligned_cols=125  Identities=20%  Similarity=0.192  Sum_probs=52.4

Q ss_pred             eeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCC
Q psy1548         153 LCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHN  232 (448)
Q Consensus       153 li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~  232 (448)
                      ++.|+-|-|||.+..+.+...+...  ..+++|.+|+.+=++.+++.+..-.... +.+..    ..........+....
T Consensus         1 VltA~RGRGKSa~lGl~~a~l~~~~--~~~I~vtAP~~~~~~~lf~~~~~~l~~~-~~~~~----~~~~~~~~~~~~~~~   73 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAALIQKG--KIRILVTAPSPENVQTLFEFAEKGLKAL-GYKEE----KKKRIGQIIKLRFNK   73 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCCSSS-------EEEE-SS--S-HHHHHCC-------------------------------C
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHhc--CceEEEecCCHHHHHHHHHHHHhhcccc-ccccc----ccccccccccccccc
Confidence            4789999999987665554433222  2579999999987777666554433222 22210    000000011111123


Q ss_pred             CcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCc
Q psy1548         233 PQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSK  300 (448)
Q Consensus       233 ~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~  300 (448)
                      ..|-+..|+.+...-       ...+++|||||=.+.-     +.+..+++..    ..++||.|+..
T Consensus        74 ~~i~f~~Pd~l~~~~-------~~~DlliVDEAAaIp~-----p~L~~ll~~~----~~vv~stTi~G  125 (177)
T PF05127_consen   74 QRIEFVAPDELLAEK-------PQADLLIVDEAAAIPL-----PLLKQLLRRF----PRVVFSTTIHG  125 (177)
T ss_dssp             CC--B--HHHHCCT-----------SCEEECTGGGS-H-----HHHHHHHCCS----SEEEEEEEBSS
T ss_pred             ceEEEECCHHHHhCc-------CCCCEEEEechhcCCH-----HHHHHHHhhC----CEEEEEeeccc
Confidence            567777787654321       2347899999985533     2344443322    35677888753

This domain is often N-terminal to a GCN5-related N-acetyltransferase domain IPR000182 from INTERPRO and C-terminal to IPR013562 from INTERPRO.; PDB: 2ZPA_B.

>PRK08084 DNA replication initiation factor; Provisional

Probab=95.85  E-value=0.025  Score=52.68  Aligned_cols=18  Identities=17%  Similarity=0.327  Sum_probs=15.2

Q ss_pred             CcceeeeccCCChhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~  166 (448)
                      +..+++.||+|+|||-..
T Consensus        45 ~~~l~l~Gp~G~GKThLl   62 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLL   62 (235)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            468999999999999553

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=95.80  E-value=0.0082  Score=63.49  Aligned_cols=47  Identities=36%  Similarity=0.425  Sum_probs=42.1

Q ss_pred             hccceeEeeccccCCcccc---cce-----eEeeccCCCCchhhhhhhccccccc
Q psy1548          97 DCWRILVATNLFGRGMDIE---RVN-----IVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        97 ~~~~~~~~~~~~~~~~d~~---~~~-----~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      ..+.|+||||+++||+|++   +|.     .|++++.|...+.|.+.+||+||..
T Consensus       520 ~~g~VlVATdmAgRGtDI~l~~~V~~~GGLhVI~~d~P~s~r~y~hr~GRTGRqG  574 (656)
T PRK12898        520 QRGRITVATNMAGRGTDIKLEPGVAARGGLHVILTERHDSARIDRQLAGRCGRQG  574 (656)
T ss_pred             CCCcEEEEccchhcccCcCCccchhhcCCCEEEEcCCCCCHHHHHHhcccccCCC
Confidence            3468999999999999999   676     8999999999999999999999943

>KOG0326|consensus

Probab=95.80  E-value=0.0066  Score=57.36  Aligned_cols=43  Identities=58%  Similarity=1.126  Sum_probs=41.3

Q ss_pred             ceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548         100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus       100 ~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      +.+|||+++.||||...+..|+||++|...+.|-+.+||+||.
T Consensus       374 rnLVctDL~TRGIDiqavNvVINFDfpk~aEtYLHRIGRsGRF  416 (459)
T KOG0326|consen  374 RNLVCTDLFTRGIDIQAVNVVINFDFPKNAETYLHRIGRSGRF  416 (459)
T ss_pred             ceeeehhhhhcccccceeeEEEecCCCCCHHHHHHHccCCccC
Confidence            7899999999999999999999999999999999999999983

>KOG0329|consensus

Probab=95.77  E-value=0.0041  Score=56.87  Aligned_cols=41  Identities=98%  Similarity=1.509  Sum_probs=39.2

Q ss_pred             eEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548         102 LVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus       102 ~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      .|+|+++|||+|...+..++||+.|..-+.|-+..+||||.
T Consensus       302 ~vat~lfgrgmdiervNi~~NYdmp~~~DtYlHrv~rAgrf  342 (387)
T KOG0329|consen  302 LVATDLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  342 (387)
T ss_pred             hHHhhhhccccCcccceeeeccCCCCCchHHHHHhhhhhcc
Confidence            79999999999999999999999999999999999999883

>KOG0350|consensus

Probab=95.77  E-value=0.0058  Score=61.02  Aligned_cols=60  Identities=32%  Similarity=0.592  Sum_probs=46.2

Q ss_pred             ceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHH
Q psy1548         100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTA  164 (448)
Q Consensus       100 ~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~  164 (448)
                      .|+||+++..||||..++..|+||+.|-....|=+.+||++||...   |  ..+..-++-|+++
T Consensus       485 ~vLIcSD~laRGiDv~~v~~VINYd~P~~~ktyVHR~GRTARAgq~---G--~a~tll~~~~~r~  544 (620)
T KOG0350|consen  485 NVLICSDALARGIDVNDVDNVINYDPPASDKTYVHRAGRTARAGQD---G--YAITLLDKHEKRL  544 (620)
T ss_pred             eEEEehhhhhcCCcccccceEeecCCCchhhHHHHhhcccccccCC---c--eEEEeeccccchH
Confidence            8999999999999999999999999999998888887776664322   1  2233445556664

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=95.76  E-value=0.028  Score=58.17  Aligned_cols=135  Identities=13%  Similarity=0.153  Sum_probs=77.7

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhh-ccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHH
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLE-TTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL  228 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~-~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l  228 (448)
                      +.+++..|-|.|||......++..+. ....+..+++.+++++-|..+++.++.+....|.+....  +.     ..  .
T Consensus        23 ~~~~l~v~RkNGKS~l~a~i~ly~l~~~g~~~~~i~~~A~~~~QA~~~f~~~~~~i~~~~~l~~~~--~~-----~~--~   93 (477)
T PF03354_consen   23 REVYLEVPRKNGKSTLAAAIALYMLFLDGEPGAEIYCAANTRDQAKIVFDEAKKMIEASPELRKRK--KP-----KI--I   93 (477)
T ss_pred             EEEEEEEcCccCccHHHHHHHHHHHhcCCccCceEEEEeCCHHHHHHHHHHHHHHHHhChhhccch--hh-----hh--h
Confidence            56788899999999776555554443 334567899999999999999999998877654332110  00     00  0


Q ss_pred             hcCCCcEEEEcHHHHHHHHHC--CCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         229 KTHNPQIVVGTPGRILALVRN--KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       229 ~~~~~~IlV~Tp~~l~~~l~~--~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      ....-.|.....+.....+..  +..+-.+..++|+||+|.+-+. .....+..-+... ++.+++..|
T Consensus        94 ~~~~~~i~~~~~~s~~~~~s~~~~~~dG~~~~~~i~DE~h~~~~~-~~~~~l~~g~~~r-~~pl~~~IS  160 (477)
T PF03354_consen   94 KSNKKEIEFPKTGSFFKALSSDADSLDGLNPSLAIFDELHAHKDD-ELYDALESGMGAR-PNPLIIIIS  160 (477)
T ss_pred             hhhceEEEEcCCCcEEEEEecCCCCccCCCCceEEEeCCCCCCCH-HHHHHHHhhhccC-CCceEEEEe
Confidence            000012222221222222211  2233345689999999988664 4555555544443 344555443

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PLN03025 replication factor C subunit; Provisional

Probab=95.75  E-value=0.11  Score=50.81  Aligned_cols=39  Identities=21%  Similarity=0.261  Sum_probs=25.6

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      ...+++++||+|.|...  ....+...+...+..+.+++.+
T Consensus        98 ~~~kviiiDE~d~lt~~--aq~aL~~~lE~~~~~t~~il~~  136 (319)
T PLN03025         98 GRHKIVILDEADSMTSG--AQQALRRTMEIYSNTTRFALAC  136 (319)
T ss_pred             CCeEEEEEechhhcCHH--HHHHHHHHHhcccCCceEEEEe
Confidence            35789999999988663  3444555566555566655543

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=95.70  E-value=0.059  Score=58.81  Aligned_cols=118  Identities=14%  Similarity=0.102  Sum_probs=67.6

Q ss_pred             hhhhhhccccccceeeeeC-cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCC
Q psy1548         131 TYLHRVARAGRFGTKAVLG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  209 (448)
Q Consensus       131 ~yQ~~~~~~~~~~~~~~~g-~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  209 (448)
                      +-|..      ++..++.+ +-+++.|+.|+|||... -.+...+..  .+.+++.++||-.-+..+.    .-.    +
T Consensus       355 ~~Q~~------Av~~i~~s~~~~il~G~aGTGKTtll-~~i~~~~~~--~g~~V~~~ApTg~Aa~~L~----~~~----g  417 (744)
T TIGR02768       355 EEQYE------AVRHVTGSGDIAVVVGRAGTGKSTML-KAAREAWEA--AGYRVIGAALSGKAAEGLQ----AES----G  417 (744)
T ss_pred             HHHHH------HHHHHhcCCCEEEEEecCCCCHHHHH-HHHHHHHHh--CCCeEEEEeCcHHHHHHHH----hcc----C
Confidence            33888      88777764 56799999999999653 334333332  2457999999986554432    111    1


Q ss_pred             ceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHh-CCCC
Q psy1548         210 IKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRS-SPHT  288 (448)
Q Consensus       210 ~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~-l~~~  288 (448)
                      +..                         .|..+++.-.......+...++|||||+-++... .+    ..++.. ....
T Consensus       418 ~~a-------------------------~Ti~~~~~~~~~~~~~~~~~~llIvDEasMv~~~-~~----~~Ll~~~~~~~  467 (744)
T TIGR02768       418 IES-------------------------RTLASLEYAWANGRDLLSDKDVLVIDEAGMVGSR-QM----ARVLKEAEEAG  467 (744)
T ss_pred             Cce-------------------------eeHHHHHhhhccCcccCCCCcEEEEECcccCCHH-HH----HHHHHHHHhcC
Confidence            111                         1222221111222233567789999999966443 33    334442 2356


Q ss_pred             CeEEEEe
Q psy1548         289 KQVMMFS  295 (448)
Q Consensus       289 ~q~i~~S  295 (448)
                      .++|++.
T Consensus       468 ~kliLVG  474 (744)
T TIGR02768       468 AKVVLVG  474 (744)
T ss_pred             CEEEEEC
Confidence            6777766

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>PRK06921 hypothetical protein; Provisional

Probab=95.68  E-value=0.051  Score=51.61  Aligned_cols=45  Identities=24%  Similarity=0.124  Sum_probs=27.5

Q ss_pred             eCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ  195 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q  195 (448)
                      .+.++++.|++|+|||... .++...+... .+..++++. ..++..+
T Consensus       116 ~~~~l~l~G~~G~GKThLa-~aia~~l~~~-~g~~v~y~~-~~~l~~~  160 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLL-TAAANELMRK-KGVPVLYFP-FVEGFGD  160 (266)
T ss_pred             CCCeEEEECCCCCcHHHHH-HHHHHHHhhh-cCceEEEEE-HHHHHHH
Confidence            3678999999999999653 3444444332 134556554 4444444

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=95.66  E-value=0.039  Score=51.97  Aligned_cols=51  Identities=16%  Similarity=0.303  Sum_probs=33.9

Q ss_pred             eeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHH
Q psy1548         147 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYE  201 (448)
Q Consensus       147 ~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  201 (448)
                      ..++++++.||+|+|||..+. ++.+.+.  ..+ ..++.+++.+|+.++...+.
T Consensus       103 ~~~~nl~l~G~~G~GKThLa~-Ai~~~l~--~~g-~sv~f~~~~el~~~Lk~~~~  153 (254)
T COG1484         103 ERGENLVLLGPPGVGKTHLAI-AIGNELL--KAG-ISVLFITAPDLLSKLKAAFD  153 (254)
T ss_pred             ccCCcEEEECCCCCcHHHHHH-HHHHHHH--HcC-CeEEEEEHHHHHHHHHHHHh
Confidence            378999999999999997643 3444444  223 34555677778777554433

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=95.62  E-value=0.14  Score=52.48  Aligned_cols=38  Identities=13%  Similarity=0.250  Sum_probs=25.0

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeec
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH  188 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~P  188 (448)
                      ..+++.||+|+|||... -++.+.+.....+.+++++..
T Consensus       131 n~l~lyG~~G~GKTHLl-~ai~~~l~~~~~~~~v~yi~~  168 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLL-QSIGNYVVQNEPDLRVMYITS  168 (440)
T ss_pred             CeEEEEcCCCCcHHHHH-HHHHHHHHHhCCCCeEEEEEH
Confidence            46899999999999653 344454444333446776653

>PRK08727 hypothetical protein; Validated

Probab=95.53  E-value=0.058  Score=50.16  Aligned_cols=35  Identities=17%  Similarity=0.080  Sum_probs=21.0

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC  187 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~  187 (448)
                      ..+++.||+|+|||-... ++...+...  +.+++++.
T Consensus        42 ~~l~l~G~~G~GKThL~~-a~~~~~~~~--~~~~~y~~   76 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLAL-ALCAAAEQA--GRSSAYLP   76 (233)
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHHHHc--CCcEEEEe
Confidence            358999999999995433 333333222  33566654

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=95.53  E-value=0.061  Score=59.85  Aligned_cols=118  Identities=13%  Similarity=0.060  Sum_probs=69.1

Q ss_pred             hhhhccccccceeeeeCcc-eeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCce
Q psy1548         133 LHRVARAGRFGTKAVLGMD-ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIK  211 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~g~~-vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~  211 (448)
                      |.+      ++..++.+++ ++++|+.|+|||.+ +-++...+..  .+.+++.++||-.-+..+.    .   .. ++.
T Consensus       351 Qr~------Av~~il~s~~v~vv~G~AGTGKTT~-l~~~~~~~e~--~G~~V~~~ApTGkAA~~L~----e---~t-Gi~  413 (988)
T PRK13889        351 QAD------ALAHVTDGRDLGVVVGYAGTGKSAM-LGVAREAWEA--AGYEVRGAALSGIAAENLE----G---GS-GIA  413 (988)
T ss_pred             HHH------HHHHHhcCCCeEEEEeCCCCCHHHH-HHHHHHHHHH--cCCeEEEecCcHHHHHHHh----h---cc-Ccc
Confidence            888      8888887654 68999999999976 3344443332  3557999999986554332    1   11 111


Q ss_pred             EEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhC-CCCCe
Q psy1548         212 VGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSS-PHTKQ  290 (448)
Q Consensus       212 v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l-~~~~q  290 (448)
                      .                         .|..+++.-...+...+...++|||||+-++...     .+..+++.. +...+
T Consensus       414 a-------------------------~TI~sll~~~~~~~~~l~~~~vlIVDEASMv~~~-----~m~~LL~~a~~~gar  463 (988)
T PRK13889        414 S-------------------------RTIASLEHGWGQGRDLLTSRDVLVIDEAGMVGTR-----QLERVLSHAADAGAK  463 (988)
T ss_pred             h-------------------------hhHHHHHhhhcccccccccCcEEEEECcccCCHH-----HHHHHHHhhhhCCCE
Confidence            0                         1222222111122233556689999999955433     334455433 45677


Q ss_pred             EEEEecc
Q psy1548         291 VMMFSAT  297 (448)
Q Consensus       291 ~i~~SAT  297 (448)
                      +|++.=+
T Consensus       464 vVLVGD~  470 (988)
T PRK13889        464 VVLVGDP  470 (988)
T ss_pred             EEEECCH
Confidence            8777655

>KOG0347|consensus

Probab=95.51  E-value=0.0087  Score=60.50  Aligned_cols=58  Identities=31%  Similarity=0.576  Sum_probs=48.5

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCC
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSG  159 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTG  159 (448)
                      .-|++||+.+.||+|.+.|..|+||.-|...+-|=+.-||+.|   +-..|-.+++++|--
T Consensus       514 ~~VLiaTDVAARGLDIp~V~HVIHYqVPrtseiYVHRSGRTAR---A~~~Gvsvml~~P~e  571 (731)
T KOG0347|consen  514 SGVLIATDVAARGLDIPGVQHVIHYQVPRTSEIYVHRSGRTAR---ANSEGVSVMLCGPQE  571 (731)
T ss_pred             CeEEEeehhhhccCCCCCcceEEEeecCCccceeEeccccccc---ccCCCeEEEEeChHH
Confidence            3799999999999999999999999999999777777666555   555677888888865

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.50  E-value=0.056  Score=55.19  Aligned_cols=19  Identities=21%  Similarity=0.343  Sum_probs=15.3

Q ss_pred             cceeeeccCCChhHHHHHH
Q psy1548         150 MDILCQAKSGMGKTAVFVL  168 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l  168 (448)
                      +.+|+.||.|+|||.++.+
T Consensus        41 ha~Lf~GP~GtGKTTlAri   59 (484)
T PRK14956         41 HAYIFFGPRGVGKTTIARI   59 (484)
T ss_pred             eEEEEECCCCCCHHHHHHH
Confidence            3479999999999977543

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=95.50  E-value=0.09  Score=53.75  Aligned_cols=50  Identities=8%  Similarity=0.207  Sum_probs=28.1

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhC-CCCCeEEEEeccCCccHHH
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSS-PHTKQVMMFSATLSKEIRP  304 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l-~~~~q~i~~SAT~~~~~~~  304 (448)
                      .+.++++|||+|.+.........+..++..+ ....|+++.|.+.|..+..
T Consensus       201 ~~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~  251 (445)
T PRK12422        201 RNVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKA  251 (445)
T ss_pred             ccCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhh
Confidence            3567899999998754312233333444332 2356666666555555443

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.48  E-value=0.21  Score=53.87  Aligned_cols=131  Identities=10%  Similarity=0.162  Sum_probs=66.5

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeec-c-HHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH-T-RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE  226 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~P-t-~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~  226 (448)
                      |+-+.+.||||+|||.+...-+...... .++.++.++.- + +.=+   .++++.+...+ ++.+              
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~-~G~kkV~lit~Dt~RigA---~eQL~~~a~~~-gvpv--------------  245 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAR-EGADQLALLTTDSFRIGA---LEQLRIYGRIL-GVPV--------------  245 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHH-cCCCeEEEecCcccchHH---HHHHHHHHHhC-CCCc--------------
Confidence            5668899999999997754333222112 22224444432 2 2112   23445554443 3322              


Q ss_pred             HHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCc-cHHHH
Q psy1548         227 YLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSK-EIRPV  305 (448)
Q Consensus       227 ~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~-~~~~~  305 (448)
                              .++.+|..+...+..    +.+.++++||=+=+..........+..+.....+...++.+|||... .+.+.
T Consensus       246 --------~~~~~~~~l~~al~~----~~~~D~VLIDTAGRs~~d~~l~eel~~l~~~~~p~e~~LVLsAt~~~~~l~~i  313 (767)
T PRK14723        246 --------HAVKDAADLRFALAA----LGDKHLVLIDTVGMSQRDRNVSEQIAMLCGVGRPVRRLLLLNAASHGDTLNEV  313 (767)
T ss_pred             --------cccCCHHHHHHHHHH----hcCCCEEEEeCCCCCccCHHHHHHHHHHhccCCCCeEEEEECCCCcHHHHHHH
Confidence                    223356655555542    23446777877765433212333344444344445567788888654 34455


Q ss_pred             HHHhc
Q psy1548         306 CKKFM  310 (448)
Q Consensus       306 ~~~~l  310 (448)
                      ++.|-
T Consensus       314 ~~~f~  318 (767)
T PRK14723        314 VHAYR  318 (767)
T ss_pred             HHHHh
Confidence            55553

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=95.45  E-value=0.044  Score=63.26  Aligned_cols=97  Identities=21%  Similarity=0.141  Sum_probs=63.7

Q ss_pred             ceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCC
Q psy1548         100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDS  179 (448)
Q Consensus       100 ~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~  179 (448)
                      ++.|||+...+|||.++++.|+++..|..+..|.|.+||||+.    ..|....+..|+. -+-+.....++..+..+.-
T Consensus       329 rvLVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~----~gg~s~gli~p~~-r~dlle~~~~ve~~l~g~i  403 (1490)
T PRK09751        329 RCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQ----VGGVSKGLFFPRT-RRDLVDSAVIVECMFAGRL  403 (1490)
T ss_pred             eEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCC----CCCccEEEEEeCc-HHHHHhhHHHHHHHhcCCC
Confidence            8999999999999999999999999999999999999999984    2233333334443 2222222333444433333


Q ss_pred             CeEEEEeeccHHHHHHHHHHHH
Q psy1548         180 NVYVLVMCHTRELAFQISKEYE  201 (448)
Q Consensus       180 ~~~~lil~Pt~~L~~q~~~~~~  201 (448)
                      ......-.|.--|++|+...+.
T Consensus       404 E~~~~p~nplDVLaqqiva~a~  425 (1490)
T PRK09751        404 ENLTPPHNPLDVLAQQTVAAAA  425 (1490)
T ss_pred             CccCCCCChHHHHHHHHHHHHh
Confidence            3323333455556888766544

>KOG0338|consensus

Probab=95.45  E-value=0.012  Score=59.11  Aligned_cols=56  Identities=41%  Similarity=0.698  Sum_probs=45.4

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeecc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAK  157 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~ap  157 (448)
                      -.|+|||++++||+|...|.-|+||..|..++.|-+..||+.|+.   ..|++|-+++.
T Consensus       477 idvLiaTDvAsRGLDI~gV~tVINy~mP~t~e~Y~HRVGRTARAG---RaGrsVtlvgE  532 (691)
T KOG0338|consen  477 IDVLIATDVASRGLDIEGVQTVINYAMPKTIEHYLHRVGRTARAG---RAGRSVTLVGE  532 (691)
T ss_pred             CCEEEEechhhccCCccceeEEEeccCchhHHHHHHHhhhhhhcc---cCcceEEEecc
Confidence            378999999999999999999999999999999999888866533   33555554443

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=95.44  E-value=0.1  Score=49.36  Aligned_cols=18  Identities=28%  Similarity=0.512  Sum_probs=15.6

Q ss_pred             CcceeeeccCCChhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~  166 (448)
                      ..++++.||+|+|||..+
T Consensus        42 ~~~vll~GppGtGKTtlA   59 (261)
T TIGR02881        42 VLHMIFKGNPGTGKTTVA   59 (261)
T ss_pred             cceEEEEcCCCCCHHHHH
Confidence            468999999999999765

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>PRK12377 putative replication protein; Provisional

Probab=95.42  E-value=0.085  Score=49.44  Aligned_cols=45  Identities=16%  Similarity=0.222  Sum_probs=27.4

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQIS  197 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~  197 (448)
                      ..++++.||+|+|||... .++.+.+...  +..+ +..+..+|..++.
T Consensus       101 ~~~l~l~G~~GtGKThLa-~AIa~~l~~~--g~~v-~~i~~~~l~~~l~  145 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLA-AAIGNRLLAK--GRSV-IVVTVPDVMSRLH  145 (248)
T ss_pred             CCeEEEECCCCCCHHHHH-HHHHHHHHHc--CCCe-EEEEHHHHHHHHH
Confidence            368999999999999553 3444444332  3234 4445556665543

>PRK08116 hypothetical protein; Validated

Probab=95.40  E-value=0.087  Score=50.10  Aligned_cols=43  Identities=23%  Similarity=0.268  Sum_probs=26.8

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHH
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI  196 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~  196 (448)
                      ..+++.|++|+|||..+ .++.+.+...  +..++++ +..++...+
T Consensus       115 ~gl~l~G~~GtGKThLa-~aia~~l~~~--~~~v~~~-~~~~ll~~i  157 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLA-ACIANELIEK--GVPVIFV-NFPQLLNRI  157 (268)
T ss_pred             ceEEEECCCCCCHHHHH-HHHHHHHHHc--CCeEEEE-EHHHHHHHH
Confidence            45999999999999664 3455555443  3344444 455555543

>PRK13767 ATP-dependent helicase; Provisional

Probab=95.38  E-value=0.026  Score=62.73  Aligned_cols=43  Identities=26%  Similarity=0.518  Sum_probs=41.3

Q ss_pred             ceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548         100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus       100 ~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ++.|||+.+++|||.++++.|+++..|..+..|-|.+|||||.
T Consensus       342 ~vLVaTs~Le~GIDip~Vd~VI~~~~P~sv~~ylQRiGRaGR~  384 (876)
T PRK13767        342 KVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAGHR  384 (876)
T ss_pred             eEEEECChHHhcCCCCCCcEEEEeCCCCCHHHHHHhcccCCCC
Confidence            8999999999999999999999999999999999999999984

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=95.38  E-value=0.096  Score=48.20  Aligned_cols=20  Identities=20%  Similarity=0.169  Sum_probs=16.5

Q ss_pred             eCcceeeeccCCChhHHHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVFV  167 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~  167 (448)
                      .+.++++.||+|+|||....
T Consensus        37 ~~~~lll~G~~G~GKT~la~   56 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHLLQ   56 (226)
T ss_pred             CCCeEEEECCCCCCHHHHHH
Confidence            35789999999999996643

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=95.38  E-value=0.17  Score=51.42  Aligned_cols=132  Identities=12%  Similarity=0.130  Sum_probs=65.0

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee--ccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE  226 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~  226 (448)
                      ...++++|++|+|||.+..--+. .+...  +.++++++  +.+.-+   .++++.++... ++.+.......       
T Consensus        95 p~vI~lvG~~GsGKTTtaakLA~-~L~~~--g~kV~lV~~D~~R~aa---~eQL~~la~~~-gvp~~~~~~~~-------  160 (437)
T PRK00771         95 PQTIMLVGLQGSGKTTTAAKLAR-YFKKK--GLKVGLVAADTYRPAA---YDQLKQLAEKI-GVPFYGDPDNK-------  160 (437)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHH-HHHHc--CCeEEEecCCCCCHHH---HHHHHHHHHHc-CCcEEecCCcc-------
Confidence            45688999999999977543332 33322  23455444  223322   23344444433 33321111000       


Q ss_pred             HHhcCCCcEEEEcHHH-HHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHH
Q psy1548         227 YLKTHNPQIVVGTPGR-ILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPV  305 (448)
Q Consensus       227 ~l~~~~~~IlV~Tp~~-l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~  305 (448)
                                  .|.. +.+.+..    ....+++|+|.+-+..........+..+.....+..-++.++|+...+..+.
T Consensus       161 ------------d~~~i~~~al~~----~~~~DvVIIDTAGr~~~d~~lm~El~~l~~~~~pdevlLVvda~~gq~av~~  224 (437)
T PRK00771        161 ------------DAVEIAKEGLEK----FKKADVIIVDTAGRHALEEDLIEEMKEIKEAVKPDEVLLVIDATIGQQAKNQ  224 (437)
T ss_pred             ------------CHHHHHHHHHHH----hhcCCEEEEECCCcccchHHHHHHHHHHHHHhcccceeEEEeccccHHHHHH
Confidence                        1111 1222222    1112678888884332221445555566555555556777777776655555


Q ss_pred             HHHhc
Q psy1548         306 CKKFM  310 (448)
Q Consensus       306 ~~~~l  310 (448)
                      ++.|.
T Consensus       225 a~~F~  229 (437)
T PRK00771        225 AKAFH  229 (437)
T ss_pred             HHHHH
Confidence            55543

>KOG0340|consensus

Probab=95.35  E-value=0.016  Score=55.65  Aligned_cols=43  Identities=49%  Similarity=0.852  Sum_probs=40.1

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR  141 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~  141 (448)
                      -+|.+||+.++||+|.|.|..|+||+.|...++|=+..||+.|
T Consensus       305 ~~iliaTDVAsRGLDIP~V~LVvN~diPr~P~~yiHRvGRtAR  347 (442)
T KOG0340|consen  305 ARILIATDVASRGLDIPTVELVVNHDIPRDPKDYIHRVGRTAR  347 (442)
T ss_pred             ccEEEEechhhcCCCCCceeEEEecCCCCCHHHHHHhhcchhc
Confidence            4899999999999999999999999999999999999888655

>KOG0332|consensus

Probab=95.33  E-value=0.017  Score=55.77  Aligned_cols=72  Identities=33%  Similarity=0.608  Sum_probs=51.2

Q ss_pred             hccCceeeeccCCcccCCCCHHHHHHHhh-ccceeEeeccccCCcccccceeEeeccCCCCc------hhhhhhhccccc
Q psy1548          69 EVKGAYVSIHSSGFRDFLLKPEILRAIVD-CWRILVATNLFGRGMDIERVNIVFNYDMPEDS------DTYLHRVARAGR  141 (448)
Q Consensus        69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~------~~yQ~~~~~~~~  141 (448)
                      ...|..++.-+.+...-.. ..++....+ ..+|+|+||...||||...|..|+||+.|...      +.|=+.+||+||
T Consensus       351 ~~~Gh~V~~l~G~l~~~~R-~~ii~~Fr~g~~kVLitTnV~ARGiDv~qVs~VvNydlP~~~~~~pD~etYlHRiGRtGR  429 (477)
T KOG0332|consen  351 RAEGHQVSLLHGDLTVEQR-AAIIDRFREGKEKVLITTNVCARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGR  429 (477)
T ss_pred             HhcCceeEEeeccchhHHH-HHHHHHHhcCcceEEEEechhhcccccceEEEEEecCCccccCCCCCHHHHHHHhccccc
Confidence            3446666665554443322 233333333 34999999999999999999999999999764      667788888887

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=95.33  E-value=0.012  Score=63.69  Aligned_cols=46  Identities=39%  Similarity=0.467  Sum_probs=42.5

Q ss_pred             ccceeEeeccccCCccc---ccce-----eEeeccCCCCchhhhhhhccccccc
Q psy1548          98 CWRILVATNLFGRGMDI---ERVN-----IVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~---~~~~-----~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      .|.|+|||+++|||+|+   ++|.     .|+++..|...+.|.+..||+||..
T Consensus       476 ~g~VlIATdmAgRG~DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~GRtGR~G  529 (790)
T PRK09200        476 KGAVTVATNMAGRGTDIKLGEGVHELGGLAVIGTERMESRRVDLQLRGRSGRQG  529 (790)
T ss_pred             CCeEEEEccchhcCcCCCcccccccccCcEEEeccCCCCHHHHHHhhccccCCC
Confidence            46999999999999999   6898     9999999999999999999999944

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=95.26  E-value=0.16  Score=49.44  Aligned_cols=40  Identities=20%  Similarity=0.409  Sum_probs=28.0

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEec
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSA  296 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SA  296 (448)
                      ...+++++||||.|..  +....+...+..-+.+..+++.+-
T Consensus       108 ~~~kviiidead~mt~--~A~nallk~lEep~~~~~~il~~n  147 (325)
T COG0470         108 GGYKVVIIDEADKLTE--DAANALLKTLEEPPKNTRFILITN  147 (325)
T ss_pred             CCceEEEeCcHHHHhH--HHHHHHHHHhccCCCCeEEEEEcC
Confidence            6788999999998877  455555666666566666665543

>TIGR00376 DNA helicase, putative

Probab=95.24  E-value=0.027  Score=60.24  Aligned_cols=65  Identities=17%  Similarity=0.082  Sum_probs=48.4

Q ss_pred             chhhhhhhccccccceeeeeC-cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         129 SDTYLHRVARAGRFGTKAVLG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       129 ~~~yQ~~~~~~~~~~~~~~~g-~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      +...|..      ++..++.. ..++|+||+|+|||.+..-.+.+.+.   .+.++|+++||..-+.++.+.+..
T Consensus       158 ln~~Q~~------Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~---~g~~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       158 LNESQKE------AVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVK---RGLRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CCHHHHH------HHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHH---cCCCEEEEcCcHHHHHHHHHHHHh
Confidence            4556999      88777765 67889999999999664433333332   234899999999998888777765

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

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=95.17  E-value=0.043  Score=54.67  Aligned_cols=46  Identities=26%  Similarity=0.364  Sum_probs=31.9

Q ss_pred             eeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHH
Q psy1548         147 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ  195 (448)
Q Consensus       147 ~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q  195 (448)
                      ..|.++.+.|+-|+|||..+ -.+.+.+..  .+..+++++||-.-|..
T Consensus        20 ~~~~~~fv~G~~GtGKs~l~-~~i~~~~~~--~~~~~~~~a~tg~AA~~   65 (364)
T PF05970_consen   20 EEGLNFFVTGPAGTGKSFLI-KAIIDYLRS--RGKKVLVTAPTGIAAFN   65 (364)
T ss_pred             cCCcEEEEEcCCCCChhHHH-HHHHHHhcc--ccceEEEecchHHHHHh
Confidence            56889999999999999764 223333322  34578889999765443

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PRK09183 transposase/IS protein; Provisional

Probab=95.16  E-value=0.13  Score=48.72  Aligned_cols=22  Identities=27%  Similarity=0.347  Sum_probs=18.6

Q ss_pred             eeeCcceeeeccCCChhHHHHH
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFV  167 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~  167 (448)
                      +..|.++++.||+|+|||....
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~  120 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAI  120 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHH
Confidence            5678999999999999996543

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=95.13  E-value=0.088  Score=48.61  Aligned_cols=139  Identities=14%  Similarity=0.140  Sum_probs=69.3

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCC----CceEEEEEcCcc
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS----NIKVGVFFGGLP  220 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~----~~~v~~~~g~~~  220 (448)
                      -+..|..+++.|++|+|||...+--+.+.+...  +-++++++- .+-..++.+.++.+.-...    .-....+... +
T Consensus        15 Gip~gs~~li~G~~GsGKT~l~~q~l~~~~~~~--ge~vlyvs~-ee~~~~l~~~~~s~g~d~~~~~~~g~l~~~d~~-~   90 (226)
T PF06745_consen   15 GIPKGSVVLISGPPGSGKTTLALQFLYNGLKNF--GEKVLYVSF-EEPPEELIENMKSFGWDLEEYEDSGKLKIIDAF-P   90 (226)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHHH--T--EEEEES-SS-HHHHHHHHHTTTS-HHHHHHTTSEEEEESS-G
T ss_pred             CCCCCcEEEEEeCCCCCcHHHHHHHHHHhhhhc--CCcEEEEEe-cCCHHHHHHHHHHcCCcHHHHhhcCCEEEEecc-c
Confidence            455678999999999999966544444444431  225777773 3344666666666542110    0011111111 0


Q ss_pred             cHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHh---hhhhHHHHHHHHHhCCCCCeEEEEecc
Q psy1548         221 IQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLE---QLEMRRDVQEIFRSSPHTKQVMMFSAT  297 (448)
Q Consensus       221 ~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~---~~~~~~~~~~i~~~l~~~~q~i~~SAT  297 (448)
                      .....        .  -..++.+...+....- -...+.+|||-...+..   ...++..+..+...+.....+.++++.
T Consensus        91 ~~~~~--------~--~~~~~~l~~~i~~~i~-~~~~~~vVIDsls~l~~~~~~~~~r~~l~~l~~~l~~~~~t~llt~~  159 (226)
T PF06745_consen   91 ERIGW--------S--PNDLEELLSKIREAIE-ELKPDRVVIDSLSALLLYDDPEELRRFLRALIKFLKSRGVTTLLTSE  159 (226)
T ss_dssp             GGST---------T--SCCHHHHHHHHHHHHH-HHTSSEEEEETHHHHTTSSSGGGHHHHHHHHHHHHHHTTEEEEEEEE
T ss_pred             ccccc--------c--ccCHHHHHHHHHHHHH-hcCCCEEEEECHHHHhhcCCHHHHHHHHHHHHHHHHHCCCEEEEEEc
Confidence            00000        0  1133333333322100 11227899999998721   124566677676666555556666666


Q ss_pred             C
Q psy1548         298 L  298 (448)
Q Consensus       298 ~  298 (448)
                      .
T Consensus       160 ~  160 (226)
T PF06745_consen  160 M  160 (226)
T ss_dssp             E
T ss_pred             c
Confidence            3

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>PF13173 AAA_14: AAA domain

Probab=95.13  E-value=0.25  Score=41.07  Aligned_cols=38  Identities=8%  Similarity=0.150  Sum_probs=25.0

Q ss_pred             CeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEecc
Q psy1548         256 LLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSAT  297 (448)
Q Consensus       256 ~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT  297 (448)
                      .-.+++|||+|.+.+|   ...+..+.... ++.++++.+..
T Consensus        61 ~~~~i~iDEiq~~~~~---~~~lk~l~d~~-~~~~ii~tgS~   98 (128)
T PF13173_consen   61 GKKYIFIDEIQYLPDW---EDALKFLVDNG-PNIKIILTGSS   98 (128)
T ss_pred             CCcEEEEehhhhhccH---HHHHHHHHHhc-cCceEEEEccc
Confidence            4457999999988554   55555555544 45677665554

>CHL00181 cbbX CbbX; Provisional

Probab=95.07  E-value=0.19  Score=48.34  Aligned_cols=20  Identities=30%  Similarity=0.499  Sum_probs=17.0

Q ss_pred             eCcceeeeccCCChhHHHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVFV  167 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~  167 (448)
                      .|.++++.||+|+|||.++-
T Consensus        58 ~~~~ill~G~pGtGKT~lAr   77 (287)
T CHL00181         58 PGLHMSFTGSPGTGKTTVAL   77 (287)
T ss_pred             CCceEEEECCCCCCHHHHHH
Confidence            46789999999999997754

>KOG0344|consensus

Probab=95.03  E-value=0.022  Score=58.11  Aligned_cols=58  Identities=40%  Similarity=0.785  Sum_probs=46.2

Q ss_pred             ceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCC
Q psy1548         100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGM  160 (448)
Q Consensus       100 ~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGs  160 (448)
                      -|++||++.+||||+.+++.|+||+.|...-.|=+.+||.||+.+.   |+-+.+-..+++
T Consensus       440 wvLicTdll~RGiDf~gvn~VInyD~p~s~~syihrIGRtgRag~~---g~Aitfytd~d~  497 (593)
T KOG0344|consen  440 WVLICTDLLARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGRAGRS---GKAITFYTDQDM  497 (593)
T ss_pred             eEEEehhhhhccccccCcceEEecCCCchhHHHHHHhhccCCCCCC---cceEEEeccccc
Confidence            5679999999999999999999999999997788888888885544   444444444443

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=95.02  E-value=0.16  Score=49.37  Aligned_cols=40  Identities=15%  Similarity=0.230  Sum_probs=27.6

Q ss_pred             CeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEec
Q psy1548         256 LLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSA  296 (448)
Q Consensus       256 ~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SA  296 (448)
                      ..+++||||+|.+... .....+..++...+..+++|+.|.
T Consensus       100 ~~~vliiDe~d~l~~~-~~~~~L~~~le~~~~~~~~Ilt~n  139 (316)
T PHA02544        100 GGKVIIIDEFDRLGLA-DAQRHLRSFMEAYSKNCSFIITAN  139 (316)
T ss_pred             CCeEEEEECcccccCH-HHHHHHHHHHHhcCCCceEEEEcC
Confidence            4578999999988333 445566666777777777776543

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.97  E-value=0.34  Score=48.89  Aligned_cols=135  Identities=11%  Similarity=0.177  Sum_probs=64.6

Q ss_pred             eeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHH
Q psy1548         147 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE  226 (448)
Q Consensus       147 ~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~  226 (448)
                      ..|.-+.+.||||+|||.....-+-..+.........++.+.+.-..  ..+++..++..+ ++.+...           
T Consensus       189 ~~g~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~v~~i~~d~~rig--alEQL~~~a~il-Gvp~~~v-----------  254 (420)
T PRK14721        189 EQGGVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIG--GHEQLRIYGKLL-GVSVRSI-----------  254 (420)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecCCcchh--HHHHHHHHHHHc-CCceecC-----------
Confidence            35677899999999999775433222222212122345555553332  222344444443 4433222           


Q ss_pred             HHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCcc-HHHH
Q psy1548         227 YLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKE-IRPV  305 (448)
Q Consensus       227 ~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~-~~~~  305 (448)
                                 .++..+...+..    +.+.+.+.+|.+=+..........+..+.....+...++.+|||.... +.+.
T Consensus       255 -----------~~~~dl~~al~~----l~~~d~VLIDTaGrsqrd~~~~~~l~~l~~~~~~~~~~LVl~at~~~~~~~~~  319 (420)
T PRK14721        255 -----------KDIADLQLMLHE----LRGKHMVLIDTVGMSQRDQMLAEQIAMLSQCGTQVKHLLLLNATSSGDTLDEV  319 (420)
T ss_pred             -----------CCHHHHHHHHHH----hcCCCEEEecCCCCCcchHHHHHHHHHHhccCCCceEEEEEcCCCCHHHHHHH
Confidence                       223333222221    344566777775322111022233333322223345678899997544 5555


Q ss_pred             HHHhc
Q psy1548         306 CKKFM  310 (448)
Q Consensus       306 ~~~~l  310 (448)
                      ...|-
T Consensus       320 ~~~f~  324 (420)
T PRK14721        320 ISAYQ  324 (420)
T ss_pred             HHHhc
Confidence            65554

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]

Probab=94.94  E-value=0.14  Score=52.66  Aligned_cols=152  Identities=14%  Similarity=0.067  Sum_probs=87.1

Q ss_pred             cCCCCchhhhhhhccccccceeeee------C----cceeeeccCCChhHHHHH-HHHHHhhhccCCCeEEEEeeccHHH
Q psy1548         124 DMPEDSDTYLHRVARAGRFGTKAVL------G----MDILCQAKSGMGKTAVFV-LATLQQLETTDSNVYVLVMCHTREL  192 (448)
Q Consensus       124 ~~p~~~~~yQ~~~~~~~~~~~~~~~------g----~~vli~apTGsGKT~~~~-l~~l~~l~~~~~~~~~lil~Pt~~L  192 (448)
                      ..|.++.+||+-      .+-.++-      |    +-.+|..|-+-|||.... +.....+.....+....|++|+.+-
T Consensus        57 ~~p~~l~PwQkF------iia~l~G~~~k~T~~rrf~e~fI~v~RkngKt~l~A~i~~~~~l~~~~~~~~~~i~A~s~~q  130 (546)
T COG4626          57 GFPESLEPWQKF------IVAALFGFYDKQTGIRRFKEAFIFIPRKNGKSTLAAGIMMTALLLNWRSGAGIYILAPSVEQ  130 (546)
T ss_pred             CCccccchHHHH------HHHHHhceeecCCCceEEEEEEEEEecCCchHHHHHHHHHHHHHhhhhcCCcEEEEeccHHH
Confidence            468888999999      5544441      1    467999999999996654 3333333333566789999999999


Q ss_pred             HHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHC--CCCcCCCeeEEEecchhHHHh
Q psy1548         193 AFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRN--KKLNLSLLKHFILDECDKMLE  270 (448)
Q Consensus       193 ~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~--~~~~~~~i~~lViDEah~l~~  270 (448)
                      +.+....++......++++..            .........|...--......+..  +..+-.+..+.|+||.|....
T Consensus       131 a~~~F~~ar~mv~~~~~l~~~------------~~~q~~s~~i~~~~~~s~ik~~aa~~~~~Dg~~~~~~I~DEih~f~~  198 (546)
T COG4626         131 AANSFNPARDMVKRDDDLRDL------------CNVQTHSRTITHRKTDSTIKAVAADPNTVDGLNSVGAIIDELHLFGK  198 (546)
T ss_pred             HHHhhHHHHHHHHhCcchhhh------------hccccceeEEEecccceeeeeeccCCCcccCCCcceEEEehhhhhcC
Confidence            999888888766554211110            000111011222111111222222  334445567899999997655


Q ss_pred             hhhhHHHHHHHHHhC--CCCCeEEEEec
Q psy1548         271 QLEMRRDVQEIFRSS--PHTKQVMMFSA  296 (448)
Q Consensus       271 ~~~~~~~~~~i~~~l--~~~~q~i~~SA  296 (448)
                      . +  ..+..+..-+  .++.+++..|.
T Consensus       199 ~-~--~~~~~~~~g~~ar~~~l~~~ITT  223 (546)
T COG4626         199 Q-E--DMYSEAKGGLGARPEGLVVYITT  223 (546)
T ss_pred             H-H--HHHHHHHhhhccCcCceEEEEec
Confidence            3 2  4444443333  24566776665

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=94.93  E-value=0.3  Score=46.88  Aligned_cols=19  Identities=26%  Similarity=0.371  Sum_probs=16.5

Q ss_pred             eCcceeeeccCCChhHHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~  166 (448)
                      .+.++++.||+|+|||.++
T Consensus        57 ~~~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        57 PTLHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             CCceEEEEcCCCCCHHHHH
Confidence            4568999999999999765

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=94.90  E-value=0.14  Score=56.28  Aligned_cols=39  Identities=23%  Similarity=0.304  Sum_probs=28.5

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      .+.+++||||+|+|...  -...+.++++..+..+.+|+.+
T Consensus       119 ~~~KV~IIDEad~lt~~--a~NaLLK~LEEpP~~~~fIl~t  157 (824)
T PRK07764        119 SRYKIFIIDEAHMVTPQ--GFNALLKIVEEPPEHLKFIFAT  157 (824)
T ss_pred             CCceEEEEechhhcCHH--HHHHHHHHHhCCCCCeEEEEEe
Confidence            56789999999998763  4445666777777777777654

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=94.90  E-value=0.022  Score=60.88  Aligned_cols=52  Identities=27%  Similarity=0.264  Sum_probs=44.5

Q ss_pred             HHHHhhccceeEeeccccCCccccc-------ceeEeeccCCCCchhhhhhhccccccc
Q psy1548          92 LRAIVDCWRILVATNLFGRGMDIER-------VNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~~~~d~~~-------~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      ...-...+.|.||||++|||.|+..       ...|+++..|...+.|.|..||+||..
T Consensus       447 i~~ag~~g~VtIATnmAgRGtDI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~GRtGRqG  505 (745)
T TIGR00963       447 IAQAGRKGAVTIATNMAGRGTDIKLEEVKELGGLYVIGTERHESRRIDNQLRGRSGRQG  505 (745)
T ss_pred             HHhcCCCceEEEEeccccCCcCCCccchhhcCCcEEEecCCCCcHHHHHHHhccccCCC
Confidence            3333455799999999999999998       459999999999999999999999944

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.

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=94.89  E-value=0.13  Score=50.43  Aligned_cols=40  Identities=15%  Similarity=0.326  Sum_probs=26.6

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEec
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSA  296 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SA  296 (448)
                      ...+++|+||+|.+..  .....+..++...+...++|+.+.
T Consensus       124 ~~~~vlilDe~~~l~~--~~~~~L~~~le~~~~~~~~Il~~~  163 (337)
T PRK12402        124 ADYKTILLDNAEALRE--DAQQALRRIMEQYSRTCRFIIATR  163 (337)
T ss_pred             CCCcEEEEeCcccCCH--HHHHHHHHHHHhccCCCeEEEEeC
Confidence            4457899999997754  334456666666666676666443

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.88  E-value=0.49  Score=49.00  Aligned_cols=133  Identities=14%  Similarity=0.176  Sum_probs=64.8

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee--ccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccH
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQ  222 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~  222 (448)
                      .+..|+.+.+.||||+|||.....-+...... ..+.++.++.  +.+.-+.+   +++.+...+ ++.+..        
T Consensus       346 ~l~~G~vIaLVGPtGvGKTTtaakLAa~la~~-~~gkkVaLIdtDtyRigA~E---QLk~ya~iL-gv~v~~--------  412 (559)
T PRK12727        346 PLERGGVIALVGPTGAGKTTTIAKLAQRFAAQ-HAPRDVALVTTDTQRVGGRE---QLHSYGRQL-GIAVHE--------  412 (559)
T ss_pred             cccCCCEEEEECCCCCCHHHHHHHHHHHHHHh-cCCCceEEEecccccccHHH---HHHHhhccc-CceeEe--------
Confidence            34457889999999999997653322222222 1122344443  23433322   334433332 222211        


Q ss_pred             HhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCc-c
Q psy1548         223 KDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSK-E  301 (448)
Q Consensus       223 ~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~-~  301 (448)
                                    +.+++.+...+..    +.+.++|+||.+-...........+..+... .....+++++++... +
T Consensus       413 --------------a~d~~~L~~aL~~----l~~~DLVLIDTaG~s~~D~~l~eeL~~L~aa-~~~a~lLVLpAtss~~D  473 (559)
T PRK12727        413 --------------ADSAESLLDLLER----LRDYKLVLIDTAGMGQRDRALAAQLNWLRAA-RQVTSLLVLPANAHFSD  473 (559)
T ss_pred             --------------cCcHHHHHHHHHH----hccCCEEEecCCCcchhhHHHHHHHHHHHHh-hcCCcEEEEECCCChhH
Confidence                          1133444444442    3456789999987543221222233333222 233456777887643 4


Q ss_pred             HHHHHHHh
Q psy1548         302 IRPVCKKF  309 (448)
Q Consensus       302 ~~~~~~~~  309 (448)
                      +.+.++.|
T Consensus       474 l~eii~~f  481 (559)
T PRK12727        474 LDEVVRRF  481 (559)
T ss_pred             HHHHHHHH
Confidence            55555554

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=94.79  E-value=0.18  Score=53.16  Aligned_cols=134  Identities=13%  Similarity=0.103  Sum_probs=79.8

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccC-CCceEEEEEcCcccHHhHHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYM-SNIKVGVFFGGLPIQKDEEY  227 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~v~~~~g~~~~~~~~~~  227 (448)
                      .+-.++..|--.|||+... +++..+...-.+.++++++|.+..++.+++.+....... +.-.+....| ...   ...
T Consensus       254 qk~tVflVPRR~GKTwivv-~iI~~ll~s~~Gi~IgytAH~~~ts~~vF~eI~~~le~~f~~~~v~~vkG-e~I---~i~  328 (738)
T PHA03368        254 QRATVFLVPRRHGKTWFLV-PLIALALATFRGIKIGYTAHIRKATEPVFEEIGARLRQWFGASRVDHVKG-ETI---SFS  328 (738)
T ss_pred             ccceEEEecccCCchhhHH-HHHHHHHHhCCCCEEEEEcCcHHHHHHHHHHHHHHHhhhcchhheeeecC-cEE---EEE
Confidence            3567899999999998655 665554444447799999999999999998888765431 1111222222 111   001


Q ss_pred             HhcCC-CcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEecc
Q psy1548         228 LKTHN-PQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSAT  297 (448)
Q Consensus       228 l~~~~-~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT  297 (448)
                      +.++. ..|.++|.      -..+...-..++++|+|||+-+-+. .+...+ -.+  ...+.++|.+|.|
T Consensus       329 f~nG~kstI~FaSa------rntNsiRGqtfDLLIVDEAqFIk~~-al~~il-p~l--~~~n~k~I~ISS~  389 (738)
T PHA03368        329 FPDGSRSTIVFASS------HNTNGIRGQDFNLLFVDEANFIRPD-AVQTIM-GFL--NQTNCKIIFVSST  389 (738)
T ss_pred             ecCCCccEEEEEec------cCCCCccCCcccEEEEechhhCCHH-HHHHHH-HHH--hccCccEEEEecC
Confidence            11221 24555432      1123344457889999999977553 222222 222  2247788999988

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.77  E-value=0.19  Score=54.99  Aligned_cols=43  Identities=12%  Similarity=0.248  Sum_probs=27.7

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCc
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSK  300 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~  300 (448)
                      ...+++||||+|+|..  .....+.+.+..-|..+.+|+. +|-+.
T Consensus       118 gk~KViIIDEAh~LT~--eAqNALLKtLEEPP~~vrFILa-TTe~~  160 (944)
T PRK14949        118 GRFKVYLIDEVHMLSR--SSFNALLKTLEEPPEHVKFLLA-TTDPQ  160 (944)
T ss_pred             CCcEEEEEechHhcCH--HHHHHHHHHHhccCCCeEEEEE-CCCch
Confidence            4568899999998865  3344455566665666666664 44333

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=94.77  E-value=0.16  Score=54.55  Aligned_cols=40  Identities=10%  Similarity=0.293  Sum_probs=26.4

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEec
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSA  296 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SA  296 (448)
                      .+.+++||||+|.|... . ...+.+++..-+.+..+|+.|.
T Consensus       118 gr~KVIIIDEah~LT~~-A-~NALLKtLEEPP~~v~FILaTt  157 (830)
T PRK07003        118 ARFKVYMIDEVHMLTNH-A-FNAMLKTLEEPPPHVKFILATT  157 (830)
T ss_pred             CCceEEEEeChhhCCHH-H-HHHHHHHHHhcCCCeEEEEEEC
Confidence            45689999999988664 3 3344455666666666666543

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=94.75  E-value=0.067  Score=58.42  Aligned_cols=67  Identities=13%  Similarity=0.167  Sum_probs=58.2

Q ss_pred             CcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCc
Q psy1548         233 PQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSK  300 (448)
Q Consensus       233 ~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~  300 (448)
                      ..|+++||..+..-+..+.+++..+..+|+||||++.+. .....+..+++...+..-+.+|||....
T Consensus         8 ggi~~~T~rIl~~DlL~~ri~~~~itgiiv~~Ahr~~~~-~~eaFI~rlyr~~n~~gfIkafSdsP~~   74 (814)
T TIGR00596         8 GGIFSITSRILVVDLLTGIIPPELITGILVLRADRIIES-SQEAFILRLYRQKNKTGFIKAFSDNPEA   74 (814)
T ss_pred             CCEEEEechhhHhHHhcCCCCHHHccEEEEeeccccccc-ccHHHHHHHHHHhCCCcceEEecCCCcc
Confidence            469999999999888889999999999999999999887 6777777888777777789999999654

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

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=94.75  E-value=0.41  Score=39.48  Aligned_cols=15  Identities=40%  Similarity=0.587  Sum_probs=13.0

Q ss_pred             eeeeccCCChhHHHH
Q psy1548         152 ILCQAKSGMGKTAVF  166 (448)
Q Consensus       152 vli~apTGsGKT~~~  166 (448)
                      +++.||.|+|||...
T Consensus         1 ill~G~~G~GKT~l~   15 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLA   15 (132)
T ss_dssp             EEEESSTTSSHHHHH
T ss_pred             CEEECcCCCCeeHHH
Confidence            589999999999764

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=94.75  E-value=0.11  Score=49.57  Aligned_cols=39  Identities=13%  Similarity=0.222  Sum_probs=23.9

Q ss_pred             CCeeEEEecchhHHHhhhhh--HHHHHHHHHhCCCCC--eEEEE
Q psy1548         255 SLLKHFILDECDKMLEQLEM--RRDVQEIFRSSPHTK--QVMMF  294 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~--~~~~~~i~~~l~~~~--q~i~~  294 (448)
                      -.++++||||+|.++.. ..  ...+...++.+....  .++++
T Consensus       144 ~~vrmLIIDE~H~lLaG-s~~~qr~~Ln~LK~L~NeL~ipiV~v  186 (302)
T PF05621_consen  144 LGVRMLIIDEFHNLLAG-SYRKQREFLNALKFLGNELQIPIVGV  186 (302)
T ss_pred             cCCcEEEeechHHHhcc-cHHHHHHHHHHHHHHhhccCCCeEEe
Confidence            46789999999998875 32  223334455554433  44544

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>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=94.74  E-value=0.17  Score=44.11  Aligned_cols=42  Identities=21%  Similarity=0.398  Sum_probs=31.2

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccC
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATL  298 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~  298 (448)
                      ...+.+||||||.|..  .....+.+.+..-|.+..++++|...
T Consensus       101 ~~~KviiI~~ad~l~~--~a~NaLLK~LEepp~~~~fiL~t~~~  142 (162)
T PF13177_consen  101 GKYKVIIIDEADKLTE--EAQNALLKTLEEPPENTYFILITNNP  142 (162)
T ss_dssp             SSSEEEEEETGGGS-H--HHHHHHHHHHHSTTTTEEEEEEES-G
T ss_pred             CCceEEEeehHhhhhH--HHHHHHHHHhcCCCCCEEEEEEECCh
Confidence            5688999999999877  46666777777777787777776554

...

>KOG0991|consensus

Probab=94.73  E-value=0.054  Score=49.36  Aligned_cols=44  Identities=20%  Similarity=0.242  Sum_probs=31.0

Q ss_pred             CcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEecc
Q psy1548         252 LNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSAT  297 (448)
Q Consensus       252 ~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT  297 (448)
                      +...+.+.+|+||||.|.+  +.-..++..+....+.+++.+...+
T Consensus       109 lp~grhKIiILDEADSMT~--gAQQAlRRtMEiyS~ttRFalaCN~  152 (333)
T KOG0991|consen  109 LPPGRHKIIILDEADSMTA--GAQQALRRTMEIYSNTTRFALACNQ  152 (333)
T ss_pred             CCCCceeEEEeeccchhhh--HHHHHHHHHHHHHcccchhhhhhcc
Confidence            3457788999999999977  5666666666666666666554444

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.72  E-value=0.4  Score=45.50  Aligned_cols=131  Identities=17%  Similarity=0.205  Sum_probs=69.0

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee--ccH-HHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTR-ELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE  225 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~--Pt~-~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~  225 (448)
                      +..+.+.+|+|+|||..+..-+... .. . +.++.++.  +.+ ..+.|+    +.+.... ++.+             
T Consensus        75 ~~~i~~~G~~g~GKTtl~~~l~~~l-~~-~-~~~v~~i~~D~~ri~~~~ql----~~~~~~~-~~~~-------------  133 (270)
T PRK06731         75 VQTIALIGPTGVGKTTTLAKMAWQF-HG-K-KKTVGFITTDHSRIGTVQQL----QDYVKTI-GFEV-------------  133 (270)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHHHH-HH-c-CCeEEEEecCCCCHHHHHHH----HHHhhhc-CceE-------------
Confidence            4678999999999998765433332 21 1 22344443  222 334443    3333222 2222             


Q ss_pred             HHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCC-ccHHH
Q psy1548         226 EYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLS-KEIRP  304 (448)
Q Consensus       226 ~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~-~~~~~  304 (448)
                               +...+|..+...+..- -...+.+++++|-+=+..........+..++....+..-++.+|||.. .+..+
T Consensus       134 ---------~~~~~~~~l~~~l~~l-~~~~~~D~ViIDt~Gr~~~~~~~l~el~~~~~~~~~~~~~LVl~a~~~~~d~~~  203 (270)
T PRK06731        134 ---------IAVRDEAAMTRALTYF-KEEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKDMIE  203 (270)
T ss_pred             ---------EecCCHHHHHHHHHHH-HhcCCCCEEEEECCCCCcCCHHHHHHHHHHHhhhCCCeEEEEEcCccCHHHHHH
Confidence                     1113454444433210 011346789999986653221334445555555545445778999865 46777


Q ss_pred             HHHHhc
Q psy1548         305 VCKKFM  310 (448)
Q Consensus       305 ~~~~~l  310 (448)
                      .++.|-
T Consensus       204 ~~~~f~  209 (270)
T PRK06731        204 IITNFK  209 (270)
T ss_pred             HHHHhC
Confidence            777764

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.62  E-value=0.22  Score=51.19  Aligned_cols=21  Identities=24%  Similarity=0.218  Sum_probs=17.0

Q ss_pred             eCcceeeeccCCChhHHHHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVFVL  168 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l  168 (448)
                      .|+-+.+.||||+|||.+...
T Consensus       255 ~g~Vi~LvGpnGvGKTTTiaK  275 (484)
T PRK06995        255 RGGVFALMGPTGVGKTTTTAK  275 (484)
T ss_pred             CCcEEEEECCCCccHHHHHHH
Confidence            466788999999999987543

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=94.60  E-value=0.031  Score=41.88  Aligned_cols=44  Identities=41%  Similarity=0.786  Sum_probs=40.2

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR  141 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~  141 (448)
                      ...+.++|+..+.|+|.+.+..|+.+..|.....|+|.+||++|
T Consensus        37 ~~~vli~t~~~~~Gi~~~~~~~vi~~~~~~~~~~~~Q~~gR~~R   80 (82)
T smart00490       37 KIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGR   80 (82)
T ss_pred             CCeEEEECChhhCCcChhcCCEEEEeCCCCCHHHHHHhhccccc
Confidence            34899999999999999999999999999999899999999877

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=94.57  E-value=0.36  Score=46.85  Aligned_cols=39  Identities=13%  Similarity=0.288  Sum_probs=25.9

Q ss_pred             CeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEec
Q psy1548         256 LLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSA  296 (448)
Q Consensus       256 ~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SA  296 (448)
                      ..+++++||+|.+...  ....+..++...+....+|+.+.
T Consensus       102 ~~~vviiDe~~~l~~~--~~~~L~~~le~~~~~~~lIl~~~  140 (319)
T PRK00440        102 PFKIIFLDEADNLTSD--AQQALRRTMEMYSQNTRFILSCN  140 (319)
T ss_pred             CceEEEEeCcccCCHH--HHHHHHHHHhcCCCCCeEEEEeC
Confidence            4578999999987553  33455666666666666666543

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=94.56  E-value=0.39  Score=52.38  Aligned_cols=17  Identities=29%  Similarity=0.374  Sum_probs=13.8

Q ss_pred             eeeeccCCChhHHHHHH
Q psy1548         152 ILCQAKSGMGKTAVFVL  168 (448)
Q Consensus       152 vli~apTGsGKT~~~~l  168 (448)
                      ++|.|+||+|||++.-.
T Consensus       784 LYIyG~PGTGKTATVK~  800 (1164)
T PTZ00112        784 LYISGMPGTGKTATVYS  800 (1164)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            35999999999987543

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=94.55  E-value=0.19  Score=46.44  Aligned_cols=18  Identities=11%  Similarity=0.233  Sum_probs=15.2

Q ss_pred             CcceeeeccCCChhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~  166 (448)
                      +..+++.||+|+|||...
T Consensus        42 ~~~~~l~G~~G~GKT~La   59 (227)
T PRK08903         42 DRFFYLWGEAGSGRSHLL   59 (227)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            467999999999999543

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=94.54  E-value=0.24  Score=49.25  Aligned_cols=24  Identities=33%  Similarity=0.499  Sum_probs=17.9

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhh
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQL  174 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l  174 (448)
                      .++++.||+|+|||.+. -.++..+
T Consensus        41 ~~i~I~G~~GtGKT~l~-~~~~~~l   64 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVT-KYVMKEL   64 (365)
T ss_pred             CcEEEECCCCCCHHHHH-HHHHHHH
Confidence            57999999999999664 3444444

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=94.50  E-value=0.29  Score=43.72  Aligned_cols=39  Identities=13%  Similarity=0.265  Sum_probs=24.9

Q ss_pred             CCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEE
Q psy1548         254 LSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMF  294 (448)
Q Consensus       254 ~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~  294 (448)
                      ....+++||||+|.+...  ....+...+...++..-+++.
T Consensus        94 ~~~~kviiide~~~l~~~--~~~~Ll~~le~~~~~~~~il~  132 (188)
T TIGR00678        94 ESGRRVVIIEDAERMNEA--AANALLKTLEEPPPNTLFILI  132 (188)
T ss_pred             cCCeEEEEEechhhhCHH--HHHHHHHHhcCCCCCeEEEEE
Confidence            356789999999988663  334455555554545555544

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>KOG1805|consensus

Probab=94.47  E-value=0.075  Score=57.47  Aligned_cols=120  Identities=22%  Similarity=0.137  Sum_probs=69.0

Q ss_pred             hhhhccccccceeeeeCcc-eeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCce
Q psy1548         133 LHRVARAGRFGTKAVLGMD-ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIK  211 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~g~~-vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~  211 (448)
                      |++      |+-.++..+| .+|.|-.|+|||..... ++..+..  .+.++|..+-|..-+..+.-.++.+.     +.
T Consensus       674 Qr~------A~~k~L~aedy~LI~GMPGTGKTTtI~~-LIkiL~~--~gkkVLLtsyThsAVDNILiKL~~~~-----i~  739 (1100)
T KOG1805|consen  674 QRQ------ALLKALAAEDYALILGMPGTGKTTTISL-LIKILVA--LGKKVLLTSYTHSAVDNILIKLKGFG-----IY  739 (1100)
T ss_pred             HHH------HHHHHHhccchheeecCCCCCchhhHHH-HHHHHHH--cCCeEEEEehhhHHHHHHHHHHhccC-----cc
Confidence            888      8877777655 78899999999976432 2222222  23478888888876666655555442     22


Q ss_pred             EEEEEcCcccHHhH-----------------HHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhh
Q psy1548         212 VGVFFGGLPIQKDE-----------------EYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQ  271 (448)
Q Consensus       212 v~~~~g~~~~~~~~-----------------~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~  271 (448)
                      +..+-.+....++.                 .... +.+.|+.+|==.+..    ..+....+++.|+|||-.+...
T Consensus       740 ~lRLG~~~kih~~v~e~~~~~~~s~ks~~~l~~~~-~~~~IVa~TClgi~~----plf~~R~FD~cIiDEASQI~lP  811 (1100)
T KOG1805|consen  740 ILRLGSEEKIHPDVEEFTLTNETSEKSYADLKKFL-DQTSIVACTCLGINH----PLFVNRQFDYCIIDEASQILLP  811 (1100)
T ss_pred             eeecCCccccchHHHHHhcccccchhhHHHHHHHh-CCCcEEEEEccCCCc----hhhhccccCEEEEccccccccc
Confidence            22111111111111                 1122 246788777432222    2233466889999999977543

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=94.45  E-value=0.54  Score=44.60  Aligned_cols=42  Identities=24%  Similarity=0.229  Sum_probs=27.0

Q ss_pred             eeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee
Q psy1548         144 TKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC  187 (448)
Q Consensus       144 ~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~  187 (448)
                      -.+..|.-+++.|++|+|||....--+.+....  .+..++++.
T Consensus        25 gG~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~--~g~~vl~iS   66 (271)
T cd01122          25 KGLRKGELIILTAGTGVGKTTFLREYALDLITQ--HGVRVGTIS   66 (271)
T ss_pred             EEEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHh--cCceEEEEE
Confidence            355567889999999999996544333333222  134677776

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.40  E-value=0.69  Score=46.59  Aligned_cols=128  Identities=15%  Similarity=0.161  Sum_probs=64.4

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee--ccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE  226 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~  226 (448)
                      +.-+++.+|+|+|||....--+......  .+.++.++.  +.+..+.+   +++.++... ++...             
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~~~~~--~G~~V~Lit~Dt~R~aA~e---QLk~yAe~l-gvp~~-------------  283 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAKYFLH--MGKSVSLYTTDNYRIAAIE---QLKRYADTM-GMPFY-------------  283 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHh--cCCeEEEecccchhhhHHH---HHHHHHHhc-CCCee-------------
Confidence            3457899999999997754433322111  122444443  44444443   344443332 32211             


Q ss_pred             HHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCC---CCCeEEEEeccCCc-cH
Q psy1548         227 YLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSP---HTKQVMMFSATLSK-EI  302 (448)
Q Consensus       227 ~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~---~~~q~i~~SAT~~~-~~  302 (448)
                               .+..+..+...+..     ...++++||=+-+..........+..++....   +...++.+|||... .+
T Consensus       284 ---------~~~~~~~l~~~l~~-----~~~D~VLIDTaGr~~rd~~~l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~~~  349 (432)
T PRK12724        284 ---------PVKDIKKFKETLAR-----DGSELILIDTAGYSHRNLEQLERMQSFYSCFGEKDSVENLLVLSSTSSYHHT  349 (432)
T ss_pred             ---------ehHHHHHHHHHHHh-----CCCCEEEEeCCCCCccCHHHHHHHHHHHHhhcCCCCCeEEEEEeCCCCHHHH
Confidence                     11112233333331     34567888866544222133444455554431   23457888999876 45


Q ss_pred             HHHHHHh
Q psy1548         303 RPVCKKF  309 (448)
Q Consensus       303 ~~~~~~~  309 (448)
                      ....+.|
T Consensus       350 ~~~~~~f  356 (432)
T PRK12724        350 LTVLKAY  356 (432)
T ss_pred             HHHHHHh
Confidence            5566555

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.34  E-value=0.3  Score=51.74  Aligned_cols=39  Identities=10%  Similarity=0.272  Sum_probs=26.1

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      ...+++||||+|+|...  ....+.+.+...+....+|+.+
T Consensus       117 gk~KV~IIDEVh~LS~~--A~NALLKtLEEPP~~v~FILaT  155 (702)
T PRK14960        117 GRFKVYLIDEVHMLSTH--SFNALLKTLEEPPEHVKFLFAT  155 (702)
T ss_pred             CCcEEEEEechHhcCHH--HHHHHHHHHhcCCCCcEEEEEE
Confidence            35689999999977653  3344555666666666666644

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.32  E-value=0.28  Score=50.55  Aligned_cols=18  Identities=28%  Similarity=0.396  Sum_probs=14.7

Q ss_pred             ceeeeccCCChhHHHHHH
Q psy1548         151 DILCQAKSGMGKTAVFVL  168 (448)
Q Consensus       151 ~vli~apTGsGKT~~~~l  168 (448)
                      .+|+.||.|+|||..+.+
T Consensus        38 ~~Lf~GPpGtGKTTlA~~   55 (472)
T PRK14962         38 AYIFAGPRGTGKTTVARI   55 (472)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            469999999999976543

>PRK06835 DNA replication protein DnaC; Validated

Probab=94.31  E-value=0.53  Score=46.14  Aligned_cols=44  Identities=20%  Similarity=0.203  Sum_probs=27.3

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI  196 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~  196 (448)
                      +.++++.||||+|||... .++...+...  +..++++ +..+|..++
T Consensus       183 ~~~Lll~G~~GtGKThLa-~aIa~~l~~~--g~~V~y~-t~~~l~~~l  226 (329)
T PRK06835        183 NENLLFYGNTGTGKTFLS-NCIAKELLDR--GKSVIYR-TADELIEIL  226 (329)
T ss_pred             CCcEEEECCCCCcHHHHH-HHHHHHHHHC--CCeEEEE-EHHHHHHHH
Confidence            588999999999999654 3444444332  3345554 445555443

>PRK07952 DNA replication protein DnaC; Validated

Probab=94.31  E-value=0.41  Score=44.76  Aligned_cols=42  Identities=19%  Similarity=0.271  Sum_probs=25.2

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHH
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ  195 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q  195 (448)
                      ..+++.|++|+|||..+ ..+...+...  +..++++ +..+|...
T Consensus       100 ~~~~l~G~~GtGKThLa-~aia~~l~~~--g~~v~~i-t~~~l~~~  141 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLA-AAICNELLLR--GKSVLII-TVADIMSA  141 (244)
T ss_pred             ceEEEECCCCCCHHHHH-HHHHHHHHhc--CCeEEEE-EHHHHHHH
Confidence            47899999999999654 3444444332  3345544 44444433

>PHA02653 RNA helicase NPH-II; Provisional

Probab=94.28  E-value=0.031  Score=59.90  Aligned_cols=53  Identities=25%  Similarity=0.415  Sum_probs=41.8

Q ss_pred             HHHHHHh--hccceeEeeccccCCcccccceeEeecc---CCC---------Cchhhhhhhcccccc
Q psy1548          90 EILRAIV--DCWRILVATNLFGRGMDIERVNIVFNYD---MPE---------DSDTYLHRVARAGRF  142 (448)
Q Consensus        90 ~~~~~~~--~~~~~~~~~~~~~~~~d~~~~~~v~~~~---~p~---------~~~~yQ~~~~~~~~~  142 (448)
                      +.++.+.  ...+|.|||+++++|+|.++++.|+++.   .|.         +-..|.|.+|||||.
T Consensus       436 q~l~~ff~~gk~kILVATdIAERGIDIp~V~~VID~G~~k~p~~~~g~~~~iSkasa~QRaGRAGR~  502 (675)
T PHA02653        436 EILEKVYSSKNPSIIISTPYLESSVTIRNATHVYDTGRVYVPEPFGGKEMFISKSMRTQRKGRVGRV  502 (675)
T ss_pred             HHHHHHhccCceeEEeccChhhccccccCeeEEEECCCccCCCcccCcccccCHHHHHHhccCcCCC
Confidence            3445553  2348999999999999999999999997   554         345778999999995

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.24  E-value=0.31  Score=51.61  Aligned_cols=41  Identities=10%  Similarity=0.331  Sum_probs=27.0

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEecc
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSAT  297 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT  297 (448)
                      .+.+++||||+|+|... .+. .+.+.+..-+.++.+|+.|.-
T Consensus       123 gr~KViIIDEah~Ls~~-AaN-ALLKTLEEPP~~v~FILaTte  163 (700)
T PRK12323        123 GRFKVYMIDEVHMLTNH-AFN-AMLKTLEEPPEHVKFILATTD  163 (700)
T ss_pred             CCceEEEEEChHhcCHH-HHH-HHHHhhccCCCCceEEEEeCC
Confidence            45789999999988764 443 344445555667777766543

>PF05729 NACHT: NACHT domain

Probab=94.21  E-value=0.36  Score=41.56  Aligned_cols=39  Identities=21%  Similarity=0.291  Sum_probs=24.3

Q ss_pred             EEEecchhHHHhhhh------hHHHHHHHHHh-CCCCCeEEEEecc
Q psy1548         259 HFILDECDKMLEQLE------MRRDVQEIFRS-SPHTKQVMMFSAT  297 (448)
Q Consensus       259 ~lViDEah~l~~~~~------~~~~~~~i~~~-l~~~~q~i~~SAT  297 (448)
                      ++|+|-+|.+.....      +...+..++.. ++++.++++.|.+
T Consensus        84 llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~  129 (166)
T PF05729_consen   84 LLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRP  129 (166)
T ss_pred             EEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcC
Confidence            389999998876311      33445555554 4567777776654

>KOG4284|consensus

Probab=94.20  E-value=0.033  Score=57.56  Aligned_cols=44  Identities=59%  Similarity=1.054  Sum_probs=42.1

Q ss_pred             ceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548         100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus       100 ~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      +|+|+|++-.||||.+.+..|+|++.|.....|-+.+|||||..
T Consensus       324 rILVsTDLtaRGIDa~~vNLVVNiD~p~d~eTY~HRIGRAgRFG  367 (980)
T KOG4284|consen  324 RILVSTDLTARGIDADNVNLVVNIDAPADEETYFHRIGRAGRFG  367 (980)
T ss_pred             EEEEecchhhccCCccccceEEecCCCcchHHHHHHhhhccccc
Confidence            89999999999999999999999999999999999999999943

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=94.15  E-value=0.24  Score=57.33  Aligned_cols=118  Identities=22%  Similarity=0.163  Sum_probs=72.8

Q ss_pred             hhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceE
Q psy1548         133 LHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKV  212 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v  212 (448)
                      |++      +|.  ..|++++|.|..|||||.+..--++..+..+....++++|+=|++-+..+.+.+..-....  +. 
T Consensus         6 Q~~------ai~--~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~~~~~il~~tFt~~aa~e~~~ri~~~l~~~--~~-   74 (1232)
T TIGR02785         6 QWQ------AIY--TRGQNILVSASAGSGKTAVLVERIIKKILRGVDIDRLLVVTFTNAAAREMKERIEEALQKA--LQ-   74 (1232)
T ss_pred             HHH------HHh--CCCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCHhhEEEEeccHHHHHHHHHHHHHHHHHH--Hh-
Confidence            888      775  3689999999999999988766666665444333469999999999999888877644321  10 


Q ss_pred             EEEEcCcccHHhH-HHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCe--eEEEecchhH
Q psy1548         213 GVFFGGLPIQKDE-EYLKTHNPQIVVGTPGRILALVRNKKLNLSLL--KHFILDECDK  267 (448)
Q Consensus       213 ~~~~g~~~~~~~~-~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i--~~lViDEah~  267 (448)
                           ..+..... ..+.. -...-|+|-..++..+-+.....-++  .+=|.||...
T Consensus        75 -----~~p~~~~L~~q~~~-~~~~~i~Tihsf~~~~~~~~~~~l~ldP~F~i~de~e~  126 (1232)
T TIGR02785        75 -----QEPNSKHLRRQLAL-LNTANISTLHSFCLKVIRKHYYLLDLDPSFRILTDTEQ  126 (1232)
T ss_pred             -----cCchhHHHHHHHhh-ccCCeEeeHHHHHHHHHHHhhhhcCCCCCceeCCHHHH
Confidence                 00111111 11111 24678999988865443322211111  2345888875

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species.

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=94.14  E-value=0.32  Score=51.59  Aligned_cols=40  Identities=13%  Similarity=0.226  Sum_probs=27.0

Q ss_pred             CCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         254 LSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       254 ~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      +...+++||||+|.|...  -...+.+.+...+..+.+|+.+
T Consensus       130 ~a~~KVvIIDEad~Ls~~--a~naLLKtLEePp~~~~fIl~t  169 (598)
T PRK09111        130 SARYKVYIIDEVHMLSTA--AFNALLKTLEEPPPHVKFIFAT  169 (598)
T ss_pred             cCCcEEEEEEChHhCCHH--HHHHHHHHHHhCCCCeEEEEEe
Confidence            456789999999988653  3344445566666677776654

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=94.06  E-value=0.26  Score=55.51  Aligned_cols=122  Identities=14%  Similarity=0.081  Sum_probs=69.1

Q ss_pred             chhhhhhhccccccceeeee-CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccC
Q psy1548         129 SDTYLHRVARAGRFGTKAVL-GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYM  207 (448)
Q Consensus       129 ~~~yQ~~~~~~~~~~~~~~~-g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  207 (448)
                      +.+=|.+      ++..+.. ++-++++|+.|+|||.+. -++...+..  .+.+++.++||-.-+..+    ..-.   
T Consensus       382 Ls~eQ~~------Av~~i~~~~r~~~v~G~AGTGKTt~l-~~~~~~~e~--~G~~V~g~ApTgkAA~~L----~e~~---  445 (1102)
T PRK13826        382 LSDEQKT------AIEHVAGPARIAAVVGRAGAGKTTMM-KAAREAWEA--AGYRVVGGALAGKAAEGL----EKEA---  445 (1102)
T ss_pred             CCHHHHH------HHHHHhccCCeEEEEeCCCCCHHHHH-HHHHHHHHH--cCCeEEEEcCcHHHHHHH----HHhh---
Confidence            3334888      6666544 456889999999999653 344443332  345789999998655443    2211   


Q ss_pred             CCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCC-
Q psy1548         208 SNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSP-  286 (448)
Q Consensus       208 ~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~-  286 (448)
                       ++..                         .|..+++-....+...+..-++|||||+-++..     ..+..+++..+ 
T Consensus       446 -Gi~a-------------------------~TIas~ll~~~~~~~~l~~~~vlVIDEAsMv~~-----~~m~~Ll~~~~~  494 (1102)
T PRK13826        446 -GIQS-------------------------RTLSSWELRWNQGRDQLDNKTVFVLDEAGMVAS-----RQMALFVEAVTR  494 (1102)
T ss_pred             -CCCe-------------------------eeHHHHHhhhccCccCCCCCcEEEEECcccCCH-----HHHHHHHHHHHh
Confidence             2221                         122222111111223345567899999995533     23444555554 


Q ss_pred             CCCeEEEEecc
Q psy1548         287 HTKQVMMFSAT  297 (448)
Q Consensus       287 ~~~q~i~~SAT  297 (448)
                      ...+++++.=+
T Consensus       495 ~garvVLVGD~  505 (1102)
T PRK13826        495 AGAKLVLVGDP  505 (1102)
T ss_pred             cCCEEEEECCH
Confidence            46778877655

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=94.06  E-value=1.6  Score=52.74  Aligned_cols=231  Identities=10%  Similarity=0.073  Sum_probs=118.7

Q ss_pred             hhhhccccccceeeeeC--cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCc
Q psy1548         133 LHRVARAGRFGTKAVLG--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI  210 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~g--~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~  210 (448)
                      |.+      ++..++..  +=.+++++.|+|||.+ +-.++..+..  .+.+++.++||..-+..+.+...        .
T Consensus       434 Q~~------Av~~il~s~~~v~ii~G~aGTGKTt~-l~~l~~~~~~--~G~~V~~lAPTgrAA~~L~e~~g--------~  496 (1960)
T TIGR02760       434 NKD------AVSTLFTSTKRFIIINGFGGTGSTEI-AQLLLHLASE--QGYEIQIITAGSLSAQELRQKIP--------R  496 (1960)
T ss_pred             HHH------HHHHHHhCCCCeEEEEECCCCCHHHH-HHHHHHHHHh--cCCeEEEEeCCHHHHHHHHHHhc--------c
Confidence            888      77777764  5678999999999965 3344443332  35689999999976555433211        1


Q ss_pred             eEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhC-CCCC
Q psy1548         211 KVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSS-PHTK  289 (448)
Q Consensus       211 ~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l-~~~~  289 (448)
                      ....      .......+..   ..-..|...++    .....+..-++||||||-++..     ..+..+++.. +.+.
T Consensus       497 ~A~T------i~~~l~~l~~---~~~~~tv~~fl----~~~~~l~~~~vlIVDEAsMl~~-----~~~~~Ll~~a~~~ga  558 (1960)
T TIGR02760       497 LAST------FITWVKNLFN---DDQDHTVQGLL----DKSSPFSNKDIFVVDEANKLSN-----NELLKLIDKAEQHNS  558 (1960)
T ss_pred             hhhh------HHHHHHhhcc---cccchhHHHhh----cccCCCCCCCEEEEECCCCCCH-----HHHHHHHHHHhhcCC
Confidence            1000      0000111111   11122333332    1222345667999999995533     3345555544 4678


Q ss_pred             eEEEEecc--CCc----cHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhC--CCCeEEEEE
Q psy1548         290 QVMMFSAT--LSK----EIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVL--EFNQVVIFV  361 (448)
Q Consensus       290 q~i~~SAT--~~~----~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~--~~~~~IIF~  361 (448)
                      ++|++.=+  ++.    .+..++.... -+... .... ......+  .........+...+.+.+-..  ...+++|+.
T Consensus       559 rvVlvGD~~QL~sV~aG~~f~~L~~~g-v~t~~-l~~i-~rq~~~v--~i~~~~~~~r~~~ia~~y~~L~~~r~~tliv~  633 (1960)
T TIGR02760       559 KLILLNDSAQRQGMSAGSAIDLLKEGG-VTTYA-WVDT-KQQKASV--EISEAVDKLRVDYIASAWLDLTPDRQNSQVLA  633 (1960)
T ss_pred             EEEEEcChhhcCccccchHHHHHHHCC-CcEEE-eecc-cccCcce--eeeccCchHHHHHHHHHHHhcccccCceEEEc
Confidence            88887665  222    2333333321 12221 1111 1111112  122222233444444444332  233589999


Q ss_pred             CccHHHHHHHHHHHh----CC------CcEEEEe-CCCCHHHHHHHHHHHhcCC
Q psy1548         362 KSVTRCIALSTLLSE----QN------FPAVSIH-RGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       362 ~s~~~a~~l~~~L~~----~g------~~~~~lh-~~~~~~eR~~~l~~F~~g~  404 (448)
                      .+.+....|....+.    .|      .....+. ..|+..++... ..|+.|.
T Consensus       634 ~t~~dr~~Ln~~iR~~L~~~G~L~~~~~~~~~L~p~~lt~~e~r~~-~~Yr~Gd  686 (1960)
T TIGR02760       634 TTHREQQDLTQIIRNALKQEGQLSRQEVTVPTLKPVNLTGIQRRNA-AHYKQGM  686 (1960)
T ss_pred             CCcHHHHHHHHHHHHHHHHcCCcCCCceEEEEeccCCCCHHHHhhH-hhcCCCC
Confidence            998888888876654    22      2233333 46888888744 6666655

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.06  E-value=0.6  Score=46.37  Aligned_cols=24  Identities=25%  Similarity=0.185  Sum_probs=18.4

Q ss_pred             eeCcceeeeccCCChhHHHHHHHH
Q psy1548         147 VLGMDILCQAKSGMGKTAVFVLAT  170 (448)
Q Consensus       147 ~~g~~vli~apTGsGKT~~~~l~~  170 (448)
                      ..++-+++.||+|+|||....--+
T Consensus       204 ~~~~ii~lvGptGvGKTTt~akLA  227 (407)
T PRK12726        204 SNHRIISLIGQTGVGKTTTLVKLG  227 (407)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHH
Confidence            346788999999999997654433

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=94.05  E-value=0.067  Score=52.12  Aligned_cols=46  Identities=17%  Similarity=0.312  Sum_probs=32.1

Q ss_pred             eeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHH
Q psy1548         147 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELA  193 (448)
Q Consensus       147 ~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~  193 (448)
                      ..+++++++|+||||||.. +-.++..+...+...+++.+=.+.||.
T Consensus       142 ~~~~nilI~G~tGSGKTTl-l~aL~~~i~~~~~~~rivtiEd~~El~  187 (323)
T PRK13833        142 DSRLNIVISGGTGSGKTTL-ANAVIAEIVASAPEDRLVILEDTAEIQ  187 (323)
T ss_pred             HcCCeEEEECCCCCCHHHH-HHHHHHHHhcCCCCceEEEecCCcccc
Confidence            3478999999999999954 455666554333344777777777763

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=94.02  E-value=0.39  Score=51.70  Aligned_cols=42  Identities=10%  Similarity=0.289  Sum_probs=37.4

Q ss_pred             eEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCc
Q psy1548         258 KHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSK  300 (448)
Q Consensus       258 ~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~  300 (448)
                      -++|+|+.|.+.+. .....+..++++.|++...++.|-+-|.
T Consensus       131 l~LVlDDyHli~~~-~l~~~l~fLl~~~P~~l~lvv~SR~rP~  172 (894)
T COG2909         131 LYLVLDDYHLISDP-ALHEALRFLLKHAPENLTLVVTSRSRPQ  172 (894)
T ss_pred             eEEEeccccccCcc-cHHHHHHHHHHhCCCCeEEEEEeccCCC
Confidence            58999999999887 8889999999999999999999887554

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=93.99  E-value=1.1  Score=40.05  Aligned_cols=145  Identities=13%  Similarity=0.111  Sum_probs=76.5

Q ss_pred             eCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEY  227 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~  227 (448)
                      ...++++..++|.|||.+++--++..+..   +.+++++-=.+--.  -......+.. ++++.....-.+.....+   
T Consensus        21 ~~g~v~v~~g~GkGKtt~a~g~a~ra~g~---G~~V~ivQFlKg~~--~~GE~~~l~~-l~~v~~~~~g~~~~~~~~---   91 (191)
T PRK05986         21 EKGLLIVHTGNGKGKSTAAFGMALRAVGH---GKKVGVVQFIKGAW--STGERNLLEF-GGGVEFHVMGTGFTWETQ---   91 (191)
T ss_pred             cCCeEEEECCCCCChHHHHHHHHHHHHHC---CCeEEEEEEecCCC--ccCHHHHHhc-CCCcEEEECCCCCcccCC---
Confidence            45789999999999998876555554433   34566654222110  0011222211 123333322111111000   


Q ss_pred             HhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhh--HHHHHHHHHhCCCCCeEEEEeccCCccHHHH
Q psy1548         228 LKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEM--RRDVQEIFRSSPHTKQVMMFSATLSKEIRPV  305 (448)
Q Consensus       228 l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~--~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~  305 (448)
                         . ..--.......+...+ ..+.-..++++|+||+-..++. ++  ...+..+++..|...-+|+..-..|+++.+.
T Consensus        92 ---~-~~e~~~~~~~~~~~a~-~~l~~~~ydlvVLDEi~~Al~~-gli~~eevi~~L~~rp~~~evVlTGR~~p~~Lie~  165 (191)
T PRK05986         92 ---D-RERDIAAAREGWEEAK-RMLADESYDLVVLDELTYALKY-GYLDVEEVLEALNARPGMQHVVITGRGAPRELIEA  165 (191)
T ss_pred             ---C-cHHHHHHHHHHHHHHH-HHHhCCCCCEEEEehhhHHHHC-CCccHHHHHHHHHcCCCCCEEEEECCCCCHHHHHh
Confidence               0 0000001111111111 1122356788999999988776 54  5677778888888888888888888877666


Q ss_pred             HH
Q psy1548         306 CK  307 (448)
Q Consensus       306 ~~  307 (448)
                      +.
T Consensus       166 AD  167 (191)
T PRK05986        166 AD  167 (191)
T ss_pred             Cc
Confidence            54

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=93.97  E-value=0.41  Score=48.16  Aligned_cols=46  Identities=7%  Similarity=0.288  Sum_probs=27.9

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHH
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIR  303 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~  303 (448)
                      ...++++|||+|.|...  ....+.+.+..-+++..+|+.|.+ +..+.
T Consensus       116 ~~~kViiIDead~m~~~--aanaLLk~LEep~~~~~fIL~a~~-~~~ll  161 (394)
T PRK07940        116 GRWRIVVIEDADRLTER--AANALLKAVEEPPPRTVWLLCAPS-PEDVL  161 (394)
T ss_pred             CCcEEEEEechhhcCHH--HHHHHHHHhhcCCCCCeEEEEECC-hHHCh
Confidence            56688999999999764  334455555554555555554444 44433

>PRK11054 helD DNA helicase IV; Provisional

Probab=93.96  E-value=0.098  Score=56.38  Aligned_cols=72  Identities=18%  Similarity=0.122  Sum_probs=51.6

Q ss_pred             CCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhcc-CCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         126 PEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-DSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       126 p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .+++.+-|++      ++-.  ...+++|.|..|||||.+..--+...+... ..+.++|+++.|+..|..+.+.+....
T Consensus       194 ~~~L~~~Q~~------av~~--~~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~l  265 (684)
T PRK11054        194 SSPLNPSQAR------AVVN--GEDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRERL  265 (684)
T ss_pred             CCCCCHHHHH------HHhC--CCCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHhc
Confidence            4667777888      5532  235689999999999988655544444332 234589999999999999998887655


Q ss_pred             c
Q psy1548         205 K  205 (448)
Q Consensus       205 ~  205 (448)
                      +
T Consensus       266 g  266 (684)
T PRK11054        266 G  266 (684)
T ss_pred             C
Confidence            4

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.96  E-value=0.39  Score=50.01  Aligned_cols=39  Identities=10%  Similarity=0.323  Sum_probs=27.1

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      .+.+++||||+|.|... .+ ..+.+.+...|..+.+|+.+
T Consensus       118 ~~~kV~iIDE~~~ls~~-a~-naLLk~LEepp~~~~fIlat  156 (509)
T PRK14958        118 GRFKVYLIDEVHMLSGH-SF-NALLKTLEEPPSHVKFILAT  156 (509)
T ss_pred             CCcEEEEEEChHhcCHH-HH-HHHHHHHhccCCCeEEEEEE
Confidence            45689999999988664 33 44555666666777777654

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=93.96  E-value=0.086  Score=50.97  Aligned_cols=45  Identities=31%  Similarity=0.436  Sum_probs=32.3

Q ss_pred             eeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHH
Q psy1548         147 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTREL  192 (448)
Q Consensus       147 ~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L  192 (448)
                      ..+++++++|+||||||.. +-.++..+.......+++++-.+.|+
T Consensus       130 ~~~~~ilI~G~tGSGKTTl-l~al~~~i~~~~~~~ri~tiEd~~El  174 (299)
T TIGR02782       130 LARKNILVVGGTGSGKTTL-ANALLAEIAKNDPTDRVVIIEDTREL  174 (299)
T ss_pred             HcCCeEEEECCCCCCHHHH-HHHHHHHhhccCCCceEEEECCchhh
Confidence            3468999999999999954 45566665443334478888777776

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=93.94  E-value=0.14  Score=51.85  Aligned_cols=26  Identities=27%  Similarity=0.339  Sum_probs=21.5

Q ss_pred             cceeeeeCcceeeeccCCChhHHHHH
Q psy1548         142 FGTKAVLGMDILCQAKSGMGKTAVFV  167 (448)
Q Consensus       142 ~~~~~~~g~~vli~apTGsGKT~~~~  167 (448)
                      .+..+..++++++.+|+|+|||..+.
T Consensus       187 l~~~L~~~~~iil~GppGtGKT~lA~  212 (459)
T PRK11331        187 ILKRLTIKKNIILQGPPGVGKTFVAR  212 (459)
T ss_pred             HHHHHhcCCCEEEECCCCCCHHHHHH
Confidence            45566679999999999999997653

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=93.93  E-value=0.82  Score=42.38  Aligned_cols=55  Identities=15%  Similarity=0.089  Sum_probs=33.4

Q ss_pred             eeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      +..|.-+++.+++|+|||...+--+...+.   .+.++++++.. +-..+..+.+..+.
T Consensus        21 i~~g~~~~i~G~~G~GKTtl~~~~~~~~~~---~g~~~~yi~~e-~~~~~~~~~~~~~g   75 (230)
T PRK08533         21 IPAGSLILIEGDESTGKSILSQRLAYGFLQ---NGYSVSYVSTQ-LTTTEFIKQMMSLG   75 (230)
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHHHh---CCCcEEEEeCC-CCHHHHHHHHHHhC
Confidence            344788999999999999664333333222   23467888743 33455555555543

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=93.88  E-value=0.63  Score=49.34  Aligned_cols=54  Identities=9%  Similarity=0.181  Sum_probs=40.7

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhc
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK  205 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  205 (448)
                      +-.++.+|-|.|||.+..+.+...+..  .+.+++|.+|...-+.++++.++.+..
T Consensus       188 ~~tV~taPRqrGKS~iVgi~l~~La~f--~Gi~IlvTAH~~~ts~evF~rv~~~le  241 (752)
T PHA03333        188 CYTAATVPRRCGKTTIMAIILAAMISF--LEIDIVVQAQRKTMCLTLYNRVETVVH  241 (752)
T ss_pred             cceEEEeccCCCcHHHHHHHHHHHHHh--cCCeEEEECCChhhHHHHHHHHHHHHH
Confidence            456788999999998765554433322  256899999999999998888777665

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=93.83  E-value=0.87  Score=43.37  Aligned_cols=134  Identities=16%  Similarity=0.255  Sum_probs=63.9

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee--ccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE  226 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~  226 (448)
                      ++-+++.+|+|+|||.+..--+.. +..  .+.+++++.  +.|.-+.+   +++.|.... ++.+  +..+....    
T Consensus        72 ~~vi~l~G~~G~GKTTt~akLA~~-l~~--~g~~V~li~~D~~r~~a~~---ql~~~~~~~-~i~~--~~~~~~~d----  138 (272)
T TIGR00064        72 PNVILFVGVNGVGKTTTIAKLANK-LKK--QGKSVLLAAGDTFRAAAIE---QLEEWAKRL-GVDV--IKQKEGAD----  138 (272)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHH-HHh--cCCEEEEEeCCCCCHHHHH---HHHHHHHhC-CeEE--EeCCCCCC----
Confidence            356778899999999765443332 222  233566665  34443332   444444443 4332  22211100    


Q ss_pred             HHhcCCCcEEEEcHHH-HHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCC------CCCeEEEEeccCC
Q psy1548         227 YLKTHNPQIVVGTPGR-ILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSP------HTKQVMMFSATLS  299 (448)
Q Consensus       227 ~l~~~~~~IlV~Tp~~-l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~------~~~q~i~~SAT~~  299 (448)
                                   |.. ....+..  ....+.+++++|=+-++.........+..+.+..+      +.--++.++|+..
T Consensus       139 -------------p~~~~~~~l~~--~~~~~~D~ViIDT~G~~~~d~~~~~el~~~~~~~~~~~~~~~~~~~LVl~a~~~  203 (272)
T TIGR00064       139 -------------PAAVAFDAIQK--AKARNIDVVLIDTAGRLQNKVNLMDELKKIKRVIKKVDKDAPDEVLLVLDATTG  203 (272)
T ss_pred             -------------HHHHHHHHHHH--HHHCCCCEEEEeCCCCCcchHHHHHHHHHHHHHHhcccCCCCceEEEEEECCCC
Confidence                         111 1111110  00133456666666544322134445555554443      4556788899876


Q ss_pred             ccHHHHHHHhc
Q psy1548         300 KEIRPVCKKFM  310 (448)
Q Consensus       300 ~~~~~~~~~~l  310 (448)
                      .+....+..|.
T Consensus       204 ~~~~~~~~~f~  214 (272)
T TIGR00064       204 QNALEQAKVFN  214 (272)
T ss_pred             HHHHHHHHHHH
Confidence            55444444444

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>PRK13342 recombination factor protein RarA; Reviewed

Probab=93.81  E-value=0.47  Score=48.15  Aligned_cols=18  Identities=22%  Similarity=0.314  Sum_probs=15.0

Q ss_pred             cceeeeccCCChhHHHHH
Q psy1548         150 MDILCQAKSGMGKTAVFV  167 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~  167 (448)
                      .++++.||+|+|||..+.
T Consensus        37 ~~ilL~GppGtGKTtLA~   54 (413)
T PRK13342         37 SSMILWGPPGTGKTTLAR   54 (413)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            478999999999996643

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=93.81  E-value=0.29  Score=43.57  Aligned_cols=106  Identities=16%  Similarity=0.165  Sum_probs=58.2

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL  228 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l  228 (448)
                      |+=-++.+|..||||.-.+-.+-. ..  -.+.++++..|-..-         ++.    .-.+..-.|-.         
T Consensus         4 g~l~~i~gpM~SGKT~eLl~r~~~-~~--~~g~~v~vfkp~iD~---------R~~----~~~V~Sr~G~~---------   58 (201)
T COG1435           4 GWLEFIYGPMFSGKTEELLRRARR-YK--EAGMKVLVFKPAIDT---------RYG----VGKVSSRIGLS---------   58 (201)
T ss_pred             EEEEEEEccCcCcchHHHHHHHHH-HH--HcCCeEEEEeccccc---------ccc----cceeeeccCCc---------
Confidence            344578999999999753332222 22  234577887776431         111    11111111211         


Q ss_pred             hcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhC
Q psy1548         229 KTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSS  285 (448)
Q Consensus       229 ~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l  285 (448)
                         .+-++|-.+..+...+......+. ++++.||||+-+ +. ..-..+..+...+
T Consensus        59 ---~~A~~i~~~~~i~~~i~~~~~~~~-~~~v~IDEaQF~-~~-~~v~~l~~lad~l  109 (201)
T COG1435          59 ---SEAVVIPSDTDIFDEIAALHEKPP-VDCVLIDEAQFF-DE-ELVYVLNELADRL  109 (201)
T ss_pred             ---ccceecCChHHHHHHHHhcccCCC-cCEEEEehhHhC-CH-HHHHHHHHHHhhc
Confidence               134666677777777765433332 789999999944 33 4445555555543

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=93.81  E-value=0.052  Score=58.62  Aligned_cols=47  Identities=32%  Similarity=0.401  Sum_probs=42.5

Q ss_pred             hccceeEeeccccCCcccc---cce-----eEeeccCCCCchhhhhhhccccccc
Q psy1548          97 DCWRILVATNLFGRGMDIE---RVN-----IVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        97 ~~~~~~~~~~~~~~~~d~~---~~~-----~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      ..|.|.||||++|||.|+.   .|.     .|+++..|...+-|.|..|||||..
T Consensus       487 ~~g~VtIATnmAGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql~GRtGRqG  541 (796)
T PRK12906        487 QRGAVTIATNMAGRGTDIKLGPGVKELGGLAVIGTERHESRRIDNQLRGRSGRQG  541 (796)
T ss_pred             CCceEEEEeccccCCCCCCCCcchhhhCCcEEEeeecCCcHHHHHHHhhhhccCC
Confidence            4579999999999999994   788     9999999999999999999999943

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.79  E-value=0.56  Score=48.39  Aligned_cols=39  Identities=13%  Similarity=0.284  Sum_probs=25.4

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      ...+++||||+|.+... .+ ..+.+.+..-|+...+|+.+
T Consensus       115 ~~~KVvIIDEah~Ls~~-A~-NaLLK~LEePp~~v~fIlat  153 (491)
T PRK14964        115 SKFKVYIIDEVHMLSNS-AF-NALLKTLEEPAPHVKFILAT  153 (491)
T ss_pred             CCceEEEEeChHhCCHH-HH-HHHHHHHhCCCCCeEEEEEe
Confidence            56789999999977653 33 34455555555666666544

>TIGR01075 uvrD DNA helicase II

Probab=93.74  E-value=0.21  Score=54.56  Aligned_cols=65  Identities=17%  Similarity=0.123  Sum_probs=49.9

Q ss_pred             hhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhc-cCCCeEEEEeeccHHHHHHHHHHHHHhhc
Q psy1548         133 LHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRELAFQISKEYERFSK  205 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  205 (448)
                      |++      ++..  ...+++|.|..|||||.+..--+...+.. +-...++|+++.|+.-|..+.+.+.++..
T Consensus         9 Q~~------av~~--~~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkAA~em~~Rl~~~~~   74 (715)
T TIGR01075         9 QRE------AVAA--PPGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGALLG   74 (715)
T ss_pred             HHH------HHcC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHHHHHHHHHHHHHhc
Confidence            888      6543  24689999999999998865555555543 22345899999999999999999988765

Designed to identify uvrD members of the uvrD/rep subfamily.

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=93.74  E-value=0.054  Score=53.78  Aligned_cols=61  Identities=21%  Similarity=0.347  Sum_probs=42.5

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChh
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGK  162 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGK  162 (448)
                      ..++|||+++++|+|.+ +..++++..  +++.|-|.+||+||.......+.++++--+...++
T Consensus       279 ~~ilvaT~~~~~GiDi~-~~~vi~~~~--~~~~~iqr~GR~gR~g~~~~~~~~~~v~~~~~~~~  339 (358)
T TIGR01587       279 KFVIVATQVIEASLDIS-ADVMITELA--PIDSLIQRLGRLHRYGRKNGENFEVYIITIAPEGK  339 (358)
T ss_pred             CeEEEECcchhceeccC-CCEEEEcCC--CHHHHHHHhccccCCCCCCCCCCeEEEEeecCCCC
Confidence            36999999999999995 677777644  47889999999999654322223555444433333

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.

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=93.68  E-value=0.37  Score=48.27  Aligned_cols=157  Identities=14%  Similarity=0.161  Sum_probs=76.6

Q ss_pred             CeeEEEecchhHHHhhhhhHHHHHHHHHhCC-CCCeEEEEeccCCccHHHH---HHHhcCCCeEEEEcCcccccccceeE
Q psy1548         256 LLKHFILDECDKMLEQLEMRRDVQEIFRSSP-HTKQVMMFSATLSKEIRPV---CKKFMHDPMEVYVDDEAKLTLHGLQQ  331 (448)
Q Consensus       256 ~i~~lViDEah~l~~~~~~~~~~~~i~~~l~-~~~q~i~~SAT~~~~~~~~---~~~~l~~~~~i~~~~~~~~~~~~i~~  331 (448)
                      ++++++||.++.+.........+-.++..+. ...|+++.|...|.++..+   ++.-+.--..+.+.+           
T Consensus       175 ~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~~-----------  243 (408)
T COG0593         175 SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEP-----------  243 (408)
T ss_pred             ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHHHHhceeEEeeCC-----------
Confidence            6788999999977554122333444444443 4558888888877764422   221111112222211           


Q ss_pred             EEEEcCcchHHHHHHHHHhhCCC---CeEEEE-----ECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcC
Q psy1548         332 HYVKLKENEKNKKLFELLDVLEF---NQVVIF-----VKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDF  403 (448)
Q Consensus       332 ~~~~~~~~~k~~~L~~ll~~~~~---~~~IIF-----~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g  403 (448)
                          ...+.+...|.........   ..++-|     ..+..+.+...+.|..   -+......++.+--.++++++...
T Consensus       244 ----Pd~e~r~aiL~kka~~~~~~i~~ev~~~la~~~~~nvReLegaL~~l~~---~a~~~~~~iTi~~v~e~L~~~~~~  316 (408)
T COG0593         244 ----PDDETRLAILRKKAEDRGIEIPDEVLEFLAKRLDRNVRELEGALNRLDA---FALFTKRAITIDLVKEILKDLLRA  316 (408)
T ss_pred             ----CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccHHHHHHHHHHHHH---HHHhcCccCcHHHHHHHHHHhhcc
Confidence                1223344444443322110   011111     1222223332222221   122223367777777788777664


Q ss_pred             CCceEEEEecChhhHHHHHHHHHHhcCCCCCCCcc
Q psy1548         404 HKGLAITFASDENDAKILNNVQDRFDVSISELPDE  438 (448)
Q Consensus       404 ~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~  438 (448)
                      ..    . +|.   ...++.+-+.|+++..++-..
T Consensus       317 ~~----~-iti---e~I~~~Va~~y~v~~~dl~s~  343 (408)
T COG0593         317 GE----K-ITI---EDIQKIVAEYYNVKVSDLLSK  343 (408)
T ss_pred             cc----c-CCH---HHHHHHHHHHhCCCHHHhhcc
Confidence            43    2 332   356677888888888776443

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=93.65  E-value=0.22  Score=45.61  Aligned_cols=56  Identities=11%  Similarity=0.230  Sum_probs=29.9

Q ss_pred             cHHHHHHHHHCCCCcCCCeeEEEecchhHHH-h---hhhhHHHHHHHHHhCCC-CCeEEEEeccC
Q psy1548         239 TPGRILALVRNKKLNLSLLKHFILDECDKML-E---QLEMRRDVQEIFRSSPH-TKQVMMFSATL  298 (448)
Q Consensus       239 Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~-~---~~~~~~~~~~i~~~l~~-~~q~i~~SAT~  298 (448)
                      +...+...+......    -+||+||+|.+. .   ...+...+..++..... ....+.++++-
T Consensus       105 ~l~~~~~~l~~~~~~----~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~v~~~S~  165 (234)
T PF01637_consen  105 ALERLLEKLKKKGKK----VIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQNVSIVITGSS  165 (234)
T ss_dssp             -HHHHHHHHHHCHCC----EEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----TTEEEEEEESS
T ss_pred             HHHHHHHHHHhcCCc----EEEEEecHHHHhhcccchHHHHHHHHHHHhhccccCCceEEEECCc
Confidence            344455555443221    579999999998 1   12566667777666332 22334445543

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>KOG0327|consensus

Probab=93.63  E-value=0.069  Score=51.88  Aligned_cols=76  Identities=33%  Similarity=0.604  Sum_probs=59.0

Q ss_pred             hhccCceeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548          68 KEVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        68 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      ....+..++.-+...++.....-+.+.-....+|+|.|...+||||...+..|++|..|.....|=+.+||+||+.
T Consensus       283 L~~~~~~~s~~~~d~~q~~R~~~~~ef~~gssrvlIttdl~argidv~~~slvinydlP~~~~~yihR~gr~gr~g  358 (397)
T KOG0327|consen  283 LRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRVLITTDLLARGIDVQQVSLVVNYDLPARKENYIHRIGRAGRFG  358 (397)
T ss_pred             HhhCCceEEEeecccchhhhhHHHHHhhcCCceEEeeccccccccchhhcceeeeeccccchhhhhhhcccccccC
Confidence            3344555555555556655555555555666799999999999999999999999999999988888888888843

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=93.62  E-value=0.29  Score=49.42  Aligned_cols=67  Identities=18%  Similarity=0.219  Sum_probs=48.0

Q ss_pred             hhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         130 DTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       130 ~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      +..|..      +.-..-.|+. .|.+-.|||||...+.-+.. +......-++++.+-|+.|+.++...+.+|.
T Consensus       164 D~~Q~k------aa~~~~~G~q-rIrGLAGSGKT~~La~Kaa~-lh~knPd~~I~~Tfftk~L~s~~r~lv~~F~  230 (660)
T COG3972         164 DTDQTK------AAFQSGFGKQ-RIRGLAGSGKTELLAHKAAE-LHSKNPDSRIAFTFFTKILASTMRTLVPEFF  230 (660)
T ss_pred             cchhhe------eeeecCCchh-hhhcccCCCchhHHHHHHHH-HhcCCCCceEEEEeehHHHHHHHHHHHHHHH
Confidence            444777      4445555666 78899999999875544433 3333344589999999999999988888776

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=93.58  E-value=0.25  Score=53.90  Aligned_cols=65  Identities=18%  Similarity=0.164  Sum_probs=49.4

Q ss_pred             hhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhc-cCCCeEEEEeeccHHHHHHHHHHHHHhhc
Q psy1548         133 LHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRELAFQISKEYERFSK  205 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  205 (448)
                      |++      ++..  ...+++|.|+.|||||.+..--+...+.. +-...++|+|+-|+.-|.++.+.+.++.+
T Consensus        14 Q~~------av~~--~~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~~~   79 (721)
T PRK11773         14 QRE------AVAA--PLGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQLLG   79 (721)
T ss_pred             HHH------HHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHHhc
Confidence            888      5543  24689999999999998865555555432 22345799999999999999999988764

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=93.53  E-value=1  Score=44.81  Aligned_cols=26  Identities=31%  Similarity=0.526  Sum_probs=18.5

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhc
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLET  176 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~  176 (448)
                      .|+++.|+||+|||.+.-. ++..+..
T Consensus        43 ~n~~iyG~~GTGKT~~~~~-v~~~l~~   68 (366)
T COG1474          43 SNIIIYGPTGTGKTATVKF-VMEELEE   68 (366)
T ss_pred             ccEEEECCCCCCHhHHHHH-HHHHHHh
Confidence            4799999999999977433 3344433

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=93.45  E-value=0.48  Score=49.39  Aligned_cols=39  Identities=15%  Similarity=0.319  Sum_probs=27.8

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      ...+++||||||.|...  ....+.+.+...|+...+|+.+
T Consensus       116 ~~~KVvIIDEad~Lt~~--A~NALLK~LEEpp~~t~FIL~t  154 (535)
T PRK08451        116 ARFKIFIIDEVHMLTKE--AFNALLKTLEEPPSYVKFILAT  154 (535)
T ss_pred             CCeEEEEEECcccCCHH--HHHHHHHHHhhcCCceEEEEEE
Confidence            56789999999988663  3445555666667777777665

>PRK11823 DNA repair protein RadA; Provisional

Probab=93.36  E-value=0.45  Score=48.78  Aligned_cols=56  Identities=27%  Similarity=0.334  Sum_probs=35.3

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      -+..|.-+++.+++|+|||...+--+. ....  .+.+++|+.- .+-..|+...+.++.
T Consensus        76 Gi~~Gs~~lI~G~pG~GKTtL~lq~a~-~~a~--~g~~vlYvs~-Ees~~qi~~ra~rlg  131 (446)
T PRK11823         76 GLVPGSVVLIGGDPGIGKSTLLLQVAA-RLAA--AGGKVLYVSG-EESASQIKLRAERLG  131 (446)
T ss_pred             CccCCEEEEEECCCCCCHHHHHHHHHH-HHHh--cCCeEEEEEc-cccHHHHHHHHHHcC
Confidence            344567889999999999965433332 2221  2447888874 445567766666654

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

Probab=93.34  E-value=0.091  Score=53.00  Aligned_cols=58  Identities=29%  Similarity=0.532  Sum_probs=46.7

Q ss_pred             ccCCCCHHHHHHHhhc-----cceeEeeccccCCcccccceeEeecc-CCCCchhhhhhhccccc
Q psy1548          83 RDFLLKPEILRAIVDC-----WRILVATNLFGRGMDIERVNIVFNYD-MPEDSDTYLHRVARAGR  141 (448)
Q Consensus        83 ~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~d~~~~~~v~~~~-~p~~~~~yQ~~~~~~~~  141 (448)
                      .+.|+++..++.+.+.     ..|+|||++...|+|.|+++.|+=|+ -|++|+.-|.. ||+||
T Consensus       405 ~~~GMsQkeQ~eiI~~Fr~Ge~nVLVaTSVgEEGLDIp~vDlVifYEpvpSeIR~IQR~-GRTGR  468 (542)
T COG1111         405 GDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRK-GRTGR  468 (542)
T ss_pred             cccccCHHHHHHHHHHHhcCCceEEEEcccccccCCCCcccEEEEecCCcHHHHHHHhh-Ccccc
Confidence            3467777666555433     48999999999999999999998776 78889888988 88877

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=93.34  E-value=0.94  Score=41.76  Aligned_cols=55  Identities=18%  Similarity=0.208  Sum_probs=32.7

Q ss_pred             eeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      +..|..+++.+++|+|||....--+...+..   +..+++++- .+...++.+.++.+.
T Consensus        17 i~~G~~~~i~G~~G~GKT~l~~~~~~~~~~~---g~~~~~is~-e~~~~~i~~~~~~~g   71 (229)
T TIGR03881        17 IPRGFFVAVTGEPGTGKTIFCLHFAYKGLRD---GDPVIYVTT-EESRESIIRQAAQFG   71 (229)
T ss_pred             CcCCeEEEEECCCCCChHHHHHHHHHHHHhc---CCeEEEEEc-cCCHHHHHHHHHHhC
Confidence            4457899999999999996544333333322   335666663 333455555555443

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=93.22  E-value=1.1  Score=45.36  Aligned_cols=59  Identities=17%  Similarity=0.138  Sum_probs=31.9

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee--ccHHHHHHHHHHHHHhhccCCCceEEEE
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGVF  215 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~v~~~  215 (448)
                      .-++++|++|+|||.+..--+. .+..  .+.++++++  |.|.-+.+   +++.++... ++.+...
T Consensus       101 ~vi~lvG~~GvGKTTtaaKLA~-~l~~--~G~kV~lV~~D~~R~aA~e---QLk~~a~~~-~vp~~~~  161 (429)
T TIGR01425       101 NVIMFVGLQGSGKTTTCTKLAY-YYQR--KGFKPCLVCADTFRAGAFD---QLKQNATKA-RIPFYGS  161 (429)
T ss_pred             eEEEEECCCCCCHHHHHHHHHH-HHHH--CCCCEEEEcCcccchhHHH---HHHHHhhcc-CCeEEee
Confidence            3578999999999966432222 2222  233555555  45554444   444455443 5554433

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>PF03237 Terminase_6: Terminase-like family; InterPro: IPR004921 The terminase is a component of the molecular motor that translocates genomic DNA into empty capsids during DNA packaging []

Probab=93.20  E-value=3.1  Score=40.91  Aligned_cols=147  Identities=15%  Similarity=0.087  Sum_probs=63.0

Q ss_pred             eeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHH---HHHHhhccCCCceEEEEEcCcccHHhHHHHh
Q psy1548         153 LCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK---EYERFSKYMSNIKVGVFFGGLPIQKDEEYLK  229 (448)
Q Consensus       153 li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~---~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~  229 (448)
                      ++.++.|+|||.+..+.++..+...+....+++...+..+...+..   .+..+................ ..     +.
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~-----~~   74 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPPGRRVIIASTYRQARDIFGRFWKGIIELLPSWFEIKFNEWNDRK-II-----LP   74 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS--EEEEEESSHHHHHHHHHHHHHHHHTS-TTTS--EEEE-SSE-EE-----ET
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCCCcEEEEecCHHHHHHHHHHhHHHHHHHHHHhcCcccccCCCCc-EE-----ec
Confidence            4678999999999887777776665544456666444444443332   222322221011111111111 00     02


Q ss_pred             cCCCcEEEEcHHHH--HHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCC--ccHHHH
Q psy1548         230 THNPQIVVGTPGRI--LALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLS--KEIRPV  305 (448)
Q Consensus       230 ~~~~~IlV~Tp~~l--~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~--~~~~~~  305 (448)
                      ++ ..|.+.+-..-  ..-+.     -..++++++||+-.+.+. .+...+........... .+.+|.|..  .....+
T Consensus        75 nG-~~i~~~~~~~~~~~~~~~-----G~~~~~i~iDE~~~~~~~-~~~~~~~~~~~~~~~~~-~~~~s~p~~~~~~~~~~  146 (384)
T PF03237_consen   75 NG-SRIQFRGADSPDSGDNIR-----GFEYDLIIIDEAAKVPDD-AFSELIRRLRATWGGSI-RMYISTPPNPGGWFYEI  146 (384)
T ss_dssp             TS--EEEEES-----SHHHHH-----TS--SEEEEESGGGSTTH-HHHHHHHHHHHCSTT---EEEEEE---SSSHHHHH
T ss_pred             Cc-eEEEEecccccccccccc-----ccccceeeeeecccCchH-HHHHHHHhhhhcccCcc-eEEeecCCCCCCceeee
Confidence            33 45666653321  11222     155678999999877554 44444433333332222 224444432  235555


Q ss_pred             HHHhcCCC
Q psy1548         306 CKKFMHDP  313 (448)
Q Consensus       306 ~~~~l~~~  313 (448)
                      ......+.
T Consensus       147 ~~~~~~~~  154 (384)
T PF03237_consen  147 FQRNLDDD  154 (384)
T ss_dssp             HHHHHCTS
T ss_pred             eehhhcCC
Confidence            55555444

The large subunit heterodimerises with the small terminase protein, which is docked on the capsid portal protein. The latter forms a ring through which genomic DNA is translocated into the capsid. The terminase protein may have or induce an endonuclease activity to cleave DNA after encapsidation. This entry represents a family of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2O0K_A 3CPE_A 2O0J_A 2O0H_A 3C6H_A 3C6A_A.

>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2

Probab=93.19  E-value=2.2  Score=37.47  Aligned_cols=141  Identities=18%  Similarity=0.259  Sum_probs=64.2

Q ss_pred             eeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcC
Q psy1548         152 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTH  231 (448)
Q Consensus       152 vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~  231 (448)
                      +.+-...|-|||.+++=-++..+   ..+.+++++-=.+-  ..-......+.. ++++.+...--+-........    
T Consensus         6 i~vytG~GKGKTTAAlGlalRA~---G~G~rV~ivQFlKg--~~~~GE~~~l~~-l~~~~~~~~g~~f~~~~~~~~----   75 (172)
T PF02572_consen    6 IQVYTGDGKGKTTAALGLALRAA---GHGMRVLIVQFLKG--GRYSGELKALKK-LPNVEIERFGKGFVWRMNEEE----   75 (172)
T ss_dssp             EEEEESSSS-HHHHHHHHHHHHH---CTT--EEEEESS----SS--HHHHHHGG-GT--EEEE--TT----GGGHH----
T ss_pred             EEEEeCCCCCchHHHHHHHHHHH---hCCCEEEEEEEecC--CCCcCHHHHHHh-CCeEEEEEcCCcccccCCCcH----
Confidence            45667889999987665555443   34557777764443  011122233222 224333222111110000000    


Q ss_pred             CCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhh--HHHHHHHHHhCCCCCeEEEEeccCCccHHHHHH
Q psy1548         232 NPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEM--RRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCK  307 (448)
Q Consensus       232 ~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~--~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~  307 (448)
                       .+  .......++..+ ..+.-...+++|+||+-..++. ++  ...+..+++..|...-+|+..-.+|+++.+.+.
T Consensus        76 -~~--~~~~~~~~~~a~-~~i~~~~~dlvILDEi~~a~~~-gll~~~~v~~~l~~rp~~~evVlTGR~~~~~l~e~AD  148 (172)
T PF02572_consen   76 -ED--RAAAREGLEEAK-EAISSGEYDLVILDEINYAVDY-GLLSEEEVLDLLENRPESLEVVLTGRNAPEELIEAAD  148 (172)
T ss_dssp             -HH--HHHHHHHHHHHH-HHTT-TT-SEEEEETHHHHHHT-TSS-HHHHHHHHHTS-TT-EEEEE-SS--HHHHHH-S
T ss_pred             -HH--HHHHHHHHHHHH-HHHhCCCCCEEEEcchHHHhHC-CCccHHHHHHHHHcCCCCeEEEEECCCCCHHHHHhCC
Confidence             00  000111122211 2223456789999999988776 54  566777888888888888888888887776654

5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) []. Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type [], EutT-type [] and PduO-type []. Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represents the ATP:cob(I)alamin adenosyltransferases CobA (Salmonella typhimurium), CobO (Pseudomonas denitrificans), and ButR (Escherichia coli). There is a high degree of sequence identity between these proteins []. CobA is responsible for attaching the adenosyl moiety from ATP to the cobalt ion of the corrin ring, necessary for the convertion of cobalamin to adenosylcobalamin [, ]. ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process; PDB: 1G64_A 1G5T_A 1G5R_A.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.18  E-value=0.48  Score=47.22  Aligned_cols=39  Identities=13%  Similarity=0.357  Sum_probs=24.9

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      ...+++||||+|.+... .+ ..+.+.+...|....+|+.+
T Consensus       118 ~~~kviIIDEa~~l~~~-a~-naLLk~lEe~~~~~~fIl~t  156 (363)
T PRK14961        118 SRFKVYLIDEVHMLSRH-SF-NALLKTLEEPPQHIKFILAT  156 (363)
T ss_pred             CCceEEEEEChhhcCHH-HH-HHHHHHHhcCCCCeEEEEEc
Confidence            45679999999988653 22 33444455555566666654

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=93.15  E-value=0.28  Score=47.00  Aligned_cols=20  Identities=30%  Similarity=0.385  Sum_probs=16.6

Q ss_pred             eCcceeeeccCCChhHHHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVFV  167 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~  167 (448)
                      .++.+++.||||+|||....
T Consensus       193 ~~~vi~~vGptGvGKTTt~~  212 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLA  212 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            46788999999999997654

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=93.14  E-value=0.087  Score=51.36  Aligned_cols=46  Identities=26%  Similarity=0.352  Sum_probs=31.9

Q ss_pred             eeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHH
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTREL  192 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L  192 (448)
                      +..+++++++|+|||||| .++-.++..+...+...+++++-.+.||
T Consensus       145 v~~~~~ilI~G~tGSGKT-Tll~aL~~~~~~~~~~~rivtIEd~~El  190 (319)
T PRK13894        145 VRAHRNILVIGGTGSGKT-TLVNAIINEMVIQDPTERVFIIEDTGEI  190 (319)
T ss_pred             HHcCCeEEEECCCCCCHH-HHHHHHHHhhhhcCCCceEEEEcCCCcc
Confidence            345789999999999999 4455555544322334477777777776

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=93.10  E-value=0.45  Score=50.72  Aligned_cols=38  Identities=11%  Similarity=0.294  Sum_probs=25.2

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEE
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMF  294 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~  294 (448)
                      ...+++||||+|+|... . ...+.+.+..-|..+.+|+.
T Consensus       118 g~~KV~IIDEah~Ls~~-a-~NALLKtLEEPp~~v~FIL~  155 (647)
T PRK07994        118 GRFKVYLIDEVHMLSRH-S-FNALLKTLEEPPEHVKFLLA  155 (647)
T ss_pred             CCCEEEEEechHhCCHH-H-HHHHHHHHHcCCCCeEEEEe
Confidence            46789999999988764 3 34444455655666666665

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=93.08  E-value=0.17  Score=54.78  Aligned_cols=65  Identities=14%  Similarity=0.042  Sum_probs=49.1

Q ss_pred             hhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhc-cCCCeEEEEeeccHHHHHHHHHHHHHhhc
Q psy1548         133 LHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRELAFQISKEYERFSK  205 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  205 (448)
                      |++      ++..  ...+++|.|+.|||||.+...-+...+.. +-...++|+++.|+.-|.++.+.+..+.+
T Consensus         7 Q~~------av~~--~~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v~p~~IL~lTFT~kAA~em~~Rl~~~l~   72 (672)
T PRK10919          7 QQQ------AVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQTLG   72 (672)
T ss_pred             HHH------HHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHHhC
Confidence            777      5543  24678899999999998866666665543 22345799999999999999998887654

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.07  E-value=0.55  Score=49.58  Aligned_cols=39  Identities=18%  Similarity=0.241  Sum_probs=26.4

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      ...+++||||+|.|...  -...+.+.+...|....+|+.+
T Consensus       117 ~~~KVvIIDEah~Lt~~--A~NALLK~LEEpp~~~~fIL~t  155 (584)
T PRK14952        117 SRYRIFIVDEAHMVTTA--GFNALLKIVEEPPEHLIFIFAT  155 (584)
T ss_pred             CCceEEEEECCCcCCHH--HHHHHHHHHhcCCCCeEEEEEe
Confidence            56789999999988663  3344455566666666666655

>PRK06904 replicative DNA helicase; Validated

Probab=93.05  E-value=0.54  Score=48.53  Aligned_cols=117  Identities=21%  Similarity=0.131  Sum_probs=55.4

Q ss_pred             eeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEE-EcCcccHHh
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVF-FGGLPIQKD  224 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~-~g~~~~~~~  224 (448)
                      +..|.=+++.|.+|+|||... +-+...+... .+..+++++. ..-..|+...+-....   ++....+ .|..-...+
T Consensus       218 l~~G~LiiIaarPg~GKTafa-lnia~~~a~~-~g~~Vl~fSl-EMs~~ql~~Rlla~~s---~v~~~~i~~g~~l~~~e  291 (472)
T PRK06904        218 LQPSDLIIVAARPSMGKTTFA-MNLCENAAMA-SEKPVLVFSL-EMPAEQIMMRMLASLS---RVDQTKIRTGQNLDQQD  291 (472)
T ss_pred             cCCCcEEEEEeCCCCChHHHH-HHHHHHHHHh-cCCeEEEEec-cCCHHHHHHHHHHhhC---CCCHHHhccCCCCCHHH
Confidence            344566788999999999644 4333333221 1335666652 2333444433332222   2222222 221111111


Q ss_pred             HH-------HHhcCCCcEEEE-----cHHHHHHHHHCCCCcCCCeeEEEecchhHHH
Q psy1548         225 EE-------YLKTHNPQIVVG-----TPGRILALVRNKKLNLSLLKHFILDECDKML  269 (448)
Q Consensus       225 ~~-------~l~~~~~~IlV~-----Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~  269 (448)
                      ..       .+... +++.|-     |+..+...+++-......++++|||-.+.|.
T Consensus       292 ~~~~~~a~~~l~~~-~~l~I~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~  347 (472)
T PRK06904        292 WAKISSTVGMFKQK-PNLYIDDSSGLTPTELRSRARRVYRENGGLSLIMVDYLQLMR  347 (472)
T ss_pred             HHHHHHHHHHHhcC-CCEEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEecHHhcC
Confidence            11       22222 446663     5555554443211111357899999999774

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=92.87  E-value=0.77  Score=47.68  Aligned_cols=19  Identities=26%  Similarity=0.268  Sum_probs=15.7

Q ss_pred             cceeeeccCCChhHHHHHH
Q psy1548         150 MDILCQAKSGMGKTAVFVL  168 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l  168 (448)
                      +.+|++||.|+|||.++.+
T Consensus        44 ~a~Lf~Gp~G~GKTT~Ari   62 (507)
T PRK06645         44 GGYLLTGIRGVGKTTSARI   62 (507)
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            4689999999999977543

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=92.87  E-value=1.2  Score=42.09  Aligned_cols=18  Identities=33%  Similarity=0.357  Sum_probs=14.7

Q ss_pred             cceeeeccCCChhHHHHH
Q psy1548         150 MDILCQAKSGMGKTAVFV  167 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~  167 (448)
                      ..+++.||+|+|||....
T Consensus        44 ~~~~l~G~~G~GKTtl~~   61 (269)
T TIGR03015        44 GFILITGEVGAGKTTLIR   61 (269)
T ss_pred             CEEEEEcCCCCCHHHHHH
Confidence            368899999999996643

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=92.86  E-value=1.3  Score=38.98  Aligned_cols=52  Identities=17%  Similarity=0.273  Sum_probs=40.6

Q ss_pred             CCeeEEEecchhHHHhhhhh--HHHHHHHHHhCCCCCeEEEEeccCCccHHHHHH
Q psy1548         255 SLLKHFILDECDKMLEQLEM--RRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCK  307 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~--~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~  307 (448)
                      ..++++|+||+-..++. ++  ...+..+++..|+..-+|+..-..|+.+.+.+.
T Consensus        96 ~~~DlvVLDEi~~A~~~-gli~~~~v~~lL~~rp~~~evVlTGR~~p~~l~e~AD  149 (173)
T TIGR00708        96 PELDLVLLDELTYALKY-GYLDVEEVVEALQERPGHQHVIITGRGCPQDLLELAD  149 (173)
T ss_pred             CCCCEEEehhhHHHHHC-CCcCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhCc
Confidence            56789999999987775 43  456777888888888888888888887766654

Alternate name: corrinoid adenosyltransferase.

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=92.86  E-value=0.66  Score=51.80  Aligned_cols=80  Identities=13%  Similarity=0.198  Sum_probs=63.0

Q ss_pred             CeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhH---HHHhcCCCcEEEEcHHHHHHHHHCCCCcCCC
Q psy1548         180 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTHNPQIVVGTPGRILALVRNKKLNLSL  256 (448)
Q Consensus       180 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~---~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~  256 (448)
                      +.+++|+||+.+-+..+.+.++++.   |+.++..++|+.+.....   ..+.++..+|+|+|.      +-...+++.+
T Consensus       660 g~qv~if~n~i~~~e~l~~~L~~~~---p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~------iie~GIDIp~  730 (926)
T TIGR00580       660 GGQVFYVHNRIESIEKLATQLRELV---PEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTT------IIETGIDIPN  730 (926)
T ss_pred             CCeEEEEECCcHHHHHHHHHHHHhC---CCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECC------hhhccccccc
Confidence            4589999999998888877777653   478999999998755443   345677799999996      3456788999


Q ss_pred             eeEEEecchhHH
Q psy1548         257 LKHFILDECDKM  268 (448)
Q Consensus       257 i~~lViDEah~l  268 (448)
                      ++++|++.++..
T Consensus       731 v~~VIi~~a~~~  742 (926)
T TIGR00580       731 ANTIIIERADKF  742 (926)
T ss_pred             CCEEEEecCCCC
Confidence            999999999853

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.

>TIGR00959 ffh signal recognition particle protein

Probab=92.86  E-value=1.3  Score=45.09  Aligned_cols=59  Identities=20%  Similarity=0.194  Sum_probs=30.8

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee--ccHHHHHHHHHHHHHhhccCCCceEEE
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGV  214 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~v~~  214 (448)
                      .-+++++++|+|||.+..--+.. +... .+.+++++.  +.|.-+.+   +++.++... ++.+..
T Consensus       100 ~vi~~vG~~GsGKTTtaakLA~~-l~~~-~g~kV~lV~~D~~R~~a~~---QL~~~a~~~-gvp~~~  160 (428)
T TIGR00959       100 TVILMVGLQGSGKTTTCGKLAYY-LKKK-QGKKVLLVACDLYRPAAIE---QLKVLGQQV-GVPVFA  160 (428)
T ss_pred             EEEEEECCCCCcHHHHHHHHHHH-HHHh-CCCeEEEEeccccchHHHH---HHHHHHHhc-CCceEe
Confidence            35789999999999775433333 2211 123455554  34444433   344444433 454433

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=92.84  E-value=0.6  Score=46.21  Aligned_cols=40  Identities=15%  Similarity=0.273  Sum_probs=27.3

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEec
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSA  296 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SA  296 (448)
                      ...+++||||||.|...  ....+.+.+...+....++++|.
T Consensus       140 g~~rVviIDeAd~l~~~--aanaLLk~LEEpp~~~~fiLit~  179 (351)
T PRK09112        140 GNWRIVIIDPADDMNRN--AANAILKTLEEPPARALFILISH  179 (351)
T ss_pred             CCceEEEEEchhhcCHH--HHHHHHHHHhcCCCCceEEEEEC
Confidence            45689999999998764  34446666666556666666653

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.84  E-value=0.46  Score=50.46  Aligned_cols=39  Identities=13%  Similarity=0.324  Sum_probs=24.3

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      ...+++||||+|+|... .+ ..+.+.+..-|....+|+.+
T Consensus       123 g~~KV~IIDEvh~Ls~~-a~-NaLLKtLEEPP~~~~fIL~T  161 (618)
T PRK14951        123 GRFKVFMIDEVHMLTNT-AF-NAMLKTLEEPPEYLKFVLAT  161 (618)
T ss_pred             CCceEEEEEChhhCCHH-HH-HHHHHhcccCCCCeEEEEEE
Confidence            46789999999988764 33 23334444445555665544

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=92.81  E-value=0.29  Score=45.53  Aligned_cols=49  Identities=22%  Similarity=0.171  Sum_probs=30.4

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee---ccHHHHHH
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC---HTRELAFQ  195 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~---Pt~~L~~q  195 (448)
                      -+..|.-+++.|++|+|||...+--+++.....  +..+++++   |..+++..
T Consensus         9 Gl~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~--g~~vly~s~E~~~~~~~~r   60 (242)
T cd00984           9 GLQPGDLIIIAARPSMGKTAFALNIAENIAKKQ--GKPVLFFSLEMSKEQLLQR   60 (242)
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhC--CCceEEEeCCCCHHHHHHH
Confidence            445678899999999999965443334433321  34677777   44444443

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=92.80  E-value=0.41  Score=46.94  Aligned_cols=41  Identities=7%  Similarity=0.139  Sum_probs=27.3

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEecc
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSAT  297 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT  297 (448)
                      ...+.+||||||.|...  ....+.+.+..-|.+..+|+.|..
T Consensus       105 ~~~kv~iI~~a~~m~~~--aaNaLLK~LEEPp~~~~fiL~t~~  145 (328)
T PRK05707        105 GGRKVVLIEPAEAMNRN--AANALLKSLEEPSGDTVLLLISHQ  145 (328)
T ss_pred             CCCeEEEECChhhCCHH--HHHHHHHHHhCCCCCeEEEEEECC
Confidence            45678999999999773  445555566665556666655443

>KOG0391|consensus

Probab=92.78  E-value=0.24  Score=54.76  Aligned_cols=74  Identities=23%  Similarity=0.292  Sum_probs=62.8

Q ss_pred             hHHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC-----------Cc
Q psy1548         340 EKNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH-----------KG  406 (448)
Q Consensus       340 ~k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~-----------~g  406 (448)
                      .|+..|..+|+++  .+.++|||....+-.+-|...|.-+|+-..-+.|..+-++|...++.|+...           .|
T Consensus      1260 GKLQtLAiLLqQLk~eghRvLIfTQMtkmLDVLeqFLnyHgylY~RLDg~t~vEqRQaLmerFNaD~RIfcfILSTrSgg 1339 (1958)
T KOG0391|consen 1260 GKLQTLAILLQQLKSEGHRVLIFTQMTKMLDVLEQFLNYHGYLYVRLDGNTSVEQRQALMERFNADRRIFCFILSTRSGG 1339 (1958)
T ss_pred             chHHHHHHHHHHHHhcCceEEehhHHHHHHHHHHHHHhhcceEEEEecCCccHHHHHHHHHHhcCCCceEEEEEeccCCc
Confidence            4667777777654  4679999999999999999999999999999999999999999999999887           56


Q ss_pred             eEEEEec
Q psy1548         407 LAITFAS  413 (448)
Q Consensus       407 ~~I~~~t  413 (448)
                      ++|++..
T Consensus      1340 vGiNLtg 1346 (1958)
T KOG0391|consen 1340 VGINLTG 1346 (1958)
T ss_pred             ccccccc
Confidence            6666543

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.77  E-value=0.48  Score=49.26  Aligned_cols=17  Identities=29%  Similarity=0.372  Sum_probs=14.2

Q ss_pred             ceeeeccCCChhHHHHH
Q psy1548         151 DILCQAKSGMGKTAVFV  167 (448)
Q Consensus       151 ~vli~apTGsGKT~~~~  167 (448)
                      -+|+.||.|+|||.++.
T Consensus        38 a~Lf~GppGtGKTTlA~   54 (504)
T PRK14963         38 AYLFSGPRGVGKTTTAR   54 (504)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            35999999999997754

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=92.77  E-value=0.19  Score=56.03  Aligned_cols=45  Identities=20%  Similarity=0.426  Sum_probs=42.0

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      .+|+|||++.++|+|+..+..|++|+.|.....|.|.+||++|..
T Consensus       547 ~~VLIsTdvgseGlNlq~a~~VInfDlP~nP~~~eQRIGR~~RiG  591 (956)
T PRK04914        547 AQVLLCSEIGSEGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRIG  591 (956)
T ss_pred             ccEEEechhhccCCCcccccEEEEecCCCCHHHHHHHhcccccCC
Confidence            479999999999999999999999999999999999999998843

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=92.75  E-value=0.76  Score=45.73  Aligned_cols=41  Identities=15%  Similarity=0.280  Sum_probs=27.3

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEecc
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSAT  297 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT  297 (448)
                      ...+++||||+|.|..  .....+.+.+...+....+|++|..
T Consensus       140 ~~~kVviIDead~m~~--~aanaLLK~LEepp~~~~~IL~t~~  180 (365)
T PRK07471        140 GGWRVVIVDTADEMNA--NAANALLKVLEEPPARSLFLLVSHA  180 (365)
T ss_pred             CCCEEEEEechHhcCH--HHHHHHHHHHhcCCCCeEEEEEECC
Confidence            5677899999998865  3444555666665556656665544

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.71  E-value=0.77  Score=46.37  Aligned_cols=40  Identities=10%  Similarity=0.169  Sum_probs=24.0

Q ss_pred             CCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         254 LSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       254 ~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      +...+++||||+|.|... . ...+.+.+...++...+|+.+
T Consensus       125 ~~~~kvvIIdea~~l~~~-~-~~~LLk~LEep~~~t~~Il~t  164 (397)
T PRK14955        125 KGRYRVYIIDEVHMLSIA-A-FNAFLKTLEEPPPHAIFIFAT  164 (397)
T ss_pred             cCCeEEEEEeChhhCCHH-H-HHHHHHHHhcCCCCeEEEEEe
Confidence            456789999999988653 2 233444445444444455443

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=92.71  E-value=0.8  Score=49.00  Aligned_cols=39  Identities=13%  Similarity=0.280  Sum_probs=26.2

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      ...+++||||+|.|...  ....+.+.+...+..+.+|+.+
T Consensus       118 gk~KVIIIDEad~Ls~~--A~NALLKtLEEPp~~v~fILaT  156 (709)
T PRK08691        118 GKYKVYIIDEVHMLSKS--AFNAMLKTLEEPPEHVKFILAT  156 (709)
T ss_pred             CCcEEEEEECccccCHH--HHHHHHHHHHhCCCCcEEEEEe
Confidence            45689999999977553  3344555566556677776655

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.70  E-value=0.61  Score=49.39  Aligned_cols=20  Identities=25%  Similarity=0.348  Sum_probs=15.9

Q ss_pred             cceeeeccCCChhHHHHHHH
Q psy1548         150 MDILCQAKSGMGKTAVFVLA  169 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~  169 (448)
                      ..+|+.+|.|+|||.++.+-
T Consensus        39 ha~Lf~GPpG~GKTtiAril   58 (624)
T PRK14959         39 PAYLFSGTRGVGKTTIARIF   58 (624)
T ss_pred             ceEEEECCCCCCHHHHHHHH
Confidence            35789999999999876443

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=92.69  E-value=1.9  Score=37.36  Aligned_cols=53  Identities=17%  Similarity=0.252  Sum_probs=41.1

Q ss_pred             CCCeeEEEecchhHHHhhhh--hHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHH
Q psy1548         254 LSLLKHFILDECDKMLEQLE--MRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCK  307 (448)
Q Consensus       254 ~~~i~~lViDEah~l~~~~~--~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~  307 (448)
                      ....+++|+||+-..+.. +  -...+..+++..|...-+|+.+-.+|+++.+.+.
T Consensus        93 ~~~~dLlVLDEi~~a~~~-gli~~~~v~~ll~~rp~~~evIlTGr~~p~~l~e~AD  147 (159)
T cd00561          93 SGEYDLVILDEINYALGY-GLLDVEEVVDLLKAKPEDLELVLTGRNAPKELIEAAD  147 (159)
T ss_pred             cCCCCEEEEechHhHhhC-CCCCHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhCc
Confidence            456789999999977665 4  3567777888888888889988888887766653

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.

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=92.64  E-value=0.098  Score=51.48  Aligned_cols=44  Identities=20%  Similarity=0.271  Sum_probs=30.8

Q ss_pred             eeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHH
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELA  193 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~  193 (448)
                      +..+++++++||||||||.. +-.++..+..   ..+++.+-.+.||.
T Consensus       159 v~~~~nilI~G~tGSGKTTl-l~aLl~~i~~---~~rivtiEd~~El~  202 (344)
T PRK13851        159 VVGRLTMLLCGPTGSGKTTM-SKTLISAIPP---QERLITIEDTLELV  202 (344)
T ss_pred             HHcCCeEEEECCCCccHHHH-HHHHHcccCC---CCCEEEECCCcccc
Confidence            33578999999999999954 4555555432   33677777777763

>KOG0738|consensus

Probab=92.60  E-value=0.6  Score=45.93  Aligned_cols=17  Identities=29%  Similarity=0.399  Sum_probs=15.1

Q ss_pred             cceeeeccCCChhHHHH
Q psy1548         150 MDILCQAKSGMGKTAVF  166 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~  166 (448)
                      +.+|..+|.|+|||+.+
T Consensus       246 kgvLm~GPPGTGKTlLA  262 (491)
T KOG0738|consen  246 KGVLMVGPPGTGKTLLA  262 (491)
T ss_pred             ceeeeeCCCCCcHHHHH
Confidence            78999999999999754

>PRK10867 signal recognition particle protein; Provisional

Probab=92.57  E-value=1.5  Score=44.56  Aligned_cols=58  Identities=19%  Similarity=0.188  Sum_probs=31.2

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee--ccHHHHHHHHHHHHHhhccCCCceEE
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVG  213 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~v~  213 (448)
                      .-+++++++|+|||.+..--+.. +... .+.+++++.  +.|.-+..   +++.++... ++.+.
T Consensus       101 ~vI~~vG~~GsGKTTtaakLA~~-l~~~-~G~kV~lV~~D~~R~aa~e---QL~~~a~~~-gv~v~  160 (433)
T PRK10867        101 TVIMMVGLQGAGKTTTAGKLAKY-LKKK-KKKKVLLVAADVYRPAAIE---QLKTLGEQI-GVPVF  160 (433)
T ss_pred             EEEEEECCCCCcHHHHHHHHHHH-HHHh-cCCcEEEEEccccchHHHH---HHHHHHhhc-CCeEE
Confidence            35788999999999765433332 2222 133455554  45554432   344444443 55543

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.51  E-value=0.83  Score=48.46  Aligned_cols=39  Identities=18%  Similarity=0.281  Sum_probs=26.2

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      ...+++||||+|.|...  -...+.+.+...|....+|+.+
T Consensus       118 ~~~KVvIIdev~~Lt~~--a~naLLk~LEepp~~~~fIl~t  156 (576)
T PRK14965        118 SRYKIFIIDEVHMLSTN--AFNALLKTLEEPPPHVKFIFAT  156 (576)
T ss_pred             CCceEEEEEChhhCCHH--HHHHHHHHHHcCCCCeEEEEEe
Confidence            56789999999987653  3345555566656666666544

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=92.49  E-value=0.77  Score=49.87  Aligned_cols=44  Identities=11%  Similarity=0.181  Sum_probs=25.5

Q ss_pred             CeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHH
Q psy1548         256 LLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPV  305 (448)
Q Consensus       256 ~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~  305 (448)
                      .-.+++|||+|.+... . .   ..++..+ .+.++++.++|-++....+
T Consensus       109 ~~~IL~IDEIh~Ln~~-q-Q---daLL~~l-E~g~IiLI~aTTenp~~~l  152 (725)
T PRK13341        109 KRTILFIDEVHRFNKA-Q-Q---DALLPWV-ENGTITLIGATTENPYFEV  152 (725)
T ss_pred             CceEEEEeChhhCCHH-H-H---HHHHHHh-cCceEEEEEecCCChHhhh
Confidence            3457999999987553 1 1   2223322 3456788888765443333

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=92.45  E-value=0.62  Score=49.19  Aligned_cols=43  Identities=14%  Similarity=0.247  Sum_probs=24.7

Q ss_pred             CCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCC
Q psy1548         254 LSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLS  299 (448)
Q Consensus       254 ~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~  299 (448)
                      ....+++||||+|.|... .+ ..+.+.+...|....+|+ .+|-+
T Consensus       117 ~~~~kViIIDE~~~Lt~~-a~-naLLKtLEepp~~~ifIl-att~~  159 (559)
T PRK05563        117 EAKYKVYIIDEVHMLSTG-AF-NALLKTLEEPPAHVIFIL-ATTEP  159 (559)
T ss_pred             cCCeEEEEEECcccCCHH-HH-HHHHHHhcCCCCCeEEEE-EeCCh
Confidence            356789999999988663 33 333344444444444444 34533

>TIGR00767 rho transcription termination factor Rho

Probab=92.39  E-value=1.1  Score=44.74  Aligned_cols=31  Identities=23%  Similarity=0.156  Sum_probs=21.6

Q ss_pred             eeeCcceeeeccCCChhHHHHHHHHHHhhhcc
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETT  177 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~  177 (448)
                      +-.|.-+++.||+|+|||... ..+...+..+
T Consensus       165 ig~Gq~~~IvG~~g~GKTtL~-~~i~~~I~~n  195 (415)
T TIGR00767       165 IGKGQRGLIVAPPKAGKTVLL-QKIAQAITRN  195 (415)
T ss_pred             eCCCCEEEEECCCCCChhHHH-HHHHHhhccc
Confidence            345889999999999999653 3344444333

Members of this family differ in the specificity of RNA binding.

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=92.37  E-value=0.89  Score=45.35  Aligned_cols=55  Identities=25%  Similarity=0.309  Sum_probs=34.0

Q ss_pred             eeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      +..|.-+++.+++|+|||...+-- ...+..  .+.+++|+.-. +-..|+...+.++.
T Consensus        79 i~~GslvLI~G~pG~GKStLllq~-a~~~a~--~g~~VlYvs~E-Es~~qi~~Ra~rlg  133 (372)
T cd01121          79 LVPGSVILIGGDPGIGKSTLLLQV-AARLAK--RGGKVLYVSGE-ESPEQIKLRADRLG  133 (372)
T ss_pred             ccCCeEEEEEeCCCCCHHHHHHHH-HHHHHh--cCCeEEEEECC-cCHHHHHHHHHHcC
Confidence            445678899999999999654333 333222  23478888754 33456665555553

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=92.34  E-value=0.56  Score=47.74  Aligned_cols=41  Identities=24%  Similarity=0.170  Sum_probs=25.4

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC  187 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~  187 (448)
                      .+..|.=+++.|++|+|||...+--+.+....  .+..+++++
T Consensus       190 G~~~g~liviag~pg~GKT~~al~ia~~~a~~--~g~~v~~fS  230 (421)
T TIGR03600       190 GLVKGDLIVIGARPSMGKTTLALNIAENVALR--EGKPVLFFS  230 (421)
T ss_pred             CCCCCceEEEEeCCCCCHHHHHHHHHHHHHHh--CCCcEEEEE
Confidence            44556778999999999996544333333212  233567776

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=92.21  E-value=0.39  Score=51.99  Aligned_cols=65  Identities=14%  Similarity=0.053  Sum_probs=49.2

Q ss_pred             hhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhc-cCCCeEEEEeeccHHHHHHHHHHHHHhhc
Q psy1548         133 LHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRELAFQISKEYERFSK  205 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  205 (448)
                      |++      ++..  ...+++|.|+.|||||.+..--+...+.. .....++++|+.|+.-+.++.+.+.+..+
T Consensus         6 Q~~------av~~--~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~~Aa~em~~Rl~~~l~   71 (664)
T TIGR01074         6 QQE------AVEY--VTGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKTLG   71 (664)
T ss_pred             HHH------HHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHhC
Confidence            777      5533  35689999999999998876666666543 22445799999999999999998887654

Designed to identify rep members of the uvrD/rep subfamily.

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=92.17  E-value=0.17  Score=44.88  Aligned_cols=48  Identities=21%  Similarity=0.205  Sum_probs=27.6

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHH
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQI  196 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~  196 (448)
                      .+-.++++++.||+|+|||..+. ++...+..  .+..+++ ++..+|...+
T Consensus        43 ~~~~~~~l~l~G~~G~GKThLa~-ai~~~~~~--~g~~v~f-~~~~~L~~~l   90 (178)
T PF01695_consen   43 FIENGENLILYGPPGTGKTHLAV-AIANEAIR--KGYSVLF-ITASDLLDEL   90 (178)
T ss_dssp             S-SC--EEEEEESTTSSHHHHHH-HHHHHHHH--TT--EEE-EEHHHHHHHH
T ss_pred             CcccCeEEEEEhhHhHHHHHHHH-HHHHHhcc--CCcceeE-eecCceeccc
Confidence            34468899999999999997643 34443333  2334555 4555666553

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>KOG2170|consensus

Probab=92.13  E-value=0.5  Score=44.88  Aligned_cols=51  Identities=20%  Similarity=0.277  Sum_probs=35.5

Q ss_pred             eEEEecchhHHHhhhhhHHHHHHHHHhCCC-------CCeEEEEeccCCccHHHHHHHhc
Q psy1548         258 KHFILDECDKMLEQLEMRRDVQEIFRSSPH-------TKQVMMFSATLSKEIRPVCKKFM  310 (448)
Q Consensus       258 ~~lViDEah~l~~~~~~~~~~~~i~~~l~~-------~~q~i~~SAT~~~~~~~~~~~~l  310 (448)
                      .++|+||+|.|..  +..+.+.-.+.+.|.       ..-+|++|.+-..++-+++..+.
T Consensus       180 slFIFDE~DKmp~--gLld~lkpfLdyyp~v~gv~frkaIFIfLSN~gg~eI~~~aL~~~  237 (344)
T KOG2170|consen  180 SLFIFDEVDKLPP--GLLDVLKPFLDYYPQVSGVDFRKAIFIFLSNAGGSEIARIALENA  237 (344)
T ss_pred             ceEEechhhhcCH--hHHHHHhhhhccccccccccccceEEEEEcCCcchHHHHHHHHHH
Confidence            4799999999877  566666666665442       33578999887776665555444

>KOG1133|consensus

Probab=92.12  E-value=0.089  Score=54.91  Aligned_cols=51  Identities=18%  Similarity=0.216  Sum_probs=37.3

Q ss_pred             eccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhh
Q psy1548         122 NYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQL  174 (448)
Q Consensus       122 ~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l  174 (448)
                      +|.+|....+.|.++++.  ....+-.|+=.|+.+|||+|||+..+-+++.++
T Consensus         9 ~F~fPy~PYdIQ~~lM~e--lyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL   59 (821)
T KOG1133|consen    9 EFPFPYTPYDIQEDLMRE--LYRVLEEGKIGIFESPTGTGKSLSLICAALTWL   59 (821)
T ss_pred             ccCCCCCchhHHHHHHHH--HHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHH
Confidence            355565555559996664  223444689889999999999998887777776

>PRK08006 replicative DNA helicase; Provisional

Probab=92.09  E-value=1  Score=46.43  Aligned_cols=142  Identities=18%  Similarity=0.094  Sum_probs=64.8

Q ss_pred             eeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEE-EcCcccHHh
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVF-FGGLPIQKD  224 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~-~g~~~~~~~  224 (448)
                      +..|.=+++.|.+|+|||..++--+.+....  .+..++|++.- .-..|+...+-....   ++....+ .|..+ ..+
T Consensus       221 l~~G~LiiIaarPgmGKTafalnia~~~a~~--~g~~V~~fSlE-M~~~ql~~Rlla~~~---~v~~~~i~~~~l~-~~e  293 (471)
T PRK08006        221 LQPSDLIIVAARPSMGKTTFAMNLCENAAML--QDKPVLIFSLE-MPGEQIMMRMLASLS---RVDQTRIRTGQLD-DED  293 (471)
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHHHHHHHHHh--cCCeEEEEecc-CCHHHHHHHHHHHhc---CCCHHHhhcCCCC-HHH
Confidence            3345667889999999995543333332222  23356666422 223343333332211   2222112 22222 122


Q ss_pred             HH-------HHhcCCCcEEEE-----cHHHHHHHHHCCCCcCCCeeEEEecchhHHHhh---hhhHHHHHHHHHhCC---
Q psy1548         225 EE-------YLKTHNPQIVVG-----TPGRILALVRNKKLNLSLLKHFILDECDKMLEQ---LEMRRDVQEIFRSSP---  286 (448)
Q Consensus       225 ~~-------~l~~~~~~IlV~-----Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~---~~~~~~~~~i~~~l~---  286 (448)
                      +.       .+... ..+.|-     |+..+...+++-......++++|||=.|.|...   ......+..+.+.+.   
T Consensus       294 ~~~~~~a~~~~~~~-~~l~I~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~~~~~~~~r~~ei~~isr~LK~lA  372 (471)
T PRK08006        294 WARISGTMGILLEK-RNMYIDDSSGLTPTEVRSRARRIFREHGGLSLIMIDYLQLMRVPSLSDNRTLEIAEISRSLKALA  372 (471)
T ss_pred             HHHHHHHHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccHHHccCCCCCCCcHHHHHHHHHHHHHHH
Confidence            11       12121 345553     455554444321111135789999999977421   012233444433332   


Q ss_pred             --CCCeEEEEe
Q psy1548         287 --HTKQVMMFS  295 (448)
Q Consensus       287 --~~~q~i~~S  295 (448)
                        -++.+|++|
T Consensus       373 kel~ipVi~Ls  383 (471)
T PRK08006        373 KELQVPVVALS  383 (471)
T ss_pred             HHhCCeEEEEE
Confidence              256677775

>PRK04195 replication factor C large subunit; Provisional

Probab=92.08  E-value=0.45  Score=49.35  Aligned_cols=18  Identities=28%  Similarity=0.412  Sum_probs=15.4

Q ss_pred             CcceeeeccCCChhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~  166 (448)
                      .+.+++.||+|+|||...
T Consensus        39 ~~~lLL~GppG~GKTtla   56 (482)
T PRK04195         39 KKALLLYGPPGVGKTSLA   56 (482)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            467999999999999664

>KOG0058|consensus

Probab=92.07  E-value=0.24  Score=52.40  Aligned_cols=39  Identities=28%  Similarity=0.319  Sum_probs=28.9

Q ss_pred             CCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEE
Q psy1548         254 LSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMM  293 (448)
Q Consensus       254 ~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~  293 (448)
                      +++-+.+|+|||-.-+|. .....+++.+..+..++-++.
T Consensus       620 lr~P~VLILDEATSALDa-eSE~lVq~aL~~~~~~rTVlv  658 (716)
T KOG0058|consen  620 LRNPRVLILDEATSALDA-ESEYLVQEALDRLMQGRTVLV  658 (716)
T ss_pred             hcCCCEEEEechhhhcch-hhHHHHHHHHHHhhcCCeEEE
Confidence            355678999999988887 777778888877766644443

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.06  E-value=0.9  Score=47.59  Aligned_cols=39  Identities=13%  Similarity=0.273  Sum_probs=27.2

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      ...+++||||+|+|...  ....+.+.+...|....+|+.+
T Consensus       118 g~~kViIIDEa~~ls~~--a~naLLK~LEepp~~v~fIL~T  156 (546)
T PRK14957        118 GRYKVYLIDEVHMLSKQ--SFNALLKTLEEPPEYVKFILAT  156 (546)
T ss_pred             CCcEEEEEechhhccHH--HHHHHHHHHhcCCCCceEEEEE
Confidence            45689999999988663  3445556666666677676655

>KOG0741|consensus

Probab=92.05  E-value=1.2  Score=45.70  Aligned_cols=44  Identities=16%  Similarity=0.477  Sum_probs=26.3

Q ss_pred             CCeeEEEecchhHHHhhhh----hHH----HHHHHHHhCC-CCCeEEEEeccC
Q psy1548         255 SLLKHFILDECDKMLEQLE----MRR----DVQEIFRSSP-HTKQVMMFSATL  298 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~----~~~----~~~~i~~~l~-~~~q~i~~SAT~  298 (448)
                      +.+.++|+|+..++++|..    |..    .+.-+++..| +.++++.+..|=
T Consensus       597 S~lsiivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS  649 (744)
T KOG0741|consen  597 SPLSIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTS  649 (744)
T ss_pred             CcceEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEeccc
Confidence            4567899999999998822    222    2222334444 355677766653

>PRK08939 primosomal protein DnaI; Reviewed

Probab=92.05  E-value=1.1  Score=43.36  Aligned_cols=27  Identities=19%  Similarity=0.240  Sum_probs=19.4

Q ss_pred             eCcceeeeccCCChhHHHHHHHHHHhhh
Q psy1548         148 LGMDILCQAKSGMGKTAVFVLATLQQLE  175 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l~~l~~l~  175 (448)
                      .++.+++.||+|+|||.... ++.+.+.
T Consensus       155 ~~~gl~L~G~~G~GKThLa~-Aia~~l~  181 (306)
T PRK08939        155 KVKGLYLYGDFGVGKSYLLA-AIANELA  181 (306)
T ss_pred             CCCeEEEECCCCCCHHHHHH-HHHHHHH
Confidence            35789999999999996643 4444443

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=92.04  E-value=0.13  Score=55.27  Aligned_cols=45  Identities=24%  Similarity=0.265  Sum_probs=38.8

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCCC-Cchhhhhhhcccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMPE-DSDTYLHRVARAGRF  142 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~-~~~~yQ~~~~~~~~~  142 (448)
                      ..+|+|||+++++|+|.++++.|+++..|. .+..+.|.+||+||.
T Consensus       508 ~~~ILVaT~vie~GvDiP~v~~VIi~~~~r~gls~lhQ~~GRvGR~  553 (630)
T TIGR00643       508 EVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRG  553 (630)
T ss_pred             CCCEEEECceeecCcccCCCcEEEEeCCCcCCHHHHHHHhhhcccC
Confidence            348999999999999999999999998775 566677888999983

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=92.00  E-value=0.26  Score=53.36  Aligned_cols=44  Identities=23%  Similarity=0.274  Sum_probs=37.8

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCC-Cchhhhhhhcccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPE-DSDTYLHRVARAGRF  142 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~-~~~~yQ~~~~~~~~~  142 (448)
                      ..|+|||+++++|+|.++++.|+++..|. .+..+-|.+||+||.
T Consensus       532 ~~ILVaT~vie~GiDip~v~~VIi~~~~r~gls~lhQ~~GRvGR~  576 (681)
T PRK10917        532 IDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRG  576 (681)
T ss_pred             CCEEEECcceeeCcccCCCcEEEEeCCCCCCHHHHHHHhhcccCC
Confidence            38999999999999999999999998875 455667788999983

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=91.97  E-value=0.26  Score=45.11  Aligned_cols=18  Identities=28%  Similarity=0.399  Sum_probs=14.4

Q ss_pred             cceeeeccCCChhHHHHH
Q psy1548         150 MDILCQAKSGMGKTAVFV  167 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~  167 (448)
                      .++|+.||.|.|||..+.
T Consensus        51 ~h~lf~GPPG~GKTTLA~   68 (233)
T PF05496_consen   51 DHMLFYGPPGLGKTTLAR   68 (233)
T ss_dssp             -EEEEESSTTSSHHHHHH
T ss_pred             ceEEEECCCccchhHHHH
Confidence            368999999999996543

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>PHA00729 NTP-binding motif containing protein

Probab=91.92  E-value=0.87  Score=41.88  Aligned_cols=75  Identities=9%  Similarity=0.082  Sum_probs=35.9

Q ss_pred             cEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhH----HHHHHHHHhCCCCCeEEEEeccCCccHHHHHHH
Q psy1548         234 QIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMR----RDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKK  308 (448)
Q Consensus       234 ~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~----~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~  308 (448)
                      ..++.+.+.+...+....-....++++|+||+=.-.....+.    .....+...+.+.++++.+...-+.++...++.
T Consensus        60 ~~~fid~~~Ll~~L~~a~~~~~~~dlLIIDd~G~~~~~~~wh~~~~~~yf~L~~aLrSR~~l~il~~ls~edL~~~Lr~  138 (226)
T PHA00729         60 NSYFFELPDALEKIQDAIDNDYRIPLIIFDDAGIWLSKYVWYEDYMKTFYKIYALIRTRVSAVIFTTPSPEDLAFYLRE  138 (226)
T ss_pred             cEEEEEHHHHHHHHHHHHhcCCCCCEEEEeCCchhhcccchhhhccchHHHHHHHHHhhCcEEEEecCCHHHHHHHHHh
Confidence            455556666655554311112345789999943221110011    122223333344556677766655555555554

>PF03668 ATP_bind_2: P-loop ATPase protein family; InterPro: IPR005337 This entry represents UPF0042 nucleotide-binding proteins

Probab=91.89  E-value=0.61  Score=44.24  Aligned_cols=29  Identities=28%  Similarity=0.416  Sum_probs=25.0

Q ss_pred             CccHHHHHHHHHHHhCCCcEEEEeCCCCH
Q psy1548         362 KSVTRCIALSTLLSEQNFPAVSIHRGMTQ  390 (448)
Q Consensus       362 ~s~~~a~~l~~~L~~~g~~~~~lh~~~~~  390 (448)
                      .|+.-|+.|++.|++.|..+..-|-+|.+
T Consensus       255 RSV~iae~La~~L~~~~~~v~v~HRdl~k  283 (284)
T PF03668_consen  255 RSVAIAERLAERLREKGYTVVVRHRDLEK  283 (284)
T ss_pred             cHHHHHHHHHHHHHhcCCcceEEcCCCCC
Confidence            34677999999999999999999998864

This is a family of putative P-loop ATPases [], as they contain an ATP-binding site and display ATPase and GTPase activities.; GO: 0005524 ATP binding

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=91.72  E-value=4.2  Score=35.55  Aligned_cols=54  Identities=13%  Similarity=0.223  Sum_probs=27.7

Q ss_pred             CeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHh
Q psy1548         256 LLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKF  309 (448)
Q Consensus       256 ~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~  309 (448)
                      ..+++|+|..............+..+........-++.++|..+.+..+....+
T Consensus        82 ~~d~viiDt~g~~~~~~~~l~~l~~l~~~~~~~~~~lVv~~~~~~~~~~~~~~~  135 (173)
T cd03115          82 NFDVVIVDTAGRLQIDENLMEELKKIKRVVKPDEVLLVVDAMTGQDAVNQAKAF  135 (173)
T ss_pred             CCCEEEEECcccchhhHHHHHHHHHHHhhcCCCeEEEEEECCCChHHHHHHHHH
Confidence            456788888875421113334444444333344456666666554444444444

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=91.69  E-value=0.16  Score=54.86  Aligned_cols=46  Identities=30%  Similarity=0.406  Sum_probs=38.8

Q ss_pred             hccceeEeeccccCCcccc---------cceeEeeccCCCCchhhhhhhccccccc
Q psy1548          97 DCWRILVATNLFGRGMDIE---------RVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        97 ~~~~~~~~~~~~~~~~d~~---------~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      ..|.|.||||++|||+|++         .+..|++|..|+.-.+ -+..||+||..
T Consensus       471 ~~g~VlIATdmAgRGtDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr~GRtGRqG  525 (762)
T TIGR03714       471 QKGAVTVATSMAGRGTDIKLGKGVAELGGLAVIGTERMENSRVD-LQLRGRSGRQG  525 (762)
T ss_pred             CCCeEEEEccccccccCCCCCccccccCCeEEEEecCCCCcHHH-HHhhhcccCCC
Confidence            3469999999999999999         8899999999987444 77789998844

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.

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=91.66  E-value=0.17  Score=48.04  Aligned_cols=42  Identities=24%  Similarity=0.330  Sum_probs=29.8

Q ss_pred             eCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTREL  192 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L  192 (448)
                      .+.+++++|+||||||.. +-.++..+...  ..+++++-.+.|+
T Consensus       126 ~~~~ili~G~tGSGKTT~-l~all~~i~~~--~~~iv~iEd~~E~  167 (270)
T PF00437_consen  126 GRGNILISGPTGSGKTTL-LNALLEEIPPE--DERIVTIEDPPEL  167 (270)
T ss_dssp             TTEEEEEEESTTSSHHHH-HHHHHHHCHTT--TSEEEEEESSS-S
T ss_pred             cceEEEEECCCccccchH-HHHHhhhcccc--ccceEEeccccce
Confidence            368999999999999955 45666665444  3477777766665

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=91.64  E-value=0.34  Score=52.01  Aligned_cols=126  Identities=16%  Similarity=0.157  Sum_probs=71.5

Q ss_pred             ceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhc
Q psy1548         151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKT  230 (448)
Q Consensus       151 ~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~  230 (448)
                      -+++.|.-|=|||.+.-+.+........ ..+++|.+|+.+=++.+...+.+-...+ +.+-.+.....   ........
T Consensus       233 ~~vlTAdRGRGKSA~lGi~~~~~~~~~~-~~~iiVTAP~~~nv~~Lf~fa~~~l~~l-g~~~~v~~d~~---g~~~~~~~  307 (758)
T COG1444         233 ALVLTADRGRGKSAALGIALAAAARLAG-SVRIIVTAPTPANVQTLFEFAGKGLEFL-GYKRKVAPDAL---GEIREVSG  307 (758)
T ss_pred             eEEEEcCCCCcHhHHHhHHHHHHHHhcC-CceEEEeCCCHHHHHHHHHHHHHhHHHh-CCccccccccc---cceeeecC
Confidence            6788999999999988877643322222 5689999999998877766555433333 32211111110   00000010


Q ss_pred             CCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCc
Q psy1548         231 HNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSK  300 (448)
Q Consensus       231 ~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~  300 (448)
                      ....|=+.+|....         .. -+++|+|||=.+.-     +.+..++...    +.++||.|+..
T Consensus       308 ~~~~i~y~~P~~a~---------~~-~DllvVDEAAaIpl-----plL~~l~~~~----~rv~~sTTIhG  358 (758)
T COG1444         308 DGFRIEYVPPDDAQ---------EE-ADLLVVDEAAAIPL-----PLLHKLLRRF----PRVLFSTTIHG  358 (758)
T ss_pred             CceeEEeeCcchhc---------cc-CCEEEEehhhcCCh-----HHHHHHHhhc----CceEEEeeecc
Confidence            11235556665432         11 56899999985532     3344444443    35888999754

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=91.61  E-value=0.46  Score=50.08  Aligned_cols=126  Identities=11%  Similarity=0.064  Sum_probs=71.3

Q ss_pred             chhhhhhhccccccceeeee--CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHH-HHHHHhhc
Q psy1548         129 SDTYLHRVARAGRFGTKAVL--GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQIS-KEYERFSK  205 (448)
Q Consensus       129 ~~~yQ~~~~~~~~~~~~~~~--g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~-~~~~~~~~  205 (448)
                      .-+||.+      .+..+..  -+.|.+..++-+|||.+.+..+...+...+.  .+|++.||.++|.+.. ..+..+..
T Consensus        17 ~~Py~~e------imd~~~~~~v~~Vv~~k~aQ~GkT~~~~n~~g~~i~~~P~--~~l~v~Pt~~~a~~~~~~rl~Pmi~   88 (557)
T PF05876_consen   17 RTPYLRE------IMDALSDPSVREVVVMKSAQVGKTELLLNWIGYSIDQDPG--PMLYVQPTDDAAKDFSKERLDPMIR   88 (557)
T ss_pred             CChhHHH------HHHhcCCcCccEEEEEEcchhhHhHHHHhhceEEEEeCCC--CEEEEEEcHHHHHHHHHHHHHHHHH
Confidence            3456888      4444443  2689999999999999655555445544443  5999999999998765 45555555


Q ss_pred             cCCCceEEEEE---cCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHh
Q psy1548         206 YMSNIKVGVFF---GGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLE  270 (448)
Q Consensus       206 ~~~~~~v~~~~---g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~  270 (448)
                      ..|.++-.+--   ...........+. + ..+.++....      -..+.-..++++++||+|.+..
T Consensus        89 ~sp~l~~~~~~~~~~~~~~t~~~k~f~-g-g~l~~~ga~S------~~~l~s~~~r~~~~DEvD~~p~  148 (557)
T PF05876_consen   89 ASPVLRRKLSPSKSRDSGNTILYKRFP-G-GFLYLVGANS------PSNLRSRPARYLLLDEVDRYPD  148 (557)
T ss_pred             hCHHHHHHhCchhhcccCCchhheecC-C-CEEEEEeCCC------CcccccCCcCEEEEechhhccc
Confidence            44433311111   0000011111111 2 2343333211      1233346688999999998843

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=91.57  E-value=1.2  Score=47.09  Aligned_cols=39  Identities=13%  Similarity=0.227  Sum_probs=23.7

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      ...+++||||+|.|..  +....+...+...|...-+|+++
T Consensus       118 ~~~KVIIIDEad~Lt~--~A~NaLLKtLEEPp~~tvfIL~T  156 (605)
T PRK05896        118 FKYKVYIIDEAHMLST--SAWNALLKTLEEPPKHVVFIFAT  156 (605)
T ss_pred             CCcEEEEEechHhCCH--HHHHHHHHHHHhCCCcEEEEEEC
Confidence            3467899999998755  33344555555555555444443

>PRK02362 ski2-like helicase; Provisional

Probab=91.55  E-value=0.17  Score=55.40  Aligned_cols=72  Identities=22%  Similarity=0.347  Sum_probs=50.8

Q ss_pred             cCCCCHHHHHHHhhc---c--ceeEeeccccCCcccccceeEee----cc-----CCCCchhhhhhhccccccceeeeeC
Q psy1548          84 DFLLKPEILRAIVDC---W--RILVATNLFGRGMDIERVNIVFN----YD-----MPEDSDTYLHRVARAGRFGTKAVLG  149 (448)
Q Consensus        84 ~~~~~~~~~~~~~~~---~--~~~~~~~~~~~~~d~~~~~~v~~----~~-----~p~~~~~yQ~~~~~~~~~~~~~~~g  149 (448)
                      .-++++...+.+.+.   |  +|+|||+.+++|+|.|..+.|++    |+     .|.+..+|+|.+|||||.-.. -.|
T Consensus       310 Hagl~~~eR~~ve~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g~d-~~G  388 (737)
T PRK02362        310 HAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLD-PYG  388 (737)
T ss_pred             cCCCCHHHHHHHHHHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCCCC-CCc
Confidence            335555544444333   2  89999999999999999998886    54     577889999999999994321 125


Q ss_pred             cceeeec
Q psy1548         150 MDILCQA  156 (448)
Q Consensus       150 ~~vli~a  156 (448)
                      ..++++.
T Consensus       389 ~~ii~~~  395 (737)
T PRK02362        389 EAVLLAK  395 (737)
T ss_pred             eEEEEec
Confidence            5555553

>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=91.52  E-value=0.15  Score=42.06  Aligned_cols=55  Identities=42%  Similarity=0.782  Sum_probs=45.0

Q ss_pred             HHHHHHHhhcc-ceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548          89 PEILRAIVDCW-RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        89 ~~~~~~~~~~~-~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      ..+...+.+.. .+.++|+.++.|+|.+....++.+..|.....+.|.+||++|..
T Consensus        68 ~~~~~~f~~~~~~ili~t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~  123 (131)
T cd00079          68 EEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAG  123 (131)
T ss_pred             HHHHHHHHcCCCcEEEEcChhhcCcChhhCCEEEEeCCCCCHHHheecccccccCC
Confidence            33444444433 79999999999999999999999999999988899999998843

>KOG0339|consensus

Probab=91.50  E-value=0.2  Score=50.61  Aligned_cols=106  Identities=31%  Similarity=0.392  Sum_probs=73.6

Q ss_pred             hhhhhccCceeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccce
Q psy1548          65 AKQKEVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGT  144 (448)
Q Consensus        65 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~  144 (448)
                      ......++..+...+..-..-.....|.+.-.....|.|+|+.+.+|.|.++.+.|++|+....++.|-+.+||.||+..
T Consensus       485 ~a~Lklk~~~v~llhgdkdqa~rn~~ls~fKkk~~~VlvatDvaargldI~~ikTVvnyD~ardIdththrigrtgRag~  564 (731)
T KOG0339|consen  485 AANLKLKGFNVSLLHGDKDQAERNEVLSKFKKKRKPVLVATDVAARGLDIPSIKTVVNYDFARDIDTHTHRIGRTGRAGE  564 (731)
T ss_pred             HHHhccccceeeeecCchhhHHHHHHHHHHhhcCCceEEEeeHhhcCCCccccceeecccccchhHHHHHHhhhcccccc
Confidence            44455556566655554444444445555555667999999999999999999999999999999999999999999554


Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhcc
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETT  177 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~  177 (448)
                      .   |  +.-..-  +-|-..|.-++++.+..-
T Consensus       565 k---G--vayTlv--TeKDa~fAG~LVnnLe~a  590 (731)
T KOG0339|consen  565 K---G--VAYTLV--TEKDAEFAGHLVNNLEGA  590 (731)
T ss_pred             c---c--eeeEEe--chhhHHHhhHHHHHHhhc
Confidence            3   2  111111  234456777777776543

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=91.42  E-value=0.87  Score=44.98  Aligned_cols=38  Identities=13%  Similarity=0.256  Sum_probs=21.9

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEE
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMF  294 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~  294 (448)
                      ..-+++|+||+|.+... . ...+...+...|....+|+.
T Consensus       116 ~~~~vviidea~~l~~~-~-~~~Ll~~le~~~~~~~lIl~  153 (355)
T TIGR02397       116 GKYKVYIIDEVHMLSKS-A-FNALLKTLEEPPEHVVFILA  153 (355)
T ss_pred             CCceEEEEeChhhcCHH-H-HHHHHHHHhCCccceeEEEE
Confidence            45678999999988553 2 22333344444445444443

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>PRK14701 reverse gyrase; Provisional

Probab=91.42  E-value=0.14  Score=60.17  Aligned_cols=40  Identities=18%  Similarity=0.278  Sum_probs=34.4

Q ss_pred             hhccceeEee----ccccCCccccc-ceeEeeccCCC---Cchhhhhh
Q psy1548          96 VDCWRILVAT----NLFGRGMDIER-VNIVFNYDMPE---DSDTYLHR  135 (448)
Q Consensus        96 ~~~~~~~~~~----~~~~~~~d~~~-~~~v~~~~~p~---~~~~yQ~~  135 (448)
                      .....|+|+|    ++++||||+|+ |++|+||+.|.   +++.|++.
T Consensus       376 ~G~~~VLVaT~s~~gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~  423 (1638)
T PRK14701        376 EGEIDYLIGVATYYGTLVRGLDLPERIRFAVFYGVPKFRFRVDLEDPT  423 (1638)
T ss_pred             cCCCCEEEEecCCCCeeEecCccCCccCEEEEeCCCCCCcchhhcccc
Confidence            3445899999    57889999998 99999999999   88777766

>PRK08840 replicative DNA helicase; Provisional

Probab=91.39  E-value=1.3  Score=45.69  Aligned_cols=41  Identities=20%  Similarity=0.178  Sum_probs=23.9

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC  187 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~  187 (448)
                      .+..|.=+++.|.+|+|||...+ -+....... .+..+++++
T Consensus       213 G~~~g~LiviaarPg~GKTafal-nia~~~a~~-~~~~v~~fS  253 (464)
T PRK08840        213 GLQGSDLIIVAARPSMGKTTFAM-NLCENAAMD-QDKPVLIFS  253 (464)
T ss_pred             CCCCCceEEEEeCCCCchHHHHH-HHHHHHHHh-CCCeEEEEe
Confidence            34446678889999999996543 333322211 233566665

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=91.37  E-value=0.22  Score=45.93  Aligned_cols=14  Identities=29%  Similarity=0.598  Sum_probs=12.2

Q ss_pred             eeeeccCCChhHHH
Q psy1548         152 ILCQAKSGMGKTAV  165 (448)
Q Consensus       152 vli~apTGsGKT~~  165 (448)
                      ++|.|+.|+|||..
T Consensus         1 ~vv~G~pGsGKSt~   14 (234)
T PF01443_consen    1 IVVHGVPGSGKSTL   14 (234)
T ss_pred             CEEEcCCCCCHHHH
Confidence            47899999999964

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

>PRK04841 transcriptional regulator MalT; Provisional

Probab=91.31  E-value=1.5  Score=49.19  Aligned_cols=42  Identities=14%  Similarity=0.348  Sum_probs=33.9

Q ss_pred             eEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCc
Q psy1548         258 KHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSK  300 (448)
Q Consensus       258 ~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~  300 (448)
                      -++|||++|.+-+. .....+..+++..|.+..+++.|-+.|+
T Consensus       123 ~~lvlDD~h~~~~~-~~~~~l~~l~~~~~~~~~lv~~sR~~~~  164 (903)
T PRK04841        123 LYLVIDDYHLITNP-EIHEAMRFFLRHQPENLTLVVLSRNLPP  164 (903)
T ss_pred             EEEEEeCcCcCCCh-HHHHHHHHHHHhCCCCeEEEEEeCCCCC
Confidence            47999999987554 6677888889999999999888877543

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=91.30  E-value=0.2  Score=49.15  Aligned_cols=41  Identities=20%  Similarity=0.295  Sum_probs=28.6

Q ss_pred             eCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTREL  192 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L  192 (448)
                      .+++++++|+||||||.. +-.++..+..   ..+++.+=-+.||
T Consensus       159 ~~~nili~G~tgSGKTTl-l~aL~~~ip~---~~ri~tiEd~~El  199 (332)
T PRK13900        159 SKKNIIISGGTSTGKTTF-TNAALREIPA---IERLITVEDAREI  199 (332)
T ss_pred             cCCcEEEECCCCCCHHHH-HHHHHhhCCC---CCeEEEecCCCcc
Confidence            478999999999999954 4556665533   3366666555555

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=91.30  E-value=2.3  Score=39.32  Aligned_cols=55  Identities=18%  Similarity=0.158  Sum_probs=33.7

Q ss_pred             eeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      +-.|.-+++.+++|+|||.....-+...+.   .+.+++++.--.. ..++.+.+..+.
T Consensus        22 ~~~g~~~~i~G~~GsGKt~l~~~~~~~~~~---~g~~~~y~~~e~~-~~~~~~~~~~~g   76 (234)
T PRK06067         22 IPFPSLILIEGDHGTGKSVLSQQFVYGALK---QGKKVYVITTENT-SKSYLKQMESVK   76 (234)
T ss_pred             CcCCcEEEEECCCCCChHHHHHHHHHHHHh---CCCEEEEEEcCCC-HHHHHHHHHHCC
Confidence            334678899999999999654433333332   2446777765433 345555566553

>KOG2228|consensus

Probab=91.24  E-value=2.5  Score=41.02  Aligned_cols=44  Identities=23%  Similarity=0.263  Sum_probs=25.4

Q ss_pred             HHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhC
Q psy1548         241 GRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSS  285 (448)
Q Consensus       241 ~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l  285 (448)
                      ..++..++.+....+.--.+|+||+|..... ..-..+-.++...
T Consensus       122 ~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h-~rQtllYnlfDis  165 (408)
T KOG2228|consen  122 SKLLEALKKGDETTSGKVIFILDEFDLFAPH-SRQTLLYNLFDIS  165 (408)
T ss_pred             HHHHHHHhcCCCCCCceEEEEeehhhccccc-hhhHHHHHHHHHH
Confidence            4566667665554444457999999955443 3333344444443

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]

Probab=91.23  E-value=1.2  Score=47.23  Aligned_cols=39  Identities=18%  Similarity=0.275  Sum_probs=25.4

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEE
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMF  294 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~  294 (448)
                      ++-+++|+|||..-+|. .....+.+.+..+.+++.++..
T Consensus       482 ~~~~ILILDEaTSalD~-~tE~~I~~~l~~l~~~rT~iiI  520 (567)
T COG1132         482 RNPPILILDEATSALDT-ETEALIQDALKKLLKGRTTLII  520 (567)
T ss_pred             cCCCEEEEeccccccCH-HhHHHHHHHHHHHhcCCEEEEE
Confidence            44467899999887776 6666666666655455444443

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.17  E-value=0.89  Score=47.64  Aligned_cols=39  Identities=13%  Similarity=0.302  Sum_probs=26.1

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      ...+++||||+|.|... . ...+.+.+...|....+|+.+
T Consensus       118 ~~~kVvIIDEad~ls~~-a-~naLLK~LEepp~~~~fIL~t  156 (527)
T PRK14969        118 GRFKVYIIDEVHMLSKS-A-FNAMLKTLEEPPEHVKFILAT  156 (527)
T ss_pred             CCceEEEEcCcccCCHH-H-HHHHHHHHhCCCCCEEEEEEe
Confidence            56789999999988663 3 334445555556667677655

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=91.05  E-value=1.4  Score=43.91  Aligned_cols=92  Identities=15%  Similarity=0.052  Sum_probs=46.6

Q ss_pred             CCcccccceeEeeccCCCCchhhhhhhccc-------cccceee---eeCcceeeeccCCChhHHHHHHHHHHhhhccCC
Q psy1548         110 RGMDIERVNIVFNYDMPEDSDTYLHRVARA-------GRFGTKA---VLGMDILCQAKSGMGKTAVFVLATLQQLETTDS  179 (448)
Q Consensus       110 ~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~-------~~~~~~~---~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~  179 (448)
                      +|.++.......+|+..+++.+.....-..       .|++..+   -.|...+|.||.|+|||.. +--+.+.+..+..
T Consensus       120 ng~~~~~~~~r~~f~~l~p~~p~~R~~le~~~~~~~~~rvID~l~PIGkGQR~lIvgppGvGKTTL-aK~Ian~I~~nhF  198 (416)
T PRK09376        120 NGEDPEKARNRPLFENLTPLYPNERLRLETGNPEDLSTRIIDLIAPIGKGQRGLIVAPPKAGKTVL-LQNIANSITTNHP  198 (416)
T ss_pred             CCCCHHHhcCCCCcccCCCCChhhcccccCCCCcccceeeeeeecccccCceEEEeCCCCCChhHH-HHHHHHHHHhhcC
Confidence            345555555555566555554444442111       1233322   3478999999999999954 3334454443322


Q ss_pred             CeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         180 NVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       180 ~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      ... ++++-..+-...+.+..+.+
T Consensus       199 Dv~-~~VvLIgER~~EVtdiqrsI  221 (416)
T PRK09376        199 EVH-LIVLLIDERPEEVTDMQRSV  221 (416)
T ss_pred             CeE-EEEEEeCCchhHHHHHHHHh
Confidence            323 33333333333444444444

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=91.02  E-value=0.099  Score=50.57  Aligned_cols=50  Identities=28%  Similarity=0.307  Sum_probs=32.7

Q ss_pred             cceeeeeC-cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHH
Q psy1548         142 FGTKAVLG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ  195 (448)
Q Consensus       142 ~~~~~~~g-~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q  195 (448)
                      .+..+..+ .|+|+++.||||||.. +-.++..+...   -++|.+--|.||--+
T Consensus       165 ~L~~av~~r~NILisGGTGSGKTTl-LNal~~~i~~~---eRvItiEDtaELql~  215 (355)
T COG4962         165 FLRRAVGIRCNILISGGTGSGKTTL-LNALSGFIDSD---ERVITIEDTAELQLA  215 (355)
T ss_pred             HHHHHHhhceeEEEeCCCCCCHHHH-HHHHHhcCCCc---ccEEEEeehhhhccC
Confidence            44444444 5999999999999954 33333333322   278888888887443

>PRK05748 replicative DNA helicase; Provisional

Probab=91.02  E-value=1  Score=46.20  Aligned_cols=116  Identities=20%  Similarity=0.125  Sum_probs=54.9

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEE-EcCcccHH
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVF-FGGLPIQK  223 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~-~g~~~~~~  223 (448)
                      .+..|.-++|.|++|+|||... +-++...... .+..+++++ ...-..|+...+-....   ++....+ .|... ..
T Consensus       199 G~~~G~livIaarpg~GKT~~a-l~ia~~~a~~-~g~~v~~fS-lEms~~~l~~R~l~~~~---~v~~~~i~~~~l~-~~  271 (448)
T PRK05748        199 GLQPNDLIIVAARPSVGKTAFA-LNIAQNVATK-TDKNVAIFS-LEMGAESLVMRMLCAEG---NIDAQRLRTGQLT-DD  271 (448)
T ss_pred             CCCCCceEEEEeCCCCCchHHH-HHHHHHHHHh-CCCeEEEEe-CCCCHHHHHHHHHHHhc---CCCHHHhhcCCCC-HH
Confidence            3445677899999999999554 4444333221 123455554 23334444444432111   2111111 12222 11


Q ss_pred             hHH-------HHhcCCCcEEEE-----cHHHHHHHHHCCCCcCCCeeEEEecchhHHH
Q psy1548         224 DEE-------YLKTHNPQIVVG-----TPGRILALVRNKKLNLSLLKHFILDECDKML  269 (448)
Q Consensus       224 ~~~-------~l~~~~~~IlV~-----Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~  269 (448)
                      +..       .+..  ..+.|.     |+..+...++.-......++++|||=.+.|-
T Consensus       272 e~~~~~~a~~~l~~--~~~~i~d~~~~ti~~i~~~~r~~~~~~~~~~~vvIDyL~li~  327 (448)
T PRK05748        272 DWPKLTIAMGSLSD--APIYIDDTPGIKVTEIRARCRRLAQEHGGLGLILIDYLQLIQ  327 (448)
T ss_pred             HHHHHHHHHHHHhc--CCEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEccchhcC
Confidence            211       2222  235443     4455544433211111257899999999774

>PRK07004 replicative DNA helicase; Provisional

Probab=91.01  E-value=0.55  Score=48.34  Aligned_cols=142  Identities=18%  Similarity=0.151  Sum_probs=64.0

Q ss_pred             eeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEE-EcCcccHHh
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVF-FGGLPIQKD  224 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~-~g~~~~~~~  224 (448)
                      +..|.=+++.|.+|+|||... +-+...+.... +..+++++ ...-..|+...+-....   ++....+ .|..+ ..+
T Consensus       210 ~~~g~liviaarpg~GKT~~a-l~ia~~~a~~~-~~~v~~fS-lEM~~~ql~~R~la~~~---~v~~~~i~~g~l~-~~e  282 (460)
T PRK07004        210 MHGGELIIVAGRPSMGKTAFS-MNIGEYVAVEY-GLPVAVFS-MEMPGTQLAMRMLGSVG---RLDQHRMRTGRLT-DED  282 (460)
T ss_pred             CCCCceEEEEeCCCCCccHHH-HHHHHHHHHHc-CCeEEEEe-CCCCHHHHHHHHHHhhc---CCCHHHHhcCCCC-HHH
Confidence            444667889999999999554 33333322111 23455554 22222333333221111   1211111 12222 222


Q ss_pred             H-------HHHhcCCCcEEEE-----cHHHHHHHHHCCCCcCCCeeEEEecchhHHHhh---hhhHHHHHHHHHhCC---
Q psy1548         225 E-------EYLKTHNPQIVVG-----TPGRILALVRNKKLNLSLLKHFILDECDKMLEQ---LEMRRDVQEIFRSSP---  286 (448)
Q Consensus       225 ~-------~~l~~~~~~IlV~-----Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~---~~~~~~~~~i~~~l~---  286 (448)
                      .       ..+..  ..+.|.     |+..+...+++-......+++||||=.+.|...   ......+..+.+.+.   
T Consensus       283 ~~~~~~a~~~l~~--~~l~I~d~~~~~~~~i~~~~r~l~~~~~~~~lviIDYLql~~~~~~~~~r~~ei~~Isr~LK~lA  360 (460)
T PRK07004        283 WPKLTHAVQKMSE--AQLFIDETGGLNPMELRSRARRLARQCGKLGLIIIDYLQLMSGSSQGENRATEISEISRSLKSLA  360 (460)
T ss_pred             HHHHHHHHHHHhc--CCEEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEChhhhccCCCCCCcHHHHHHHHHHHHHHHH
Confidence            2       22222  346553     444444433221111234789999999987522   012333444443332   


Q ss_pred             --CCCeEEEEec
Q psy1548         287 --HTKQVMMFSA  296 (448)
Q Consensus       287 --~~~q~i~~SA  296 (448)
                        .++.++++|.
T Consensus       361 kel~ipVi~lsQ  372 (460)
T PRK07004        361 KELDVPVIALSQ  372 (460)
T ss_pred             HHhCCeEEEEec
Confidence              2566776654

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.99  E-value=0.82  Score=48.81  Aligned_cols=38  Identities=13%  Similarity=0.307  Sum_probs=23.1

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEE
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMF  294 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~  294 (448)
                      ...+++||||||.|...  ....+.+.+..-+....+|+.
T Consensus       120 ~~~KViIIDEad~Lt~~--a~naLLK~LEePp~~tvfIL~  157 (620)
T PRK14948        120 ARWKVYVIDECHMLSTA--AFNALLKTLEEPPPRVVFVLA  157 (620)
T ss_pred             CCceEEEEECccccCHH--HHHHHHHHHhcCCcCeEEEEE
Confidence            45689999999988653  333444445544444444443

>PLN02165 adenylate isopentenyltransferase

Probab=90.99  E-value=0.19  Score=48.97  Aligned_cols=39  Identities=15%  Similarity=0.105  Sum_probs=29.5

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFV  167 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~  167 (448)
                      ...|......|++      +.-.-..|+-++|.||||+|||..+.
T Consensus        23 ~~~~~~~~~~~~~------~~~~~~~g~iivIiGPTGSGKStLA~   61 (334)
T PLN02165         23 LPPPRSVVTMTSV------AMEQNCKDKVVVIMGATGSGKSRLSV   61 (334)
T ss_pred             CCCCccccccccc------ccccCCCCCEEEEECCCCCcHHHHHH
Confidence            5667777777888      54444457789999999999997654

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.91  E-value=1.6  Score=46.53  Aligned_cols=40  Identities=10%  Similarity=0.190  Sum_probs=24.6

Q ss_pred             CCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         254 LSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       254 ~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      +..-+++||||+|.|... . ...+.+.+...|...-+|+.+
T Consensus       125 ~~~~KVvIIdEad~Lt~~-a-~naLLK~LEePp~~tv~IL~t  164 (620)
T PRK14954        125 KGRYRVYIIDEVHMLSTA-A-FNAFLKTLEEPPPHAIFIFAT  164 (620)
T ss_pred             cCCCEEEEEeChhhcCHH-H-HHHHHHHHhCCCCCeEEEEEe
Confidence            456789999999988653 2 334444455545555555544

>KOG0742|consensus

Probab=90.89  E-value=1.4  Score=43.68  Aligned_cols=29  Identities=14%  Similarity=0.015  Sum_probs=19.8

Q ss_pred             EeCCCCHHHHHHHHHHHhcCCCceEEEEe
Q psy1548         384 IHRGMTQEERLKKYQEFKDFHKGLAITFA  412 (448)
Q Consensus       384 lh~~~~~~eR~~~l~~F~~g~~g~~I~~~  412 (448)
                      ...||+-.+-.+.+..++..--|-.=++.
T Consensus       572 kTeGfSGREiakLva~vQAavYgsedcvL  600 (630)
T KOG0742|consen  572 KTEGFSGREIAKLVASVQAAVYGSEDCVL  600 (630)
T ss_pred             hccCCcHHHHHHHHHHHHHHHhcccchhh
Confidence            35678888888888888877654333333

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=90.89  E-value=0.76  Score=53.72  Aligned_cols=58  Identities=17%  Similarity=0.137  Sum_probs=39.4

Q ss_pred             hhhhhccccccceeeeeC--cceeeeccCCChhHHHH--HHHHHHhhhccCCCeEEEEeeccHHHHHHH
Q psy1548         132 YLHRVARAGRFGTKAVLG--MDILCQAKSGMGKTAVF--VLATLQQLETTDSNVYVLVMCHTRELAFQI  196 (448)
Q Consensus       132 yQ~~~~~~~~~~~~~~~g--~~vli~apTGsGKT~~~--~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~  196 (448)
                      -|.+      ++..++.+  +-++|+|..|+|||.+.  ++.++..+. ...+..++.++||-.-+..+
T Consensus       839 ~Qr~------Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~-e~~g~~V~glAPTgkAa~~L  900 (1623)
T PRK14712        839 GQRA------ATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLP-ESERPRVVGLGPTHRAVGEM  900 (1623)
T ss_pred             HHHH------HHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHh-hccCceEEEEechHHHHHHH
Confidence            3888      77777754  67899999999999763  222333222 22345788899998766553

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=90.86  E-value=0.29  Score=46.49  Aligned_cols=27  Identities=22%  Similarity=0.383  Sum_probs=20.6

Q ss_pred             ceeeeccCCChhHHHHHHHHHHhhhccC
Q psy1548         151 DILCQAKSGMGKTAVFVLATLQQLETTD  178 (448)
Q Consensus       151 ~vli~apTGsGKT~~~~l~~l~~l~~~~  178 (448)
                      =+||.||||||||.. +.++++.+....
T Consensus       127 LILVTGpTGSGKSTT-lAamId~iN~~~  153 (353)
T COG2805         127 LILVTGPTGSGKSTT-LAAMIDYINKHK  153 (353)
T ss_pred             eEEEeCCCCCcHHHH-HHHHHHHHhccC
Confidence            478999999999965 566777765543

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=90.81  E-value=1.3  Score=44.01  Aligned_cols=111  Identities=13%  Similarity=0.134  Sum_probs=61.5

Q ss_pred             eeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHH
Q psy1548         147 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE  226 (448)
Q Consensus       147 ~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~  226 (448)
                      ...+.+.+.|+.|.|||...-+ ..+.+ +.+.+.++    +..+...++.+.+..+.+            +..      
T Consensus        60 ~~~~GlYl~G~vG~GKT~Lmd~-f~~~l-p~~~k~R~----HFh~Fm~~vh~~l~~~~~------------~~~------  115 (362)
T PF03969_consen   60 PPPKGLYLWGPVGRGKTMLMDL-FYDSL-PIKRKRRV----HFHEFMLDVHSRLHQLRG------------QDD------  115 (362)
T ss_pred             CCCceEEEECCCCCchhHHHHH-HHHhC-Cccccccc----cccHHHHHHHHHHHHHhC------------CCc------
Confidence            3468899999999999975322 22222 22222222    556777777777777641            110      


Q ss_pred             HHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhC-CCCCeEEEEeccCCcc
Q psy1548         227 YLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSS-PHTKQVMMFSATLSKE  301 (448)
Q Consensus       227 ~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l-~~~~q~i~~SAT~~~~  301 (448)
                              -   -+ .+.+.+      .+...+|++||+| +.+. +-.-.+..++..+ ....-+++.|-+.|++
T Consensus       116 --------~---l~-~va~~l------~~~~~lLcfDEF~-V~Di-aDAmil~rLf~~l~~~gvvlVaTSN~~P~~  171 (362)
T PF03969_consen  116 --------P---LP-QVADEL------AKESRLLCFDEFQ-VTDI-ADAMILKRLFEALFKRGVVLVATSNRPPED  171 (362)
T ss_pred             --------c---HH-HHHHHH------HhcCCEEEEeeee-ccch-hHHHHHHHHHHHHHHCCCEEEecCCCChHH
Confidence                    0   01 111112      2345579999999 3332 2233344444433 4567788888887764

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

>KOG1016|consensus

Probab=90.77  E-value=2  Score=45.82  Aligned_cols=147  Identities=12%  Similarity=0.158  Sum_probs=85.2

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCC--------CceEEEEEcCcc
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS--------NIKVGVFFGGLP  220 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~--------~~~v~~~~g~~~  220 (448)
                      |--+|+.-..|.|||+.. +.....+.+.-....+|+|+|-..|-+ |+..+..|...++        ...+.++..+..
T Consensus       282 GFGCILAHSMGLGKTlQV-isF~diflRhT~AKtVL~ivPiNTlQN-WlsEfnmWiP~y~sD~~vrpR~F~vf~LnD~~K  359 (1387)
T KOG1016|consen  282 GFGCILAHSMGLGKTLQV-ISFSDIFLRHTKAKTVLVIVPINTLQN-WLSEFNMWIPKYFSDTGVRPRSFEVFLLNDGVK  359 (1387)
T ss_pred             CcceeeeeccccCceeEE-eehhHHHhhcCccceEEEEEehHHHHH-HHHHhhhhcCCCcccCCCccceeEEEEecCchh
Confidence            446788888999999763 444444444445568999999988754 4556776665431        245555555543


Q ss_pred             cHHhHHH-----HhcCCCcEEEEcHHHHHHHHHC-----C-------C-----Cc-------------------CCCeeE
Q psy1548         221 IQKDEEY-----LKTHNPQIVVGTPGRILALVRN-----K-------K-----LN-------------------LSLLKH  259 (448)
Q Consensus       221 ~~~~~~~-----l~~~~~~IlV~Tp~~l~~~l~~-----~-------~-----~~-------------------~~~i~~  259 (448)
                      .-.+...     ...|  .|+..-.+.+.-++..     +       .     +.                   -..-++
T Consensus       360 T~~~Rakvi~~Wv~~G--GVlLvGYemfRLL~lk~~~~~grpkkt~kr~~~~~i~~d~eD~~qe~~~li~~AL~~PGPDl  437 (1387)
T KOG1016|consen  360 TFDQRAKVIEQWVQTG--GVLLVGYEMFRLLILKTLPKKGRPKKTLKRISSGFIKDDSEDQRQEAYSLIRSALLEPGPDL  437 (1387)
T ss_pred             hHHHHHHHHHHHhccC--CEEEehHHHHHHHHHhcccccCCccccccccCCcccCCchhhhHHHHHHHHHHHhcCCCCCe
Confidence            3222221     2233  4555556544222211     0       0     00                   012467


Q ss_pred             EEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccH
Q psy1548         260 FILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEI  302 (448)
Q Consensus       260 lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~  302 (448)
                      +|+||-|++-.-   ...+...++.+...+++++....+-+.+
T Consensus       438 VICDEGHrIKN~---~A~iS~aLk~IrtrRRiVLTGYPLQNNL  477 (1387)
T KOG1016|consen  438 VICDEGHRIKNI---TAEISMALKAIRTRRRIVLTGYPLQNNL  477 (1387)
T ss_pred             EEecCCceeccc---hHHHHHHHHHhhhceeEEEeccccccch
Confidence            999999988553   3444445666666778888877776653

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=90.71  E-value=1.8  Score=45.52  Aligned_cols=21  Identities=24%  Similarity=0.314  Sum_probs=17.8

Q ss_pred             eeeeCcceeeeccCCChhHHH
Q psy1548         145 KAVLGMDILCQAKSGMGKTAV  165 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~  165 (448)
                      .+..|+-+.+.||+|+|||..
T Consensus       357 ~i~~G~~vaIvG~SGsGKSTL  377 (529)
T TIGR02868       357 DLPPGERVAILGPSGSGKSTL  377 (529)
T ss_pred             EEcCCCEEEEECCCCCCHHHH
Confidence            445689999999999999964

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=90.68  E-value=0.19  Score=55.18  Aligned_cols=53  Identities=30%  Similarity=0.362  Sum_probs=42.0

Q ss_pred             HHHHHhhccceeEeeccccCCcccc---ccee-----EeeccCCCCchhhhhhhccccccc
Q psy1548          91 ILRAIVDCWRILVATNLFGRGMDIE---RVNI-----VFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~d~~---~~~~-----v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      +...-...+.|.||||++|||+|+.   .|..     |++...|...+-|-|..|||||..
T Consensus       639 Iia~AG~~g~VtIATNMAGRGtDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~GRtGRqG  699 (1025)
T PRK12900        639 IVAEAGQKGAVTIATNMAGRGTDIKLGEGVRELGGLFILGSERHESRRIDRQLRGRAGRQG  699 (1025)
T ss_pred             HHHhcCCCCeEEEeccCcCCCCCcCCccchhhhCCceeeCCCCCchHHHHHHHhhhhhcCC
Confidence            3333445579999999999999999   5543     377888888888999999999933

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=90.62  E-value=2  Score=44.97  Aligned_cols=125  Identities=14%  Similarity=0.137  Sum_probs=78.6

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHH----HHhhccCCCceEEEEEcCcccHHh
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEY----ERFSKYMSNIKVGVFFGGLPIQKD  224 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~----~~~~~~~~~~~v~~~~g~~~~~~~  224 (448)
                      .|-.+...|---|||+ ++.|++..+...-.+.++.|+++-+--++-+.+++    ++|..   .-.+...-+       
T Consensus       202 QkaTVFLVPRRHGKTW-f~VpiIsllL~s~~gI~IGYvAHqKhvs~~Vf~EI~~~lrrwF~---~~~vi~~k~-------  270 (668)
T PHA03372        202 QKATVFLVPRRHGKTW-FIIPIISFLLKNIIGISIGYVAHQKHVSQFVLKEVEFRCRRMFP---RKHTIENKD-------  270 (668)
T ss_pred             ccceEEEecccCCcee-hHHHHHHHHHHhhcCceEEEEeeHHHHHHHHHHHHHHHHhhhcC---ccceeeecC-------
Confidence            3566788999999995 57888888877777889999999988776655544    34432   111211111       


Q ss_pred             HHHHhcCCCcEEEEcHHHH-----HHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhC-CCCCeEEEEecc
Q psy1548         225 EEYLKTHNPQIVVGTPGRI-----LALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSS-PHTKQVMMFSAT  297 (448)
Q Consensus       225 ~~~l~~~~~~IlV~Tp~~l-----~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l-~~~~q~i~~SAT  297 (448)
                              -.|.+.-|+.-     ...-+.+.+.-.+..++++||||-+..     ..+..++..+ .+++++|..|.|
T Consensus       271 --------~tI~~s~pg~Kst~~fasc~n~NsiRGQ~fnll~VDEA~FI~~-----~a~~tilgfm~q~~~KiIfISS~  336 (668)
T PHA03372        271 --------NVISIDHRGAKSTALFASCYNTNSIRGQNFHLLLVDEAHFIKK-----DAFNTILGFLAQNTTKIIFISST  336 (668)
T ss_pred             --------cEEEEecCCCcceeeehhhccCccccCCCCCEEEEehhhccCH-----HHHHHhhhhhcccCceEEEEeCC
Confidence                    12444433321     111233455567788999999995533     2344455444 467788888887

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=90.60  E-value=0.19  Score=50.52  Aligned_cols=48  Identities=23%  Similarity=0.162  Sum_probs=37.3

Q ss_pred             ceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       151 ~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      ++++.||||||||.++++|-+-..     ...++|+=|--++........+..
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~~-----~~s~vv~D~Kge~~~~t~~~r~~~   48 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLTW-----PGSVVVLDPKGENFELTSEHRRAL   48 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhcC-----CCCEEEEccchhHHHHHHHHHHHc
Confidence            578999999999999988876542     236888889999987766655543

These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer to plant cells and is required for virulence.

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=90.55  E-value=0.21  Score=47.79  Aligned_cols=21  Identities=29%  Similarity=0.314  Sum_probs=17.2

Q ss_pred             eeCcceeeeccCCChhHHHHH
Q psy1548         147 VLGMDILCQAKSGMGKTAVFV  167 (448)
Q Consensus       147 ~~g~~vli~apTGsGKT~~~~  167 (448)
                      +...|+++.+|||||||+.+.
T Consensus        95 L~KSNILLiGPTGsGKTlLAq  115 (408)
T COG1219          95 LSKSNILLIGPTGSGKTLLAQ  115 (408)
T ss_pred             eeeccEEEECCCCCcHHHHHH
Confidence            345689999999999998653

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=90.54  E-value=0.36  Score=48.03  Aligned_cols=42  Identities=17%  Similarity=0.110  Sum_probs=26.7

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE  191 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~  191 (448)
                      +..++++||||||||.. +-.++..+.......+++.+--..|
T Consensus       149 ~GlilI~G~TGSGKTT~-l~al~~~i~~~~~~~~IvtiEdp~E  190 (372)
T TIGR02525       149 AGLGLICGETGSGKSTL-AASIYQHCGETYPDRKIVTYEDPIE  190 (372)
T ss_pred             CCEEEEECCCCCCHHHH-HHHHHHHHHhcCCCceEEEEecCch
Confidence            45789999999999955 4556666543333335555544433

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.52  E-value=0.82  Score=48.63  Aligned_cols=39  Identities=15%  Similarity=0.263  Sum_probs=23.3

Q ss_pred             CCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEE
Q psy1548         254 LSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMF  294 (448)
Q Consensus       254 ~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~  294 (448)
                      +...+++||||+|.|...  ....+.+.+...+....+|+.
T Consensus       118 ~~~~kVvIIDEa~~L~~~--a~naLLk~LEepp~~tv~Il~  156 (585)
T PRK14950        118 LARYKVYIIDEVHMLSTA--AFNALLKTLEEPPPHAIFILA  156 (585)
T ss_pred             cCCeEEEEEeChHhCCHH--HHHHHHHHHhcCCCCeEEEEE
Confidence            356789999999987653  233344444554445444443

>cd01131 PilT Pilus retraction ATPase PilT

Probab=90.52  E-value=0.36  Score=43.64  Aligned_cols=38  Identities=18%  Similarity=0.349  Sum_probs=23.5

Q ss_pred             eeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHH
Q psy1548         152 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE  191 (448)
Q Consensus       152 vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~  191 (448)
                      ++++||||||||... ..++..+.... +.+++.+....+
T Consensus         4 ilI~GptGSGKTTll-~~ll~~~~~~~-~~~i~t~e~~~E   41 (198)
T cd01131           4 VLVTGPTGSGKSTTL-AAMIDYINKNK-THHILTIEDPIE   41 (198)
T ss_pred             EEEECCCCCCHHHHH-HHHHHHhhhcC-CcEEEEEcCCcc
Confidence            689999999999663 44555554332 235555554434

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=90.47  E-value=0.47  Score=44.17  Aligned_cols=55  Identities=15%  Similarity=0.125  Sum_probs=36.7

Q ss_pred             eeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      +..|..+++.||+|+|||...+--+...+..   +-.++|++ +.+-..++.+.+..+.
T Consensus        18 ~~~gs~~lI~G~pGsGKT~la~~~l~~~~~~---ge~~lyvs-~ee~~~~i~~~~~~~g   72 (237)
T TIGR03877        18 IPERNVVLLSGGPGTGKSIFSQQFLWNGLQM---GEPGIYVA-LEEHPVQVRRNMAQFG   72 (237)
T ss_pred             CcCCeEEEEEcCCCCCHHHHHHHHHHHHHHc---CCcEEEEE-eeCCHHHHHHHHHHhC
Confidence            3357889999999999997654434444422   34677777 4455667777676654

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=90.46  E-value=0.19  Score=49.93  Aligned_cols=40  Identities=25%  Similarity=0.538  Sum_probs=33.0

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAG  140 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~  140 (448)
                      ...|+|||++++||+|++.+ .|+ +. |.+.+.|-|.+||+|
T Consensus       318 ~~~iLVaTdv~~rGiDi~~~-~vi-~~-p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       318 QFDILLGTSTVDVGVDFKRD-WLI-FS-ARDAAAFWQRLGRLG  357 (357)
T ss_pred             cCCEEEEecHHhcccCCCCc-eEE-EC-CCCHHHHhhhcccCC
Confidence            35799999999999999876 555 44 888989999988865

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.

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=90.44  E-value=0.29  Score=49.84  Aligned_cols=26  Identities=38%  Similarity=0.535  Sum_probs=20.0

Q ss_pred             ceeeeccCCChhHHHHHHHHHHhhhcc
Q psy1548         151 DILCQAKSGMGKTAVFVLATLQQLETT  177 (448)
Q Consensus       151 ~vli~apTGsGKT~~~~l~~l~~l~~~  177 (448)
                      =+|+.||||||||.. +..+++.+...
T Consensus       260 liLvTGPTGSGKTTT-LY~~L~~ln~~  285 (500)
T COG2804         260 LILVTGPTGSGKTTT-LYAALSELNTP  285 (500)
T ss_pred             EEEEeCCCCCCHHHH-HHHHHHHhcCC
Confidence            378999999999965 67777776544

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=90.41  E-value=1.9  Score=42.05  Aligned_cols=58  Identities=10%  Similarity=0.187  Sum_probs=34.8

Q ss_pred             EEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEec
Q psy1548         235 IVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSA  296 (448)
Q Consensus       235 IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SA  296 (448)
                      |-|-....+.+.+..... ....+++|||+||.|..  .....+.+.+..-| +..+|++|.
T Consensus       104 I~id~ir~i~~~l~~~p~-~~~~kVvII~~ae~m~~--~aaNaLLK~LEEPp-~~~fILi~~  161 (314)
T PRK07399        104 IRLEQIREIKRFLSRPPL-EAPRKVVVIEDAETMNE--AAANALLKTLEEPG-NGTLILIAP  161 (314)
T ss_pred             CcHHHHHHHHHHHccCcc-cCCceEEEEEchhhcCH--HHHHHHHHHHhCCC-CCeEEEEEC
Confidence            444344444444544333 25678999999999876  34455555666655 665665554

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=90.37  E-value=0.21  Score=54.97  Aligned_cols=44  Identities=25%  Similarity=0.481  Sum_probs=37.3

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCc------------------hhhhhhhcccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDS------------------DTYLHRVARAGRF  142 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~------------------~~yQ~~~~~~~~~  142 (448)
                      .+|.||||++++|||.++|+.|+|+..|...                  ..|.|.+|||||.
T Consensus       263 rkVlVATnIAErgItIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRAGR~  324 (819)
T TIGR01970       263 RKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRL  324 (819)
T ss_pred             eEEEEecchHhhcccccCceEEEEcCcccccccccccCCceeeEEEECHHHHHhhhhhcCCC
Confidence            4899999999999999999999999877532                  1367889999984

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.

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=90.35  E-value=1.4  Score=43.75  Aligned_cols=19  Identities=26%  Similarity=0.370  Sum_probs=15.8

Q ss_pred             cceeeeccCCChhHHHHHH
Q psy1548         150 MDILCQAKSGMGKTAVFVL  168 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l  168 (448)
                      .++|+-||.|+|||..+-+
T Consensus        49 ~SmIl~GPPG~GKTTlA~l   67 (436)
T COG2256          49 HSMILWGPPGTGKTTLARL   67 (436)
T ss_pred             ceeEEECCCCCCHHHHHHH
Confidence            4899999999999976543

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=90.34  E-value=0.32  Score=50.29  Aligned_cols=49  Identities=22%  Similarity=0.254  Sum_probs=38.5

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      .++++.||||||||..+++|.+-.  . + + .+||.=|--+|.......+++.
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll~--~-~-~-s~iV~D~KgEl~~~t~~~r~~~   93 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLLN--Y-P-G-SMIVTDPKGELYEKTAGYRKKR   93 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHHh--c-c-C-CEEEEECCCcHHHHHHHHHHHC
Confidence            479999999999999999997643  1 2 2 5888889999988777666654

These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems [, ].; GO: 0009291 unidirectional conjugation, 0016020 membrane

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=90.33  E-value=3.6  Score=40.12  Aligned_cols=41  Identities=12%  Similarity=0.210  Sum_probs=29.7

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEecc
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSAT  297 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT  297 (448)
                      ...+++|||+||.|..  .....+.+.+..-|.++.+|+.|..
T Consensus       112 g~~kV~iI~~ae~m~~--~AaNaLLKtLEEPp~~~~fiL~~~~  152 (319)
T PRK08769        112 GIAQVVIVDPADAINR--AACNALLKTLEEPSPGRYLWLISAQ  152 (319)
T ss_pred             CCcEEEEeccHhhhCH--HHHHHHHHHhhCCCCCCeEEEEECC
Confidence            4678999999999976  3445555566766677777777654

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=90.31  E-value=0.9  Score=49.74  Aligned_cols=65  Identities=17%  Similarity=0.153  Sum_probs=49.2

Q ss_pred             hhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhcc-CCCeEEEEeeccHHHHHHHHHHHHHhhc
Q psy1548         133 LHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-DSNVYVLVMCHTRELAFQISKEYERFSK  205 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~  205 (448)
                      |++      ++..  ...+++|.|+.|||||.+..--+...+... -..-++|+++-|+.-|..+.+.+..+.+
T Consensus         9 Q~~------av~~--~~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i~P~~IL~lTFT~kAA~em~~Rl~~~~~   74 (726)
T TIGR01073         9 QRE------AVKT--TEGPLLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTNKAAREMKERVEKLLG   74 (726)
T ss_pred             HHH------HHhC--CCCCEEEEeCCCCCHHHHHHHHHHHHHHcCCCCHHHeeeeeccHHHHHHHHHHHHHHhc
Confidence            888      6643  346899999999999988666665555432 2334799999999999999988887754

Designed to identify pcrA members of the uvrD/rep subfamily.

>COG2109 BtuR ATP:corrinoid adenosyltransferase [Coenzyme metabolism]

Probab=90.31  E-value=6.6  Score=34.88  Aligned_cols=52  Identities=17%  Similarity=0.296  Sum_probs=40.0

Q ss_pred             CCeeEEEecchhHHHhhhhh--HHHHHHHHHhCCCCCeEEEEeccCCccHHHHHH
Q psy1548         255 SLLKHFILDECDKMLEQLEM--RRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCK  307 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~--~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~  307 (448)
                      ..++++|+||....+.. ++  ...+..+++.-|....+|+..-..|+.+.+.+.
T Consensus       121 ~~ydlviLDEl~~al~~-g~l~~eeV~~~l~~kP~~~~vIiTGr~ap~~lie~AD  174 (198)
T COG2109         121 GKYDLVILDELNYALRY-GLLPLEEVVALLKARPEHTHVIITGRGAPPELIELAD  174 (198)
T ss_pred             CCCCEEEEehhhHHHHc-CCCCHHHHHHHHhcCCCCcEEEEECCCCCHHHHHHHH
Confidence            35778999999988775 43  566777788778888888888778888777654

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=90.24  E-value=4  Score=36.92  Aligned_cols=40  Identities=15%  Similarity=0.152  Sum_probs=26.6

Q ss_pred             eeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeecc
Q psy1548         147 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT  189 (448)
Q Consensus       147 ~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt  189 (448)
                      ..|.-+.+.||+|+|||...+-.+.+...   .+.+++++.-.
T Consensus        10 ~~g~i~~i~G~~GsGKT~l~~~~~~~~~~---~g~~v~yi~~e   49 (209)
T TIGR02237        10 ERGTITQIYGPPGSGKTNICMILAVNAAR---QGKKVVYIDTE   49 (209)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHh---CCCeEEEEECC
Confidence            34677899999999999765544443332   23467777654

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=90.17  E-value=0.22  Score=54.82  Aligned_cols=44  Identities=25%  Similarity=0.481  Sum_probs=37.3

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCc------------------hhhhhhhcccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDS------------------DTYLHRVARAGRF  142 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~------------------~~yQ~~~~~~~~~  142 (448)
                      .+|.||||++.+|+|.++++.|+|+..+...                  ..|.|.+|||||.
T Consensus       266 rkVlvATnIAErsLtIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRaGR~  327 (812)
T PRK11664        266 RKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRL  327 (812)
T ss_pred             eEEEEecchHHhcccccCceEEEECCCcccccccccCCcceeEEEeechhhhhhhccccCCC
Confidence            4899999999999999999999997766432                  2578899999984

>KOG1131|consensus

Probab=90.16  E-value=0.64  Score=47.25  Aligned_cols=86  Identities=16%  Similarity=0.089  Sum_probs=47.6

Q ss_pred             cccccceeEeeccCCCCchhhhhhhcccccccee-eeeCcceeeeccCCChhHHHHHHHHHHhhhccC-CCeEEEEeecc
Q psy1548         112 MDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK-AVLGMDILCQAKSGMGKTAVFVLATLQQLETTD-SNVYVLVMCHT  189 (448)
Q Consensus       112 ~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~-~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~-~~~~~lil~Pt  189 (448)
                      ++..++.-.|+|+.-.|-   |.+-++   -+.. +-.+.+.++..|+|+|||.+.+--++......+ ...+.++-.-|
T Consensus         3 ~~id~l~v~FPY~~iYPE---Q~~YM~---elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRT   76 (755)
T KOG1131|consen    3 FYIDDLLVYFPYDYIYPE---QYEYMR---ELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRT   76 (755)
T ss_pred             eeecCeeEecCCcccCHH---HHHHHH---HHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCc
Confidence            344555555666554444   554222   2222 334678999999999999775444443323333 33455665555


Q ss_pred             HHHHHHHHHHHHHh
Q psy1548         190 RELAFQISKEYERF  203 (448)
Q Consensus       190 ~~L~~q~~~~~~~~  203 (448)
                      ..-......+++.+
T Consensus        77 vpEieK~l~El~~l   90 (755)
T KOG1131|consen   77 VPEIEKALEELKRL   90 (755)
T ss_pred             chHHHHHHHHHHHH
Confidence            55555555555554

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=90.07  E-value=1.1  Score=52.95  Aligned_cols=58  Identities=16%  Similarity=0.099  Sum_probs=39.3

Q ss_pred             hhhhhhccccccceeeeeC--cceeeeccCCChhHHHHHHHHHHhhh--ccCCCeEEEEeeccHHHHHH
Q psy1548         131 TYLHRVARAGRFGTKAVLG--MDILCQAKSGMGKTAVFVLATLQQLE--TTDSNVYVLVMCHTRELAFQ  195 (448)
Q Consensus       131 ~yQ~~~~~~~~~~~~~~~g--~~vli~apTGsGKT~~~~l~~l~~l~--~~~~~~~~lil~Pt~~L~~q  195 (448)
                      +-|.+      ++..++.+  +-++|+|..|+|||... -.++..+.  ....+..++.++||-.-+..
T Consensus       970 ~~Q~~------Av~~il~s~dr~~~I~G~AGTGKTT~l-~~v~~~~~~l~~~~~~~V~glAPTgrAAk~ 1031 (1747)
T PRK13709        970 SGQRA------ATRMILESTDRFTVVQGYAGVGKTTQF-RAVMSAVNTLPESERPRVVGLGPTHRAVGE 1031 (1747)
T ss_pred             HHHHH------HHHHHHhCCCcEEEEEeCCCCCHHHHH-HHHHHHHHHhhcccCceEEEECCcHHHHHH
Confidence            33888      88777775  56899999999999663 23333322  12234578889999876654

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=90.03  E-value=0.6  Score=48.42  Aligned_cols=58  Identities=21%  Similarity=0.141  Sum_probs=41.8

Q ss_pred             eCcceeeeccCCChhHHHHHHHHHHhhhcc---CCCeEEEEeeccHHHHHHHHHHHHHhhc
Q psy1548         148 LGMDILCQAKSGMGKTAVFVLATLQQLETT---DSNVYVLVMCHTRELAFQISKEYERFSK  205 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l~~l~~l~~~---~~~~~~lil~Pt~~L~~q~~~~~~~~~~  205 (448)
                      .++-++|+|..|||||.+++--+...+...   -....+||+.|.+-+..-+.+.+-.++.
T Consensus       225 k~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~vFleYis~VLPeLGe  285 (747)
T COG3973         225 KNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNRVFLEYISRVLPELGE  285 (747)
T ss_pred             CCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEcCcHHHHHHHHHhchhhcc
Confidence            466789999999999988765443333221   1233499999999998888888777654

>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated

Probab=89.97  E-value=9.6  Score=33.67  Aligned_cols=52  Identities=13%  Similarity=0.300  Sum_probs=40.7

Q ss_pred             CCeeEEEecchhHHHhhhhh--HHHHHHHHHhCCCCCeEEEEeccCCccHHHHHH
Q psy1548         255 SLLKHFILDECDKMLEQLEM--RRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCK  307 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~--~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~  307 (448)
                      ..++++|+||+-..++. ++  ...+..+++..|+..-+|+..-..|+++.+.+.
T Consensus       114 ~~~dlvVLDEi~~Al~~-gli~~eeVl~~L~~rp~~~evILTGR~~p~~Lie~AD  167 (178)
T PRK07414        114 GRYSLVVLDELSLAIQF-GLIPETEVLEFLEKRPSHVDVILTGPEMPESLLAIAD  167 (178)
T ss_pred             CCCCEEEEehhHHHHHC-CCccHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhCC
Confidence            56788999999988776 54  566777888888888888888888887766543

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=89.90  E-value=0.86  Score=42.98  Aligned_cols=141  Identities=20%  Similarity=0.170  Sum_probs=68.6

Q ss_pred             eeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeec---cHHHHHHHHHHHHHhhccCCCceEEEEEcCcccH
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH---TRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQ  222 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~P---t~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~  222 (448)
                      +..|.=+++.|++|.|||...+--+.+.....  +..++|++.   ..+++..+....   +    ++....+..+.-..
T Consensus        16 ~~~g~L~vi~a~pg~GKT~~~l~ia~~~a~~~--~~~vly~SlEm~~~~l~~R~la~~---s----~v~~~~i~~g~l~~   86 (259)
T PF03796_consen   16 LRPGELTVIAARPGVGKTAFALQIALNAALNG--GYPVLYFSLEMSEEELAARLLARL---S----GVPYNKIRSGDLSD   86 (259)
T ss_dssp             B-TT-EEEEEESTTSSHHHHHHHHHHHHHHTT--SSEEEEEESSS-HHHHHHHHHHHH---H----TSTHHHHHCCGCHH
T ss_pred             CCcCcEEEEEecccCCchHHHHHHHHHHHHhc--CCeEEEEcCCCCHHHHHHHHHHHh---h----cchhhhhhccccCH
Confidence            33456688999999999966554444444322  357888874   344433332222   1    11111111111111


Q ss_pred             Hh-------HHHHhcCCCcEEE-E----cHHHHHHHHHCCCCcCCCeeEEEecchhHHHhh---hhhHHHHHHHHHhCC-
Q psy1548         223 KD-------EEYLKTHNPQIVV-G----TPGRILALVRNKKLNLSLLKHFILDECDKMLEQ---LEMRRDVQEIFRSSP-  286 (448)
Q Consensus       223 ~~-------~~~l~~~~~~IlV-~----Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~---~~~~~~~~~i~~~l~-  286 (448)
                      .+       ...+...  .+.| .    |++.+.+.+..-......+++||||-.|.+...   .+.+..+..+.+.+. 
T Consensus        87 ~e~~~~~~~~~~l~~~--~l~i~~~~~~~~~~i~~~i~~~~~~~~~~~~v~IDyl~ll~~~~~~~~~~~~~~~i~~~Lk~  164 (259)
T PF03796_consen   87 EEFERLQAAAEKLSDL--PLYIEDTPSLTIDDIESKIRRLKREGKKVDVVFIDYLQLLKSEDSSDNRRQEIGEISRELKA  164 (259)
T ss_dssp             HHHHHHHHHHHHHHTS--EEEEEESSS-BHHHHHHHHHHHHHHSTTEEEEEEEEGGGSBTSCSSSCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhC--cEEEECCCCCCHHHHHHHHHHHHhhccCCCEEEechHHHhcCCCCCCCHHHHHHHHHHHHHH
Confidence            11       1123332  3433 3    445565555432222267899999999977542   123444444433321 


Q ss_pred             ----CCCeEEEEecc
Q psy1548         287 ----HTKQVMMFSAT  297 (448)
Q Consensus       287 ----~~~q~i~~SAT  297 (448)
                          .++.++++|..
T Consensus       165 lA~~~~i~vi~~sQl  179 (259)
T PF03796_consen  165 LAKELNIPVIALSQL  179 (259)
T ss_dssp             HHHHHTSEEEEEEEB
T ss_pred             HHHHcCCeEEEcccc
Confidence                25667776654

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>PRK10689 transcription-repair coupling factor; Provisional

Probab=89.89  E-value=2.7  Score=48.25  Aligned_cols=80  Identities=10%  Similarity=0.192  Sum_probs=62.0

Q ss_pred             CeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhH---HHHhcCCCcEEEEcHHHHHHHHHCCCCcCCC
Q psy1548         180 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTHNPQIVVGTPGRILALVRNKKLNLSL  256 (448)
Q Consensus       180 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~---~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~  256 (448)
                      +.+++|+||+.+-+..+.+.+.+..   |+.++..++|+.+.....   ..+.++..+|+|+|.      +-...+++.+
T Consensus       809 ~gqv~vf~n~i~~ie~la~~L~~~~---p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTd------IierGIDIP~  879 (1147)
T PRK10689        809 GGQVYYLYNDVENIQKAAERLAELV---PEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT------IIETGIDIPT  879 (1147)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHhC---CCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECc------hhhccccccc
Confidence            4589999999998888777777654   477889999998755433   345667799999995      3456788999


Q ss_pred             eeEEEecchhHH
Q psy1548         257 LKHFILDECDKM  268 (448)
Q Consensus       257 i~~lViDEah~l  268 (448)
                      ++++|++.++++
T Consensus       880 v~~VIi~~ad~f  891 (1147)
T PRK10689        880 ANTIIIERADHF  891 (1147)
T ss_pred             CCEEEEecCCCC
Confidence            999999999854

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=89.89  E-value=3.8  Score=38.17  Aligned_cols=32  Identities=25%  Similarity=0.247  Sum_probs=22.2

Q ss_pred             cceeeeeCc-ceeeeccCCChhHHHHHHHHHHhh
Q psy1548         142 FGTKAVLGM-DILCQAKSGMGKTAVFVLATLQQL  174 (448)
Q Consensus       142 ~~~~~~~g~-~vli~apTGsGKT~~~~l~~l~~l  174 (448)
                      +-+.+..|+ -+.++++-|||||...- +++..+
T Consensus        43 l~~~i~d~qg~~~vtGevGsGKTv~~R-al~~s~   75 (269)
T COG3267          43 LHAAIADGQGILAVTGEVGSGKTVLRR-ALLASL   75 (269)
T ss_pred             HHHHHhcCCceEEEEecCCCchhHHHH-HHHHhc
Confidence            344555565 67899999999998765 444443

>KOG0743|consensus

Probab=89.76  E-value=0.29  Score=48.97  Aligned_cols=64  Identities=27%  Similarity=0.418  Sum_probs=44.0

Q ss_pred             ccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeecc
Q psy1548          78 HSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAK  157 (448)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~ap  157 (448)
                      |+.+|+.+.+++++.+.+.+.-                        .....-.+|....|+|++        +--|+-||
T Consensus       196 HpstF~TlaMd~~~K~~I~~Dl------------------------~~F~k~k~~YkrvGkawK--------RGYLLYGP  243 (457)
T KOG0743|consen  196 HPSTFETLAMDPDLKERIIDDL------------------------DDFIKGKDFYKRVGKAWK--------RGYLLYGP  243 (457)
T ss_pred             CCCCccccccChhHHHHHHHHH------------------------HHHHhcchHHHhcCcchh--------ccceeeCC
Confidence            5578999999999988887653                        111222344777666554        56788999


Q ss_pred             CCChhHHHHHHHHHHhh
Q psy1548         158 SGMGKTAVFVLATLQQL  174 (448)
Q Consensus       158 TGsGKT~~~~l~~l~~l  174 (448)
                      +|+||| .++.++.+.+
T Consensus       244 PGTGKS-S~IaAmAn~L  259 (457)
T KOG0743|consen  244 PGTGKS-SFIAAMANYL  259 (457)
T ss_pred             CCCCHH-HHHHHHHhhc
Confidence            999999 4455555555

>TIGR00665 DnaB replicative DNA helicase

Probab=89.71  E-value=1.9  Score=44.08  Aligned_cols=40  Identities=23%  Similarity=0.157  Sum_probs=24.2

Q ss_pred             eeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC  187 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~  187 (448)
                      +..|.=+++.|++|+|||... +-+...+... .+..+++++
T Consensus       192 ~~~G~l~vi~g~pg~GKT~~~-l~~a~~~a~~-~g~~vl~~S  231 (434)
T TIGR00665       192 LQPSDLIILAARPSMGKTAFA-LNIAENAAIK-EGKPVAFFS  231 (434)
T ss_pred             CCCCeEEEEEeCCCCChHHHH-HHHHHHHHHh-CCCeEEEEe
Confidence            444677899999999999554 3333332221 133566665

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=89.70  E-value=0.38  Score=51.02  Aligned_cols=49  Identities=27%  Similarity=0.087  Sum_probs=40.2

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      .++++.||||||||..+++|-+-..     +..++|+=|--|+........++.
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~~-----~~S~VV~DpKGEl~~~Ta~~R~~~  207 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLFW-----EDSVVVHDIKLENYELTSGWREKQ  207 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHhC-----CCCEEEEeCcHHHHHHHHHHHHHC
Confidence            5899999999999999999987653     235888889999998877666654

>KOG1513|consensus

Probab=89.59  E-value=0.26  Score=52.28  Aligned_cols=133  Identities=17%  Similarity=0.249  Sum_probs=76.9

Q ss_pred             eeeeccC--CChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEE----cCcccHHhH
Q psy1548         152 ILCQAKS--GMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFF----GGLPIQKDE  225 (448)
Q Consensus       152 vli~apT--GsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~----g~~~~~~~~  225 (448)
                      .||-...  |-|.|.+-  .|+.....  +..++|++.-+..|-.+..+.++.+...  ++.|..+.    +..+.. ..
T Consensus       292 fLiGDGAGVGKGRTvAg--iIfeNyLk--GRKrAlW~SVSsDLKfDAERDL~DigA~--~I~V~alnK~KYakIss~-en  364 (1300)
T KOG1513|consen  292 FLIGDGAGVGKGRTVAG--IIFENYLK--GRKRALWFSVSSDLKFDAERDLRDIGAT--GIAVHALNKFKYAKISSK-EN  364 (1300)
T ss_pred             eeeccCcccCCCceeEE--EEehhhhc--ccceeEEEEeccccccchhhchhhcCCC--Cccceehhhccccccccc-cc
Confidence            3444444  44555442  23333333  3348999999999998888888887643  56655442    111111 11


Q ss_pred             HHHhcCCCcEEEEcHHHHH---------------HHHHCCCCcCCCeeEEEecchhHHHhh--------hhhHHHHHHHH
Q psy1548         226 EYLKTHNPQIVVGTPGRIL---------------ALVRNKKLNLSLLKHFILDECDKMLEQ--------LEMRRDVQEIF  282 (448)
Q Consensus       226 ~~l~~~~~~IlV~Tp~~l~---------------~~l~~~~~~~~~i~~lViDEah~l~~~--------~~~~~~~~~i~  282 (448)
                      ...+   -.|+++|...|.               +++..-.-++  =..||+||||+--..        ...+..+..+-
T Consensus       365 ~n~k---rGViFaTYtaLIGEs~~~~~kyrtR~rQllqW~Ge~f--eGvIvfDECHkAKNL~p~~~~k~TKtG~tVLdLQ  439 (1300)
T KOG1513|consen  365 TNTK---RGVIFATYTALIGESQGKGGKYRTRFRQLLQWCGEDF--EGVIVFDECHKAKNLVPTAGAKSTKTGKTVLDLQ  439 (1300)
T ss_pred             CCcc---ceeEEEeeHhhhhhccccCchHHHHHHHHHHHhhhcc--ceeEEehhhhhhcccccccCCCcCcccHhHHHHH
Confidence            1122   359999976553               2222111112  246999999976431        23566777777


Q ss_pred             HhCCCCCeEEEEecc
Q psy1548         283 RSSPHTKQVMMFSAT  297 (448)
Q Consensus       283 ~~l~~~~q~i~~SAT  297 (448)
                      +.+| +.+++..|||
T Consensus       440 k~LP-~ARVVYASAT  453 (1300)
T KOG1513|consen  440 KKLP-NARVVYASAT  453 (1300)
T ss_pred             HhCC-CceEEEeecc
Confidence            7776 5678999999

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=89.58  E-value=0.34  Score=52.03  Aligned_cols=44  Identities=27%  Similarity=0.516  Sum_probs=39.3

Q ss_pred             cceeEeeccccCCcccccceeEeecc-----CCCCchhhhhhhcccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYD-----MPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~-----~p~~~~~yQ~~~~~~~~~  142 (448)
                      ..|+|||+.+++|+|.+++..|+.++     .|.....|-|.+|||||.
T Consensus       493 i~VLV~t~~L~rGfDiP~v~lVvi~DadifG~p~~~~~~iqriGRagR~  541 (655)
T TIGR00631       493 FDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN  541 (655)
T ss_pred             ceEEEEcChhcCCeeeCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCC
Confidence            36788899999999999999999877     788888899999999994

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

>PTZ00293 thymidine kinase; Provisional

Probab=89.48  E-value=2.8  Score=38.12  Aligned_cols=40  Identities=15%  Similarity=0.156  Sum_probs=25.6

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE  191 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~  191 (448)
                      |+=-++.||+++|||.- ++-.+.....  .+.+++++-|...
T Consensus         4 G~i~vi~GpMfSGKTte-LLr~i~~y~~--ag~kv~~~kp~~D   43 (211)
T PTZ00293          4 GTISVIIGPMFSGKTTE-LMRLVKRFTY--SEKKCVVIKYSKD   43 (211)
T ss_pred             eEEEEEECCCCChHHHH-HHHHHHHHHH--cCCceEEEEeccc
Confidence            44567899999999954 3333443332  2346888888653

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=89.42  E-value=0.53  Score=46.49  Aligned_cols=42  Identities=14%  Similarity=0.222  Sum_probs=27.3

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTREL  192 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L  192 (448)
                      +..++++||||||||.. +-.++..+... .+.+++.+-...++
T Consensus       122 ~g~ili~G~tGSGKTT~-l~al~~~i~~~-~~~~i~tiEdp~E~  163 (343)
T TIGR01420       122 RGLILVTGPTGSGKSTT-LASMIDYINKN-AAGHIITIEDPIEY  163 (343)
T ss_pred             CcEEEEECCCCCCHHHH-HHHHHHhhCcC-CCCEEEEEcCChhh
Confidence            57899999999999965 34455555432 23356666555544

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=89.36  E-value=2  Score=46.43  Aligned_cols=39  Identities=15%  Similarity=0.268  Sum_probs=23.7

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      ...+++||||||.|...  ....+...+...|....+|+.+
T Consensus       117 g~~KV~IIDEa~~LT~~--A~NALLKtLEEPP~~tifILaT  155 (725)
T PRK07133        117 SKYKIYIIDEVHMLSKS--AFNALLKTLEEPPKHVIFILAT  155 (725)
T ss_pred             CCCEEEEEEChhhCCHH--HHHHHHHHhhcCCCceEEEEEc
Confidence            56789999999987653  3333444455545555445443

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=89.19  E-value=2.4  Score=41.55  Aligned_cols=41  Identities=15%  Similarity=0.277  Sum_probs=27.6

Q ss_pred             CCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEec
Q psy1548         254 LSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSA  296 (448)
Q Consensus       254 ~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SA  296 (448)
                      ....+++||||+|.|..  .....+.+.+..-|++..+|+.|.
T Consensus       108 ~~~~kvviI~~a~~~~~--~a~NaLLK~LEEPp~~~~~Il~t~  148 (329)
T PRK08058        108 ESNKKVYIIEHADKMTA--SAANSLLKFLEEPSGGTTAILLTE  148 (329)
T ss_pred             ccCceEEEeehHhhhCH--HHHHHHHHHhcCCCCCceEEEEeC
Confidence            35678999999998866  344455556666566666666443

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=89.03  E-value=7.3  Score=37.99  Aligned_cols=56  Identities=14%  Similarity=0.277  Sum_probs=30.0

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhC------CCCCeEEEEeccCCccHHHHHHHhc
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSS------PHTKQVMMFSATLSKEIRPVCKKFM  310 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l------~~~~q~i~~SAT~~~~~~~~~~~~l  310 (448)
                      .+.+++++|=+-++.........+..+.+..      .+..-++.++||...+....+..+.
T Consensus       195 ~~~D~ViIDTaGr~~~~~~l~~eL~~~~~v~~~~~~~~p~~~~LVl~a~~g~~~~~~a~~f~  256 (318)
T PRK10416        195 RGIDVLIIDTAGRLHNKTNLMEELKKIKRVIKKADPDAPHEVLLVLDATTGQNALSQAKAFH  256 (318)
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHHHHHHhhhcCCCCceEEEEEECCCChHHHHHHHHHH
Confidence            4456777777765532213334444444322      2334578889997655434445443

>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

Probab=88.96  E-value=2.9  Score=45.16  Aligned_cols=68  Identities=16%  Similarity=0.158  Sum_probs=48.0

Q ss_pred             HHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCc-EEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         343 KKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFP-AVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       343 ~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~-~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                      ..+..++...+ ++++||++|.+..+.+++.++..... ....+|..+.   ...++.|+.+..+ .+++++..
T Consensus       469 ~~i~~~~~~~~-~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~~~~---~~~l~~f~~~~~~-~~lv~~gs  537 (654)
T COG1199         469 AYLREILKASP-GGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGEDER---EELLEKFKASGEG-LILVGGGS  537 (654)
T ss_pred             HHHHHHHhhcC-CCEEEEeccHHHHHHHHHHHhhcCccceeeecCCCcH---HHHHHHHHHhcCC-eEEEeecc
Confidence            34444455444 48999999999999999999987653 3455555444   4889999887765 66666653

>PRK14873 primosome assembly protein PriA; Provisional

Probab=88.95  E-value=2.2  Score=45.91  Aligned_cols=66  Identities=9%  Similarity=0.092  Sum_probs=56.2

Q ss_pred             chHHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhC-C-CcEEEEeCCCCHHHHHHHHHHHhcCC
Q psy1548         339 NEKNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQ-N-FPAVSIHRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       339 ~~k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~-g-~~~~~lh~~~~~~eR~~~l~~F~~g~  404 (448)
                      ..|.+....++...  .++++||.++....+..+...|++. | ..+..+|++++..+|.+.....++|+
T Consensus       171 SGKTevyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~  240 (665)
T PRK14873        171 EDWARRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQ  240 (665)
T ss_pred             CcHHHHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCC
Confidence            35777766666543  4678999999999999999999875 4 67999999999999999999999998

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=88.92  E-value=3.5  Score=42.84  Aligned_cols=52  Identities=15%  Similarity=0.139  Sum_probs=35.7

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      |.-+++.+|+|+|||...+--+...+.   .+-+++|++ ..+-..|+...++.+.
T Consensus       263 gs~~li~G~~G~GKt~l~~~f~~~~~~---~ge~~~y~s-~eEs~~~i~~~~~~lg  314 (484)
T TIGR02655       263 DSIILATGATGTGKTLLVSKFLENACA---NKERAILFA-YEESRAQLLRNAYSWG  314 (484)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHH---CCCeEEEEE-eeCCHHHHHHHHHHcC
Confidence            567899999999999754433333322   234678776 5666778888887764

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>PF10412 TrwB_AAD_bind: Type IV secretion-system coupling protein DNA-binding domain; InterPro: IPR019476 The plasmid conjugative coupling protein TraD (also known as TrwB) is a basic integral inner-membrane nucleoside-triphosphate-binding protein

Probab=88.90  E-value=0.52  Score=47.40  Aligned_cols=53  Identities=19%  Similarity=0.134  Sum_probs=35.3

Q ss_pred             cceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHH
Q psy1548         142 FGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQIS  197 (448)
Q Consensus       142 ~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~  197 (448)
                      -+|.-...+++++.|.||+|||. ++-.++..+...  +-+++|.=|.-+.....+
T Consensus         8 ~l~~~~e~~~~li~G~~GsGKT~-~i~~ll~~~~~~--g~~~iI~D~kg~~~~~f~   60 (386)
T PF10412_consen    8 PLPKDSENRHILIIGATGSGKTQ-AIRHLLDQIRAR--GDRAIIYDPKGEFTERFY   60 (386)
T ss_dssp             EE-GGGGGG-EEEEE-TTSSHHH-HHHHHHHHHHHT--T-EEEEEEETTHHHHHH-
T ss_pred             ecccchhhCcEEEECCCCCCHHH-HHHHHHHHHHHc--CCEEEEEECCchHHHHhc
Confidence            55666667999999999999996 456777766544  347888888877655433

It is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells []. This protein forms hexamers from six structurally very similar protomers []. This hexamer contains a central channel running from the cytosolic pole (formed by the all-alpha domains) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB all-alpha domain appears to be the DNA-binding domain of the structure. ; PDB: 1E9S_D 1E9R_F 1GKI_B 1GL7_G 1GL6_A.

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=88.61  E-value=12  Score=36.81  Aligned_cols=15  Identities=27%  Similarity=0.392  Sum_probs=12.4

Q ss_pred             ceeeeccCCChhHHH
Q psy1548         151 DILCQAKSGMGKTAV  165 (448)
Q Consensus       151 ~vli~apTGsGKT~~  165 (448)
                      -+-+.|+.|+|||..
T Consensus        58 ~igi~G~~GaGKSTl   72 (332)
T PRK09435         58 RIGITGVPGVGKSTF   72 (332)
T ss_pred             EEEEECCCCCCHHHH
Confidence            467889999999954

>KOG0346|consensus

Probab=88.57  E-value=0.32  Score=48.33  Aligned_cols=49  Identities=33%  Similarity=0.556  Sum_probs=39.5

Q ss_pred             cccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548         107 LFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus       107 ~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      -++||||+-.|..|+||++|.....|=+.+||++|+.   ..|-.+-++.|+
T Consensus       362 GVsRGIDF~~V~~VlNFD~P~t~~sYIHRvGRTaRg~---n~GtalSfv~P~  410 (569)
T KOG0346|consen  362 GVSRGIDFHHVSNVLNFDFPETVTSYIHRVGRTARGN---NKGTALSFVSPK  410 (569)
T ss_pred             chhccccchheeeeeecCCCCchHHHHHhccccccCC---CCCceEEEecch
Confidence            3789999999999999999999999999999988833   335555555554

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=88.50  E-value=3  Score=42.81  Aligned_cols=39  Identities=15%  Similarity=0.320  Sum_probs=24.6

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      ...+++||||+|.|...  ....+.+.+...+....+|+.+
T Consensus       120 ~~~kvvIIdead~lt~~--~~n~LLk~lEep~~~~~~Il~t  158 (451)
T PRK06305        120 SRYKIYIIDEVHMLTKE--AFNSLLKTLEEPPQHVKFFLAT  158 (451)
T ss_pred             CCCEEEEEecHHhhCHH--HHHHHHHHhhcCCCCceEEEEe
Confidence            45678999999988653  2334455555555555555543

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=88.48  E-value=3.4  Score=45.28  Aligned_cols=19  Identities=32%  Similarity=0.373  Sum_probs=16.1

Q ss_pred             CcceeeeccCCChhHHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVFV  167 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~  167 (448)
                      ..|+++.||+|+|||...-
T Consensus       203 ~~n~lL~G~pG~GKT~l~~  221 (731)
T TIGR02639       203 KNNPLLVGEPGVGKTAIAE  221 (731)
T ss_pred             CCceEEECCCCCCHHHHHH
Confidence            3589999999999997653

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=88.45  E-value=2.6  Score=46.16  Aligned_cols=19  Identities=37%  Similarity=0.405  Sum_probs=16.2

Q ss_pred             CcceeeeccCCChhHHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVFV  167 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~  167 (448)
                      ..++++.||+|+|||...-
T Consensus       207 ~~n~LLvGppGvGKT~lae  225 (758)
T PRK11034        207 KNNPLLVGESGVGKTAIAE  225 (758)
T ss_pred             CCCeEEECCCCCCHHHHHH
Confidence            4689999999999997643

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=88.42  E-value=3.2  Score=40.58  Aligned_cols=41  Identities=5%  Similarity=0.080  Sum_probs=27.9

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEecc
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSAT  297 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT  297 (448)
                      ...+.+|||+||.|..  .....+.+.+.--|++..+|+.|..
T Consensus       106 g~~KV~iI~~a~~m~~--~AaNaLLKtLEEPp~~~~fiL~t~~  146 (325)
T PRK06871        106 GGNKVVYIQGAERLTE--AAANALLKTLEEPRPNTYFLLQADL  146 (325)
T ss_pred             CCceEEEEechhhhCH--HHHHHHHHHhcCCCCCeEEEEEECC
Confidence            5678999999999977  3455555566665666666665443

>PRK06321 replicative DNA helicase; Provisional

Probab=88.40  E-value=1.7  Score=44.89  Aligned_cols=113  Identities=15%  Similarity=0.132  Sum_probs=53.2

Q ss_pred             eeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEE-EcCcccHHhH
Q psy1548         147 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVF-FGGLPIQKDE  225 (448)
Q Consensus       147 ~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~-~g~~~~~~~~  225 (448)
                      ..|.=+++.|.+|+|||... +-+...+.... +..+++++ ...-..|+...+-....   ++...-+ .|... ..+.
T Consensus       224 ~~G~LiiiaarPgmGKTafa-l~ia~~~a~~~-g~~v~~fS-LEMs~~ql~~Rlla~~s---~v~~~~i~~~~l~-~~e~  296 (472)
T PRK06321        224 SPSNLMILAARPAMGKTALA-LNIAENFCFQN-RLPVGIFS-LEMTVDQLIHRIICSRS---EVESKKISVGDLS-GRDF  296 (472)
T ss_pred             CCCcEEEEEeCCCCChHHHH-HHHHHHHHHhc-CCeEEEEe-ccCCHHHHHHHHHHhhc---CCCHHHhhcCCCC-HHHH
Confidence            33556788999999999554 43444332111 23455554 22223343333332221   2222111 22222 1121


Q ss_pred             -------HHHhcCCCcEEEE-----cHHHHHHHHHCCCCcCCCeeEEEecchhHHH
Q psy1548         226 -------EYLKTHNPQIVVG-----TPGRILALVRNKKLNLSLLKHFILDECDKML  269 (448)
Q Consensus       226 -------~~l~~~~~~IlV~-----Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~  269 (448)
                             ..+..  ..+.|-     |...+...++.-.. -..++++|||=.+.|.
T Consensus       297 ~~~~~a~~~l~~--~~~~idd~~~~ti~~i~~~~r~~~~-~~~~~lvvIDyLql~~  349 (472)
T PRK06321        297 QRIVSVVNEMQE--HTLLIDDQPGLKITDLRARARRMKE-SYDIQFLIIDYLQLLS  349 (472)
T ss_pred             HHHHHHHHHHHc--CCEEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHHcC
Confidence                   22222  246554     44555444432111 1347899999999874

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=88.35  E-value=0.33  Score=55.34  Aligned_cols=45  Identities=24%  Similarity=0.388  Sum_probs=37.2

Q ss_pred             cceeEeeccccCCcccccceeEeeccC---------------C---CCchhhhhhhccccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDM---------------P---EDSDTYLHRVARAGRFG  143 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~---------------p---~~~~~yQ~~~~~~~~~~  143 (448)
                      .+|.||||++++|+|.++++.|+|+..               |   .+...|.|.+|||||.-
T Consensus       338 rkIIVATNIAEtSITIpgI~yVID~Gl~k~~~Yd~~~~~~~Lp~~~iSkasa~QRaGRAGR~~  400 (1294)
T PRK11131        338 RRIVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVS  400 (1294)
T ss_pred             eeEEEeccHHhhccccCcceEEEECCCccccccccccCcccCCeeecCHhhHhhhccccCCCC
Confidence            489999999999999999999999742               2   22356899999999953

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=88.29  E-value=2.6  Score=41.49  Aligned_cols=41  Identities=10%  Similarity=0.137  Sum_probs=27.7

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEecc
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSAT  297 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT  297 (448)
                      ...+++|||+||.|...  ....+.+.+..-|++.-+|++|..
T Consensus       131 ~~~kV~iI~~ae~m~~~--AaNaLLKtLEEPp~~t~fiL~t~~  171 (342)
T PRK06964        131 GGARVVVLYPAEALNVA--AANALLKTLEEPPPGTVFLLVSAR  171 (342)
T ss_pred             CCceEEEEechhhcCHH--HHHHHHHHhcCCCcCcEEEEEECC
Confidence            56789999999999773  444555556655566666665544

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=88.21  E-value=2.4  Score=44.77  Aligned_cols=38  Identities=13%  Similarity=0.210  Sum_probs=22.5

Q ss_pred             CCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEE
Q psy1548         254 LSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMM  293 (448)
Q Consensus       254 ~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~  293 (448)
                      ....+++||||+|.|...  ....+.+.+...|...-+|+
T Consensus       117 ~~~~KVvIIDEa~~Ls~~--a~naLLK~LEepp~~~vfI~  154 (563)
T PRK06647        117 SSRYRVYIIDEVHMLSNS--AFNALLKTIEEPPPYIVFIF  154 (563)
T ss_pred             cCCCEEEEEEChhhcCHH--HHHHHHHhhccCCCCEEEEE
Confidence            356789999999988653  23334444444444444443

>PRK08760 replicative DNA helicase; Provisional

Probab=88.20  E-value=1.9  Score=44.56  Aligned_cols=114  Identities=20%  Similarity=0.150  Sum_probs=54.3

Q ss_pred             eeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEE-EcCcccHHh
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVF-FGGLPIQKD  224 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~-~g~~~~~~~  224 (448)
                      +..|.=++|.|.+|+|||...+ -+...+... .+..+++++. ..-..|+...+.......   ....+ .|... ..+
T Consensus       226 ~~~G~LivIaarPg~GKTafal-~iA~~~a~~-~g~~V~~fSl-EMs~~ql~~Rl~a~~s~i---~~~~i~~g~l~-~~e  298 (476)
T PRK08760        226 LQPTDLIILAARPAMGKTTFAL-NIAEYAAIK-SKKGVAVFSM-EMSASQLAMRLISSNGRI---NAQRLRTGALE-DED  298 (476)
T ss_pred             CCCCceEEEEeCCCCChhHHHH-HHHHHHHHh-cCCceEEEec-cCCHHHHHHHHHHhhCCC---cHHHHhcCCCC-HHH
Confidence            3445668889999999996543 333332211 1224666642 222345544444433222   11111 22211 111


Q ss_pred             H-------HHHhcCCCcEEEE-----cHHHHHHHHHCCCCcCCCeeEEEecchhHHH
Q psy1548         225 E-------EYLKTHNPQIVVG-----TPGRILALVRNKKLNLSLLKHFILDECDKML  269 (448)
Q Consensus       225 ~-------~~l~~~~~~IlV~-----Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~  269 (448)
                      .       ..+..  ..+.|.     |++.+...++.-.. -..+++||||=.+.|.
T Consensus       299 ~~~~~~a~~~l~~--~~l~I~d~~~~t~~~I~~~~r~l~~-~~~~~lVvIDyLql~~  352 (476)
T PRK08760        299 WARVTGAIKMLKE--TKIFIDDTPGVSPEVLRSKCRRLKR-EHDLGLIVIDYLQLMS  352 (476)
T ss_pred             HHHHHHHHHHHhc--CCEEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEecHHhcC
Confidence            1       12222  245444     45555444332111 1347899999999774

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=88.13  E-value=0.66  Score=46.05  Aligned_cols=39  Identities=18%  Similarity=0.260  Sum_probs=24.8

Q ss_pred             eCcceeeeccCCChhHHHHHHHHHHhhhccC-CCeEEEEee
Q psy1548         148 LGMDILCQAKSGMGKTAVFVLATLQQLETTD-SNVYVLVMC  187 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l~~l~~l~~~~-~~~~~lil~  187 (448)
                      .+.-++++||||||||.. +-.++..+.... .+.+++.+-
T Consensus       133 ~~glilI~GpTGSGKTTt-L~aLl~~i~~~~~~~~~Ivt~E  172 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTL-LAAIIRELAEAPDSHRKILTYE  172 (358)
T ss_pred             cCCEEEEECCCCCCHHHH-HHHHHHHHhhcCCCCcEEEEeC
Confidence            467899999999999965 345555554332 222444443

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>KOG2227|consensus

Probab=88.08  E-value=4.1  Score=41.29  Aligned_cols=51  Identities=22%  Similarity=0.217  Sum_probs=30.2

Q ss_pred             eeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeecc-HHHHHHHHH
Q psy1548         147 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT-RELAFQISK  198 (448)
Q Consensus       147 ~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt-~~L~~q~~~  198 (448)
                      ..+.++.|+|.+|+|||++.. -++..+......+.++++--+ ...+..++.
T Consensus       173 ~t~gSlYVsG~PGtgkt~~l~-rvl~~~~~~~~~~~~v~inc~sl~~~~aiF~  224 (529)
T KOG2227|consen  173 NTSGSLYVSGQPGTGKTALLS-RVLDSLSKSSKSPVTVYINCTSLTEASAIFK  224 (529)
T ss_pred             ccCcceEeeCCCCcchHHHHH-HHHHhhhhhcccceeEEEeeccccchHHHHH
Confidence            346789999999999998743 244444333344454555433 345555443

>PRK08506 replicative DNA helicase; Provisional

Probab=87.86  E-value=2.1  Score=44.20  Aligned_cols=114  Identities=19%  Similarity=0.145  Sum_probs=55.0

Q ss_pred             eeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEE-EcCcccHHh
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVF-FGGLPIQKD  224 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~-~g~~~~~~~  224 (448)
                      +..|.=+++.|.+|+|||...+--+.+.. .  .+..+++++. ..-..|+...+-....   ++....+ .|..+ ..+
T Consensus       189 ~~~G~LivIaarpg~GKT~fal~ia~~~~-~--~g~~V~~fSl-EMs~~ql~~Rlla~~s---~v~~~~i~~~~l~-~~e  260 (472)
T PRK08506        189 FNKGDLIIIAARPSMGKTTLCLNMALKAL-N--QDKGVAFFSL-EMPAEQLMLRMLSAKT---SIPLQNLRTGDLD-DDE  260 (472)
T ss_pred             CCCCceEEEEcCCCCChHHHHHHHHHHHH-h--cCCcEEEEeC-cCCHHHHHHHHHHHhc---CCCHHHHhcCCCC-HHH
Confidence            44466788999999999965443343332 2  2335666642 2334444443332222   2211111 12222 111


Q ss_pred             H-------HHHhcCCCcEEEE-----cHHHHHHHHHCCCCcCCCeeEEEecchhHHH
Q psy1548         225 E-------EYLKTHNPQIVVG-----TPGRILALVRNKKLNLSLLKHFILDECDKML  269 (448)
Q Consensus       225 ~-------~~l~~~~~~IlV~-----Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~  269 (448)
                      .       ..+..  ..+.|-     |+..+...++.-......++++|||=.+.|.
T Consensus       261 ~~~~~~a~~~l~~--~~l~I~d~~~~ti~~I~~~~r~l~~~~~~~~lvvIDyLql~~  315 (472)
T PRK08506        261 WERLSDACDELSK--KKLFVYDSGYVNIHQVRAQLRKLKSQHPEIGLAVIDYLQLMS  315 (472)
T ss_pred             HHHHHHHHHHHHc--CCeEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEcChhhcc
Confidence            1       12223  234442     4555544443211112357899999999775

>TIGR02012 tigrfam_recA protein RecA

Probab=87.85  E-value=1.1  Score=43.59  Aligned_cols=46  Identities=15%  Similarity=0.034  Sum_probs=29.0

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHH
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELA  193 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~  193 (448)
                      -+..|+-+.|.+|+|+|||...+-.+.....   .+..++++..-..+-
T Consensus        51 Glp~G~iteI~G~~GsGKTtLaL~~~~~~~~---~g~~v~yId~E~~~~   96 (321)
T TIGR02012        51 GLPRGRIIEIYGPESSGKTTLALHAIAEAQK---AGGTAAFIDAEHALD   96 (321)
T ss_pred             CCcCCeEEEEECCCCCCHHHHHHHHHHHHHH---cCCcEEEEcccchhH
Confidence            3445678899999999999665433333322   234677776544443

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>TIGR00763 lon ATP-dependent protease La

Probab=87.80  E-value=1.9  Score=47.60  Aligned_cols=19  Identities=26%  Similarity=0.266  Sum_probs=15.8

Q ss_pred             eCcceeeeccCCChhHHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~  166 (448)
                      .|..+++.||+|+|||..+
T Consensus       346 ~~~~lll~GppG~GKT~lA  364 (775)
T TIGR00763       346 KGPILCLVGPPGVGKTSLG  364 (775)
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            3567999999999999654

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>PRK00254 ski2-like helicase; Provisional

Probab=87.74  E-value=0.49  Score=51.76  Aligned_cols=57  Identities=16%  Similarity=0.300  Sum_probs=40.8

Q ss_pred             ceeEeeccccCCcccccceeEee-------ccCC-CCchhhhhhhccccccceeeeeCcceeeecc
Q psy1548         100 RILVATNLFGRGMDIERVNIVFN-------YDMP-EDSDTYLHRVARAGRFGTKAVLGMDILCQAK  157 (448)
Q Consensus       100 ~~~~~~~~~~~~~d~~~~~~v~~-------~~~p-~~~~~yQ~~~~~~~~~~~~~~~g~~vli~ap  157 (448)
                      +|+|||+.+++|+|.+.++.|+.       +..| .++.+|+|.+|||||.. .=..|..++++.+
T Consensus       323 ~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~~-~d~~G~~ii~~~~  387 (720)
T PRK00254        323 KVITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRPK-YDEVGEAIIVATT  387 (720)
T ss_pred             eEEEeCcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCCC-cCCCceEEEEecC
Confidence            89999999999999999998873       3332 25667899999999932 1123555555443

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=87.70  E-value=3.9  Score=45.69  Aligned_cols=19  Identities=26%  Similarity=0.370  Sum_probs=16.0

Q ss_pred             CcceeeeccCCChhHHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVFV  167 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~  167 (448)
                      ..+.++.||+|+|||...-
T Consensus       194 ~~n~lL~G~pGvGKT~l~~  212 (852)
T TIGR03346       194 KNNPVLIGEPGVGKTAIVE  212 (852)
T ss_pred             CCceEEEcCCCCCHHHHHH
Confidence            3689999999999997653

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=87.61  E-value=0.57  Score=47.49  Aligned_cols=51  Identities=12%  Similarity=0.086  Sum_probs=35.1

Q ss_pred             cceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHH
Q psy1548         142 FGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ  195 (448)
Q Consensus       142 ~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q  195 (448)
                      .+|.-...+++++.|+||+|||.+ +..++..+...  +.+++|+=|..++...
T Consensus        35 ~~~~~~~~~h~~i~g~tGsGKt~~-i~~l~~~~~~~--~~~~vi~D~kg~~~~~   85 (410)
T cd01127          35 PFPKDAEEAHTMIIGTTGTGKTTQ-IRELLASIRAR--GDRAIIYDPNGGFVSK   85 (410)
T ss_pred             eCCcchhhccEEEEcCCCCCHHHH-HHHHHHHHHhc--CCCEEEEeCCcchhHh
Confidence            445555568999999999999975 44445444333  3368888888876543

TrwB is a homohexamer encoded by conjugative plasmids in Gram-negative bacteria. TrwB also has an all alpha domain which has been hypothesized to be responsible for DNA binding. TrwB is a component of Type IV secretion and is responsible for the horizontal transfer of DNA between bacteria.

>PRK09165 replicative DNA helicase; Provisional

Probab=87.54  E-value=3.5  Score=42.89  Aligned_cols=117  Identities=15%  Similarity=0.051  Sum_probs=55.8

Q ss_pred             eeeCcceeeeccCCChhHHHHHHHHHHhhhcc------------CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEE
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETT------------DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  213 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~------------~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~  213 (448)
                      +..|.=+++.|++|+|||...+--+.+.....            ..+..++|++ ...-..|+...+.......   ...
T Consensus       214 ~~~g~livIaarpg~GKT~~al~ia~~~a~~~~~~~~~~~~~~~~~g~~vl~fS-lEMs~~ql~~R~la~~s~v---~~~  289 (497)
T PRK09165        214 LHPSDLIILAGRPSMGKTALATNIAFNAAKAYRREAQPDGSKKAVNGGVVGFFS-LEMSAEQLATRILSEQSEI---SSS  289 (497)
T ss_pred             CCCCceEEEEeCCCCChHHHHHHHHHHHHHhhcccccccccccccCCCeEEEEe-CcCCHHHHHHHHHHHhcCC---CHH
Confidence            44456788999999999965443333322211            1234566664 3333445544443332222   111


Q ss_pred             EEEcCcccHHhHH-------HHhcCCCcEEEE-----cHHHHHHHHHCCCCcCCCeeEEEecchhHHH
Q psy1548         214 VFFGGLPIQKDEE-------YLKTHNPQIVVG-----TPGRILALVRNKKLNLSLLKHFILDECDKML  269 (448)
Q Consensus       214 ~~~g~~~~~~~~~-------~l~~~~~~IlV~-----Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~  269 (448)
                      .+..+.-...+..       .+..  ..+.|-     |+..+...+++-.. -..++++|||=.+.|.
T Consensus       290 ~i~~~~l~~~e~~~l~~a~~~l~~--~~l~I~d~~~~ti~~i~~~ir~l~~-~~~~~lvvIDyLqli~  354 (497)
T PRK09165        290 KIRRGKISEEDFEKLVDASQELQK--LPLYIDDTPALSISQLRARARRLKR-QHGLDLLVVDYLQLIR  354 (497)
T ss_pred             HHhcCCCCHHHHHHHHHHHHHHhc--CCeEEeCCCCCCHHHHHHHHHHHHH-hcCCCEEEEcchHhcc
Confidence            1111111111111       1222  235543     45555444432111 1347899999999775

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=87.54  E-value=0.85  Score=43.03  Aligned_cols=39  Identities=18%  Similarity=0.123  Sum_probs=23.8

Q ss_pred             eeeeccCCChhHHHHHHHHHHh-hhc--cCCCeEEEEeeccH
Q psy1548         152 ILCQAKSGMGKTAVFVLATLQQ-LET--TDSNVYVLVMCHTR  190 (448)
Q Consensus       152 vli~apTGsGKT~~~~l~~l~~-l~~--~~~~~~~lil~Pt~  190 (448)
                      .=++|+.|+|||-..+-.++.. +..  ...+.+++|+.-..
T Consensus        41 tEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~   82 (256)
T PF08423_consen   41 TEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEG   82 (256)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSS
T ss_pred             EEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCC
Confidence            3478999999995544333333 322  22345899997444

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>PRK10865 protein disaggregation chaperone; Provisional

Probab=87.42  E-value=3.6  Score=45.90  Aligned_cols=19  Identities=26%  Similarity=0.370  Sum_probs=15.9

Q ss_pred             CcceeeeccCCChhHHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVFV  167 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~  167 (448)
                      ..++++.||+|+|||...-
T Consensus       199 ~~n~lL~G~pGvGKT~l~~  217 (857)
T PRK10865        199 KNNPVLIGEPGVGKTAIVE  217 (857)
T ss_pred             cCceEEECCCCCCHHHHHH
Confidence            3589999999999997653

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	448
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		1e-138
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		1e-138
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		1e-137
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		3e-93
1t5i_A	172	Crystal Structure Of The C-Terminal Domain Of Uap56		5e-40
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		5e-33
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		6e-33
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		6e-33
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		2e-32
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		2e-32
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-32
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		2e-32
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		4e-32
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		6e-32
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		7e-32
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		5e-31
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		3e-27
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		2e-26
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		3e-26
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		4e-26
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		1e-24
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		8e-23
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		4e-22
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		4e-22
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		4e-21
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		4e-21
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		4e-20
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		1e-18
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		1e-18
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		2e-18
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		2e-18
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		4e-18
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		4e-18
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		5e-18
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		5e-18
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		5e-18
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		5e-18
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		1e-17
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		2e-17
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		3e-16
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		6e-16
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		3e-15
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		2e-14
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		1e-13
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		1e-13
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		1e-10
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		1e-10
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		1e-10
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		4e-04
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		2e-10
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		9e-10
3ly5_A	262	Ddx18 Dead-Domain Length = 262		4e-09
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		4e-09
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		5e-09
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		6e-09
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		8e-09
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		1e-08
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		2e-08
2jgn_A	185	Ddx3 Helicase Domain Length = 185		4e-07
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		2e-06
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		2e-05
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		4e-04

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score =  489 bits (1259), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 257/414 (62%), Positives = 284/414 (68%), Gaps = 78/414 (18%)
Query: 79  SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVAR 138
           SSGFRDFLLKPE+LRAIVDC                        ++ P +     H    
Sbjct: 7   SSGFRDFLLKPELLRAIVDC-----------------------GFEHPSEVQ---HECI- 39
Query: 139 AGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK 198
                 +A+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQISK
Sbjct: 40  -----PQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISK 94
Query: 199 EYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLK 258
           EYERFSKYM N+KV VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK LNL  +K
Sbjct: 95  EYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIK 154
Query: 259 HFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
           HFILDECDKMLEQL+MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++V
Sbjct: 155 HFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 214
Query: 319 DDEAKLTLHGLQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQN 378
           DDE KLTLHGLQQ+YV               DVLEFNQVVIFVKSV RCIAL+ LL EQN
Sbjct: 215 DDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQN 274
Query: 379 FPAVSIHRGMTQEERLKKYQEFKDFH---------------------------------- 404
           FPA++IHRGM QEERL +YQ+FKDF                                   
Sbjct: 275 FPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTY 334
Query: 405 ------------KGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIE 446
                       KGLAITF SDENDAKILN+VQDRF+V+ISELPDEID+S+YIE
Sbjct: 335 LHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIE 388

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score =  486 bits (1251), Expect = e-138,   Method: Compositional matrix adjust.
 Identities = 256/415 (61%), Positives = 283/415 (68%), Gaps = 78/415 (18%)
Query: 78  HSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVA 137
           H SGFRDFLLKPE+LRAIVDC                        ++ P +     H   
Sbjct: 5   HMSGFRDFLLKPELLRAIVDC-----------------------GFEHPSEVQ---HECI 38
Query: 138 RAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQIS 197
                  +A+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQIS
Sbjct: 39  ------PQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQIS 92
Query: 198 KEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLL 257
           KEYERFSKYM N+KV VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK LNL  +
Sbjct: 93  KEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHI 152
Query: 258 KHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVY 317
           KHFILDE DKMLEQL+MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++
Sbjct: 153 KHFILDEADKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIF 212
Query: 318 VDDEAKLTLHGLQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQ 377
           VDDE KLTLHGLQQ+YV               DVLEFNQVVIFVKSV RCIAL+ LL EQ
Sbjct: 213 VDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQ 272
Query: 378 NFPAVSIHRGMTQEERLKKYQEFKDFH--------------------------------- 404
           NFPA++IHRGM QEERL +YQ+FKDF                                  
Sbjct: 273 NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDT 332
Query: 405 -------------KGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIE 446
                        KGLAITF SDENDAKILN+VQDRF+V+ISELPDEID+S+YIE
Sbjct: 333 YLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIE 387

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score =  485 bits (1248), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 255/412 (61%), Positives = 282/412 (68%), Gaps = 78/412 (18%)
Query: 79  SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVAR 138
           SSGFRDFLLKPE+LRAIVDC         F    +++   I                   
Sbjct: 7   SSGFRDFLLKPELLRAIVDCG--------FEHPSEVQHECI------------------- 39
Query: 139 AGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK 198
                 +A+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQISK
Sbjct: 40  -----PQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISK 94
Query: 199 EYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLK 258
           EYERFSKYM N+KV VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK LNL  +K
Sbjct: 95  EYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIK 154
Query: 259 HFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
           HFILDECDKMLEQL+MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++V
Sbjct: 155 HFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 214
Query: 319 DDEAKLTLHGLQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQN 378
           DDE KLTLHGLQQ+YV               DVLEFNQVVIFVKSV RCIAL+ LL EQN
Sbjct: 215 DDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQN 274
Query: 379 FPAVSIHRGMTQEERLKKYQEFKDFH---------------------------------- 404
           FPA++IHRGM QEERL +YQ+FKDF                                   
Sbjct: 275 FPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTY 334
Query: 405 ------------KGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTY 444
                       KGLAITF SDENDAKILN+VQDRF+V+ISELPDEID+S+Y
Sbjct: 335 LHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDISSY 386

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score =  338 bits (868), Expect = 3e-93,   Method: Compositional matrix adjust.
 Identities = 171/250 (68%), Positives = 189/250 (75%), Gaps = 32/250 (12%)
Query: 69  EVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPED 128
           +VKG+YVSIHSSGFRDFLLKPE+LRAIVDC                        ++ P +
Sbjct: 3   DVKGSYVSIHSSGFRDFLLKPELLRAIVDC-----------------------GFEHPSE 39
Query: 129 SDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH 188
                H          +A+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCH
Sbjct: 40  VQ---HECI------PQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCH 90
Query: 189 TRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVR 248
           TRELAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IVVGTPGRILAL R
Sbjct: 91  TRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALAR 150
Query: 249 NKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKK 308
           NK LNL  +KHFILDECDKMLEQL+MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+K
Sbjct: 151 NKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRK 210
Query: 309 FMHDPMEVYV 318
           FM DPME++V
Sbjct: 211 FMQDPMEIFV 220

>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56 Length = 172

Iteration: 1
 Score =  162 bits (409), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 88/168 (52%), Positives = 100/168 (59%), Gaps = 46/168 (27%)
Query: 325 TLHGLQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSI 384
           +LHGLQQ+YV               DVLEFNQVVIFVKSV RCIAL+ LL EQNFPA++I
Sbjct: 2   SLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAI 61
Query: 385 HRGMTQEERLKKYQEFKDFH---------------------------------------- 404
           HRGM QEERL +YQ+FKDF                                         
Sbjct: 62  HRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVAR 121
Query: 405 ------KGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIE 446
                 KGLAITF SDENDAKILN+VQDRF+V+ISELPDEID+S+YIE
Sbjct: 122 AGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIE 169

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score =  139 bits (349), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 85/263 (32%), Positives = 136/263 (51%), Gaps = 4/263 (1%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D++ QA+SG GKTA F ++ LQQ+E        LV+  TRELA QI K       YM 
Sbjct: 77  GYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMG 136
Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
                   GG  ++ + + L+   P I+VGTPGR+  ++  + L+   +K F+LDE D+M
Sbjct: 137 -ASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEM 195
Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHG 328
           L +   +  + +IF+      QV++ SAT+  ++  V KKFM DP+ + V  E +LTL G
Sbjct: 196 LSR-GFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKE-ELTLEG 253
Query: 329 LQQHYVXXXXXXXXXXXX-XXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRG 387
           ++Q Y+                + L   Q VIF+ +  +   L+  +  ++F   ++H  
Sbjct: 254 IRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGD 313
Query: 388 MTQEERLKKYQEFKDFHKGLAIT 410
           M Q+ER    +EF+     + IT
Sbjct: 314 MDQKERDVIMREFRSGSSRVLIT 336

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score =  138 bits (348), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 85/263 (32%), Positives = 136/263 (51%), Gaps = 4/263 (1%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D++ QA+SG GKTA F ++ LQQ+E        LV+  TRELA QI K       YM 
Sbjct: 51  GYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMG 110
Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
                   GG  ++ + + L+   P I+VGTPGR+  ++  + L+   +K F+LDE D+M
Sbjct: 111 A-SCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEM 169
Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHG 328
           L +   +  + +IF+      QV++ SAT+  ++  V KKFM DP+ + V  E +LTL G
Sbjct: 170 LSR-GFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKE-ELTLEG 227
Query: 329 LQQHYVXXXXXXXXXXXX-XXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRG 387
           ++Q Y+                + L   Q VIF+ +  +   L+  +  ++F   ++H  
Sbjct: 228 IRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGD 287
Query: 388 MTQEERLKKYQEFKDFHKGLAIT 410
           M Q+ER    +EF+     + IT
Sbjct: 288 MDQKERDVIMREFRSGSSRVLIT 310

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score =  138 bits (347), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 101/306 (33%), Positives = 153/306 (50%), Gaps = 22/306 (7%)
Query: 113 DIERVNIVFNYD--MPEDSDTYLHRVARAGRFG----------TKAVL----GMDILCQA 156
           DIE   I  NYD  + +  D  L      G FG           +A++    G D+L QA
Sbjct: 7   DIEESQIQTNYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQA 66
Query: 157 KSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFF 216
           +SG GKT  F +A LQ+++T+      L++  TRELA QI K     + +M +IKV    
Sbjct: 67  QSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHM-DIKVHACI 125
Query: 217 GGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRR 276
           GG    +D E L+  + QIVVGTPGR+   ++ ++     +K FILDE D+ML     + 
Sbjct: 126 GGTSFVEDAEGLR--DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSS-GFKE 182
Query: 277 DVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVXX 336
            + +IF   P T QV++ SAT+  ++  V  KFM +P+ + V  + +LTL G++Q YV  
Sbjct: 183 QIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKD-ELTLEGIKQFYVNV 241
Query: 337 XXXXXXXX-XXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLK 395
                         D +   Q VIF  +  +   L+T L    F   +I+  + Q+ER  
Sbjct: 242 EEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDT 301
Query: 396 KYQEFK 401
             +EF+
Sbjct: 302 IMKEFR 307

>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 413

Iteration: 1
 Score =  137 bits (344), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 84/254 (33%), Positives = 130/254 (51%), Gaps = 5/254 (1%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D++ Q++SG GKTA F ++ LQ L+        L++  TRELA QI K       YM 
Sbjct: 75  GRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYM- 133
Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
           N++     GG  + +D   L  +   +V GTPGR+  ++R + L    +K  +LDE D+M
Sbjct: 134 NVQCHACIGGTNVGEDIRKLD-YGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEM 192
Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHG 328
           L +   +  + +++R  P   QV++ SATL  EI  +  KFM DP+ + V  + +LTL G
Sbjct: 193 LNK-GFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRD-ELTLEG 250
Query: 329 LQQHYVXXXXXXXXXXXX-XXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRG 387
           ++Q +V                D L   Q VIF  +  +   L+  + E NF   S+H  
Sbjct: 251 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGD 310
Query: 388 MTQEERLKKYQEFK 401
           M Q+ER    +EF+
Sbjct: 311 MPQKERESIMKEFR 324

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score =  137 bits (344), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 84/254 (33%), Positives = 130/254 (51%), Gaps = 5/254 (1%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D++ Q++SG GKTA F ++ LQ L+        L++  TRELA QI K       YM 
Sbjct: 74  GRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYM- 132
Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
           N++     GG  + +D   L  +   +V GTPGR+  ++R + L    +K  +LDE D+M
Sbjct: 133 NVQCHACIGGTNVGEDIRKLD-YGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEM 191
Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHG 328
           L +   +  + +++R  P   QV++ SATL  EI  +  KFM DP+ + V  + +LTL G
Sbjct: 192 LNK-GFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRD-ELTLEG 249
Query: 329 LQQHYVXXXXXXXXXXXX-XXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRG 387
           ++Q +V                D L   Q VIF  +  +   L+  + E NF   S+H  
Sbjct: 250 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGD 309
Query: 388 MTQEERLKKYQEFK 401
           M Q+ER    +EF+
Sbjct: 310 MPQKERESIMKEFR 323

>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 411

Iteration: 1
 Score =  137 bits (344), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 84/254 (33%), Positives = 130/254 (51%), Gaps = 5/254 (1%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D++ Q++SG GKTA F ++ LQ L+        L++  TRELA QI K       YM 
Sbjct: 75  GRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYM- 133
Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
           N++     GG  + +D   L  +   +V GTPGR+  ++R + L    +K  +LDE D+M
Sbjct: 134 NVQCHACIGGTNVGEDIRKLD-YGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEM 192
Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHG 328
           L +   +  + +++R  P   QV++ SATL  EI  +  KFM DP+ + V  + +LTL G
Sbjct: 193 LNK-GFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRD-ELTLEG 250
Query: 329 LQQHYVXXXXXXXXXXXX-XXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRG 387
           ++Q +V                D L   Q VIF  +  +   L+  + E NF   S+H  
Sbjct: 251 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGD 310
Query: 388 MTQEERLKKYQEFK 401
           M Q+ER    +EF+
Sbjct: 311 MPQKERESIMKEFR 324

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score =  136 bits (343), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 84/254 (33%), Positives = 130/254 (51%), Gaps = 5/254 (1%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D++ Q++SG GKTA F ++ LQ L+        L++  TRELA QI K       YM 
Sbjct: 53  GRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYM- 111
Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
           N++     GG  + +D   L  +   +V GTPGR+  ++R + L    +K  +LDE D+M
Sbjct: 112 NVQCHACIGGTNVGEDIRKLD-YGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEM 170
Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHG 328
           L +   +  + +++R  P   QV++ SATL  EI  +  KFM DP+ + V  + +LTL G
Sbjct: 171 LNK-GFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRD-ELTLEG 228
Query: 329 LQQHYVXXXXXXXXXXXX-XXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRG 387
           ++Q +V                D L   Q VIF  +  +   L+  + E NF   S+H  
Sbjct: 229 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGD 288
Query: 388 MTQEERLKKYQEFK 401
           M Q+ER    +EF+
Sbjct: 289 MPQKERESIMKEFR 302

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  135 bits (341), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 83/254 (32%), Positives = 130/254 (51%), Gaps = 5/254 (1%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D++ Q++SG GKTA F ++ LQ L+        L++  TRELA Q+ K       YM 
Sbjct: 38  GRDVIAQSQSGTGKTATFSVSVLQCLDIQVRETQALILAPTRELAVQVQKGLLALGDYM- 96
Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
           N++     GG  + +D   L  +   +V GTPGR+  ++R + L    +K  +LDE D+M
Sbjct: 97  NVQCHACIGGTNVGEDIRKLD-YGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEM 155
Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHG 328
           L +   +  + +++R  P   QV++ SATL  EI  +  KFM DP+ + V  + +LTL G
Sbjct: 156 LNK-GFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRD-ELTLEG 213
Query: 329 LQQHYVXXXXXXXXXXXX-XXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRG 387
           ++Q +V                D L   Q VIF  +  +   L+  + E NF   S+H  
Sbjct: 214 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGD 273
Query: 388 MTQEERLKKYQEFK 401
           M Q+ER    +EF+
Sbjct: 274 MPQKERESIMKEFR 287

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score =  135 bits (339), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 87/256 (33%), Positives = 132/256 (51%), Gaps = 5/256 (1%)
Query: 146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK 205
           A+ G DIL +AK+G GKTA FV+ TL++++   + +  L+M  TRELA Q S+      K
Sbjct: 55  AITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGK 114
Query: 206 YMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDEC 265
           +   I   V  GG  ++ D   L      I+VGTPGR+L L   K  +LS    FI+DE 
Sbjct: 115 H-CGISCMVTTGGTNLRDDILRLN-ETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEA 172
Query: 266 DKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLT 325
           DKML + + +  +++I    P T Q ++FSAT    ++    K +H P E+ + +E  LT
Sbjct: 173 DKMLSR-DFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLMEE--LT 229
Query: 326 LHGLQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIH 385
           L G+ Q+Y                  L+ NQ +IF  S  R   L+  +++  +     H
Sbjct: 230 LKGITQYYAFVEERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSH 289
Query: 386 RGMTQEERLKKYQEFK 401
             M Q+ER K + EF+
Sbjct: 290 ARMKQQERNKVFHEFR 305

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  134 bits (338), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 82/254 (32%), Positives = 130/254 (51%), Gaps = 5/254 (1%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D++ Q++SG GKTA F ++ LQ L+        L++  TRELA Q+ K       YM 
Sbjct: 38  GRDVIAQSQSGTGKTATFSVSVLQCLDIQVRETQALILAPTRELAVQVQKGLLALGDYM- 96
Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
           N++     GG  + +D   L  +   +V GTPGR+  ++R + L    +K  +LDE D+M
Sbjct: 97  NVQSHACIGGTNVGEDIRKLD-YGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEM 155
Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHG 328
           L +   +  + +++R  P   QV++ SATL  E+  +  KFM DP+ + V  + +LTL G
Sbjct: 156 LNK-GFKEQIYDVYRYLPPATQVVLISATLPHEVLEMTNKFMTDPIRILVKRD-ELTLEG 213
Query: 329 LQQHYVXXXXXXXXXXXX-XXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRG 387
           ++Q +V                D L   Q VIF  +  +   L+  + E NF   S+H  
Sbjct: 214 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGD 273
Query: 388 MTQEERLKKYQEFK 401
           M Q+ER    +EF+
Sbjct: 274 MPQKERESIMKEFR 287

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score =  132 bits (331), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 85/254 (33%), Positives = 130/254 (51%), Gaps = 6/254 (2%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D+L QA+SG GKT  F +A LQ+++T+      L +  TRELA QI K     + +  
Sbjct: 58  GHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALXLAPTRELALQIQKVVXALA-FHX 116
Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
           +IKV    GG    +D E L+  + QIVVGTPGR+   ++ ++     +K FILDE D+ 
Sbjct: 117 DIKVHACIGGTSFVEDAEGLR--DAQIVVGTPGRVFDNIQRRRFRTDKIKXFILDEADEX 174
Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHG 328
           L     +  + +IF   P T QV++ SAT   ++  V  KF  +P+ + V  + +LTL G
Sbjct: 175 LSS-GFKEQIYQIFTLLPPTTQVVLLSATXPNDVLEVTTKFXRNPVRILVKKD-ELTLEG 232
Query: 329 LQQHYVXXXXXXXXXX-XXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRG 387
           ++Q YV                D +   Q VIF  +  +   L+T L    F   +I+  
Sbjct: 233 IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSD 292
Query: 388 MTQEERLKKYQEFK 401
           + Q+ER    +EF+
Sbjct: 293 LPQQERDTIXKEFR 306

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score =  119 bits (299), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 66/173 (38%), Positives = 97/173 (56%), Gaps = 2/173 (1%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D++ QA+SG GKTA F ++ LQQLE        LV+  TRELA QI K       YM 
Sbjct: 67  GYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMG 126
Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
                   GG  ++ + + L+   P IVVGTPGR+  ++  + L+   +K F+LDE D+M
Sbjct: 127 A-TCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEM 185
Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDE 321
           L +   +  + EIF+    + QV++ SAT+  ++  V KKFM DP+ + V  E
Sbjct: 186 LSR-GFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKE 237

>pdb|1QDE|A Chain A, Crystal Structure Of The Atpase Domain Of Translation Initiation Factor 4a From Saccharomyces Cerevisiae-The Prototype Of The Dead Box Protein Family Length = 224

Iteration: 1
 Score =  116 bits (291), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 69/179 (38%), Positives = 104/179 (58%), Gaps = 5/179 (2%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D+L QA+SG GKT  F +A LQ+++T+      L++  TRELA QI K     + +M 
Sbjct: 51  GHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHM- 109
Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
           +IKV    GG    +D E L+  + QIVVGTPGR+   ++ ++     +K FILDE D+M
Sbjct: 110 DIKVHACIGGTSFVEDAEGLR--DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEM 167
Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLH 327
           L     +  + +IF   P T QV++ SAT+  ++  V  KFM +P+ + V  + +LTL 
Sbjct: 168 LSS-GFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKD-ELTLE 224

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score =  116 bits (291), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 66/170 (38%), Positives = 99/170 (58%), Gaps = 4/170 (2%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D+L QA+SG GKT  F +A LQ+++T+      L++  TRELA QI K     + +M 
Sbjct: 58  GHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHM- 116
Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
           +IKV    GG    +D E L+  + QIVVGTPGR+   ++ ++     +K FILDE D+M
Sbjct: 117 DIKVHACIGGTSFVEDAEGLR--DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEM 174
Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
           L     +  + +IF   P T QV++ SAT+  ++  V  KFM +P+ + V
Sbjct: 175 LSS-GFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILV 223

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score =  115 bits (289), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 88/264 (33%), Positives = 138/264 (52%), Gaps = 13/264 (4%)
Query: 151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI 210
           +I+ QA++G GKTA F +  L +L   ++ +  +++  TRELA Q++ E E   K   N+
Sbjct: 46  NIVAQARTGSGKTASFAIP-LIELVNENNGIEAIILTPTRELAIQVADEIESL-KGNKNL 103
Query: 211 KVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLE 270
           K+   +GG  I    + LK  N  IVVGTPGRIL  +    LNL  +K+FILDE D+ L 
Sbjct: 104 KIAKIYGGKAIYPQIKALK--NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEXL- 160
Query: 271 QLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQ 330
                +DV++I  +    K++++FSAT  +EI  + KK+  D    Y   +AK+  + ++
Sbjct: 161 NXGFIKDVEKILNACNKDKRILLFSATXPREILNLAKKYXGD----YSFIKAKINAN-IE 215
Query: 331 QHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQ 390
           Q YV                  EF  +V F K+      L++ L +  F A +IH  ++Q
Sbjct: 216 QSYVEVNENERFEALCRLLKNKEFYGLV-FCKTKRDTKELASXLRDIGFKAGAIHGDLSQ 274
Query: 391 EERLKKYQEFKDFHKGLAITFASD 414
            +R K  + FK   K + I  A+D
Sbjct: 275 SQREKVIRLFK--QKKIRILIATD 296

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score =  110 bits (276), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 62/172 (36%), Positives = 94/172 (54%), Gaps = 2/172 (1%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G+D++ QAKSG GKT VF    L  L   + +  +L++  TRE+A QI          M 
Sbjct: 61  GLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKME 120
Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
            ++  VF GG P+ +D+  LK  +  I VG+PGRI  L+    LN   ++ FILDE DK+
Sbjct: 121 GLECHVFIGGTPLSQDKTRLKKCH--IAVGSPGRIKQLIELDYLNPGSIRLFILDEADKL 178
Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDD 320
           LE+   +  +  I+ S P +KQ++  SAT  + +     K+M DP  V ++ 
Sbjct: 179 LEEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRLNS 230

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score =  104 bits (260), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 57/172 (33%), Positives = 90/172 (52%), Gaps = 2/172 (1%)
Query: 147 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKY 206
           + G D++ QA+SG G TA F ++ LQQ+E        LV+  TRELA QI         Y
Sbjct: 50  IXGYDVIAQAQSGTGXTATFAISILQQIELDLXATQALVLAPTRELAQQIQXVVMALGDY 109
Query: 207 MSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECD 266
           M         GG  ++ + + L+   P I+VGTPGR+  ++  + L+   +  F+LDE D
Sbjct: 110 MGA-SCHACIGGTNVRAEVQXLQMEAPHIIVGTPGRVFDMLNRRYLSPXYIXMFVLDEAD 168
Query: 267 KMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
           +ML +      + +IF+      QV++ SAT+  ++  V   FM DP+ + V
Sbjct: 169 EMLSR-GFXDQIYDIFQXLNSNTQVVLLSATMPSDVLEVTXXFMRDPIRILV 219

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score =  102 bits (255), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 56/174 (32%), Positives = 99/174 (56%), Gaps = 4/174 (2%)
Query: 146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK 205
           A+ G DI+  A++G GKT  F L  L  L  T   ++ LV+  TRELAFQIS+++E    
Sbjct: 77  ALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTPTRELAFQISEQFEALGS 136
Query: 206 YMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK-LNLSLLKHFILDE 264
            +  ++  V  GG+        L    P I++ TPGR++  + N K  NL  LK+ ++DE
Sbjct: 137 SI-GVQSAVIVGGIDSMSQSLAL-AKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDE 194
Query: 265 CDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
            D++L  ++   +V +I +  P  ++  +FSAT++K+++ + +  + +P++  V
Sbjct: 195 ADRIL-NMDFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAV 247

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score =  102 bits (254), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 88/321 (27%), Positives = 154/321 (47%), Gaps = 44/321 (13%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQL-----ETTDSNVYVLVMCHTRELAFQISKEYERF 203
           G D++  A++G GKTA F+L  L +L     E       V+++  TRELA QI  E  +F
Sbjct: 93  GRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKF 152
Query: 204 SKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILD 263
           + + S +K+G+ +GG   +   E + T    +V+ TPGR+L  V    +     +  +LD
Sbjct: 153 A-FESYLKIGIVYGGTSFRHQNECI-TRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLD 210
Query: 264 ECDKMLE---QLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVD- 319
           E D+ML+     +MRR +  +     H  Q +MFSAT  +EI+ +  +F+ + + V +  
Sbjct: 211 EADRMLDMGFSEDMRRIMTHVTMRPEH--QTLMFSATFPEEIQRMAGEFLKNYVFVAIGI 268
Query: 320 -----DEAKLTLHGLQQHYVXXXXXXXXXXXXXXXDVL--EFNQVVIFVKSVTRCIALST 372
                 + K T++ + ++                 ++L  + +  ++FV++      L++
Sbjct: 269 VGGACSDVKQTIYEVNKY----------AKRSKLIEILSEQADGTIVFVETKRGADFLAS 318
Query: 373 LLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKG-----LAITFASDENDAKILNNVQDR 427
            LSE+ FP  SIH    Q +R    Q  +DF  G     +A + AS   D K + +V + 
Sbjct: 319 FLSEKEFPTTSIHGDRLQSQR---EQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINY 375
Query: 428 FDVSISELPDEIDLSTYIEGR 448
                 ++P +ID   +  GR
Sbjct: 376 ------DMPSKIDDYVHRIGR 390

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score = 99.4 bits (246), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 116/240 (48%), Gaps = 40/240 (16%)
Query: 82  FRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR 141
           F+DF LKPEIL A            L GRG+                + T +   A    
Sbjct: 3   FKDFPLKPEILEA------------LHGRGLT---------------TPTPIQAAAL--- 32
Query: 142 FGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDS---NVYVLVMCHTRELAFQISK 198
               A+ G D++ QA++G GKT  F L   ++L  +         LV+  TRELA Q++ 
Sbjct: 33  --PLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVAS 90
Query: 199 EYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLK 258
           E    +    ++KV   +GG    K +E L       VV TPGR L  +R   L+LS ++
Sbjct: 91  E---LTAVAPHLKVVAVYGGTGYGKQKEAL-LRGADAVVATPGRALDYLRQGVLDLSRVE 146
Query: 259 HFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
             +LDE D+ML  +    +V+ +  ++P ++Q ++FSATL    + + +++M +P+ + V
Sbjct: 147 VAVLDEADEML-SMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINV 205

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score = 99.0 bits (245), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 116/240 (48%), Gaps = 40/240 (16%)
Query: 82  FRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR 141
           F+DF LKPEIL A            L GRG+                + T +   A    
Sbjct: 3   FKDFPLKPEILEA------------LHGRGLT---------------TPTPIEAAAL--- 32
Query: 142 FGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDS---NVYVLVMCHTRELAFQISK 198
               A+ G D++ QA++G GKT  F L   ++L  +         LV+  TRELA Q++ 
Sbjct: 33  --PLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVAS 90
Query: 199 EYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLK 258
           E    +    ++KV   +GG    K +E L       VV TPGR L  +R   L+LS ++
Sbjct: 91  E---LTAVAPHLKVVAVYGGTGYGKQKEAL-LRGADAVVATPGRALDYLRQGVLDLSRVE 146
Query: 259 HFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
             +LDE D+ML  +    +V+ +  ++P ++Q ++FSATL    + + +++M +P+ + V
Sbjct: 147 VAVLDEADEML-SMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINV 205

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score = 95.9 bits (237), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 53/171 (30%), Positives = 96/171 (56%), Gaps = 2/171 (1%)
Query: 146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK 205
           A+ G DIL +AK+G GK+  +++  L++L+    N+  +V+  TRELA Q+S+   + SK
Sbjct: 37  ALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSK 96
Query: 206 YMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDEC 265
           +M   KV    GG  ++ D   L      +V+ TPGRIL L++     +  ++  +LDE 
Sbjct: 97  HMGGAKVMATTGGTNLRDDIMRLD-DTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEA 155
Query: 266 DKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEV 316
           DK+L Q +  + +++I  + P  +Q++++SAT    ++      +  P E+
Sbjct: 156 DKLLSQ-DFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI 205

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 90.9 bits (224), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 69/264 (26%), Positives = 123/264 (46%), Gaps = 14/264 (5%)
Query: 151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ---ISKEYERFSKYM 207
           +++ Q++SG GKTA F L  L ++   D++   + +  +RELA Q   + +E  +F+K  
Sbjct: 46  NMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKIT 105
Query: 208 SNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDK 267
           S + V   F         E  K  N Q++VGTPG +L L+R K + L  +K F+LDE D 
Sbjct: 106 SQLIVPDSF---------EKNKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADN 156
Query: 268 MLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLH 327
           ML+Q  +      + R  P   Q+++FSAT +  +R   KK + +   + +    ++ + 
Sbjct: 157 MLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTN-EVNVD 215
Query: 328 GLQQHYVX-XXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHR 386
            ++Q Y+                 V+     +IFV +      L   L  +      +H 
Sbjct: 216 AIKQLYMDCKNEADKFDVLTELYGVMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHG 275
Query: 387 GMTQEERLKKYQEFKDFHKGLAIT 410
            +  +ER +   +F++    + IT
Sbjct: 276 DLQTQERDRLIDDFREGRSKVLIT 299

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 90.9 bits (224), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 55/165 (33%), Positives = 89/165 (53%), Gaps = 12/165 (7%)
Query: 151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ---ISKEYERFSKYM 207
           +++ Q++SG GKTA F L  L ++   D++   + +  +RELA Q   + +E  +F+K  
Sbjct: 46  NMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKIT 105
Query: 208 SNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDK 267
           S + V   F         E  K  N Q++VGTPG +L L+R K + L  +K F+LDE D 
Sbjct: 106 SQLIVPDSF---------EKNKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADN 156
Query: 268 MLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHD 312
           ML+Q  +      + R  P   Q+++FSAT +  +R   KK + +
Sbjct: 157 MLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPN 201

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score = 90.1 bits (222), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 55/165 (33%), Positives = 89/165 (53%), Gaps = 12/165 (7%)
Query: 151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ---ISKEYERFSKYM 207
           +++ Q++SG GKTA F L  L ++   D++   + +  +RELA Q   + +E  +F+K  
Sbjct: 63  NMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKIT 122
Query: 208 SNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDK 267
           S + V   F         E  K  N Q++VGTPG +L L+R K + L  +K F+LDE D 
Sbjct: 123 SQLIVPDSF---------EKNKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADN 173
Query: 268 MLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHD 312
           ML+Q  +      + R  P   Q+++FSAT +  +R   KK + +
Sbjct: 174 MLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPN 218

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 90.1 bits (222), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 69/272 (25%), Positives = 126/272 (46%), Gaps = 23/272 (8%)
Query: 151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYV------------------LVMCHTREL 192
           D++  A++G GKTA F+L  L Q+ +      +                  LV+  TREL
Sbjct: 54  DLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTREL 113
Query: 193 AFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKL 252
           A QI +E  +FS Y S ++  V +GG  I +    L+     ++V TPGR++ ++   K+
Sbjct: 114 AVQIYEEARKFS-YRSRVRPCVVYGGADIGQQIRDLE-RGCHLLVATPGRLVDMMERGKI 171
Query: 253 NLSLLKHFILDECDKMLE---QLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKF 309
            L   K+ +LDE D+ML+   + ++RR V++        +  MMFSAT  KEI+ + + F
Sbjct: 172 GLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDF 231
Query: 310 MHDPMEVYVDDEAKLTLHGLQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIA 369
           + + + + V      + +  Q+                     + +  ++FV++     +
Sbjct: 232 LDEYIFLAVGRVGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADS 291
Query: 370 LSTLLSEQNFPAVSIHRGMTQEERLKKYQEFK 401
           L   L  + +   SIH   +Q +R +   +F+
Sbjct: 292 LEDFLYHEGYACTSIHGDRSQRDREEALHQFR 323

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 89.4 bits (220), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 69/262 (26%), Positives = 121/262 (46%), Gaps = 7/262 (2%)
Query: 151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI 210
           +++ Q++SG GKTA FVLA L Q+E  +     L +  T ELA Q  K  E+  K+   +
Sbjct: 133 NLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPEL 192
Query: 211 KVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK-LNLSLLKHFILDECDKML 269
           K+     G  +++ ++     + QIV+GTPG +L      K ++   +K F+LDE D M+
Sbjct: 193 KLAYAVRGNKLERGQKI----SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 248
Query: 270 EQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGL 329
                +     I R  P   Q+++FSAT    +    +K + DP  + +  E + TL  +
Sbjct: 249 ATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEE-TLDTI 307
Query: 330 QQHYVXXXXXXXX-XXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGM 388
           +Q+YV                  +   Q +IF  +      L+  LS++      +   M
Sbjct: 308 KQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEM 367
Query: 389 TQEERLKKYQEFKDFHKGLAIT 410
             E+R    + F++  + + +T
Sbjct: 368 MVEQRAAVIERFREGKEKVLVT 389

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 89.0 bits (219), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 69/262 (26%), Positives = 121/262 (46%), Gaps = 7/262 (2%)
Query: 151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI 210
           +++ Q++SG GKTA FVLA L Q+E  +     L +  T ELA Q  K  E+  K+   +
Sbjct: 82  NLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPEL 141
Query: 211 KVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK-LNLSLLKHFILDECDKML 269
           K+     G  +++ ++     + QIV+GTPG +L      K ++   +K F+LDE D M+
Sbjct: 142 KLAYAVRGNKLERGQKI----SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 197
Query: 270 EQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGL 329
                +     I R  P   Q+++FSAT    +    +K + DP  + +  E + TL  +
Sbjct: 198 ATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEE-TLDTI 256
Query: 330 QQHYVXXXXXXXX-XXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGM 388
           +Q+YV                  +   Q +IF  +      L+  LS++      +   M
Sbjct: 257 KQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEM 316
Query: 389 TQEERLKKYQEFKDFHKGLAIT 410
             E+R    + F++  + + +T
Sbjct: 317 MVEQRAAVIERFREGKEKVLVT 338

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 89.0 bits (219), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 69/262 (26%), Positives = 121/262 (46%), Gaps = 7/262 (2%)
Query: 151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI 210
           +++ Q++SG GKTA FVLA L Q+E  +     L +  T ELA Q  K  E+  K+   +
Sbjct: 66  NLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPEL 125
Query: 211 KVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK-LNLSLLKHFILDECDKML 269
           K+     G  +++ ++     + QIV+GTPG +L      K ++   +K F+LDE D M+
Sbjct: 126 KLAYAVRGNKLERGQKI----SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 181
Query: 270 EQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGL 329
                +     I R  P   Q+++FSAT    +    +K + DP  + +  E + TL  +
Sbjct: 182 ATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEE-TLDTI 240
Query: 330 QQHYVXXXXXXXX-XXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGM 388
           +Q+YV                  +   Q +IF  +      L+  LS++      +   M
Sbjct: 241 KQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEM 300
Query: 389 TQEERLKKYQEFKDFHKGLAIT 410
             E+R    + F++  + + +T
Sbjct: 301 MVEQRAAVIERFREGKEKVLVT 322

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 89.0 bits (219), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 69/262 (26%), Positives = 121/262 (46%), Gaps = 7/262 (2%)
Query: 151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI 210
           +++ Q++SG GKTA FVLA L Q+E  +     L +  T ELA Q  K  E+  K+   +
Sbjct: 103 NLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPEL 162
Query: 211 KVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK-LNLSLLKHFILDECDKML 269
           K+     G  +++ ++     + QIV+GTPG +L      K ++   +K F+LDE D M+
Sbjct: 163 KLAYAVRGNKLERGQKI----SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 218
Query: 270 EQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGL 329
                +     I R  P   Q+++FSAT    +    +K + DP  + +  E + TL  +
Sbjct: 219 ATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEE-TLDTI 277
Query: 330 QQHYVXXXXXXXX-XXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGM 388
           +Q+YV                  +   Q +IF  +      L+  LS++      +   M
Sbjct: 278 KQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEM 337
Query: 389 TQEERLKKYQEFKDFHKGLAIT 410
             E+R    + F++  + + +T
Sbjct: 338 MVEQRAAVIERFREGKEKVLVT 359

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 89.0 bits (219), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 83/299 (27%), Positives = 138/299 (46%), Gaps = 30/299 (10%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G +++ +AK+G GKTA + +  L+        +  LV+  TREL  Q++       +YM 
Sbjct: 31  GKNVVVRAKTGSGKTAAYAIPILEL------GMKSLVVTPTRELTRQVASHIRDIGRYM- 83
Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
           + KV   +GG+P +   +  +  N  IVV TPGR+L L     ++LS  +  I+DE D M
Sbjct: 84  DTKVAEVYGGMPYKA--QINRVRNADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLM 141
Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHG 328
            E +    D++ I   + + K   +FSAT+ +EIR V K F+ +    Y + EA + L  
Sbjct: 142 FE-MGFIDDIKIILAQTSNRKITGLFSATIPEEIRKVVKDFITN----YEEIEACIGLAN 196
Query: 329 LQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGM 388
           ++  +V               +  +   V++FV++  R   L  L       A+ +   +
Sbjct: 197 VEHKFVHVKDDWRSKVQALREN--KDKGVIVFVRTRNRVAKLVRLFDN----AIELRGDL 250
Query: 389 TQEERLKKYQEFKDFHKGLAIT--FASDENDAKILNNVQDRFDVSISELPDEIDLSTYI 445
            Q  R +    F++    + IT   AS   D  ++  V + FD      P   DL TYI
Sbjct: 251 PQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVIN-FDA-----PQ--DLRTYI 301

>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of Djvlgb, A Pranarian Vasa-Like Rna Helicase Length = 253

Iteration: 1
 Score = 87.8 bits (216), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 66/225 (29%), Positives = 113/225 (50%), Gaps = 27/225 (12%)
Query: 111 GMDIERVNIVFNYDMPEDSDTYLHRVARAG--------RFGTKAVL-GMDILCQAKSGMG 161
           G D    N++ N+D  +   T  + +  A         +    A+L   DI+  A++G G
Sbjct: 13  GPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSG 72
Query: 162 KTAVFVLATLQQLETTDSN-------VY--VLVMCHTRELAFQISKEYERFSKYMSNIKV 212
           KTA F++  +  L   D N        Y   L++  TRELA QI  E ++FS   + ++ 
Sbjct: 73  KTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFS-LNTPLRS 131
Query: 213 GVFFGGLPI--QKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLE 270
            V +GG     Q  E  +  H   ++V TPGR++  +   K++L   K+ +LDE D+ML+
Sbjct: 132 CVVYGGADTHSQIREVQMGCH---LLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLD 188
Query: 271 ---QLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHD 312
              + ++R+ ++E    S   +Q +MFSAT  KEI+ +   F+++
Sbjct: 189 MGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYN 233

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score = 87.0 bits (214), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 55/176 (31%), Positives = 91/176 (51%), Gaps = 5/176 (2%)
Query: 146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK 205
           A+ G   + Q+++G GKT  ++L   ++++   + V  ++   TRELA QI  E  + +K
Sbjct: 38  ALRGESXVGQSQTGTGKTHAYLLPIXEKIKPERAEVQAVITAPTRELATQIYHETLKITK 97
Query: 206 YMSN---IKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFIL 262
           +      I      GG   QK  E L    P IV+GTPGRI   +R + L++      ++
Sbjct: 98  FCPKDRXIVARCLIGGTDKQKALEKLNV-QPHIVIGTPGRINDFIREQALDVHTAHILVV 156
Query: 263 DECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
           DE D  L+      DV +I    P   Q ++FSAT+ ++++P  KK+  +P  V+V
Sbjct: 157 DEADLXLDX-GFITDVDQIAARXPKDLQXLVFSATIPEKLKPFLKKYXENPTFVHV 211

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score = 82.8 bits (203), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 52/164 (31%), Positives = 84/164 (51%), Gaps = 5/164 (3%)
Query: 151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI 210
           +++ Q++SG GKTA FVLA L Q+E  +     L +  T ELA Q  K  E+  K+   +
Sbjct: 133 NLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPEL 192
Query: 211 KVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK-LNLSLLKHFILDECDKML 269
           K+     G  +++ ++     + QIV+GTPG +L      K ++   +K F+LDE D M+
Sbjct: 193 KLAYAVRGNKLERGQKI----SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 248
Query: 270 EQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDP 313
                +     I R  P   Q+++FSAT    +    +K + DP
Sbjct: 249 ATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDP 292

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score = 82.0 bits (201), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 52/164 (31%), Positives = 84/164 (51%), Gaps = 5/164 (3%)
Query: 151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI 210
           +++ Q++SG GKTA FVLA L Q+E  +     L +  T ELA Q  K  E+  K+   +
Sbjct: 66  NLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPEL 125
Query: 211 KVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK-LNLSLLKHFILDECDKML 269
           K+     G  +++ ++     + QIV+GTPG +L      K ++   +K F+LDE D M+
Sbjct: 126 KLAYAVRGNKLERGQKI----SEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 181
Query: 270 EQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDP 313
                +     I R  P   Q+++FSAT    +    +K + DP
Sbjct: 182 ATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDP 225

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score = 80.1 bits (196), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 52/182 (28%), Positives = 99/182 (54%), Gaps = 9/182 (4%)
Query: 146 AVLGMDILCQAKSGMGKTAVFVLATLQQL----ETTDSNVYVLVMCHTRELAFQISKEYE 201
           A+ G D+L  AK+G GKT  F++  L+ L     T+   + VL++  TRELA+Q  +   
Sbjct: 59  ALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLR 118
Query: 202 RFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILA-LVRNKKLNLSLLKHF 260
           +  K   +   G+  GG  ++ + E  + +N  I+V TPGR+L  +      + + L+  
Sbjct: 119 KVGKN-HDFSAGLIIGGKDLKHEAE--RINNINILVCTPGRLLQHMDETVSFHATDLQML 175
Query: 261 ILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDD 320
           +LDE D++L+ +     +  +  + P  +Q ++FSAT +K ++ + +  + +P  V+V +
Sbjct: 176 VLDEADRILD-MGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVHE 234
Query: 321 EA 322
           +A
Sbjct: 235 KA 236

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score = 76.6 bits (187), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 50/176 (28%), Positives = 89/176 (50%), Gaps = 10/176 (5%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTD------SNVYVLVMCHTRELAFQISKEYER 202
           G+D++  A++G GKT  +++     L++        +   +LV+  TRELA  +  E  +
Sbjct: 57  GIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSK 116
Query: 203 FSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFIL 262
           +S     +K    +GG       E + +    I++ TPGR+  L  N  +NL  + + ++
Sbjct: 117 YS--YKGLKSICIYGGRNRNGQIEDI-SKGVDIIIATPGRLNDLQMNNSVNLRSITYLVI 173
Query: 263 DECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
           DE DKML+ +E    +++I       +Q +M SAT    +R +   ++ DPM VYV
Sbjct: 174 DEADKMLD-MEFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV 228

>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human Dead-Box Rna Helicase Ddx5 (P68) Length = 253

Iteration: 1
 Score = 74.3 bits (181), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 52/176 (29%), Positives = 91/176 (51%), Gaps = 16/176 (9%)
Query: 146 AVLGMDILCQAKSGMGKTAVFVLATLQQ------LETTDSNVYVLVMCHTRELAFQISKE 199
           A+ G+D++  A++G GKT  ++L  +        LE  D  +  LV+  TRELA Q+ + 
Sbjct: 77  ALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPI-CLVLAPTRELAQQVQQV 135
Query: 200 YERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKH 259
              + +    +K    +GG P       L+    +I + TPGR++  +   K NL    +
Sbjct: 136 AAEYCR-ACRLKSTCIYGGAPKGPQIRDLE-RGVEICIATPGRLIDFLECGKTNLRRTTY 193
Query: 260 FILDECDKMLE---QLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHD 312
            +LDE D+ML+   + ++R+ V +I       +Q +M+SAT  KE+R + + F+ D
Sbjct: 194 LVLDEADRMLDMGFEPQIRKIVDQIRPD----RQTLMWSATWPKEVRQLAEDFLKD 245

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 74.3 bits (181), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 88/173 (50%), Gaps = 10/173 (5%)
Query: 146 AVLGMDILCQAKSGMGKTAVFVLATLQQ------LETTDSNVYVLVMCHTRELAFQISKE 199
           A+ G+D++  A++G GKT  ++L  +        LE  D  +  LV+  TRELA Q+ + 
Sbjct: 63  ALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPI-CLVLAPTRELAQQVQQV 121
Query: 200 YERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKH 259
              + +    +K    +GG P       L+    +I + TPGR++  +   K NL    +
Sbjct: 122 AAEYCR-ACRLKSTCIYGGAPKGPQIRDLE-RGVEICIATPGRLIDFLECGKTNLRRTTY 179
Query: 260 FILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHD 312
            +LDE D+ML+ +     +++I       +Q +M+SAT  KE+R + + F+ D
Sbjct: 180 LVLDEADRMLD-MGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKD 231

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 64.7 bits (156), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 64/286 (22%), Positives = 122/286 (42%), Gaps = 28/286 (9%)
Query: 151 DILCQAKSGMGKTAVFVLATLQQLETT--DSN--VYVLVMCHTRELAFQISKEYERFSKY 206
           D++ +AK+G GKT  F++   Q L  T  DS   V  +++  TR+LA QI  E ++    
Sbjct: 62  DVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDM 121
Query: 207 MSNIKVGV---FFGGLPIQKDEEYLKTHNPQIVVGTPGRIL-ALVRNKKLNLSLLKHFIL 262
              +K        GG   +     +    P IV+ TPGR++  L +        + + +L
Sbjct: 122 NYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVL 181
Query: 263 DECDKMLEQLEMRRDVQEIF-------RSSPHTKQVMMFSATLSKEIRPVCKKFMHDPME 315
           DE D++LE +  R D++ I          S    + ++FSATL  +++ +    M+    
Sbjct: 182 DEADRLLE-IGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKEC 240
Query: 316 VYVD--DEAKLTLHG-------LQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTR 366
           +++D  D+ +   H        + + +                +     + +IF  +V  
Sbjct: 241 LFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKF 300
Query: 367 CIALSTLLS---EQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAI 409
              L ++L    +++ P +  H  +TQ +R    + FK    G+ +
Sbjct: 301 TSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILV 346

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 64.3 bits (155), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 64/286 (22%), Positives = 122/286 (42%), Gaps = 28/286 (9%)
Query: 151 DILCQAKSGMGKTAVFVLATLQQLETT--DSN--VYVLVMCHTRELAFQISKEYERFSKY 206
           D++ +AK+G GKT  F++   Q L  T  DS   V  +++  TR+LA QI  E ++    
Sbjct: 113 DVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDM 172
Query: 207 MSNIKVGV---FFGGLPIQKDEEYLKTHNPQIVVGTPGRIL-ALVRNKKLNLSLLKHFIL 262
              +K        GG   +     +    P IV+ TPGR++  L +        + + +L
Sbjct: 173 NYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVL 232
Query: 263 DECDKMLEQLEMRRDVQEIF-------RSSPHTKQVMMFSATLSKEIRPVCKKFMHDPME 315
           DE D++LE +  R D++ I          S    + ++FSATL  +++ +    M+    
Sbjct: 233 DEADRLLE-IGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKEC 291
Query: 316 VYVD--DEAKLTLHG-------LQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTR 366
           +++D  D+ +   H        + + +                +     + +IF  +V  
Sbjct: 292 LFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKF 351
Query: 367 CIALSTLLS---EQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAI 409
              L ++L    +++ P +  H  +TQ +R    + FK    G+ +
Sbjct: 352 TSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILV 397

>pdb|2WAX|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex With An Edc3-Fdf Peptide Length = 193

Iteration: 1
 Score = 63.9 bits (154), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 29/53 (54%), Positives = 40/53 (75%), Gaps = 3/53 (5%)
Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDI 152
           R LV T+LF RG+DI+ VN+V N+D P+ ++TYLHR+ R+GRFG    LG+ I
Sbjct: 96  RNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGH---LGLAI 145

>pdb|2WAX|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex With An Edc3-Fdf Peptide Length = 193

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 30/97 (30%), Positives = 42/97 (43%), Gaps = 5/97 (5%)
Query: 312 DPMEVYVDDEAKLTLHGLQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTRCIALS 371
           DP E+ + +E  LTL G+ Q+Y                  L+ NQ +IF  S  R   L+
Sbjct: 4   DPYEINLMEE--LTLKGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLA 61
Query: 372 TLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLA 408
             +S+  +    IH  M QE R +    F DF  GL 
Sbjct: 62  KKISQLGYSCFYIHAKMRQEHRNRV---FHDFRNGLC 95

>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion) Bound To Ssrna And Amp-Pnp Length = 512

Iteration: 1
 Score = 63.9 bits (154), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 64/286 (22%), Positives = 122/286 (42%), Gaps = 28/286 (9%)
Query: 151 DILCQAKSGMGKTAVFVLATLQQLETT--DSN--VYVLVMCHTRELAFQISKEYERFSKY 206
           D++ +AK+G GKT  F++   Q L  T  DS   V  +++  TR+LA QI  E ++    
Sbjct: 62  DVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDM 121
Query: 207 MSNIKVGV---FFGGLPIQKDEEYLKTHNPQIVVGTPGRIL-ALVRNKKLNLSLLKHFIL 262
              +K        GG   +     +    P IV+ TPGR++  L +        + + +L
Sbjct: 122 NYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVL 181
Query: 263 DECDKMLEQLEMRRDVQEIF-------RSSPHTKQVMMFSATLSKEIRPVCKKFMHDPME 315
           DE D++LE +  R D++ I          S    + ++FSATL  +++ +    M+    
Sbjct: 182 DEADRLLE-IGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKEC 240
Query: 316 VYVD--DEAKLTLHG-------LQQHYVXXXXXXXXXXXXXXXDVLEFNQVVIFVKSVTR 366
           +++D  D+ +   H        + + +                +     + +IF  +V  
Sbjct: 241 LFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKF 300
Query: 367 CIALSTLLS---EQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAI 409
              L ++L    +++ P +  H  +TQ +R    + FK    G+ +
Sbjct: 301 TSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILV 346

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 61.6 bits (148), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 50/171 (29%), Positives = 83/171 (48%), Gaps = 19/171 (11%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQL-ETTDSNVYVLVMCHTRELAFQISKEYERFSKYM 207
           G ++L  A +G GKT  F +  L QL +  +     L++  TRELA QI +E  + S+  
Sbjct: 66  GRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISE-- 123
Query: 208 SNIKVGVFFGGLPIQKDEEYLKTHNPQ------IVVGTPGRILALVRNKK--LNLSLLKH 259
                G  F    I K     K   P+      I+V TP R++ L++     ++L+ ++ 
Sbjct: 124 -----GTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEW 178
Query: 260 FILDECDKMLE--QLEMRRDVQEIFRS-SPHTKQVMMFSATLSKEIRPVCK 307
            ++DE DK+ E  +   R  +  IF + + H  +  MFSAT + ++   CK
Sbjct: 179 LVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCK 229

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 59.3 bits (142), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 47/165 (28%), Positives = 85/165 (51%), Gaps = 10/165 (6%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQ---QLETTDSN-VYVLVMCHTRELAFQISKEYERFS 204
           G D+L  AK+G GKT  F++  ++   +L     N   VL++  TRELA Q     +   
Sbjct: 91  GRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELM 150
Query: 205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNP-QIVVGTPGRILALVRNKK-LNLSLLKHFIL 262
            +  +   G+  GG    +  E  K  N   I+V TPGR+L  ++N        L+  ++
Sbjct: 151 THHVH-TYGLIMGG--SNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVI 207
Query: 263 DECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCK 307
           DE D++L+ +    ++++I +  P  +Q M+FSAT ++++  + +
Sbjct: 208 DEADRILD-VGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLAR 251

>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The Bacillus Subtilis Yxin Protein Length = 163

Iteration: 1
 Score = 59.3 bits (142), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 23/48 (47%), Positives = 35/48 (72%)
Query: 99  WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKA 146
           +R LVAT++  RG+DIE +++V NYD+P + ++Y+HR  R GR G K 
Sbjct: 86  YRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKG 133

>pdb|2YJT|D Chain D, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound To Regulator Of Ribonuclease Activity A (Rraa) Length = 170

Iteration: 1
 Score = 58.9 bits (141), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 28/47 (59%), Positives = 35/47 (74%), Gaps = 3/47 (6%)
Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRV---ARAGRFGT 144
           +LVAT++  RG+DI  V+ VFN+DMP   DTYLHR+   ARAGR GT
Sbjct: 83  VLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGT 129

>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25 Rna Helicase Length = 175

Iteration: 1
 Score = 58.9 bits (141), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 37/54 (68%), Gaps = 6/54 (11%)
Query: 100 RILVATNLFGRGMDIERVNIVFNYDMP------EDSDTYLHRVARAGRFGTKAV 147
           ++L+ TN+  RG+D+++V IV N+D+P       D +TYLHR+ R GRFG K +
Sbjct: 86  KVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGL 139

>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p Length = 187

Iteration: 1
 Score = 58.2 bits (139), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 35/54 (64%), Gaps = 6/54 (11%)
Query: 100 RILVATNLFGRGMDIERVNIVFNYDMP------EDSDTYLHRVARAGRFGTKAV 147
           ++L+ TN+  RG+DI  V++V NYD+P       D  TY+HR+ R GRFG K V
Sbjct: 87  KVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGV 140

>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein Dbp5 Length = 189

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 34/54 (62%), Gaps = 6/54 (11%)
Query: 100 RILVATNLFGRGMDIERVNIVFNYDMP------EDSDTYLHRVARAGRFGTKAV 147
           ++L+ TN+  RG+DI  V+ V NYD+P       D  TY+HR+ R GRFG K V
Sbjct: 89  KVLITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGV 142

>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1 H337r And Ip6 Length = 188

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 34/54 (62%), Gaps = 6/54 (11%)
Query: 100 RILVATNLFGRGMDIERVNIVFNYDMP------EDSDTYLHRVARAGRFGTKAV 147
           ++L+ TN+  RG+DI  V+ V NYD+P       D  TY+HR+ R GRFG K V
Sbjct: 88  KVLITTNVLARGIDIPTVSXVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGV 141

>pdb|2JGN|A Chain A, Ddx3 Helicase Domain Length = 185

Iteration: 1
 Score = 52.8 bits (125), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 22/44 (50%), Positives = 29/44 (65%)
Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGT 144
           ILVAT +  RG+DI  V  V N+D+P D + Y+HR+ R GR G 
Sbjct: 99  ILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGN 142

>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain Length = 191

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 30/47 (63%)
Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV 147
           +LVAT++  +G+D   +  V NYDMPE+ + Y+HR+ R G  G   +
Sbjct: 107 VLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGI 153

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 17/38 (44%), Positives = 31/38 (81%)
Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVA 137
           RIL++T+L  RG+D+++V++V NYD+P + + Y+HR+ 
Sbjct: 82  RILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIG 119

>pdb|3I32|A Chain A, Dimeric Structure Of A Hera Helicase Fragment Including The C-Terminal Reca Domain, The Dimerization Domain, And The Rna Binding Domain Length = 300

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 16/35 (45%), Positives = 27/35 (77%)
Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLH 134
           R+LVAT++  RG+DI +V++V +Y MP+ ++ Y H
Sbjct: 80  RVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQH 114

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	448
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	1e-160
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	1e-124
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	1e-107
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	5e-86
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	2e-83
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	6e-17
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	3e-83
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	3e-17
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	7e-81
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-16
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	2e-78
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	2e-17
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	5e-75
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	4e-15
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	8e-74
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	4e-15
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	4e-72
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	7e-15
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	1e-61
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	3e-12
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	2e-61
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	5e-12
3bor_A	237	Human initiation factor 4A-II; translation initiat	1e-60
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	3e-59
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	1e-58
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	2e-58
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	2e-12
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	3e-58
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	1e-12
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	3e-57
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	2e-56
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	6e-51
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	9e-12
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	1e-49
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	1e-48
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	9e-12
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	2e-47
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	3e-47
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	2e-26
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	2e-44
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	9e-44
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	7e-40
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	5e-06
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	5e-38
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	2e-37
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	2e-35
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	8e-35
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	2e-28
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	2e-22
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	2e-16
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	3e-14
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	1e-15
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	2e-13
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	3e-13
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	2e-07
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	6e-13
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	1e-12
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	1e-12
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	2e-06
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	2e-12
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	1e-09
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	4e-12
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	8e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-12
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-11
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	7e-12
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	1e-05
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	6e-09
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	8e-07
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	5e-06
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	6e-06
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	8e-06
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	4e-04
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	1e-05
3b6e_A	216	Interferon-induced helicase C domain-containing P;	2e-05
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	2e-05
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	4e-05
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	1e-04
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	2e-04
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	9e-04

>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 =  458 bits (1180), Expect = e-160
 Identities = 269/420 (64%), Positives = 299/420 (71%), Gaps = 78/420 (18%)

Query: 73  AYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTY 132
                 SSGFRDFLLKPE+LRAIVDC         F    +++   I             
Sbjct: 1   GSPGHMSSGFRDFLLKPELLRAIVDCG--------FEHPSEVQHECIP------------ 40

Query: 133 LHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTREL 192
                       +A+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTREL
Sbjct: 41  ------------QAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTREL 88

Query: 193 AFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKL 252
           AFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK L
Sbjct: 89  AFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSL 148

Query: 253 NLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHD 312
           NL  +KHFILDECDKMLEQL+MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM D
Sbjct: 149 NLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQD 208

Query: 313 PMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALST 372
           PME++VDDE KLTLHGLQQ+YVKLK+NEKN+KLF+LLDVLEFNQVVIFVKSV RCIAL+ 
Sbjct: 209 PMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQ 268

Query: 373 LLSEQNFPAVSIHRGMTQEERLKKYQEFKDF----------------------------- 403
           LL EQNFPA++IHRGM QEERL +YQ+FKDF                             
Sbjct: 269 LLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMP 328

Query: 404 -----------------HKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIE 446
                             KGLAITF SDENDAKILN+VQDRF+V+ISELPDEID+S+YIE
Sbjct: 329 EDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIE 388

>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 =  365 bits (940), Expect = e-124
 Identities = 115/426 (26%), Positives = 177/426 (41%), Gaps = 84/426 (19%)

Query: 67  QKEVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMP 126
            +      ++   + F DF LK E+L  I +          F +   I+   I       
Sbjct: 8   TRPQTDDVLNTKGNTFEDFYLKRELLMGIFEAG--------FEKPSPIQEEAIPV----- 54

Query: 127 EDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVM 186
                              A+ G DIL +AK+G GKTA FV+ TL++++   + +  L+M
Sbjct: 55  -------------------AITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIM 95

Query: 187 CHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILAL 246
             TRELA Q S+      K+   I   V  GG  ++ D   L      I+VGTPGR+L L
Sbjct: 96  VPTRELALQTSQVVRTLGKHC-GISCMVTTGGTNLRDDILRLN-ETVHILVGTPGRVLDL 153

Query: 247 VRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVC 306
              K  +LS    FI+DE DKML + + +  +++I    P T Q ++FSAT    ++   
Sbjct: 154 ASRKVADLSDCSLFIMDEADKMLSR-DFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFM 212

Query: 307 KKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTR 366
            K +H P E+ + +E  LTL G+ Q+Y  ++E +K   L  L   L+ NQ +IF  S  R
Sbjct: 213 VKHLHKPYEINLMEE--LTLKGITQYYAFVEERQKLHCLNTLFSKLQINQAIIFCNSTNR 270

Query: 367 CIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDF----------------------- 403
              L+  +++  +     H  M Q+ER K + EF+                         
Sbjct: 271 VELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVV 330

Query: 404 -----------------------HKGLAITFASDENDAKILNNVQDRFDVSISELPDEID 440
                                  H GLAI   +   D   L  ++      I+ +P  ID
Sbjct: 331 INFDFPKTAETYLHRIGRSGRFGHLGLAINLINWN-DRFNLYKIEQELGTEIAAIPATID 389

Query: 441 LSTYIE 446
            S Y+ 
Sbjct: 390 KSLYVA 395

>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 =  314 bits (808), Expect = e-107
 Identities = 171/250 (68%), Positives = 188/250 (75%), Gaps = 32/250 (12%)

Query: 69  EVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPED 128
           +VKG+YVSIHSSGFRDFLLKPE+LRAIVDC         F    +++   I         
Sbjct: 3   DVKGSYVSIHSSGFRDFLLKPELLRAIVDCG--------FEHPSEVQHECIPQ------- 47

Query: 129 SDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH 188
                            A+LGMD+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCH
Sbjct: 48  -----------------AILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCH 90

Query: 189 TRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVR 248
           TRELAFQISKEYERFSKYM N+KV VFFGGL I+KDEE LK + P IVVGTPGRILAL R
Sbjct: 91  TRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALAR 150

Query: 249 NKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKK 308
           NK LNL  +KHFILDECDKMLEQL+MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+K
Sbjct: 151 NKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRK 210

Query: 309 FMHDPMEVYV 318
           FM DPME++V
Sbjct: 211 FMQDPMEIFV 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 =  261 bits (670), Expect = 5e-86
 Identities = 71/260 (27%), Positives = 110/260 (42%), Gaps = 34/260 (13%)

Query: 60  AGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNI 119
               L+  +   G  +    + F   LL   +L  +            F R   ++   I
Sbjct: 4   TAQDLSSPRTRTGDVLLAEPADFESLLLSRPVLEGLRAAG--------FERPSPVQLKAI 55

Query: 120 VFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDS 179
                                        G+D++ QAKSG GKT VF    L  L   + 
Sbjct: 56  PL------------------------GRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENL 91

Query: 180 NVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGT 239
           +  +L++  TRE+A QI          M  ++  VF GG P+ +D+  LK     I VG+
Sbjct: 92  STQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLK--KCHIAVGS 149

Query: 240 PGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLS 299
           PGRI  L+    LN   ++ FILDE DK+LE+   +  +  I+ S P +KQ++  SAT  
Sbjct: 150 PGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYP 209

Query: 300 KEIRPVCKKFMHDPMEVYVD 319
           + +     K+M DP  V ++
Sbjct: 210 EFLANALTKYMRDPTFVRLN 229

>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 =  261 bits (670), Expect = 2e-83
 Identities = 99/335 (29%), Positives = 161/335 (48%), Gaps = 51/335 (15%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D++ QA+SG GKTA F ++ LQQ+E        LV+  TRELA QI K       YM 
Sbjct: 77  GYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYM- 135

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
                   GG  ++ + + L+   P I+VGTPGR+  ++  + L+   +K F+LDE D+M
Sbjct: 136 GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEM 195

Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHG 328
           L +   +  + +IF+      QV++ SAT+  ++  V KKFM DP+ + V  E +LTL G
Sbjct: 196 LSR-GFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKE-ELTLEG 253

Query: 329 LQQHYVKL-KENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRG 387
           ++Q Y+ + +E  K   L +L + L   Q VIF+ +  +   L+  +  ++F   ++H  
Sbjct: 254 IRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGD 313

Query: 388 MTQEERLKKYQEFK----------------------------DF---------------- 403
           M Q+ER    +EF+                            D                 
Sbjct: 314 MDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGR 373

Query: 404 --HKGLAITFASDENDAKILNNVQDRFDVSISELP 436
              KG+AI   + E D + L +++  ++ SI E+P
Sbjct: 374 FGRKGVAINMVT-EEDKRTLRDIETFYNTSIEEMP 407

>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 = 81.5 bits (202), Expect = 6e-17
 Identities = 23/48 (47%), Positives = 37/48 (77%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV 147
           R+L+ T+L  RG+D+++V++V NYD+P + + Y+HR+ R GRFG K V
Sbjct: 332 RVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGV 379

>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 =  260 bits (667), Expect = 3e-83
 Identities = 106/339 (31%), Positives = 165/339 (48%), Gaps = 53/339 (15%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D+L QA+SG GKT  F +A LQ+++T+      L++  TRELA QI K     + +M 
Sbjct: 58  GHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHM- 116

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
           +IKV    GG    +D E L+  + QIVVGTPGR+   ++ ++     +K FILDE D+M
Sbjct: 117 DIKVHACIGGTSFVEDAEGLR--DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEM 174

Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHG 328
           L     +  + +IF   P T QV++ SAT+  ++  V  KFM +P+ + V  + +LTL G
Sbjct: 175 LSS-GFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKD-ELTLEG 232

Query: 329 LQQHYVKLKENE-KNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRG 387
           ++Q YV ++E E K + L +L D +   Q VIF  +  +   L+T L    F   +I+  
Sbjct: 233 IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSD 292

Query: 388 MTQEERLKKYQEFK----------------------------DF---------------- 403
           + Q+ER    +EF+                            D                 
Sbjct: 293 LPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGR 352

Query: 404 --HKGLAITFASDENDAKILNNVQDRFDVSISELPDEID 440
              KG+AI F ++E D   +  ++  +   I ELP +I 
Sbjct: 353 FGRKGVAINFVTNE-DVGAMRELEKFYSTQIEELPSDIA 390

>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 = 82.2 bits (204), Expect = 3e-17
 Identities = 24/48 (50%), Positives = 38/48 (79%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV 147
           RIL++T+L  RG+D+++V++V NYD+P + + Y+HR+ R GRFG K V
Sbjct: 311 RILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGV 358

>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 =  254 bits (652), Expect = 7e-81
 Identities = 100/335 (29%), Positives = 158/335 (47%), Gaps = 52/335 (15%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D++ Q++SG GKTA F ++ LQ L+        L++  TRELA QI K       YM 
Sbjct: 74  GRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYM- 132

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
           N++     GG  + +D   L  +   +V GTPGR+  ++R + L    +K  +LDE D+M
Sbjct: 133 NVQCHACIGGTNVGEDIRKLD-YGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEM 191

Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHG 328
           L +   +  + +++R  P   QV++ SATL  EI  +  KFM DP+ + V  + +LTL G
Sbjct: 192 LNK-GFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRD-ELTLEG 249

Query: 329 LQQHYVKL-KENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRG 387
           ++Q +V + +E  K   L +L D L   Q VIF  +  +   L+  + E NF   S+H  
Sbjct: 250 IKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGD 309

Query: 388 MTQEERLKKYQEFK----------------------------DF---------------- 403
           M Q+ER    +EF+                            D                 
Sbjct: 310 MPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGR 369

Query: 404 --HKGLAITFASDENDAKILNNVQDRFDVSISELP 436
              KG+AI F  ++ D +IL +++  +   I E+P
Sbjct: 370 YGRKGVAINFVKND-DIRILRDIEQYYSTQIDEMP 403

>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 = 80.3 bits (199), Expect = 1e-16
 Identities = 20/48 (41%), Positives = 39/48 (81%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV 147
           R+L++T+++ RG+D+ +V+++ NYD+P + + Y+HR+ R+GR+G K V
Sbjct: 328 RVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGV 375

>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 =  239 bits (613), Expect = 5e-75
 Identities = 72/254 (28%), Positives = 124/254 (48%), Gaps = 7/254 (2%)

Query: 151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI 210
           +++ Q++SG GKTA FVLA L Q+E  +     L +  T ELA Q  K  E+  K+   +
Sbjct: 66  NLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPEL 125

Query: 211 KVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRIL-ALVRNKKLNLSLLKHFILDECDKML 269
           K+     G  +++ ++     + QIV+GTPG +L    + K ++   +K F+LDE D M+
Sbjct: 126 KLAYAVRGNKLERGQK----ISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 181

Query: 270 EQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGL 329
                +     I R  P   Q+++FSAT    +    +K + DP  + +  E + TL  +
Sbjct: 182 ATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKRE-EETLDTI 240

Query: 330 QQHYVKLK-ENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGM 388
           +Q+YV     +EK + L  L   +   Q +IF  +      L+  LS++      +   M
Sbjct: 241 KQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEM 300

Query: 389 TQEERLKKYQEFKD 402
             E+R    + F++
Sbjct: 301 MVEQRAAVIERFRE 314

>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 = 75.7 bits (187), Expect = 4e-15
 Identities = 25/54 (46%), Positives = 38/54 (70%), Gaps = 6/54 (11%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSD------TYLHRVARAGRFGTKAV 147
           ++LV TN+  RG+D+E+V++V N+D+P D D      TYLHR+ R GRFG + +
Sbjct: 318 KVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGL 371

>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 =  238 bits (610), Expect = 8e-74
 Identities = 72/254 (28%), Positives = 124/254 (48%), Gaps = 7/254 (2%)

Query: 151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI 210
           +++ Q++SG GKTA FVLA L Q+E  +     L +  T ELA Q  K  E+  K+   +
Sbjct: 133 NLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPEL 192

Query: 211 KVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRIL-ALVRNKKLNLSLLKHFILDECDKML 269
           K+     G  +++ ++     + QIV+GTPG +L    + K ++   +K F+LDE D M+
Sbjct: 193 KLAYAVRGNKLERGQK----ISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 248

Query: 270 EQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGL 329
                +     I R  P   Q+++FSAT    +    +K + DP  + +  E + TL  +
Sbjct: 249 ATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKRE-EETLDTI 307

Query: 330 QQHYVKLK-ENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGM 388
           +Q+YV     +EK + L  L   +   Q +IF  +      L+  LS++      +   M
Sbjct: 308 KQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEM 367

Query: 389 TQEERLKKYQEFKD 402
             E+R    + F++
Sbjct: 368 MVEQRAAVIERFRE 381

>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 = 76.2 bits (188), Expect = 4e-15
 Identities = 25/54 (46%), Positives = 38/54 (70%), Gaps = 6/54 (11%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSD------TYLHRVARAGRFGTKAV 147
           ++LV TN+  RG+D+E+V++V N+D+P D D      TYLHR+ R GRFG + +
Sbjct: 385 KVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGL 438

>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 =  231 bits (592), Expect = 4e-72
 Identities = 66/253 (26%), Positives = 120/253 (47%), Gaps = 8/253 (3%)

Query: 151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI 210
           +++ Q++SG GKTA F L  L ++   D++   + +  +RELA Q  +  +   K+    
Sbjct: 46  NMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKIT 105

Query: 211 KVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLE 270
              +        K        N Q++VGTPG +L L+R K + L  +K F+LDE D ML+
Sbjct: 106 SQLIVPDSFEKNKQ------INAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLD 159

Query: 271 QLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQ 330
           Q  +      + R  P   Q+++FSAT +  +R   KK + +   + +    ++ +  ++
Sbjct: 160 QQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTN-EVNVDAIK 218

Query: 331 QHYVKLK-ENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMT 389
           Q Y+  K E +K   L EL  ++     +IFV +      L   L  +      +H  + 
Sbjct: 219 QLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQ 278

Query: 390 QEERLKKYQEFKD 402
            +ER +   +F++
Sbjct: 279 TQERDRLIDDFRE 291

>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 = 74.9 bits (185), Expect = 7e-15
 Identities = 25/54 (46%), Positives = 35/54 (64%), Gaps = 6/54 (11%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMP------EDSDTYLHRVARAGRFGTKAV 147
           ++L+ TN+  RG+DI  V++V NYD+P       D  TY+HR+ R GRFG K V
Sbjct: 295 KVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGV 348

>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 =  202 bits (516), Expect = 1e-61
 Identities = 70/256 (27%), Positives = 122/256 (47%), Gaps = 24/256 (9%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G +++ +AK+G GKTA + +  L+        +  LV+  TREL  Q++       +YM 
Sbjct: 31  GKNVVVRAKTGSGKTAAYAIPILEL------GMKSLVVTPTRELTRQVASHIRDIGRYM- 83

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
           + KV   +GG+P +     ++  N  IVV TPGR+L L     ++LS  +  I+DE D M
Sbjct: 84  DTKVAEVYGGMPYKAQINRVR--NADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLM 141

Query: 269 LEQLEM--RRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTL 326
               EM    D++ I   + + K   +FSAT+ +EIR V K F+ +  E+       + L
Sbjct: 142 ---FEMGFIDDIKIILAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIEA----CIGL 194

Query: 327 HGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHR 386
             ++  +V +K  +  +   + L   +   V++FV+  TR       L      A+ +  
Sbjct: 195 ANVEHKFVHVK--DDWRSKVQALRENKDKGVIVFVR--TRNRVAK--LVRLFDNAIELRG 248

Query: 387 GMTQEERLKKYQEFKD 402
            + Q  R +    F++
Sbjct: 249 DLPQSVRNRNIDAFRE 264

>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 = 66.4 bits (163), Expect = 3e-12
 Identities = 20/44 (45%), Positives = 29/44 (65%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG 143
            +L+ T++  RG+DI  V  V N+D P+D  TY+HR+ R GR G
Sbjct: 268 DMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMG 311

>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 =  202 bits (517), Expect = 2e-61
 Identities = 87/254 (34%), Positives = 141/254 (55%), Gaps = 15/254 (5%)

Query: 151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI 210
           +I+ QA++G GKTA F +  ++ +   ++ +  +++  TRELA Q++ E E       N+
Sbjct: 46  NIVAQARTGSGKTASFAIPLIELVNE-NNGIEAIILTPTRELAIQVADEIESLKGNK-NL 103

Query: 211 KVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLE 270
           K+   +GG  I    + LK  N  IVVGTPGRIL  +    LNL  +K+FILDE D+M  
Sbjct: 104 KIAKIYGGKAIYPQIKALK--NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEM-- 159

Query: 271 QLEM--RRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHG 328
            L M   +DV++I  +    K++++FSAT+ +EI  + KK+M D   +     A +    
Sbjct: 160 -LNMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAKINANIE--- 215

Query: 329 LQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGM 388
             Q YV++ ENE+ + L  LL   EF   ++F K+      L+++L +  F A +IH  +
Sbjct: 216 --QSYVEVNENERFEALCRLLKNKEF-YGLVFCKTKRDTKELASMLRDIGFKAGAIHGDL 272

Query: 389 TQEERLKKYQEFKD 402
           +Q +R K  + FK 
Sbjct: 273 SQSQREKVIRLFKQ 286

>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 = 66.0 bits (162), Expect = 5e-12
 Identities = 21/46 (45%), Positives = 34/46 (73%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK 145
           RIL+AT++  RG+D+  +N V NY +P++ ++Y+HR+ R GR G K
Sbjct: 290 RILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKK 335

>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 =  196 bits (501), Expect = 1e-60
 Identities = 66/173 (38%), Positives = 97/173 (56%), Gaps = 2/173 (1%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D++ QA+SG GKTA F ++ LQQLE        LV+  TRELA QI K       YM 
Sbjct: 67  GYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYM- 125

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
                   GG  ++ + + L+   P IVVGTPGR+  ++  + L+   +K F+LDE D+M
Sbjct: 126 GATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEM 185

Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDE 321
           L +   +  + EIF+    + QV++ SAT+  ++  V KKFM DP+ + V  E
Sbjct: 186 LSR-GFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKKE 237

>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 =  191 bits (489), Expect = 3e-59
 Identities = 52/168 (30%), Positives = 94/168 (55%), Gaps = 2/168 (1%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G DIL +AK+G GK+  +++  L++L+    N+  +V+  TRELA Q+S+   + SK+M 
Sbjct: 40  GRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMG 99

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
             KV    GG  ++ D   L      +V+ TPGRIL L++     +  ++  +LDE DK+
Sbjct: 100 GAKVMATTGGTNLRDDIMRLD-DTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKL 158

Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEV 316
           L Q +  + +++I  + P  +Q++++SAT    ++      +  P E+
Sbjct: 159 LSQ-DFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI 205

>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 =  191 bits (487), Expect = 1e-58
 Identities = 69/178 (38%), Positives = 104/178 (58%), Gaps = 5/178 (2%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D+L QA+SG GKT  F +A LQ+++T+      L++  TRELA QI K     + +M 
Sbjct: 51  GHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHM- 109

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
           +IKV    GG    +D E L+  + QIVVGTPGR+   ++ ++     +K FILDE D+M
Sbjct: 110 DIKVHACIGGTSFVEDAEGLR--DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEM 167

Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTL 326
           L     +  + +IF   P T QV++ SAT+  ++  V  KFM +P+ + V  + +LTL
Sbjct: 168 LSS-GFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKD-ELTL 223

>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 =  200 bits (511), Expect = 2e-58
 Identities = 60/295 (20%), Positives = 117/295 (39%), Gaps = 34/295 (11%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETT----DSNVYVLVMCHTRELAFQISKEYERFS 204
             D++ +AK+G GKT  F++   Q L  T       V  +++  TR+LA QI  E ++  
Sbjct: 60  DHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIH 119

Query: 205 KY---MSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNL-SLLKHF 260
                +         GG   +     +    P IV+ TPGR++ ++          + + 
Sbjct: 120 DMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYK 179

Query: 261 ILDECDKMLEQLEM--RRDVQEIFRSSP-------HTKQVMMFSATLSKEIRPVCKKFMH 311
           +LDE D++   LE+  R D++ I               + ++FSATL  +++ +    M+
Sbjct: 180 VLDEADRL---LEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMN 236

Query: 312 DPMEVYV---DDEAKLTLHGLQQHYVKLKENEKNKKLF------ELLDVLEFNQVVIFVK 362
               +++   D         + Q  V  ++   +          ++ +     + +IF  
Sbjct: 237 KKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAP 296

Query: 363 SVTRCIALSTLLSEQN---FPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASD 414
           +V     L ++L  +     P +  H  +TQ +R    + FK       I   +D
Sbjct: 297 TVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKK--DESGILVCTD 349

>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 = 68.3 bits (167), Expect = 2e-12
 Identities = 20/51 (39%), Positives = 30/51 (58%), Gaps = 4/51 (7%)

Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRV---ARAGRFGTKAVL 148
           ILV T++  RGMD   V+ V    +P +   Y+HR+   AR+G+ G  +VL
Sbjct: 344 ILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEG-SSVL 393

>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 =  199 bits (508), Expect = 3e-58
 Identities = 60/295 (20%), Positives = 117/295 (39%), Gaps = 34/295 (11%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETT----DSNVYVLVMCHTRELAFQISKEYERFS 204
             D++ +AK+G GKT  F++   Q L  T       V  +++  TR+LA QI  E ++  
Sbjct: 111 DHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIH 170

Query: 205 KY---MSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNL-SLLKHF 260
                +         GG   +     +    P IV+ TPGR++ ++          + + 
Sbjct: 171 DMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYK 230

Query: 261 ILDECDKMLEQLEM--RRDVQEIFRSSP-------HTKQVMMFSATLSKEIRPVCKKFMH 311
           +LDE D++   LE+  R D++ I               + ++FSATL  +++ +    M+
Sbjct: 231 VLDEADRL---LEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMN 287

Query: 312 DPMEVYV---DDEAKLTLHGLQQHYVKLKENEKNKKLF------ELLDVLEFNQVVIFVK 362
               +++   D         + Q  V  ++   +          ++ +     + +IF  
Sbjct: 288 KKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAP 347

Query: 363 SVTRCIALSTLLSEQN---FPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASD 414
           +V     L ++L  +     P +  H  +TQ +R    + FK       I   +D
Sbjct: 348 TVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKK--DESGILVCTD 400

>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 = 68.7 bits (168), Expect = 1e-12
 Identities = 20/51 (39%), Positives = 30/51 (58%), Gaps = 4/51 (7%)

Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRV---ARAGRFGTKAVL 148
           ILV T++  RGMD   V+ V    +P +   Y+HR+   AR+G+ G  +VL
Sbjct: 395 ILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEG-SSVL 444

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  187 bits (477), Expect = 3e-57
 Identities = 57/175 (32%), Positives = 95/175 (54%), Gaps = 9/175 (5%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G  ++ Q+++G GKT  ++L  +++++   + V  ++   TRELA QI  E  + +K+  
Sbjct: 41  GESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCP 100

Query: 209 N---IKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDEC 265
               I      GG   QK  E L    P IV+GTPGRI   +R + L++      ++DE 
Sbjct: 101 KDRMIVARCLIGGTDKQKALEKLN-VQPHIVIGTPGRINDFIREQALDVHTAHILVVDEA 159

Query: 266 DKMLEQLEM--RRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
           D M   L+M    DV +I    P   Q+++FSAT+ ++++P  KK+M +P  V+V
Sbjct: 160 DLM---LDMGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHV 211

>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 =  188 bits (478), Expect = 2e-56
 Identities = 53/172 (30%), Positives = 88/172 (51%), Gaps = 5/172 (2%)

Query: 151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI 210
           +++ Q++SG GKTA FVLA L Q+E  +     L +  T ELA Q  K  E+  K+   +
Sbjct: 133 NLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPEL 192

Query: 211 KVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRIL-ALVRNKKLNLSLLKHFILDECDKML 269
           K+     G  +++ ++     + QIV+GTPG +L    + K ++   +K F+LDE D M+
Sbjct: 193 KLAYAVRGNKLERGQK----ISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMI 248

Query: 270 EQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDE 321
                +     I R  P   Q+++FSAT    +    +K + DP  + +  E
Sbjct: 249 ATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKRE 300

>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 =  177 bits (451), Expect = 6e-51
 Identities = 75/261 (28%), Positives = 133/261 (50%), Gaps = 14/261 (5%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNV-----YVLVMCHTRELAFQISKEYERF 203
           G D++  A++G GKTA F+L  L +L      +      V+++  TRELA QI  E  +F
Sbjct: 93  GRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKF 152

Query: 204 SKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILD 263
           + + S +K+G+ +GG   +   E +      +V+ TPGR+L  V    +     +  +LD
Sbjct: 153 A-FESYLKIGIVYGGTSFRHQNECIT-RGCHVVIATPGRLLDFVDRTFITFEDTRFVVLD 210

Query: 264 ECDKMLE---QLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDD 320
           E D+ML+     +MRR +  +  +     Q +MFSAT  +EI+ +  +F+ + + V +  
Sbjct: 211 EADRMLDMGFSEDMRRIMTHV--TMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAI-G 267

Query: 321 EAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFP 380
                   ++Q   ++ +  K  KL E+L     +  ++FV++      L++ LSE+ FP
Sbjct: 268 IVGGACSDVKQTIYEVNKYAKRSKLIEILSEQA-DGTIVFVETKRGADFLASFLSEKEFP 326

Query: 381 AVSIHRGMTQEERLKKYQEFK 401
             SIH    Q +R +  ++FK
Sbjct: 327 TTSIHGDRLQSQREQALRDFK 347

>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 = 65.6 bits (161), Expect = 9e-12
 Identities = 21/45 (46%), Positives = 30/45 (66%)

Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK 145
           +L+AT++  RG+DI+ +  V NYDMP   D Y+HR+ R GR G  
Sbjct: 353 VLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNN 397

>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 =  167 bits (425), Expect = 1e-49
 Identities = 56/175 (32%), Positives = 94/175 (53%), Gaps = 12/175 (6%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSN---VYVLVMCHTRELAFQISKEYERFSK 205
           G D++ QA++G GKT  F L   ++L  +         LV+  TRELA Q++ E    + 
Sbjct: 38  GKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAP 97

Query: 206 YMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDEC 265
           ++   KV   +GG    K +E L       VV TPGR L  +R   L+LS ++  +LDE 
Sbjct: 98  HL---KVVAVYGGTGYGKQKEALL-RGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEA 153

Query: 266 DKMLEQLEM--RRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
           D+ML    M    +V+ +  ++P ++Q ++FSATL    + + +++M +P+ + V
Sbjct: 154 DEMLS---MGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINV 205

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  170 bits (434), Expect = 1e-48
 Identities = 76/275 (27%), Positives = 134/275 (48%), Gaps = 25/275 (9%)

Query: 149 GMDILCQAKSGMGKTAVFVL---------ATLQQLETTDSNV---------YVLVMCHTR 190
             D++  A++G GKTA F+L            + L     N            LV+  TR
Sbjct: 52  KRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTR 111

Query: 191 ELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNK 250
           ELA QI +E  +FS Y S ++  V +GG  I +    L+     ++V TPGR++ ++   
Sbjct: 112 ELAVQIYEEARKFS-YRSRVRPCVVYGGADIGQQIRDLE-RGCHLLVATPGRLVDMMERG 169

Query: 251 KLNLSLLKHFILDECDKMLE---QLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCK 307
           K+ L   K+ +LDE D+ML+   + ++RR V++        +  MMFSAT  KEI+ + +
Sbjct: 170 KIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLAR 229

Query: 308 KFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQ-VVIFVKSVTR 366
            F+ + + + V      T   + Q  V ++E++K   L +LL+    +   ++FV++   
Sbjct: 230 DFLDEYIFLAV-GRVGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKG 288

Query: 367 CIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFK 401
             +L   L  + +   SIH   +Q +R +   +F+
Sbjct: 289 ADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFR 323

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score = 65.6 bits (161), Expect = 9e-12
 Identities = 22/45 (48%), Positives = 29/45 (64%)

Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK 145
           ILVAT +  RG+DI  V  V N+D+P D + Y+HR+ R GR G  
Sbjct: 329 ILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNL 373

>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 =  162 bits (412), Expect = 2e-47
 Identities = 56/175 (32%), Positives = 99/175 (56%), Gaps = 4/175 (2%)

Query: 146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK 205
           A+ G DI+  A++G GKT  F L  L  L  T   ++ LV+  TRELAFQIS+++E    
Sbjct: 77  ALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTPTRELAFQISEQFEALGS 136

Query: 206 YMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK-LNLSLLKHFILDE 264
            +  ++  V  GG+        L    P I++ TPGR++  + N K  NL  LK+ ++DE
Sbjct: 137 SI-GVQSAVIVGGIDSMSQSLALAKK-PHIIIATPGRLIDHLENTKGFNLRALKYLVMDE 194

Query: 265 CDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVD 319
            D++L  ++   +V +I +  P  ++  +FSAT++K+++ + +  + +P++  V 
Sbjct: 195 ADRILN-MDFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAVS 248

>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 Length = 172

 Score =  159 bits (405), Expect = 3e-47
 Identities = 100/168 (59%), Positives = 115/168 (68%), Gaps = 46/168 (27%)

Query: 325 TLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSI 384
           +LHGLQQ+YVKLK+NEKN+KLF+LLDVLEFNQVVIFVKSV RCIAL+ LL EQNFPA++I
Sbjct: 2   SLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAI 61

Query: 385 HRGMTQEERLKKYQEFKDF----------------------------------------- 403
           HRGM QEERL +YQ+FKDF                                         
Sbjct: 62  HRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVAR 121

Query: 404 -----HKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIE 446
                 KGLAITF SDENDAKILN+VQDRF+V+ISELPDEID+S+YIE
Sbjct: 122 AGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIE 169

>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 Length = 172

 Score =  104 bits (261), Expect = 2e-26
 Identities = 45/48 (93%), Positives = 46/48 (95%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV 147
           RILVATNLFGRGMDIERVNI FNYDMPEDSDTYLHRVARAGRFGTK +
Sbjct: 83  RILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGL 130

>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 =  154 bits (391), Expect = 2e-44
 Identities = 46/176 (26%), Positives = 87/176 (49%), Gaps = 7/176 (3%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSN-VYVLVMCHTRELAFQISKEYERFSKYM 207
           G ++L  A +G GKT  F +  L QL+   +     L++  TRELA QI +E  + S+  
Sbjct: 66  GRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEG- 124

Query: 208 SNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK--LNLSLLKHFILDEC 265
           +  ++ +        K      +    I+V TP R++ L++     ++L+ ++  ++DE 
Sbjct: 125 TGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDES 184

Query: 266 DKMLEQLEM--RRDVQEIFRS-SPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
           DK+ E  +   R  +  IF + + H  +  MFSAT + ++   CK  + + + V +
Sbjct: 185 DKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSI 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 =  152 bits (386), Expect = 9e-44
 Identities = 52/182 (28%), Positives = 97/182 (53%), Gaps = 9/182 (4%)

Query: 146 AVLGMDILCQAKSGMGKTAVFVLATLQQLE----TTDSNVYVLVMCHTRELAFQISKEYE 201
           A+ G D+L  AK+G GKT  F++  L+ L     T+   + VL++  TRELA+Q  +   
Sbjct: 59  ALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLR 118

Query: 202 RFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK-LNLSLLKHF 260
           +  K       G+  GG  ++ + E +   N  I+V TPGR+L  +      + + L+  
Sbjct: 119 KVGKNHD-FSAGLIIGGKDLKHEAERIN--NINILVCTPGRLLQHMDETVSFHATDLQML 175

Query: 261 ILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDD 320
           +LDE D++L+ +     +  +  + P  +Q ++FSAT +K ++ + +  + +P  V+V +
Sbjct: 176 VLDEADRILD-MGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVHE 234

Query: 321 EA 322
           +A
Sbjct: 235 KA 236

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  146 bits (371), Expect = 7e-40
 Identities = 44/280 (15%), Positives = 88/280 (31%), Gaps = 46/280 (16%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G      A +G+GKT   ++  L             ++  T  L  Q  +  ++ +    
Sbjct: 36  GKSFTMVAPTGVGKTTFGMMTALWLA---RKGKKSALVFPTVTLVKQTLERLQKLADE-- 90

Query: 209 NIKVGVFFGGLPIQKDEEYLK---THNPQIVVGTPGRILALVRN-KKLNLSLLKHFILDE 264
            +K+  F+  +  ++ E++ K     +  I+V +      + +N +KL+        +D+
Sbjct: 91  KVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQF---VSKNREKLSQKRFDFVFVDD 147

Query: 265 CDKMLEQLEM--RRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDE- 321
            D +L+        D   +    P       FS     +I    K      + V      
Sbjct: 148 VDAVLK---ASRNIDTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAK 204

Query: 322 ----AKLTLHGLQ---------------QHYVKLKENEKNKKLFELLDVLEFNQVVIFVK 362
                 L    L                   +  +  EK  +L E+      + ++IF +
Sbjct: 205 PRGIRPLLFRDLLNFTVGRLVSVARNITHVRISSRSKEKLVELLEIFR----DGILIFAQ 260

Query: 363 SVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKD 402
           +      L   L    F            E  K +++FK 
Sbjct: 261 TEEEGKELYEYLKRFKFNVGETWS-----EFEKNFEDFKV 295

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score = 47.4 bits (113), Expect = 5e-06
 Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 7/51 (13%)

Query: 100 RILVAT----NLFGRGMDI-ERVNIVFNYDMPEDSD--TYLHRVARAGRFG 143
            IL+          RG+D+ ER+  V  +  P   D  TY+    R+ R  
Sbjct: 299 NILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRIL 349

>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 =  136 bits (346), Expect = 5e-38
 Identities = 50/178 (28%), Positives = 86/178 (48%), Gaps = 14/178 (7%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLE------TTDSNVYVLVMCHTRELAFQISKEYER 202
           G+D++  A++G GKT  +++     L+         +   +LV+  TRELA  +  E  +
Sbjct: 57  GIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSK 116

Query: 203 FSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFIL 262
           +S     +K    +GG       E +      I++ TPGR+  L  N  +NL  + + ++
Sbjct: 117 YSY--KGLKSICIYGGRNRNGQIEDIS-KGVDIIIATPGRLNDLQMNNSVNLRSITYLVI 173

Query: 263 DECDKMLEQLEM--RRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
           DE DKML+   M     +++I       +Q +M SAT    +R +   ++ DPM VYV
Sbjct: 174 DEADKMLD---MEFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV 228

>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 =  136 bits (344), Expect = 2e-37
 Identities = 54/182 (29%), Positives = 96/182 (52%), Gaps = 14/182 (7%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNV---------YVLVMCHTRELAFQISKE 199
             DI+  A++G GKTA F++  +  L   D N            L++  TRELA QI  E
Sbjct: 60  HRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSE 119

Query: 200 YERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKH 259
            ++FS   + ++  V +GG         ++     ++V TPGR++  +   K++L   K+
Sbjct: 120 SQKFSLN-TPLRSCVVYGGADTHSQIREVQ-MGCHLLVATPGRLVDFIEKNKISLEFCKY 177

Query: 260 FILDECDKMLE---QLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEV 316
            +LDE D+ML+   + ++R+ ++E    S   +Q +MFSAT  KEI+ +   F+++ + +
Sbjct: 178 IVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFM 237

Query: 317 YV 318
            V
Sbjct: 238 TV 239

>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 =  130 bits (330), Expect = 2e-35
 Identities = 45/177 (25%), Positives = 87/177 (49%), Gaps = 9/177 (5%)

Query: 146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSN----VYVLVMCHTRELAFQISKEYE 201
            + G D+L  AK+G GKT  F++  ++ +            VL++  TRELA Q     +
Sbjct: 88  LLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLK 147

Query: 202 RFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK-LNLSLLKHF 260
               +      G+  GG     + + L  +   I+V TPGR+L  ++N        L+  
Sbjct: 148 ELMTHHV-HTYGLIMGGSNRSAEAQKLG-NGINIIVATPGRLLDHMQNTPGFMYKNLQCL 205

Query: 261 ILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKK-FMHDPMEV 316
           ++DE D++L+ +    ++++I +  P  +Q M+FSAT ++++  + +     +P+ V
Sbjct: 206 VIDEADRILD-VGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYV 261

>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 =  128 bits (325), Expect = 8e-35
 Identities = 47/177 (26%), Positives = 85/177 (48%), Gaps = 12/177 (6%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNV-----YVLVMCHTRELAFQISKEYERF 203
           G+D++  A++G GKT  ++L  +  +              LV+  TRELA Q+ +    +
Sbjct: 66  GLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEY 125

Query: 204 SKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILD 263
                 +K    +GG P       L+    +I + TPGR++  +   K NL    + +LD
Sbjct: 126 C-RACRLKSTCIYGGAPKGPQIRDLE-RGVEICIATPGRLIDFLECGKTNLRRTTYLVLD 183

Query: 264 ECDKMLEQLEM--RRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
           E D+M   L+M     +++I       +Q +M+SAT  KE+R + + F+ D + + +
Sbjct: 184 EADRM---LDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINI 237

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score =  109 bits (274), Expect = 2e-28
 Identities = 37/162 (22%), Positives = 61/162 (37%), Gaps = 48/162 (29%)

Query: 326 LHGLQQHYVKLKENE-KNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSI 384
           L G++Q YV ++E E K + L +L D +   Q VIF  +  +   L+T L    F   +I
Sbjct: 1   LEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAI 60

Query: 385 HRGMTQEERLKKYQEFKDF----------------------------------------- 403
           +  + Q+ER    +EF+                                           
Sbjct: 61  YSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGR 120

Query: 404 -----HKGLAITFASDENDAKILNNVQDRFDVSISELPDEID 440
                 KG+AI F ++E D   +  ++  +   I ELP +I 
Sbjct: 121 GGRFGRKGVAINFVTNE-DVGAMRELEKFYSTQIEELPSDIA 161

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score = 92.6 bits (231), Expect = 2e-22
 Identities = 24/48 (50%), Positives = 38/48 (79%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV 147
           RIL++T+L  RG+D+++V++V NYD+P + + Y+HR+ R GRFG K V
Sbjct: 82  RILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGV 129

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens} Length = 175

 Score = 76.1 bits (188), Expect = 2e-16
 Identities = 24/54 (44%), Positives = 37/54 (68%), Gaps = 6/54 (11%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMP------EDSDTYLHRVARAGRFGTKAV 147
           ++L+ TN+  RG+D+++V IV N+D+P       D +TYLHR+ R GRFG K +
Sbjct: 86  KVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGL 139

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens} Length = 175

 Score = 69.9 bits (172), Expect = 3e-14
 Identities = 18/82 (21%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 322 AKLTLHGLQQHYVKLK-ENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFP 380
           + LTL+ ++Q+YV  +   +K + L  +   +   Q +IF ++      L+  + +    
Sbjct: 1   SMLTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQ 60

Query: 381 AVSIHRGMTQEERLKKYQEFKD 402
              +   +T E+R    Q F+D
Sbjct: 61  VSLLSGELTVEQRASIIQRFRD 82

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score = 73.3 bits (181), Expect = 1e-15
 Identities = 23/46 (50%), Positives = 34/46 (73%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK 145
           R LVAT++  RG+DIE +++V NYD+P + ++Y+HR  R GR G K
Sbjct: 87  RYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNK 132

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score = 67.2 bits (165), Expect = 2e-13
 Identities = 21/79 (26%), Positives = 37/79 (46%)

Query: 324 LTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVS 383
           LT   ++   ++++E  K   L ++L     +  +IF ++      L+  L +  +P   
Sbjct: 5   LTTRNIEHAVIQVREENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDK 64

Query: 384 IHRGMTQEERLKKYQEFKD 402
           IH GM QE+R     EFK 
Sbjct: 65  IHGGMIQEDRFDVMNEFKR 83

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli} Length = 170

 Score = 66.4 bits (163), Expect = 3e-13
 Identities = 28/48 (58%), Positives = 35/48 (72%), Gaps = 3/48 (6%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRV---ARAGRFGT 144
            +LVAT++  RG+DI  V+ VFN+DMP   DTYLHR+   ARAGR GT
Sbjct: 82  NVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGT 129

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli} Length = 170

 Score = 49.9 bits (120), Expect = 2e-07
 Identities = 16/73 (21%), Positives = 27/73 (36%)

Query: 330 QQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMT 389
           Q +Y       K   L  LL   E  + ++FV+   R   L+  L E       +   M 
Sbjct: 6   QWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMV 65

Query: 390 QEERLKKYQEFKD 402
           Q +R +  +   +
Sbjct: 66  QGKRNEAIKRLTE 78

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score = 66.1 bits (162), Expect = 6e-13
 Identities = 19/45 (42%), Positives = 29/45 (64%)

Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK 145
           +LVAT++  +G+D   +  V NYDMPE+ + Y+HR+ R G  G  
Sbjct: 107 VLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNT 151

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score = 65.0 bits (159), Expect = 1e-12
 Identities = 26/100 (26%), Positives = 37/100 (37%), Gaps = 7/100 (7%)

Query: 309 FMHDPMEVYVDDE------AKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVK 362
             H    V +  E             + Q    +KE  K   L E L       V+IF +
Sbjct: 4   HHHHSSGVDLGTENLYFQSMGAASLDVIQEVEYVKEEAKMVYLLECLQKTP-PPVLIFAE 62

Query: 363 SVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKD 402
                 A+   L  +   AV+IH G  QEER K  + F++
Sbjct: 63  KKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFRE 102

>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 Length = 212

 Score = 65.8 bits (161), Expect = 1e-12
 Identities = 20/44 (45%), Positives = 32/44 (72%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG 143
           R+LVAT++  RG+DI +V++V +Y +P+ ++ Y HR  R GR G
Sbjct: 83  RVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAG 126

>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 Length = 212

 Score = 47.3 bits (113), Expect = 2e-06
 Identities = 14/73 (19%), Positives = 33/73 (45%)

Query: 330 QQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMT 389
           ++  V      + + L +LL V   ++ ++F ++      ++  L     PA ++H  ++
Sbjct: 7   EEEAVPAPVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLS 66

Query: 390 QEERLKKYQEFKD 402
           Q ER +    F+ 
Sbjct: 67  QGERERVLGAFRQ 79

>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 = 64.5 bits (158), Expect = 2e-12
 Identities = 22/45 (48%), Positives = 29/45 (64%)

Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK 145
           ILVAT +  RG+DI  V  V N+D+P D + Y+HR+ R GR G  
Sbjct: 99  ILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNL 143

>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 = 56.4 bits (137), Expect = 1e-09
 Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 330 QQHYVKLKENEKNKKLFELLDVLEFNQ-VVIFVKSVTRCIALSTLLSEQNFPAVSIHRGM 388
            Q  V ++E++K   L +LL+    +   ++FV++     +L   L  + +   SIH   
Sbjct: 21  TQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDR 80

Query: 389 TQEERLKKYQEFK 401
           +Q +R +   +F+
Sbjct: 81  SQRDREEALHQFR 93

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus} Length = 300

 Score = 65.9 bits (161), Expect = 4e-12
 Identities = 21/47 (44%), Positives = 32/47 (68%), Gaps = 3/47 (6%)

Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRV---ARAGRFGT 144
           +LVAT++  RG+DI +V++V +Y MP+ ++ Y HR     RAGR G 
Sbjct: 81  VLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGR 127

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus} Length = 300

 Score = 46.3 bits (110), Expect = 8e-06
 Identities = 15/73 (20%), Positives = 33/73 (45%)

Query: 330 QQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMT 389
           ++  V      + + L +LL V   ++ ++F ++      ++  L     PA ++H  M+
Sbjct: 4   EEEAVPAPVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMS 63

Query: 390 QEERLKKYQEFKD 402
           Q ER +    F+ 
Sbjct: 64  QGERERVMGAFRQ 76

>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 = 67.2 bits (163), Expect = 5e-12
 Identities = 61/446 (13%), Positives = 128/446 (28%), Gaps = 120/446 (26%)

Query: 62  DALAKQKEVKGAYVSIHS-SGF----------RDFLLKPEILRAIVDCW----------- 99
            AL + +      V I    G             + ++ ++   I   W           
Sbjct: 142 QALLELR--PAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIF--WLNLKNCNSPET 197

Query: 100 RILVATNLFGR--GMDIERVNIVFNYDMP-EDSDTYLHRVARAGRFG-----------TK 145
            + +   L  +       R +   N  +        L R+ ++  +             K
Sbjct: 198 VLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAK 257

Query: 146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDS----NVYVLVMCHTRELAFQISKEYE 201
           A    ++ C+           +L T +  + TD         + + H         +   
Sbjct: 258 AWNAFNLSCK-----------ILLTTRFKQVTDFLSAATTTHISLDHHSM-TLTPDEVKS 305

Query: 202 RFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRN--------KKLN 253
              KY     +      LP +     + T NP+ +      I   +R+        K +N
Sbjct: 306 LLLKY-----LDCRPQDLPRE-----VLTTNPRRL----SIIAESIRDGLATWDNWKHVN 351

Query: 254 LSLLKHFILDECDKMLEQLEMRRDVQE--IFRSSPH-TKQVMMF--SATLSKEIRPVCKK 308
              L   I++    +LE  E R+      +F  S H    ++       +  ++  V  K
Sbjct: 352 CDKLTT-IIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNK 410

Query: 309 FMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEK--NKKLFELLDVLEFNQVVIFVKSVTR 366
                +      E+ +++  +        ENE   ++ + +      +N        + +
Sbjct: 411 LHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVD-----HYN--------IPK 457

Query: 367 CIALSTLLSEQN----FPAVSIHRGMTQEERLKKYQEFK----DFHKGLAITFASDENDA 418
                 L+        +  +  H  +   E  ++   F+    DF       F     + 
Sbjct: 458 TFDSDDLIPPYLDQYFYSHIGHH--LKNIEHPERMTLFRMVFLDFR------FL----EQ 505

Query: 419 KILNNVQDRFDVSISELPDEIDLSTY 444
           KI  +    ++ S S L     L  Y
Sbjct: 506 KI-RHDSTAWNASGSILNTLQQLKFY 530

>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 = 63.3 bits (153), Expect = 9e-11
 Identities = 36/224 (16%), Positives = 78/224 (34%), Gaps = 56/224 (25%)

Query: 248 RNKKLNLSLLKHFILD-ECDKMLEQLE---MRRDVQEIFRSSPHTKQV-MMFSATLSKEI 302
           + K +       F+ + +C  + +  +    + ++  I  S         +F   LSK+ 
Sbjct: 17  QYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQE 76

Query: 303 RPVCKKFMHDPMEVYVDDEAKLTLHGLQQHY--------VKLKENEKNKKLF-ELLDVLE 353
             V +KF+ +                L+ +Y         + ++     +++ E  D L 
Sbjct: 77  EMV-QKFVEE---------------VLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRL- 119

Query: 354 FNQVVIFVK-SVTR---CIALSTLLSE-QNFPAVSIHRGMT------------QEERLKK 396
           +N   +F K +V+R    + L   L E +    V I  G+                +++ 
Sbjct: 120 YNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLID-GVLGSGKTWVALDVCLSYKVQC 178

Query: 397 YQEFKDFHKGLAITFA---SDENDAKILNNVQDRFDVSISELPD 437
             +FK F     +      S E   ++L  +  + D + +   D
Sbjct: 179 KMDFKIFW----LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSD 218

>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 = 2e-05
 Identities = 35/214 (16%), Positives = 69/214 (32%), Gaps = 42/214 (19%)

Query: 43  LLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEIL----RAIVDC 98
           +     + +   +V      +L + K+ K + +SI  S + +  +K E      R+IVD 
Sbjct: 395 IWFDVIKSDVMVVVNKLHKYSLVE-KQPKESTISIP-SIYLELKVKLENEYALHRSIVDH 452

Query: 99  WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTY-LHRVARAGRFG--TKAVLGMDILCQ 155
           + I    +              +++        + L  +    R        L    L +
Sbjct: 453 YNIPKTFDSDDLIPPYLD-QYFYSHIG------HHLKNIEHPERMTLFRMVFLDFRFL-E 504

Query: 156 AK---SGMGKTAV-FVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF-------- 203
            K         A   +L TLQQL+      Y+       E   ++      F        
Sbjct: 505 QKIRHDSTAWNASGSILNTLQQLKFYKP--YICDNDPKYE---RLVNAILDFLPKIEENL 559

Query: 204 --SKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQI 235
             SKY   +++ +        +DE   +  + Q+
Sbjct: 560 ICSKYTDLLRIALMA------EDEAIFEEAHKQV 587

>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 = 66.0 bits (160), Expect = 7e-12
 Identities = 28/196 (14%), Positives = 73/196 (37%), Gaps = 9/196 (4%)

Query: 145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS 204
                 + L    +G+GKT + ++    +L      V  L++  T+ L  Q ++ + R  
Sbjct: 19  AKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKV--LMLAPTKPLVLQHAESFRRLF 76

Query: 205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDE 264
                 K+    G    ++  +       +++V TP  I   +   +++L  +   + DE
Sbjct: 77  NL-PPEKIVALTGEKSPEERSKAWARA--KVIVATPQTIENDLLAGRISLEDVSLIVFDE 133

Query: 265 CDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLS---KEIRPVCKKFMHDPMEVYVDDE 321
             + +         +E  R + +   V+  +A+     ++I  V      + +E   ++ 
Sbjct: 134 AHRAVGNYAYVFIAREYKRQAKN-PLVIGLTASPGSTPEKIMEVINNLGIEHIEYRSENS 192

Query: 322 AKLTLHGLQQHYVKLK 337
             +  +     +  ++
Sbjct: 193 PDVRPYVKGIRFEWVR 208

>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 = 46.3 bits (109), Expect = 1e-05
 Identities = 14/51 (27%), Positives = 26/51 (50%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGM 150
            +LVAT++   G+D+  V++V  Y+    +   + R  R GR     V+ +
Sbjct: 421 NVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHMPGRVIIL 471

>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* Length = 720

 Score = 57.2 bits (138), Expect = 6e-09
 Identities = 40/269 (14%), Positives = 100/269 (37%), Gaps = 43/269 (15%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSN-VYVLVMCHTRELAFQISKEYERFSKYM 207
           G + L    +  GKT +  +A + ++ T     VY++     + LA +  +E++ + K  
Sbjct: 39  GKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIV---PLKALAEEKFQEFQDWEKI- 94

Query: 208 SNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDK 267
             ++V +  G    + +          I++ T  +  +L+R+    +  +K  + DE   
Sbjct: 95  -GLRVAMATGDYDSKDEW----LGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEI-H 148

Query: 268 MLEQLEMRRDVQE--IFRSSPHTKQVMMFSATLS--KEI-------------RPVCKKFM 310
           ++   + R    E  +       + + + SAT+   +E+             RPV     
Sbjct: 149 LIGSRD-RGATLEVILAHMLGKAQIIGL-SATIGNPEELAEWLNAELIVSDWRPV----- 201

Query: 311 HDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIAL 370
              +   V  +  +T        +  + +   + +++   + +    +IFV    +   +
Sbjct: 202 --KLRRGVFYQGFVTWE---DGSID-RFSSWEELVYDA--IRKKKGALIFVNMRRKAERV 253

Query: 371 STLLSEQNFPAVSIHRGMTQEERLKKYQE 399
           +  LS++    ++        E     +E
Sbjct: 254 ALELSKKVKSLLTKPEIRALNELADSLEE 282

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 50.5 bits (121), Expect = 8e-07
 Identities = 45/240 (18%), Positives = 86/240 (35%), Gaps = 47/240 (19%)

Query: 161 GKTAVFVLATLQQLETTDSN-VYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGL 219
           GKT +  +  +  L       +YV  +   R L  +    ++ +       KV +  G  
Sbjct: 58  GKTLIAEMGIISFLLKNGGKAIYVTPL---RALTNEKYLTFKDWELI--GFKVAMTSGDY 112

Query: 220 PIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRD-- 277
                       N  I++ T  ++ +L R++   L+ + +F+LDE       L    D  
Sbjct: 113 DTDDAW----LKNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDE-------LHYLNDPE 161

Query: 278 ---VQEIFRSSPHTKQVMMFSATLS--KEI-------------RPVCKKFMHDPMEVYV- 318
              V E        + ++  SAT+S  K+I             RPV       P+   V 
Sbjct: 162 RGPVVESVTIRAKRRNLLALSATISNYKQIAKWLGAEPVATNWRPV-------PLIEGVI 214

Query: 319 -DDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVL-EFNQVVIFVKSVTRCIALSTLLSE 376
             +  K   + + +     K +  +  +   LD L +  QV++F  S     + +  ++ 
Sbjct: 215 YPERKKKEYNVIFKDNTTKKVHGDDAIIAYTLDSLSKNGQVLVFRNSRKMAESTALKIAN 274

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 47.6 bits (112), Expect = 5e-06
 Identities = 24/154 (15%), Positives = 53/154 (34%), Gaps = 7/154 (4%)

Query: 145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVY--VLVMCHTRELAFQISKEYER 202
            A  G + +  A +G GKT V +L     L+         V+   +   +  Q +  + R
Sbjct: 15  PAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSR 74

Query: 203 FSKYMSNIKVGVFFGGL-PIQKDEEYLKTHNPQIVVGTPGRIL-ALVRNKKLNLSLLKHF 260
           + + +    +    G        +  ++ +   I++ TP  ++  L      +LS+    
Sbjct: 75  YFERLG-YNIASISGATSDSVSVQHIIEDN--DIIILTPQILVNNLNNGAIPSLSVFTLM 131

Query: 261 ILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMF 294
           I DEC    +     + +           +  + 
Sbjct: 132 IFDECHNTSKNHPYNQIMFRYLDHKLGESRDPLP 165

>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* 4a92_A* 1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A Length = 666

 Score = 47.7 bits (113), Expect = 6e-06
 Identities = 41/251 (16%), Positives = 70/251 (27%), Gaps = 55/251 (21%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
                  A +G GK+     A   Q         VLV+  +             F  YMS
Sbjct: 232 FQVAHLHAPTGSGKSTKVPAAYAAQ------GYKVLVLNPSVAAT-------LGFGAYMS 278

Query: 209 ---NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDEC 265
               I   +  G            T    +   T G+ LA   +   +       I DEC
Sbjct: 279 KAHGIDPNIRTGV--------RTITTGAPVTYSTYGKFLA---DGGCSGGAYDIIICDEC 327

Query: 266 DKM-LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEI---RPVCKKFMHDPMEVYVDDE 321
                  +     V +   ++     V+  +AT    +    P  ++         +   
Sbjct: 328 HSTDSTTILGIGTVLDQAETAGARLVVLA-TATPPGSVTVPHPNIEEV-ALSNTGEIPFY 385

Query: 322 AKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPA 381
            K                         ++ +   + +IF  S  +C  L+  LS     A
Sbjct: 386 GKAIP----------------------IEAIRGGRHLIFCHSKKKCDELAAKLSGLGINA 423

Query: 382 VSIHRGMTQEE 392
           V+ +RG+    
Sbjct: 424 VAYYRGLDVSV 434

>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} Length = 936

 Score = 47.3 bits (111), Expect = 8e-06
 Identities = 53/341 (15%), Positives = 98/341 (28%), Gaps = 49/341 (14%)

Query: 145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLET--TDSNVYVLVMCHTRELAFQISKEYER 202
            A+ G + L  A +G GKT V +L      +         V+ +     +  Q       
Sbjct: 259 PAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQ---KNV 315

Query: 203 FSKYMSNIKVGVFFGGLPIQKDEEYLKTH--NPQIVVGTPGRIL-ALVRNKKLNLSLLKH 259
           F  +    +     G          ++    +  I+V TP  ++ +       +LS+   
Sbjct: 316 FKHHF-ERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTL 374

Query: 260 FILDECDKML----EQLEMRRDVQEIFRSSPHTKQVMMFSATL----------------- 298
            I DEC          + M R +++ F S+    Q++  +A++                 
Sbjct: 375 MIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICS 434

Query: 299 ------------SKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLF 346
                        +E     ++FM+ P       + ++           + E E   +  
Sbjct: 435 LCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAIISNLMSETEALMRTI 494

Query: 347 ELLDVLEFNQVVIFVKS------VTRCIALSTLLSEQNFPAVSIHRGMTQE-ERLKKYQE 399
             +D L  N    F         V        L  E       I R +    E L+KY +
Sbjct: 495 AYVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYND 554

Query: 400 FKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEID 440
                +   I  A         N     +      L  +  
Sbjct: 555 ALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQ 595

>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} Length = 936

 Score = 41.9 bits (97), Expect = 4e-04
 Identities = 14/77 (18%), Positives = 33/77 (42%), Gaps = 6/77 (7%)

Query: 78  HSSGFRDFLLKPEILRAIVDCWR------ILVATNLFGRGMDIERVNIVFNYDMPEDSDT 131
                +   +     + ++D ++      +L+AT++   G+DI + N+V  Y+   +   
Sbjct: 668 RGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTK 727

Query: 132 YLHRVARAGRFGTKAVL 148
            +    R    G+K +L
Sbjct: 728 MIQVRGRGRAAGSKCIL 744

>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 Length = 702

 Score = 47.1 bits (112), Expect = 1e-05
 Identities = 50/255 (19%), Positives = 100/255 (39%), Gaps = 57/255 (22%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G ++L    +  GKT +  +A +++      ++YV+ +   R LA +  + ++++ K   
Sbjct: 40  GKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPL---RALAGEKYESFKKWEKI-- 94

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDEC--- 265
            +++G+  G    + +       +  I+V T  +  +L+RN+   +  +   ++DE    
Sbjct: 95  GLRIGISTGDYESRDEH----LGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLL 150

Query: 266 -DKM----LEQL--EMRRDVQEIFRSSPHTKQVMMFSATLS--KEI-------------R 303
             +     LE L  +MRR  + +        +V+  SAT     EI             R
Sbjct: 151 DSEKRGATLEILVTKMRRMNKAL--------RVIGLSATAPNVTEIAEWLDADYYVSDWR 202

Query: 304 PVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLD--VLEFNQVVIFV 361
           PV       P+   V  E  L      + +       +  K  EL++  V E   V++F 
Sbjct: 203 PV-------PLVEGVLCEGTL------ELFDGAFSTSRRVKFEELVEECVAENGGVLVFE 249

Query: 362 KSVTRCIALSTLLSE 376
            +       +  LS 
Sbjct: 250 STRRGAEKTAVKLSA 264

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens} Length = 216

 Score = 44.8 bits (106), Expect = 2e-05
 Identities = 30/132 (22%), Positives = 51/132 (38%), Gaps = 15/132 (11%)

Query: 145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVY---VLVMCHTRELAFQ-ISKEY 200
            A+ G +I+    +G GKT V V      L+          V+V+ +   L  Q   KE+
Sbjct: 44  PALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEF 103

Query: 201 ERFSKYMSNIKVGVFFGGLPIQKD-EEYLKTHNPQIVVGTPGRIL------ALVRNKKLN 253
           + F K     +V    G   ++    E +K+    I++ T   +           +  + 
Sbjct: 104 QPFLKKW--YRVIGLSGDTQLKISFPEVVKSC--DIIISTAQILENSLLNLENGEDAGVQ 159

Query: 254 LSLLKHFILDEC 265
           LS     I+DEC
Sbjct: 160 LSDFSLIIIDEC 171

>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} Length = 797

 Score = 45.7 bits (107), Expect = 2e-05
 Identities = 30/179 (16%), Positives = 64/179 (35%), Gaps = 9/179 (5%)

Query: 145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLET--TDSNVYVLVMCHTRELAFQISKEYER 202
            A+ G + L  A +G GKT V +L      +         V+ +     +  Q    ++ 
Sbjct: 259 PAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKH 318

Query: 203 FSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRIL-ALVRNKKLNLSLLKHFI 261
             +       G+          E+ ++     I+V TP  ++ +       +LS+    I
Sbjct: 319 HFERQGYSVQGISGENFSNVSVEKVIEDS--DIIVVTPQILVNSFEDGTLTSLSIFTLMI 376

Query: 262 LDECDKMLEQLE----MRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEV 316
            DEC            M R +++ F S+    Q++  +A++        ++ +     +
Sbjct: 377 FDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSL 435

>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* Length = 556

 Score = 44.9 bits (105), Expect = 4e-05
 Identities = 24/181 (13%), Positives = 57/181 (31%), Gaps = 13/181 (7%)

Query: 145 KAVLGMDILCQAKSGMGKT--AVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER 202
            A+ G + L  A +G GKT  ++ +     Q         V+ +     +  Q   +   
Sbjct: 18  PAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQ---QKNV 74

Query: 203 FSKYMSNIKVGVFFGGLPIQKDEEYLKTH--NPQIVVGTPGRIL-ALVRNKKLNLSLLKH 259
           F  +    +     G          ++    +  I+V TP  ++ +       +LS+   
Sbjct: 75  FKHHF-ERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTL 133

Query: 260 FILDECDKMLEQLEMRRDVQEIFRSSPHTKQ----VMMFSATLSKEIRPVCKKFMHDPME 315
            I DEC            +        ++      ++  +A++        ++ +     
Sbjct: 134 MIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICS 193

Query: 316 V 316
           +
Sbjct: 194 L 194

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12} Length = 968

 Score = 43.5 bits (102), Expect = 1e-04
 Identities = 22/165 (13%), Positives = 52/165 (31%), Gaps = 9/165 (5%)

Query: 258 KHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVY 317
           +  +    D+      + R+ +   +  P  +++      L  + +   K          
Sbjct: 401 QELVSMLMDRHGTSRVLFRNTRNGVKGFPK-RELHTIKLPLPTQYQTAIKVSGIMGARKS 459

Query: 318 VDDEAKLTLHGLQ-------QHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIAL 370
            +D A+  L+  +        +      + + + L   L      +V++        + L
Sbjct: 460 AEDRARDMLYPERIYQEFEGDNATWWNFDPRVEWLMGYLTSHRSQKVLVICAKAATALQL 519

Query: 371 -STLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASD 414
              L   +   A   H GM+  ER +    F +   G  +   S+
Sbjct: 520 EQVLREREGIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSE 564

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 43.0 bits (100), Expect = 2e-04
 Identities = 24/127 (18%), Positives = 49/127 (38%), Gaps = 5/127 (3%)

Query: 145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETT--DSNVYVLVMCHTRELAFQISKEYER 202
            A+ G + +  A +G GKT V +L     L+         V+   +   +  Q    + +
Sbjct: 24  PAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFSK 83

Query: 203 FSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRIL-ALVRNKKLNLSLLKHFI 261
           + +       G+          E+ ++ +   I++ TP  ++  L +    +LS+    I
Sbjct: 84  YFERHGYRVTGISGATAENVPVEQIVENN--DIIILTPQILVNNLKKGTIPSLSIFTLMI 141

Query: 262 LDECDKM 268
            DEC   
Sbjct: 142 FDECHNT 148

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 40.7 bits (94), Expect = 9e-04
 Identities = 14/49 (28%), Positives = 24/49 (48%)

Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVL 148
            IL+AT++   G+DI + N+V  Y+   +    +    R    G+K  L
Sbjct: 463 NILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFL 511

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	448
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	100.0
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	100.0
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	100.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	100.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	100.0
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	100.0
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	100.0
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	100.0
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	100.0
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	100.0
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	100.0
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	100.0
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	100.0
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	100.0
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	100.0
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	100.0
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	100.0
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
3bor_A	237	Human initiation factor 4A-II; translation initiat	100.0
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	100.0
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	100.0
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	100.0
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	100.0
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	100.0
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	100.0
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	100.0
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	100.0
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	100.0
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	100.0
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	100.0
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	100.0
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	100.0
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	100.0
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	100.0
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	100.0
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	100.0
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	100.0
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.98
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.98
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.97
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.97
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.97
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.97
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.97
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.97
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.97
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.97
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.97
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.96
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.96
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.96
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.95
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.95
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.94
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.94
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.94
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.93
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.93
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.93
3h1t_A	590	Type I site-specific restriction-modification syst	99.92
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.92
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.92
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.9
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.89
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.88
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.88
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.87
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.86
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.85
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.84
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.83
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.82
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.81
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.73
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.62
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.6
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.56
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.53
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.48
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.42
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.42
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.39
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.38
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.33
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	98.8
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.17
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.16
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	98.79
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.74
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	98.43
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	98.37
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	98.33
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	97.79
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	97.71
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	97.66
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	97.55
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.53
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	97.44
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	97.38
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.38
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	97.33
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	97.24
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	97.14
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	97.14
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	97.14
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	97.14
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	97.07
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	97.05
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	96.11
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	96.82
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	96.7
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	96.64
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	96.61
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	96.4
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	96.33
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	96.21
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	96.18
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	96.17
4gl2_A	699	Interferon-induced helicase C domain-containing P;	96.16
2chg_A	226	Replication factor C small subunit; DNA-binding pr	96.12
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	96.02
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	96.01
3jux_A	822	Protein translocase subunit SECA; protein transloc	95.98
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	95.97
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	95.96
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	95.95
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	95.92
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	95.91
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	95.91
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	95.88
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	95.84
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	95.78
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	95.77
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	95.67
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	95.62
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	95.62
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	95.61
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	95.59
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	95.59
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	95.33
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	95.26
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	95.23
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	95.23
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	95.19
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	95.18
3bos_A	242	Putative DNA replication factor; P-loop containing	95.16
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	95.14
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	95.04
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	95.02
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	94.95
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	94.88
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	94.72
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	94.64
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	94.57
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	94.51
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	94.46
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	94.44
1yks_A	440	Genome polyprotein [contains: flavivirin protease	94.43
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	94.38
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	94.37
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	94.27
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	94.23
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	94.22
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	94.14
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	94.12
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	94.05
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	93.93
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	93.81
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	93.77
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	93.76
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	93.59
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	93.56
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	93.52
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	93.4
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	93.39
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	93.36
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	93.31
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	93.23
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	93.21
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	93.16
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	93.15
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	93.1
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	93.04
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	93.01
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	92.99
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	92.95
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	92.89
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	92.53
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	92.52
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	92.41
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	92.29
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	92.24
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	91.98
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	91.8
3h1t_A	590	Type I site-specific restriction-modification syst	91.65
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	91.61
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	91.5
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	91.2
2r6a_A	454	DNAB helicase, replicative helicase; replication,	91.13
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	91.08
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	90.86
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	90.78
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	90.63
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	90.15
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	90.01
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	89.9
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	89.9
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	89.57
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	89.53
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	89.36
2chq_A	319	Replication factor C small subunit; DNA-binding pr	89.31
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	89.21
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	88.93
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	88.72
3io5_A	333	Recombination and repair protein; storage dimer, i	87.29
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	87.23
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	86.96
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	86.73
2l82_A	162	Designed protein OR32; structural genomics, northe	86.69
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	85.78
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	85.49
3co5_A	143	Putative two-component system transcriptional RES	83.88
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	82.19
3gk5_A	108	Uncharacterized rhodanese-related protein TVG08686	82.18
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	81.77
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	81.52
1xp8_A	366	RECA protein, recombinase A; recombination, radior	81.49
3foj_A	100	Uncharacterized protein; protein SSP1007, structur	81.43
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	80.92
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	80.61
1p9r_A	418	General secretion pathway protein E; bacterial typ	80.45
3eme_A	103	Rhodanese-like domain protein; alpha-beta-alpha sa	80.24

>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=4.7e-48  Score=392.75  Aligned_cols=335  Identities=27%  Similarity=0.402  Sum_probs=303.9

Q ss_pred             ccCceeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeC
Q psy1548          70 VKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLG  149 (448)
Q Consensus        70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g  149 (448)
                      +.+...+.+...|.++++++.+++++.+.|                       |..|+++   |++      +||.++.|
T Consensus        46 ~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g-----------------------~~~pt~i---Q~~------ai~~i~~g   93 (434)
T 2db3_A           46 VTGSDVPQPIQHFTSADLRDIIIDNVNKSG-----------------------YKIPTPI---QKC------SIPVISSG   93 (434)
T ss_dssp             EESSSCCCCCCCGGGSCCCHHHHHHHHHTT-----------------------CCSCCHH---HHH------HHHHHHTT
T ss_pred             ecCCCCCCCcCChhhcCCCHHHHHHHHHcC-----------------------CCCCCHH---HHH------HHHHHhcC
Confidence            345556666778999999999999999999                       9999999   999      99999999


Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccC-----CCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHh
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTD-----SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD  224 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~-----~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~  224 (448)
                      +|+++++|||||||++|++|++..+....     .++++||++||++|+.|+++.++++.... ++++..++|+.....+
T Consensus        94 ~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~  172 (434)
T 2db3_A           94 RDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFES-YLKIGIVYGGTSFRHQ  172 (434)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCSEEEECSSHHHHHHHHHHHHHHTTTS-SCCCCEECTTSCHHHH
T ss_pred             CCEEEECCCCCCchHHHHHHHHHHHHhcccccccCCccEEEEecCHHHHHHHHHHHHHHhccC-CcEEEEEECCCCHHHH
Confidence            99999999999999999999999876532     36799999999999999999999999876 7899999999988777


Q ss_pred             HHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhC--CCCCeEEEEeccCCccH
Q psy1548         225 EEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSS--PHTKQVMMFSATLSKEI  302 (448)
Q Consensus       225 ~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l--~~~~q~i~~SAT~~~~~  302 (448)
                      ...+..+ ++|+|+||++|.+++.+....+.+++++|+||||+|+++ +|...+..++..+  ++..|+++||||+++.+
T Consensus       173 ~~~l~~~-~~Ivv~Tp~~l~~~l~~~~~~l~~~~~lVlDEah~~~~~-gf~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~  250 (434)
T 2db3_A          173 NECITRG-CHVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDM-GFSEDMRRIMTHVTMRPEHQTLMFSATFPEEI  250 (434)
T ss_dssp             HHHHTTC-CSEEEECHHHHHHHHHTTSCCCTTCCEEEEETHHHHTST-TTHHHHHHHHHCTTSCSSCEEEEEESCCCHHH
T ss_pred             HHHhhcC-CCEEEEChHHHHHHHHhCCcccccCCeEEEccHhhhhcc-CcHHHHHHHHHhcCCCCCceEEEEeccCCHHH
Confidence            7777665 899999999999999998888999999999999999998 9999999999875  57889999999999999


Q ss_pred             HHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEE
Q psy1548         303 RPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAV  382 (448)
Q Consensus       303 ~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~  382 (448)
                      ..++..++.++..+.+... .....++.+.+..+....|...|.+++..... ++||||++++.|+.+++.|++.|+++.
T Consensus       251 ~~~~~~~l~~~~~i~~~~~-~~~~~~i~~~~~~~~~~~k~~~l~~~l~~~~~-~~lVF~~t~~~a~~l~~~L~~~~~~~~  328 (434)
T 2db3_A          251 QRMAGEFLKNYVFVAIGIV-GGACSDVKQTIYEVNKYAKRSKLIEILSEQAD-GTIVFVETKRGADFLASFLSEKEFPTT  328 (434)
T ss_dssp             HHHHHTTCSSCEEEEESST-TCCCTTEEEEEEECCGGGHHHHHHHHHHHCCT-TEEEECSSHHHHHHHHHHHHHTTCCEE
T ss_pred             HHHHHHhccCCEEEEeccc-cccccccceEEEEeCcHHHHHHHHHHHHhCCC-CEEEEEeCcHHHHHHHHHHHhCCCCEE
Confidence            9999999999998887765 44567889999999999999999999988765 499999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHhcCC----------------------------------------------CceEEEEecChh
Q psy1548         383 SIHRGMTQEERLKKYQEFKDFH----------------------------------------------KGLAITFASDEN  416 (448)
Q Consensus       383 ~lh~~~~~~eR~~~l~~F~~g~----------------------------------------------~g~~I~~~t~~~  416 (448)
                      .+||+|++.+|.+++++|++|+                                              .|.+++|+++.+
T Consensus       329 ~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v~~rGlDi~~v~~VI~~d~p~~~~~y~qriGR~gR~g~~G~a~~~~~~~~  408 (434)
T 2db3_A          329 SIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEK  408 (434)
T ss_dssp             EESTTSCHHHHHHHHHHHHTSSCSEEEECGGGTSSCCCTTCCEEEESSCCSSHHHHHHHHTTSSCTTCCEEEEEEECTTT
T ss_pred             EEeCCCCHHHHHHHHHHHHcCCCcEEEEchhhhCCCCcccCCEEEEECCCCCHHHHHHHhcccccCCCCCEEEEEEeccc
Confidence            9999999999999999999998                                              799999999777


Q ss_pred             hHHHHHHHHHHhcCCCCCCCccccc
Q psy1548         417 DAKILNNVQDRFDVSISELPDEIDL  441 (448)
Q Consensus       417 d~~~l~~i~~~~~~~~~~~p~~~~~  441 (448)
                      +...++.+.+.+....+++|+++..
T Consensus       409 ~~~~~~~l~~~l~~~~~~vp~~l~~  433 (434)
T 2db3_A          409 DRAIAADLVKILEGSGQTVPDFLRT  433 (434)
T ss_dssp             CGGGHHHHHHHHHHTTCCCCGGGC-
T ss_pred             cHHHHHHHHHHHHHcCCCCCHHHHh
Confidence            8889999999999999999999753

>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=100.00  E-value=3.2e-46  Score=373.49  Aligned_cols=338  Identities=80%  Similarity=1.221  Sum_probs=310.2

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      +.+|+++++++.+++++.+.|                       |..|+++   |.+      +++.++.|+++++.+||
T Consensus         7 ~~~f~~~~l~~~l~~~l~~~g-----------------------~~~~~~~---Q~~------~i~~~~~~~~~lv~a~T   54 (391)
T 1xti_A            7 SSGFRDFLLKPELLRAIVDCG-----------------------FEHPSEV---QHE------CIPQAILGMDVLCQAKS   54 (391)
T ss_dssp             --CGGGGCCCHHHHHHHHHHS-----------------------CCSCCHH---HHH------HHHHHTTTCCEEEECSS
T ss_pred             CCChhhcCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhcCCcEEEECCC
Confidence            357999999999999999999                       9999888   999      99999999999999999


Q ss_pred             CChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEE
Q psy1548         159 GMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVG  238 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~  238 (448)
                      |+|||++|++|++..+.....+.++||++|+++|+.|+.+.++++....+++++..+.|+.........+..+.++|+|+
T Consensus        55 GsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~  134 (391)
T 1xti_A           55 GMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVG  134 (391)
T ss_dssp             CSSHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEE
T ss_pred             CCcHHHHHHHHHHHhhcccCCCeeEEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEE
Confidence            99999999999999887666677999999999999999999999998877899999999988777777777666899999


Q ss_pred             cHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEE
Q psy1548         239 TPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV  318 (448)
Q Consensus       239 Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~  318 (448)
                      ||+++..++......+.+++++|+||||++.++.+++..+..++...++..|++++|||+++....++..++.+|..+..
T Consensus       135 T~~~l~~~~~~~~~~~~~~~~vViDEaH~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~  214 (391)
T 1xti_A          135 TPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV  214 (391)
T ss_dssp             CHHHHHHHHHTTSSCCTTCSEEEECSHHHHTSSHHHHHHHHHHHHTSCSSSEEEEEESSCCSTHHHHHHHHCSSCEEEEC
T ss_pred             CHHHHHHHHHcCCccccccCEEEEeCHHHHhhccchHHHHHHHHhhCCCCceEEEEEeeCCHHHHHHHHHHcCCCeEEEe
Confidence            99999999998888899999999999999988558889999999999999999999999999999999999999998887


Q ss_pred             cCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHH
Q psy1548         319 DDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQ  398 (448)
Q Consensus       319 ~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~  398 (448)
                      ..........+.+++..+....|...+..++.....+++||||++++.|+.+++.|++.|+.+..+||+|++++|.++++
T Consensus       215 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~  294 (391)
T 1xti_A          215 DDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQ  294 (391)
T ss_dssp             CCCCCCCCTTCEEEEEECCGGGHHHHHHHHHHHSCCSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHH
T ss_pred             cCccccCcccceEEEEEcCchhHHHHHHHHHHhcCCCcEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHH
Confidence            76655667788899999999999999999999988899999999999999999999999999999999999999999999


Q ss_pred             HHhcCC----------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCCC
Q psy1548         399 EFKDFH----------------------------------------------KGLAITFASDENDAKILNNVQDRFDVSI  432 (448)
Q Consensus       399 ~F~~g~----------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~~  432 (448)
                      .|++|+                                              .|.+++++++.++..+++.+++.+++.+
T Consensus       295 ~f~~~~~~vlv~T~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~  374 (391)
T 1xti_A          295 QFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNI  374 (391)
T ss_dssp             HHHTTCCSEEEESCCCSSCBCCTTEEEEEESSCCSSHHHHHHHHCBCSSSCCCCEEEEEECSHHHHHHHHHHHHHTTCCC
T ss_pred             HHhcCCCcEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHhcccccCCCCceEEEEEEcccchHHHHHHHHHHhcCCh
Confidence            999988                                              7899999999888899999999999999


Q ss_pred             CCCCccccccccccCC
Q psy1548         433 SELPDEIDLSTYIEGR  448 (448)
Q Consensus       433 ~~~p~~~~~~~~~~~~  448 (448)
                      .++|..++...+++.|
T Consensus       375 ~~~~~~~~~~~~~~~~  390 (391)
T 1xti_A          375 SELPDEIDISSYIEQT  390 (391)
T ss_dssp             EECCSCCCGGGTSCC-
T ss_pred             hhCCccccHHHHhhhc
Confidence            9999999988888765

>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=100.00  E-value=5.7e-45  Score=367.09  Aligned_cols=325  Identities=33%  Similarity=0.572  Sum_probs=296.2

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      ...|.++++++.+++++...|                       |..|+++   |++      +++.++.|+|+++++||
T Consensus        36 ~~~f~~~~l~~~l~~~l~~~g-----------------------~~~~~~~---Q~~------ai~~i~~~~~~lv~a~T   83 (410)
T 2j0s_A           36 TPTFDTMGLREDLLRGIYAYG-----------------------FEKPSAI---QQR------AIKQIIKGRDVIAQSQS   83 (410)
T ss_dssp             CCSGGGGCCCHHHHHHHHHHT-----------------------CCSCCHH---HHH------HHHHHHTTCCEEEECCT
T ss_pred             CCCHhhcCCCHHHHHHHHHcC-----------------------CCCCCHH---HHH------HHHHHhCCCCEEEECCC
Confidence            357999999999999999999                       9999999   999      99999999999999999


Q ss_pred             CChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEE
Q psy1548         159 GMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVG  238 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~  238 (448)
                      |+|||++|++|+++.+.....+.++||++||++|+.|+.+.++.+.... ++++..+.|+.....+...+..+ ++|+|+
T Consensus        84 GsGKT~~~~~~~~~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~-~~ivv~  161 (410)
T 2j0s_A           84 GTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLDYG-QHVVAG  161 (410)
T ss_dssp             TSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTT-TCCEEEECTTSCHHHHHHHHHHC-CSEEEE
T ss_pred             CCCchHHHHHHHHHHHhhccCCceEEEEcCcHHHHHHHHHHHHHHhccC-CeEEEEEECCCCHHHHHHHhhcC-CCEEEc
Confidence            9999999999999988665567799999999999999999999998877 88999999999877777777665 899999


Q ss_pred             cHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEE
Q psy1548         239 TPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV  318 (448)
Q Consensus       239 Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~  318 (448)
                      ||+++.+++..+.+.+.+++++|+||||++.++ ++...+..+++.+++..|++++|||+++.+.++...++.+|..+..
T Consensus       162 Tp~~l~~~l~~~~~~~~~~~~vViDEah~~~~~-~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~  240 (410)
T 2j0s_A          162 TPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNK-GFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILV  240 (410)
T ss_dssp             CHHHHHHHHHTTSSCCTTCCEEEEETHHHHTST-TTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECC
T ss_pred             CHHHHHHHHHhCCccHhheeEEEEccHHHHHhh-hhHHHHHHHHHhCccCceEEEEEcCCCHHHHHHHHHHcCCCEEEEe
Confidence            999999999998888899999999999999998 9999999999999999999999999999988888899999988876


Q ss_pred             cCcccccccceeEEEEEcCcch-HHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHH
Q psy1548         319 DDEAKLTLHGLQQHYVKLKENE-KNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKY  397 (448)
Q Consensus       319 ~~~~~~~~~~i~~~~~~~~~~~-k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l  397 (448)
                      ... .....++.+.+..+.... |...+..++.....+++||||++++.++.+++.|++.|+.+..+||+|++.+|.+++
T Consensus       241 ~~~-~~~~~~~~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~  319 (410)
T 2j0s_A          241 KRD-ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIM  319 (410)
T ss_dssp             CGG-GCSCTTEEEEEEEESSTTHHHHHHHHHHHHHTSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHH
T ss_pred             cCc-cccCCCceEEEEEeCcHHhHHHHHHHHHHhcCCCcEEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHH
Confidence            555 456677888888777654 889999999888788999999999999999999999999999999999999999999


Q ss_pred             HHHhcCC----------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCC
Q psy1548         398 QEFKDFH----------------------------------------------KGLAITFASDENDAKILNNVQDRFDVS  431 (448)
Q Consensus       398 ~~F~~g~----------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~  431 (448)
                      +.|++|+                                              .|.+++|++.. |...+++++++++..
T Consensus       320 ~~f~~g~~~vlv~T~~~~~Gidi~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~-~~~~~~~i~~~~~~~  398 (410)
T 2j0s_A          320 KEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKND-DIRILRDIEQYYSTQ  398 (410)
T ss_dssp             HHHHHTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGG-GHHHHHHHHHHTTCC
T ss_pred             HHHHCCCCCEEEECChhhCcCCcccCCEEEEECCCCCHHHHHHhcccccCCCCceEEEEEecHH-HHHHHHHHHHHhCCC
Confidence            9999998                                              78999999876 889999999999999


Q ss_pred             CCCCCcccc
Q psy1548         432 ISELPDEID  440 (448)
Q Consensus       432 ~~~~p~~~~  440 (448)
                      +.++|.++.
T Consensus       399 ~~~~~~~~~  407 (410)
T 2j0s_A          399 IDEMPMNVA  407 (410)
T ss_dssp             CEECCSCCT
T ss_pred             ceecccchh
Confidence            999998754

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=100.00  E-value=1.1e-44  Score=365.65  Aligned_cols=334  Identities=27%  Similarity=0.405  Sum_probs=295.0

Q ss_pred             CceeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcc
Q psy1548          72 GAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMD  151 (448)
Q Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~  151 (448)
                      |...+.+...|.++++++.+++++...|                       |..|+++   |++      ++|.++.|+|
T Consensus         7 ~~~~p~~~~~f~~~~l~~~l~~~l~~~~-----------------------~~~~~~~---Q~~------~i~~i~~~~~   54 (417)
T 2i4i_A            7 GNNCPPHIESFSDVEMGEIIMGNIELTR-----------------------YTRPTPV---QKH------AIPIIKEKRD   54 (417)
T ss_dssp             STTCCCCCSSGGGSCCCHHHHHHHHHHT-----------------------CCSCCHH---HHH------HHHHHHTTCC
T ss_pred             CCcCCcccCCHhhCCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHccCCC
Confidence            4455666678999999999999999999                       9999999   999      9999999999


Q ss_pred             eeeeccCCChhHHHHHHHHHHhhhccC------------------CCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEE
Q psy1548         152 ILCQAKSGMGKTAVFVLATLQQLETTD------------------SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVG  213 (448)
Q Consensus       152 vli~apTGsGKT~~~~l~~l~~l~~~~------------------~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~  213 (448)
                      +++++|||+|||++|++|+++.+....                  .++++||++||++|+.|+.+.++.+.... ++++.
T Consensus        55 ~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~  133 (417)
T 2i4i_A           55 LMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRS-RVRPC  133 (417)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTS-SCCEE
T ss_pred             EEEEcCCCCHHHHHHHHHHHHHHHhccccchhhccccccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcC-CceEE
Confidence            999999999999999999998875432                  23689999999999999999999998876 89999


Q ss_pred             EEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHh--CCC--CC
Q psy1548         214 VFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRS--SPH--TK  289 (448)
Q Consensus       214 ~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~--l~~--~~  289 (448)
                      .++|+.....+...+..+ ++|+|+||+++.+++..+.+.+.+++++|+||||++.++ +|...+..++..  ++.  ..
T Consensus       134 ~~~g~~~~~~~~~~~~~~-~~I~v~Tp~~l~~~l~~~~~~~~~~~~iViDEah~~~~~-~~~~~~~~i~~~~~~~~~~~~  211 (417)
T 2i4i_A          134 VVYGGADIGQQIRDLERG-CHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDM-GFEPQIRRIVEQDTMPPKGVR  211 (417)
T ss_dssp             EECSSSCHHHHHHHHTTC-CSEEEECHHHHHHHHHTTSBCCTTCCEEEESSHHHHHHT-TCHHHHHHHHTSSSCCCBTTB
T ss_pred             EEECCCCHHHHHHHhhCC-CCEEEEChHHHHHHHHcCCcChhhCcEEEEEChhHhhcc-CcHHHHHHHHHhccCCCcCCc
Confidence            999998877777777664 899999999999999988888999999999999999998 899999999874  333  67


Q ss_pred             eEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhC-CCCeEEEEECccHHHH
Q psy1548         290 QVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVL-EFNQVVIFVKSVTRCI  368 (448)
Q Consensus       290 q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~-~~~~~IIF~~s~~~a~  368 (448)
                      |++++|||+++.+..+...++.++..+..... .....++.+.+..+....|...+.++++.. .++++||||++++.|+
T Consensus       212 ~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~lVf~~~~~~~~  290 (417)
T 2i4i_A          212 HTMMFSATFPKEIQMLARDFLDEYIFLAVGRV-GSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGAD  290 (417)
T ss_dssp             EEEEEESCCCHHHHHHHHHHCSSCEEEEEC-----CCSSEEEEEEECCGGGHHHHHHHHHHTCCTTCEEEEECSSHHHHH
T ss_pred             EEEEEEEeCCHHHHHHHHHHcCCCEEEEeCCC-CCCccCceEEEEEeccHhHHHHHHHHHHhcCCCCeEEEEECCHHHHH
Confidence            99999999999999999999999988777655 445678889999999999999999999886 5678999999999999


Q ss_pred             HHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC--------------------------------------------
Q psy1548         369 ALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH--------------------------------------------  404 (448)
Q Consensus       369 ~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~--------------------------------------------  404 (448)
                      .+++.|++.|+.+..+||+|++++|.++++.|++|+                                            
T Consensus       291 ~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~  370 (417)
T 2i4i_A          291 SLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRV  370 (417)
T ss_dssp             HHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECHHHHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC-
T ss_pred             HHHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCCEEEEEcCCCCHHHHHHhcCccccC
Confidence            999999999999999999999999999999999998                                            


Q ss_pred             --CceEEEEecChhhHHHHHHHHHHhcCCCCCCCcccccc
Q psy1548         405 --KGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLS  442 (448)
Q Consensus       405 --~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~  442 (448)
                        .|.+++|++.. |...++.+.+.+.....++|.++..+
T Consensus       371 g~~g~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~l~~~  409 (417)
T 2i4i_A          371 GNLGLATSFFNER-NINITKDLLDLLVEAKQEVPSWLENM  409 (417)
T ss_dssp             -CCEEEEEEECGG-GGGGHHHHHHHHHHTTCCCCHHHHHH
T ss_pred             CCCceEEEEEccc-cHHHHHHHHHHHHHhcCcCCHHHHHH
Confidence              68899999876 78888999999998889999886543

>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=100.00  E-value=1e-43  Score=356.60  Aligned_cols=331  Identities=34%  Similarity=0.512  Sum_probs=297.2

Q ss_pred             ccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeecc
Q psy1548          78 HSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAK  157 (448)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~ap  157 (448)
                      ....|+++++++.+++++.+.|                       |..|+++   |++      +++.++.|+++++.+|
T Consensus        19 ~~~~f~~~~l~~~l~~~l~~~g-----------------------~~~~~~~---Q~~------~i~~i~~~~~~li~a~   66 (400)
T 1s2m_A           19 KGNTFEDFYLKRELLMGIFEAG-----------------------FEKPSPI---QEE------AIPVAITGRDILARAK   66 (400)
T ss_dssp             --CCGGGGCCCHHHHHHHHHTT-----------------------CCSCCHH---HHH------HHHHHHHTCCEEEECC
T ss_pred             ccCChhhcCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhcCCCEEEECC
Confidence            3457999999999999999999                       9999988   999      9999999999999999


Q ss_pred             CCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEE
Q psy1548         158 SGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVV  237 (448)
Q Consensus       158 TGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV  237 (448)
                      ||+|||++|++|++..+.....+.++||++|+++|+.|+.+.++.+.... ++++..+.|+.....+...+.. .++|+|
T Consensus        67 TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~-~~~Ivv  144 (400)
T 1s2m_A           67 NGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHC-GISCMVTTGGTNLRDDILRLNE-TVHILV  144 (400)
T ss_dssp             TTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTT-TCCEEEECSSSCHHHHHHHTTS-CCSEEE
T ss_pred             CCcHHHHHHHHHHHHHHhhccCCccEEEEcCCHHHHHHHHHHHHHHhccc-CceEEEEeCCcchHHHHHHhcC-CCCEEE
Confidence            99999999999999988766566789999999999999999999998877 8899999998876665555544 489999


Q ss_pred             EcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEE
Q psy1548         238 GTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVY  317 (448)
Q Consensus       238 ~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~  317 (448)
                      +||+++.+++......+.+++++|+||||++.+. ++...+..++..+++..|++++|||++..+...+..++..|..+.
T Consensus       145 ~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~-~~~~~~~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~~~~~~  223 (400)
T 1s2m_A          145 GTPGRVLDLASRKVADLSDCSLFIMDEADKMLSR-DFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEIN  223 (400)
T ss_dssp             ECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSH-HHHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEES
T ss_pred             EchHHHHHHHHhCCcccccCCEEEEeCchHhhhh-chHHHHHHHHHhCCcCceEEEEEecCCHHHHHHHHHHcCCCeEEE
Confidence            9999999999888888899999999999999987 899999999999999999999999999999999999998887765


Q ss_pred             EcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHH
Q psy1548         318 VDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKY  397 (448)
Q Consensus       318 ~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l  397 (448)
                      ....  ....++.+++..+....|...+..++.....+++||||++++.++.+++.|++.|+.+..+||+|++++|..++
T Consensus       224 ~~~~--~~~~~~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~  301 (400)
T 1s2m_A          224 LMEE--LTLKGITQYYAFVEERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVF  301 (400)
T ss_dssp             CCSS--CBCTTEEEEEEECCGGGHHHHHHHHHHHSCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHH
T ss_pred             eccc--cccCCceeEEEEechhhHHHHHHHHHhhcCCCcEEEEEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHH
Confidence            5433  45677888888899899999999999988888999999999999999999999999999999999999999999


Q ss_pred             HHHhcCC----------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCC
Q psy1548         398 QEFKDFH----------------------------------------------KGLAITFASDENDAKILNNVQDRFDVS  431 (448)
Q Consensus       398 ~~F~~g~----------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~  431 (448)
                      +.|++|+                                              .|.++++++.. |...++++++.++.+
T Consensus       302 ~~f~~g~~~vLv~T~~~~~Gidip~~~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~l~~~~-~~~~~~~i~~~~~~~  380 (400)
T 1s2m_A          302 HEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWN-DRFNLYKIEQELGTE  380 (400)
T ss_dssp             HHHHTTSSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGG-GHHHHHHHHHHHTCC
T ss_pred             HHHhcCCCcEEEEcCccccCCCccCCCEEEEeCCCCCHHHHHHhcchhcCCCCCceEEEEeccc-hHHHHHHHHHHhCCC
Confidence            9999997                                              78899999877 788999999999999


Q ss_pred             CCCCCcccccccccc
Q psy1548         432 ISELPDEIDLSTYIE  446 (448)
Q Consensus       432 ~~~~p~~~~~~~~~~  446 (448)
                      ++++|.+++...|.+
T Consensus       381 ~~~~~~~~~~~~~~~  395 (400)
T 1s2m_A          381 IAAIPATIDKSLYVA  395 (400)
T ss_dssp             CEECCSSCCGGGTCC
T ss_pred             cccccccccccceeh
Confidence            999999987766543

>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=100.00  E-value=6e-44  Score=359.66  Aligned_cols=330  Identities=32%  Similarity=0.540  Sum_probs=292.3

Q ss_pred             eeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeee
Q psy1548          76 SIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQ  155 (448)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~  155 (448)
                      ......|.++++++.+++.+.+.+                       |..|+++   |++      +++.++.|++++++
T Consensus        36 ~~~~~~f~~~~l~~~~~~~l~~~~-----------------------~~~~~~~---Q~~------~i~~~~~~~~~lv~   83 (414)
T 3eiq_A           36 NEIVDSFDDMNLSESLLRGIYAYG-----------------------FEKPSAI---QQR------AILPCIKGYDVIAQ   83 (414)
T ss_dssp             CCCCCCGGGGCCCHHHHHHHHHTT-----------------------CCSCCHH---HHH------HHHHHHTTCCEEEC
T ss_pred             cchhcCHhhCCCCHHHHHHHHHcC-----------------------CCCCCHH---HHH------HhHHHhCCCCEEEE
Confidence            334467999999999999999999                       9999998   999      99999999999999


Q ss_pred             ccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcE
Q psy1548         156 AKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQI  235 (448)
Q Consensus       156 apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~I  235 (448)
                      +|||+|||++|++|+++.+.....+.++||++|+++|+.|+.+.++.+.... +..+..++|+.....+...+..+.++|
T Consensus        84 a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~i  162 (414)
T 3eiq_A           84 AQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEAPHI  162 (414)
T ss_dssp             CCSCSSSHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHGGGS-CCCEEECCCCTTHHHHHHHHTTTCCSE
T ss_pred             CCCCCcccHHHHHHHHHHHhhcCCceeEEEEeChHHHHHHHHHHHHHHhccc-CceEEEEECCcchHHHHHHHhcCCCCE
Confidence            9999999999999999988776667799999999999999999999998877 889999999988877777777566899


Q ss_pred             EEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeE
Q psy1548         236 VVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPME  315 (448)
Q Consensus       236 lV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~  315 (448)
                      +|+||+++.+++..+.+.+.+++++|+||||++.++ ++...+..++..+++..|++++|||+++.+..+...++.+|..
T Consensus       163 iv~T~~~l~~~l~~~~~~~~~~~~vViDEah~~~~~-~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~  241 (414)
T 3eiq_A          163 IVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSR-GFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIR  241 (414)
T ss_dssp             EEECHHHHHHHHHHTSSCSTTCCEEEECSHHHHHHT-TTHHHHHHHHTTSCTTCEEEEECSCCCHHHHHHHTTTCSSCEE
T ss_pred             EEECHHHHHHHHHcCCcccccCcEEEEECHHHhhcc-CcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHcCCCEE
Confidence            999999999999988888899999999999999998 9999999999999999999999999999999999999999988


Q ss_pred             EEEcCcccccccceeEEEEEcCcc-hHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHH
Q psy1548         316 VYVDDEAKLTLHGLQQHYVKLKEN-EKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERL  394 (448)
Q Consensus       316 i~~~~~~~~~~~~i~~~~~~~~~~-~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~  394 (448)
                      +..... ......+.+.+..+... .|...+..++.....+++||||++++.|+.+++.|++.|+.+..+||+|++++|.
T Consensus       242 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~  320 (414)
T 3eiq_A          242 ILVKKE-ELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERD  320 (414)
T ss_dssp             ECCCCC-CCCTTSCCEEEEECSSSTTHHHHHHHHHHSSCCSSCEEECSCHHHHHHHHHHHHTTTCCCEEC---CHHHHHH
T ss_pred             EEecCC-ccCCCCceEEEEEeChHHhHHHHHHHHHHhCCCCcEEEEeCCHHHHHHHHHHHHhcCCeEEEecCCCCHHHHH
Confidence            877655 45667788888777665 4899999999998888999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCC----------------------------------------------CceEEEEecChhhHHHHHHHHHHh
Q psy1548         395 KKYQEFKDFH----------------------------------------------KGLAITFASDENDAKILNNVQDRF  428 (448)
Q Consensus       395 ~~l~~F~~g~----------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~  428 (448)
                      ++++.|++|+                                              .|.++++++.. +...++.+++.+
T Consensus       321 ~~~~~f~~g~~~vlv~T~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~-~~~~~~~~~~~~  399 (414)
T 3eiq_A          321 VIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEE-DKRTLRDIETFY  399 (414)
T ss_dssp             HHHHHHSCC---CEEECSSCC--CCGGGCSCEEESSCCSSTHHHHHHSCCC-------CEEEEECST-HHHHHHHHHHHT
T ss_pred             HHHHHHHcCCCcEEEECCccccCCCccCCCEEEEeCCCCCHHHhhhhcCcccCCCCCceEEEEEcHH-HHHHHHHHHHHH
Confidence            9999999988                                              68899999877 788999999999


Q ss_pred             cCCCCCCCccccc
Q psy1548         429 DVSISELPDEIDL  441 (448)
Q Consensus       429 ~~~~~~~p~~~~~  441 (448)
                      +..+.++|.++..
T Consensus       400 ~~~~~~~~~~~~~  412 (414)
T 3eiq_A          400 NTSIEEMPLNVAD  412 (414)
T ss_dssp             TCCCEECCC----
T ss_pred             cCCccccChhhhh
Confidence            9999999988653

>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=100.00  E-value=6.3e-42  Score=344.49  Aligned_cols=325  Identities=27%  Similarity=0.432  Sum_probs=287.6

Q ss_pred             eccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeC--cceee
Q psy1548          77 IHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLG--MDILC  154 (448)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g--~~vli  154 (448)
                      .....|+++++++.+++.+.+.|                       |..|+++   |.+      +++.++.|  +++++
T Consensus        22 ~~~~~f~~~~l~~~l~~~l~~~g-----------------------~~~~~~~---Q~~------~i~~~~~~~~~~~lv   69 (412)
T 3fht_A           22 YSVKSFEELRLKPQLLQGVYAMG-----------------------FNRPSKI---QEN------ALPLMLAEPPQNLIA   69 (412)
T ss_dssp             CCSSCTGGGTCCHHHHHHHHHTT-----------------------CCSCCHH---HHH------HHHHHHSSSCCCEEE
T ss_pred             cccCCHhhCCCCHHHHHHHHHcC-----------------------CCCCCHH---HHH------HHHHHhcCCCCeEEE
Confidence            34567999999999999999999                       9999999   999      99999987  99999


Q ss_pred             eccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCc
Q psy1548         155 QAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQ  234 (448)
Q Consensus       155 ~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~  234 (448)
                      ++|||+|||++|++|++..+.....++++||++|+++|+.|+.+.++.+....++..+....++.......    ...++
T Consensus        70 ~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~  145 (412)
T 3fht_A           70 QSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ----KISEQ  145 (412)
T ss_dssp             ECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTTC----CCCCS
T ss_pred             ECCCCchHHHHHHHHHHHHhhhcCCCCCEEEECCCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhhh----cCCCC
Confidence            99999999999999999998777777799999999999999999999999887788888888877644332    23479


Q ss_pred             EEEEcHHHHHHHHHC-CCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCC
Q psy1548         235 IVVGTPGRILALVRN-KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDP  313 (448)
Q Consensus       235 IlV~Tp~~l~~~l~~-~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~  313 (448)
                      |+|+||+++.+++.+ +.+.+.+++++|+||||++.+..++...+..+...+++..|++++|||+++.+..+...++.++
T Consensus       146 ivv~T~~~l~~~~~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~  225 (412)
T 3fht_A          146 IVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDP  225 (412)
T ss_dssp             EEEECHHHHHHHHTTSCSSCGGGCCEEEEETHHHHHSTTTTHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSSSC
T ss_pred             EEEECchHHHHHHHhcCCcChhhCcEEEEeCHHHHhhcCCcHHHHHHHHhhCCCCceEEEEEeecCHHHHHHHHHhcCCC
Confidence            999999999999865 6677899999999999999873388889999999999999999999999999999999999999


Q ss_pred             eEEEEcCcccccccceeEEEEEcCc-chHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHH
Q psy1548         314 MEVYVDDEAKLTLHGLQQHYVKLKE-NEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEE  392 (448)
Q Consensus       314 ~~i~~~~~~~~~~~~i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~e  392 (448)
                      ..+..... ......+.+.+..+.. ..+...+..++.....+++||||++++.|+.++..|++.|+.+..+||+|++.+
T Consensus       226 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~  304 (412)
T 3fht_A          226 NVIKLKRE-EETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQ  304 (412)
T ss_dssp             EEECCCGG-GSSCTTEEEEEEECSSHHHHHHHHHHHHHHHSSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHH
T ss_pred             eEEeeccc-cccccCceEEEEEcCChHHHHHHHHHHHhhcCCCCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHH
Confidence            88877665 4556777787777765 568888999998888889999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcCC----------------------------------------------------CceEEEEecChhhHHH
Q psy1548         393 RLKKYQEFKDFH----------------------------------------------------KGLAITFASDENDAKI  420 (448)
Q Consensus       393 R~~~l~~F~~g~----------------------------------------------------~g~~I~~~t~~~d~~~  420 (448)
                      |.++++.|++|+                                                    .|.++++++..++...
T Consensus       305 r~~~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~  384 (412)
T 3fht_A          305 RAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKHSMNI  384 (412)
T ss_dssp             HHHHHHHHHTTSCSEEEECGGGTSSCCCTTEEEEEESSCCBCSSSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHH
T ss_pred             HHHHHHHHHCCCCcEEEEcCccccCCCccCCCEEEEECCCCCCCCCcchheeecccCcccCCCCCceEEEEEcChhhHHH
Confidence            999999999998                                                    6889999998878999


Q ss_pred             HHHHHHHhcCCCCCCCcc
Q psy1548         421 LNNVQDRFDVSISELPDE  438 (448)
Q Consensus       421 l~~i~~~~~~~~~~~p~~  438 (448)
                      ++.+++.++..+.+++.+
T Consensus       385 ~~~i~~~~~~~~~~~~~~  402 (412)
T 3fht_A          385 LNRIQEHFNKKIERLDTD  402 (412)
T ss_dssp             HHHHHHHHTCCCEEC---
T ss_pred             HHHHHHHHCCccccCCCc
Confidence            999999999999998765

>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=100.00  E-value=7.1e-43  Score=349.34  Aligned_cols=329  Identities=33%  Similarity=0.499  Sum_probs=188.3

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      ...|+++++++.+++.+...|                       |..|+++   |++      +++.++.|+++++++||
T Consensus        20 ~~~f~~~~l~~~l~~~l~~~g-----------------------~~~~~~~---Q~~------~i~~i~~~~~~lv~~~T   67 (394)
T 1fuu_A           20 VYKFDDMELDENLLRGVFGYG-----------------------FEEPSAI---QQR------AIMPIIEGHDVLAQAQS   67 (394)
T ss_dssp             CCSSGGGCCCHHHHHHHHHHT-----------------------CCSCCHH---HHH------HHHHHHHTCCEEECCCS
T ss_pred             cCChhhcCCCHHHHHHHHHcC-----------------------CCCCCHH---HHH------HHHHHhCCCCEEEECCC
Confidence            457999999999999999999                       9999888   999      99999999999999999


Q ss_pred             CChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEE
Q psy1548         159 GMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVG  238 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~  238 (448)
                      |+|||++|++|++..+.....++++||++|+++|+.|+.+.+.++.... ++++..+.|+.........+..  ++|+|+
T Consensus        68 GsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~--~~i~v~  144 (394)
T 1fuu_A           68 GTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRD--AQIVVG  144 (394)
T ss_dssp             SHHHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTS-CCCEEEECSSCCHHHHHHHHHH--CSEEEE
T ss_pred             CChHHHHHHHHHHHHhhccCCCCCEEEEcCCHHHHHHHHHHHHHHhccC-CeeEEEEeCCCchHHHHhhcCC--CCEEEE
Confidence            9999999999999988776667799999999999999999999998877 8899999999887666555553  799999


Q ss_pred             cHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEE
Q psy1548         239 TPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV  318 (448)
Q Consensus       239 Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~  318 (448)
                      ||+++.+.+..+...+.+++++|+||||++.++ ++...+..++..+++..|++++|||+++...++...++.+|..+..
T Consensus       145 T~~~l~~~~~~~~~~~~~~~~vIiDEah~~~~~-~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~  223 (394)
T 1fuu_A          145 TPGRVFDNIQRRRFRTDKIKMFILDEADEMLSS-GFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILV  223 (394)
T ss_dssp             CHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHT-TCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCCSCEEEEE
T ss_pred             CHHHHHHHHHhCCcchhhCcEEEEEChHHhhCC-CcHHHHHHHHHhCCCCceEEEEEEecCHHHHHHHHHhcCCCeEEEe
Confidence            999999999988888899999999999999998 8999999999999999999999999999999999999999998887


Q ss_pred             cCcccccccceeEEEEEcCcch-HHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHH
Q psy1548         319 DDEAKLTLHGLQQHYVKLKENE-KNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKY  397 (448)
Q Consensus       319 ~~~~~~~~~~i~~~~~~~~~~~-k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l  397 (448)
                      ... .....++.+.+..+.... +...+..+++....+++||||++++.|+.+++.|++.|+.+..+||+|++.+|.+++
T Consensus       224 ~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~  302 (394)
T 1fuu_A          224 KKD-ELTLEGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIM  302 (394)
T ss_dssp             CC------------------------------------------------------------------------------
T ss_pred             cCc-cccCCCceEEEEEcCchhhHHHHHHHHHhcCCCCcEEEEECCHHHHHHHHHHHHHcCCeEEEeeCCCCHHHHHHHH
Confidence            665 445566777766665544 777888888877778999999999999999999999999999999999999999999


Q ss_pred             HHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         398 QEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       398 ~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      +.|++|+  ..|.++|+....++  ++...--+-..+.|.+...+.++.||
T Consensus       303 ~~f~~~~--~~vlv~T~~~~~Gl--di~~~~~Vi~~~~p~s~~~~~Qr~GR  349 (394)
T 1fuu_A          303 KEFRSGS--SRILISTDLLARGI--DVQQVSLVINYDLPANKENYIHRIGR  349 (394)
T ss_dssp             ---------------------------------------------------
T ss_pred             HHHHCCC--CcEEEECChhhcCC--CcccCCEEEEeCCCCCHHHHHHHcCc
Confidence            9999987  45667776544443  45444445566778888889999988

>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=100.00  E-value=7.1e-41  Score=334.56  Aligned_cols=321  Identities=26%  Similarity=0.454  Sum_probs=284.1

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeC--cceeeec
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLG--MDILCQA  156 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g--~~vli~a  156 (448)
                      ...|+++++++.+++++.+.+                       |..|+++   |.+      +++.++.|  +++++++
T Consensus         4 ~~~f~~~~l~~~l~~~l~~~~-----------------------~~~~~~~---Q~~------~i~~~~~~~~~~~lv~a   51 (395)
T 3pey_A            4 AKSFDELGLAPELLKGIYAMK-----------------------FQKPSKI---QER------ALPLLLHNPPRNMIAQS   51 (395)
T ss_dssp             CCSSTTSCCCHHHHHHHHHTT-----------------------CCSCCHH---HHH------HHHHHHCSSCCCEEEEC
T ss_pred             ccCHhhCCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHHcCCCCeEEEEC
Confidence            357999999999999999999                       9999999   999      99999998  9999999


Q ss_pred             cCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEE
Q psy1548         157 KSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV  236 (448)
Q Consensus       157 pTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~Il  236 (448)
                      |||+|||++|++|++..+.....+.++||++|+++|+.|+.+.++.+.... ++.+....++......     ...++|+
T Consensus        52 ~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~-----~~~~~ii  125 (395)
T 3pey_A           52 QSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFT-KITSQLIVPDSFEKNK-----QINAQVI  125 (395)
T ss_dssp             CTTSCHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTS-CCCEEEESTTSSCTTS-----CBCCSEE
T ss_pred             CCCCcHHHHHHHHHHHHhccCCCCccEEEECCCHHHHHHHHHHHHHHhccc-CeeEEEEecCchhhhc-----cCCCCEE
Confidence            999999999999999988776667799999999999999999999998776 7788887776543322     2247999


Q ss_pred             EEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEE
Q psy1548         237 VGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEV  316 (448)
Q Consensus       237 V~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i  316 (448)
                      |+||+++.+++......+.+++++|+||||++.+..++...+..+...+++..|++++|||+++.+..+...++.++..+
T Consensus       126 v~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~  205 (395)
T 3pey_A          126 VGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTL  205 (395)
T ss_dssp             EECHHHHHHHHHTTCBCCTTCCEEEEETHHHHHHSTTHHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSCSCEEE
T ss_pred             EEcHHHHHHHHHcCCcccccCCEEEEEChhhhcCccccHHHHHHHHHhCCCCcEEEEEEecCCHHHHHHHHHhCCCCeEE
Confidence            99999999999988888999999999999999884388999999999999999999999999999999999999988887


Q ss_pred             EEcCcccccccceeEEEEEcCc-chHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHH
Q psy1548         317 YVDDEAKLTLHGLQQHYVKLKE-NEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLK  395 (448)
Q Consensus       317 ~~~~~~~~~~~~i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~  395 (448)
                      ..... ......+.+.+..+.. ..+...+..++.....+++||||++++.|+.+++.|++.|+.+..+||+|++.+|.+
T Consensus       206 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~  284 (395)
T 3pey_A          206 ELQTN-EVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDR  284 (395)
T ss_dssp             CCCGG-GCSCTTEEEEEEECSSHHHHHHHHHHHHTTTTSSEEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHH
T ss_pred             Ecccc-ccccccccEEEEEcCchHHHHHHHHHHHHhccCCCEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHH
Confidence            76555 4456677777777644 568888888888888899999999999999999999999999999999999999999


Q ss_pred             HHHHHhcCC----------------------------------------------------CceEEEEecChhhHHHHHH
Q psy1548         396 KYQEFKDFH----------------------------------------------------KGLAITFASDENDAKILNN  423 (448)
Q Consensus       396 ~l~~F~~g~----------------------------------------------------~g~~I~~~t~~~d~~~l~~  423 (448)
                      +++.|++|+                                                    .|.++++++..++...++.
T Consensus       285 ~~~~f~~g~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~g~~g~~~~~~~~~~~~~~~~~  364 (395)
T 3pey_A          285 LIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSA  364 (395)
T ss_dssp             HHHHHHTTSCCEEEECGGGSSSCCCTTEEEEEESSCCBCTTSSBCHHHHHHHHTTSSCTTCCEEEEEEECSHHHHHHHHH
T ss_pred             HHHHHHCCCCCEEEECChhhcCCCcccCCEEEEcCCCCCCcCCCCHHHhhHhccccccCCCCceEEEEEechHHHHHHHH
Confidence            999999998                                                    5889999998888899999


Q ss_pred             HHHHhc-CCCCCCCcc
Q psy1548         424 VQDRFD-VSISELPDE  438 (448)
Q Consensus       424 i~~~~~-~~~~~~p~~  438 (448)
                      +++.++ ..+..+|..
T Consensus       365 i~~~~~~~~~~~~~~~  380 (395)
T 3pey_A          365 IQKYFGDIEMTRVPTD  380 (395)
T ss_dssp             HHHHTTSCCCEECCSS
T ss_pred             HHHHhCCceeecCChH
Confidence            999998 888877754

>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=100.00  E-value=3.3e-40  Score=326.49  Aligned_cols=314  Identities=31%  Similarity=0.472  Sum_probs=280.1

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeC-cceeeecc
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLG-MDILCQAK  157 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g-~~vli~ap  157 (448)
                      ...|+++++++.+++.+.+.|                       |..|+++   |++      +++.++.| +++++.+|
T Consensus         5 ~~~f~~~~l~~~~~~~l~~~g-----------------------~~~~~~~---Q~~------~i~~~~~~~~~~l~~~~   52 (367)
T 1hv8_A            5 YMNFNELNLSDNILNAIRNKG-----------------------FEKPTDI---QMK------VIPLFLNDEYNIVAQAR   52 (367)
T ss_dssp             CCCGGGSSCCHHHHHHHHHHT-----------------------CCSCCHH---HHH------HHHHHHHTCSEEEEECC
T ss_pred             cCchhhcCCCHHHHHHHHHcC-----------------------CCCCCHH---HHH------HHHHHhCCCCCEEEECC
Confidence            457999999999999999999                       9999998   999      99999988 79999999


Q ss_pred             CCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEE
Q psy1548         158 SGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVV  237 (448)
Q Consensus       158 TGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV  237 (448)
                      ||+|||++|++|++..+... .+.++||++|+++|+.|+.+.+..+.... ++++..+.|+.....+...+..  ++|+|
T Consensus        53 TGsGKT~~~~~~~~~~~~~~-~~~~~lil~P~~~L~~q~~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~~--~~iiv  128 (367)
T 1hv8_A           53 TGSGKTASFAIPLIELVNEN-NGIEAIILTPTRELAIQVADEIESLKGNK-NLKIAKIYGGKAIYPQIKALKN--ANIVV  128 (367)
T ss_dssp             SSSSHHHHHHHHHHHHSCSS-SSCCEEEECSCHHHHHHHHHHHHHHHCSS-CCCEEEECTTSCHHHHHHHHHT--CSEEE
T ss_pred             CCChHHHHHHHHHHHHhccc-CCCcEEEEcCCHHHHHHHHHHHHHHhCCC-CceEEEEECCcchHHHHhhcCC--CCEEE
Confidence            99999999999999876543 45689999999999999999999998776 7889999999887766666653  79999


Q ss_pred             EcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEE
Q psy1548         238 GTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVY  317 (448)
Q Consensus       238 ~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~  317 (448)
                      +||+++.+.+..+...+.+++++|+||||.+.++ ++...+..++..+++..+++++|||+++........++.++..+.
T Consensus       129 ~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~-~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~  207 (367)
T 1hv8_A          129 GTPGRILDHINRGTLNLKNVKYFILDEADEMLNM-GFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIK  207 (367)
T ss_dssp             ECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTT-TTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEE
T ss_pred             ecHHHHHHHHHcCCcccccCCEEEEeCchHhhhh-chHHHHHHHHHhCCCCceEEEEeeccCHHHHHHHHHHcCCCeEEE
Confidence            9999999999988888899999999999999998 899999999999999999999999999999899998888776655


Q ss_pred             EcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHH
Q psy1548         318 VDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKY  397 (448)
Q Consensus       318 ~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l  397 (448)
                      ...     ...+.+.+..+...+|...+..++. ...+++||||++++.++.+++.|++.|+.+..+||+|+..+|.+++
T Consensus       208 ~~~-----~~~~~~~~~~~~~~~~~~~l~~~l~-~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~  281 (367)
T 1hv8_A          208 AKI-----NANIEQSYVEVNENERFEALCRLLK-NKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVI  281 (367)
T ss_dssp             CCS-----SSSSEEEEEECCGGGHHHHHHHHHC-STTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHH
T ss_pred             ecC-----CCCceEEEEEeChHHHHHHHHHHHh-cCCCcEEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHH
Confidence            432     2467788888888999999988887 3456899999999999999999999999999999999999999999


Q ss_pred             HHHhcCC----------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCC
Q psy1548         398 QEFKDFH----------------------------------------------KGLAITFASDENDAKILNNVQDRFDVS  431 (448)
Q Consensus       398 ~~F~~g~----------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~  431 (448)
                      +.|++|+                                              .|.++.+++.. |...+..+++.++.+
T Consensus       282 ~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g~~g~~~~~~~~~-~~~~~~~i~~~~~~~  360 (367)
T 1hv8_A          282 RLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRR-EYKKLRYIERAMKLK  360 (367)
T ss_dssp             HHHHTTSSSEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTT-SHHHHHHHHHHHTCC
T ss_pred             HHHHcCCCeEEEECChhhcCCCcccCCEEEEecCCCCHHHhhhcccccccCCCccEEEEEEcHH-HHHHHHHHHHHhCCC
Confidence            9999998                                              68889998876 888999999999998


Q ss_pred             CCCCC
Q psy1548         432 ISELP  436 (448)
Q Consensus       432 ~~~~p  436 (448)
                      +.+++
T Consensus       361 ~~~~~  365 (367)
T 1hv8_A          361 IKKLK  365 (367)
T ss_dssp             CCCBC
T ss_pred             Cceec
Confidence            88765

>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=100.00  E-value=2.3e-42  Score=355.46  Aligned_cols=329  Identities=26%  Similarity=0.374  Sum_probs=182.5

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeC--cceeeec
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLG--MDILCQA  156 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g--~~vli~a  156 (448)
                      ...|.++++++.+++.+...|                       |..|+++   |.+      ++|.++.|  +++++++
T Consensus        91 ~~~f~~~~l~~~l~~~l~~~g-----------------------~~~p~~~---Q~~------ai~~il~~~~~~~l~~a  138 (479)
T 3fmp_B           91 VKSFEELRLKPQLLQGVYAMG-----------------------FNRPSKI---QEN------ALPLMLAEPPQNLIAQS  138 (479)
T ss_dssp             CCCSGGGTCCHHHHHHHHHTT-----------------------CCSCCHH---HHH------HHHHHTSBSCCEEEEEC
T ss_pred             cCCHHHcCCCHHHHHHHHHcC-----------------------CCCCCHH---HHH------HHHHHHcCCCCcEEEEc
Confidence            357999999999999999999                       9999999   999      99999987  9999999


Q ss_pred             cCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEE
Q psy1548         157 KSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV  236 (448)
Q Consensus       157 pTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~Il  236 (448)
                      |||||||++|++|++..+.....++++||++|+++|+.|+.+.++.+....+++.+....++.......    ...++|+
T Consensus       139 ~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Iv  214 (479)
T 3fmp_B          139 QSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ----KISEQIV  214 (479)
T ss_dssp             CSSSSHHHHHHHHHHTTCCTTSCSCCEEEECSSHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTTC----CCCCSEE
T ss_pred             CCCCchhHHHHHHHHHHHhhcCCCCcEEEEeChHHHHHHHHHHHHHHHhhCCCceEEEEeCCccccccc----cCCCCEE
Confidence            999999999999999988777777799999999999999999999998877678888888876543321    2247899


Q ss_pred             EEcHHHHHHHHHC-CCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeE
Q psy1548         237 VGTPGRILALVRN-KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPME  315 (448)
Q Consensus       237 V~Tp~~l~~~l~~-~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~  315 (448)
                      |+||+++.+++.+ +.+.+.++++||+||||++.+..++...+..+.+.+++.+|++++|||++..+..++..++.+|..
T Consensus       215 v~Tp~~l~~~l~~~~~~~~~~~~~iViDEah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~  294 (479)
T 3fmp_B          215 IGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNV  294 (479)
T ss_dssp             EECHHHHHHHHTTSCCCCGGGCCEEEECCHHHHHTSTTHHHHHHHHHTTSCTTSEEEEEESCCCHHHHHHHHHHSSSEEE
T ss_pred             EECchHHHHHHHhcCCcCcccCCEEEEECHHHHhhcCCcHHHHHHHHhhCCccceEEEEeCCCCHHHHHHHHHHcCCCeE
Confidence            9999999999865 566789999999999999987338888999999999999999999999999999999999999998


Q ss_pred             EEEcCcccccccceeEEEEEcCc-chHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHH
Q psy1548         316 VYVDDEAKLTLHGLQQHYVKLKE-NEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERL  394 (448)
Q Consensus       316 i~~~~~~~~~~~~i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~  394 (448)
                      +.+... ......+.+.+..+.. ..+...+..++.....+++||||++++.|+.++..|.+.|+.+..+||+|++.+|.
T Consensus       295 i~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~~~~~R~  373 (479)
T 3fmp_B          295 IKLKRE-EETLDTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRA  373 (479)
T ss_dssp             EEEC----------------------------------------------------------------------------
T ss_pred             Eecccc-ccCcCCceEEEEEeCCHHHHHHHHHHHHhhccCCceEEEeCcHHHHHHHHHHHHhCCccEEEecCCCCHHHHH
Confidence            887766 4456677777777665 56788888888877788999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCc------cccccccccCC
Q psy1548         395 KKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPD------EIDLSTYIEGR  448 (448)
Q Consensus       395 ~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~------~~~~~~~~~~~  448 (448)
                      .+++.|++|+  ..|+++|+.-..++  ++.+.--+-..++|.      +...+.++.||
T Consensus       374 ~~~~~f~~g~--~~iLv~T~~~~~Gl--Dip~v~~VI~~d~p~~~~~~~s~~~~~Qr~GR  429 (479)
T 3fmp_B          374 AVIERFREGK--EKVLVTTNVCARGI--DVEQVSVVINFDLPVDKDGNPDNETYLHRIGR  429 (479)
T ss_dssp             ------------------------------------------------------------
T ss_pred             HHHHHHHcCC--CcEEEEccccccCC--ccccCCEEEEecCCCCCccCCCHHHHHHHhcc
Confidence            9999999988  46777776544443  454444455566774      44578888887

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=100.00  E-value=1.3e-40  Score=350.17  Aligned_cols=326  Identities=21%  Similarity=0.329  Sum_probs=262.3

Q ss_pred             CCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeee--eCcceeeeccCCChhH
Q psy1548          86 LLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV--LGMDILCQAKSGMGKT  163 (448)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~--~g~~vli~apTGsGKT  163 (448)
                      .+++++++++...|                       |..|+++   |.+      +++.++  .|+|+++++|||+|||
T Consensus        27 ~l~~~l~~~l~~~g-----------------------~~~~~~~---Q~~------~i~~il~~~~~dvlv~apTGsGKT   74 (579)
T 3sqw_A           27 VLDKEIHKAITRME-----------------------FPGLTPV---QQK------TIKPILSSEDHDVIARAKTGTGKT   74 (579)
T ss_dssp             SSCHHHHHHHHTTT-----------------------CSSCCHH---HHH------HHHHHHCSSSEEEEEECCTTSCHH
T ss_pred             CCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHHccCCCeEEEEcCCCcHHH
Confidence            39999999999999                       9999999   999      999999  7899999999999999


Q ss_pred             HHHHHHHHHhhhccC----CCeEEEEeeccHHHHHHHHHHHHHhhcc---CCCceEEEEEcCcccHHhHHHHhcCCCcEE
Q psy1548         164 AVFVLATLQQLETTD----SNVYVLVMCHTRELAFQISKEYERFSKY---MSNIKVGVFFGGLPIQKDEEYLKTHNPQIV  236 (448)
Q Consensus       164 ~~~~l~~l~~l~~~~----~~~~~lil~Pt~~L~~q~~~~~~~~~~~---~~~~~v~~~~g~~~~~~~~~~l~~~~~~Il  236 (448)
                      ++|++|+++.+....    .++++|||+||++|+.|+.+.++++...   .+...+..++|+.....+...+....++|+
T Consensus        75 l~~~lpil~~l~~~~~~~~~~~~~lvl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~Il  154 (579)
T 3sqw_A           75 FAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIV  154 (579)
T ss_dssp             HHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEE
T ss_pred             HHHHHHHHHHHHhccccccCCCeEEEEcchHHHHHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEE
Confidence            999999999876542    3568999999999999999999998642   235778889999888877777766568999


Q ss_pred             EEcHHHHHHHHHCC-CCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCC-------CCCeEEEEeccCCccHHHHHHH
Q psy1548         237 VGTPGRILALVRNK-KLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSP-------HTKQVMMFSATLSKEIRPVCKK  308 (448)
Q Consensus       237 V~Tp~~l~~~l~~~-~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~-------~~~q~i~~SAT~~~~~~~~~~~  308 (448)
                      |+||+++.+++... ...+..++++|+||||+++++ +|+..+..++..++       ..+|+++||||+++.+..++..
T Consensus       155 V~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l~~~-gf~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~  233 (579)
T 3sqw_A          155 IATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEI-GFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANN  233 (579)
T ss_dssp             EECHHHHHHHHHHHHHHHCTTCCEEEEETHHHHTST-TTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTT
T ss_pred             EECHHHHHHHHHhccccccccCCEEEEEChHHhhcC-CCHHHHHHHHHHhhhhhcccccCceEEEEeccCChHHHHHHHH
Confidence            99999999988764 446788999999999999998 99999998877653       3779999999999999999999


Q ss_pred             hcCCCeEEEEcCc---ccccccceeEEEEEcCcc-hH----HHHHHHHHhh-CCCCeEEEEECccHHHHHHHHHHHhC--
Q psy1548         309 FMHDPMEVYVDDE---AKLTLHGLQQHYVKLKEN-EK----NKKLFELLDV-LEFNQVVIFVKSVTRCIALSTLLSEQ--  377 (448)
Q Consensus       309 ~l~~~~~i~~~~~---~~~~~~~i~~~~~~~~~~-~k----~~~L~~ll~~-~~~~~~IIF~~s~~~a~~l~~~L~~~--  377 (448)
                      ++.+|..+.+...   .......+.+.+...... .+    ...+...+.. ..+.++||||+|+..|+.++..|++.  
T Consensus       234 ~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~~~  313 (579)
T 3sqw_A          234 IMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFK  313 (579)
T ss_dssp             TCCSSEEEEEESSCSSSCSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHHTTTCCEEEEECSSHHHHHHHHHHHHHHHT
T ss_pred             HcCCCceEEEeecCccccccccccceEEEEecchhhhHHHHHHHHHHHHhhcCCCCcEEEECCcHHHHHHHHHHHHHhhc
Confidence            9999887766432   122345566666665542 22    2233333333 45679999999999999999999886  


Q ss_pred             -CCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         378 -NFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       378 -g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                       |+.+..+||+|++.+|.+++++|++|+  ..|+++|+...+++  ++.+.-.+-...+|.+...+.++.||
T Consensus       314 ~~~~v~~~hg~~~~~~R~~~~~~F~~g~--~~vLVaT~~~~~Gi--Dip~v~~VI~~~~p~s~~~y~Qr~GR  381 (579)
T 3sqw_A          314 KDLPILEFHGKITQNKRTSLVKRFKKDE--SGILVCTDVGARGM--DFPNVHEVLQIGVPSELANYIHRIGR  381 (579)
T ss_dssp             TTSCEEEESTTSCHHHHHHHHHHHHHCS--SEEEEECGGGTSSC--CCTTCCEEEEESCCSSTTHHHHHHTT
T ss_pred             CCCcEEEecCCCCHHHHHHHHHHhhcCC--CeEEEEcchhhcCC--CcccCCEEEEcCCCCCHHHhhhhccc
Confidence             899999999999999999999999988  56788877543332  22222223445678888888898887

>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=100.00  E-value=6.2e-40  Score=343.96  Aligned_cols=326  Identities=21%  Similarity=0.328  Sum_probs=260.4

Q ss_pred             CCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeee--eCcceeeeccCCChhH
Q psy1548          86 LLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV--LGMDILCQAKSGMGKT  163 (448)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~--~g~~vli~apTGsGKT  163 (448)
                      .+++.+++++...|                       |..|+++   |.+      +++.++  .|+|+++++|||+|||
T Consensus        78 ~l~~~l~~~l~~~g-----------------------~~~~~~~---Q~~------~i~~~l~~~~~~~lv~apTGsGKT  125 (563)
T 3i5x_A           78 VLDKEIHKAITRME-----------------------FPGLTPV---QQK------TIKPILSSEDHDVIARAKTGTGKT  125 (563)
T ss_dssp             SSCHHHHHHHHTTC-----------------------CSSCCHH---HHH------HHHHHHSSSSEEEEEECCTTSCHH
T ss_pred             CCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhcCCCCeEEEECCCCCCcc
Confidence            39999999999999                       9999999   999      999999  6799999999999999


Q ss_pred             HHHHHHHHHhhhccC----CCeEEEEeeccHHHHHHHHHHHHHhhcc---CCCceEEEEEcCcccHHhHHHHhcCCCcEE
Q psy1548         164 AVFVLATLQQLETTD----SNVYVLVMCHTRELAFQISKEYERFSKY---MSNIKVGVFFGGLPIQKDEEYLKTHNPQIV  236 (448)
Q Consensus       164 ~~~~l~~l~~l~~~~----~~~~~lil~Pt~~L~~q~~~~~~~~~~~---~~~~~v~~~~g~~~~~~~~~~l~~~~~~Il  236 (448)
                      ++|++|+++.+....    .++++|||+||++|+.|+.+.++.+...   .+...+..++|+.....+...+....++|+
T Consensus       126 l~~~lpil~~l~~~~~~~~~~~~~lil~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Ii  205 (563)
T 3i5x_A          126 FAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIV  205 (563)
T ss_dssp             HHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEE
T ss_pred             HHHHHHHHHHHHhccccccCCeeEEEEcCcHHHHHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEE
Confidence            999999999886543    2468999999999999999999997543   225678888999887777777755568999


Q ss_pred             EEcHHHHHHHHHCC-CCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCC-------CCCeEEEEeccCCccHHHHHHH
Q psy1548         237 VGTPGRILALVRNK-KLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSP-------HTKQVMMFSATLSKEIRPVCKK  308 (448)
Q Consensus       237 V~Tp~~l~~~l~~~-~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~-------~~~q~i~~SAT~~~~~~~~~~~  308 (448)
                      |+||+++.+++.+. ...+++++++|+||||+++++ +|+..+..++..++       ..+|+++||||+++.+..++..
T Consensus       206 v~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~l~~~-~f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~  284 (563)
T 3i5x_A          206 IATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEI-GFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANN  284 (563)
T ss_dssp             EECHHHHHHHHHHHHHHHCTTCCEEEEETHHHHTST-TTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTT
T ss_pred             EECcHHHHHHHHhccccccccceEEEEeCHHHHhcc-chHHHHHHHHHhhhhccccCccCceEEEEEccCCHHHHHHHHH
Confidence            99999999988764 345788999999999999998 99999998877653       3779999999999999999999


Q ss_pred             hcCCCeEEEEcCcc---cccccceeEEEEEcCcc-hH----HHHHHHHHhh-CCCCeEEEEECccHHHHHHHHHHHhC--
Q psy1548         309 FMHDPMEVYVDDEA---KLTLHGLQQHYVKLKEN-EK----NKKLFELLDV-LEFNQVVIFVKSVTRCIALSTLLSEQ--  377 (448)
Q Consensus       309 ~l~~~~~i~~~~~~---~~~~~~i~~~~~~~~~~-~k----~~~L~~ll~~-~~~~~~IIF~~s~~~a~~l~~~L~~~--  377 (448)
                      ++.++..+......   ......+.+.+...... .+    ...+...+.. ..++++||||+|++.|+.++..|++.  
T Consensus       285 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~  364 (563)
T 3i5x_A          285 IMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFK  364 (563)
T ss_dssp             TCCSSEEEEEESSCSSSCSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHT
T ss_pred             hcCCCceEEEeccCCCCccccccCceEEEECchhHhhHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhcc
Confidence            99988877664321   22344566666655542 22    2223333333 45679999999999999999999886  


Q ss_pred             -CCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         378 -NFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       378 -g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                       |+.+..+||+|++.+|.++++.|++|+  ..|+++|+...+++  ++.+.-.+-..++|.+...+.++.||
T Consensus       365 ~~~~v~~~h~~~~~~~R~~~~~~f~~g~--~~vLvaT~~~~~Gi--Dip~v~~VI~~~~p~s~~~y~Qr~GR  432 (563)
T 3i5x_A          365 KDLPILEFHGKITQNKRTSLVKRFKKDE--SGILVCTDVGARGM--DFPNVHEVLQIGVPSELANYIHRIGR  432 (563)
T ss_dssp             TTSCEEEESTTSCHHHHHHHHHHHHHCS--SEEEEECGGGTSSC--CCTTCCEEEEESCCSSTTHHHHHHTT
T ss_pred             CCceEEEecCCCCHHHHHHHHHHHhcCC--CCEEEEcchhhcCC--CcccCCEEEEECCCCchhhhhhhcCc
Confidence             899999999999999999999999988  56788877533322  22222223345678888888899888

>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=100.00  E-value=2.7e-38  Score=309.25  Aligned_cols=300  Identities=25%  Similarity=0.421  Sum_probs=252.2

Q ss_pred             CCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHH
Q psy1548          87 LKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVF  166 (448)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~  166 (448)
                      +++++.+++.+.|                       |..|++.   |++      +++.++.|+++++.+|||+|||++|
T Consensus         1 l~~~i~~~l~~~g-----------------------~~~l~~~---Q~~------~i~~i~~~~~~lv~~~TGsGKT~~~   48 (337)
T 2z0m_A            1 MNEKIEQAIREMG-----------------------FKNFTEV---QSK------TIPLMLQGKNVVVRAKTGSGKTAAY   48 (337)
T ss_dssp             CCHHHHHHHHHTT-----------------------CCSCCHH---HHH------HHHHHHTTCCEEEECCTTSSHHHHH
T ss_pred             CCHHHHHHHHHcC-----------------------CCCCCHH---HHH------HHHHHhcCCCEEEEcCCCCcHHHHH
Confidence            5788999999999                       9999888   999      9999999999999999999999999


Q ss_pred             HHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHH
Q psy1548         167 VLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILAL  246 (448)
Q Consensus       167 ~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~  246 (448)
                      ++|++..      +.++||++|+++|+.|+.+.++++.... +.++..++|+.....+...+..  ++|+|+||+++.++
T Consensus        49 ~~~~~~~------~~~~liv~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~--~~i~v~T~~~l~~~  119 (337)
T 2z0m_A           49 AIPILEL------GMKSLVVTPTRELTRQVASHIRDIGRYM-DTKVAEVYGGMPYKAQINRVRN--ADIVVATPGRLLDL  119 (337)
T ss_dssp             HHHHHHH------TCCEEEECSSHHHHHHHHHHHHHHTTTS-CCCEEEECTTSCHHHHHHHHTT--CSEEEECHHHHHHH
T ss_pred             HHHHHhh------cCCEEEEeCCHHHHHHHHHHHHHHhhhc-CCcEEEEECCcchHHHHhhcCC--CCEEEECHHHHHHH
Confidence            9999874      4589999999999999999999998777 8899999999877666555543  79999999999999


Q ss_pred             HHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccc
Q psy1548         247 VRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTL  326 (448)
Q Consensus       247 l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~  326 (448)
                      +......+.+++++|+||||++.++ ++...+..++...+...+++++|||+++.....+..++.++..+...    ...
T Consensus       120 ~~~~~~~~~~~~~iViDEah~~~~~-~~~~~~~~~~~~~~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~~~~----~~~  194 (337)
T 2z0m_A          120 WSKGVIDLSSFEIVIIDEADLMFEM-GFIDDIKIILAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIEAC----IGL  194 (337)
T ss_dssp             HHTTSCCGGGCSEEEEESHHHHHHT-TCHHHHHHHHHHCTTCSEEEEEESCCCHHHHHHHHHHSCSCEEEECS----GGG
T ss_pred             HHcCCcchhhCcEEEEEChHHhhcc-ccHHHHHHHHhhCCcccEEEEEeCcCCHHHHHHHHHhcCCceeeecc----ccc
Confidence            9888888899999999999999998 99999999999999999999999999999999999999888776432    335


Q ss_pred             cceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCc
Q psy1548         327 HGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKG  406 (448)
Q Consensus       327 ~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g  406 (448)
                      .++.+.+..+....+.  ....+....++++||||++++.++.+++.|+    ++..+||+|+..+|.+++++|++|+  
T Consensus       195 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~lvf~~~~~~~~~l~~~l~----~~~~~~~~~~~~~r~~~~~~f~~~~--  266 (337)
T 2z0m_A          195 ANVEHKFVHVKDDWRS--KVQALRENKDKGVIVFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGE--  266 (337)
T ss_dssp             GGEEEEEEECSSSSHH--HHHHHHTCCCSSEEEECSCHHHHHHHHTTCT----TEEEECTTSCHHHHHHHHHHHHTTS--
T ss_pred             CCceEEEEEeChHHHH--HHHHHHhCCCCcEEEEEcCHHHHHHHHHHhh----hhhhhcCCCCHHHHHHHHHHHHcCC--
Confidence            5677777777665443  2355666677899999999999999999887    5889999999999999999999988  


Q ss_pred             eEEEEecChhhHHHHHHHHHHhcCC------CCCCCccccccccccCC
Q psy1548         407 LAITFASDENDAKILNNVQDRFDVS------ISELPDEIDLSTYIEGR  448 (448)
Q Consensus       407 ~~I~~~t~~~d~~~l~~i~~~~~~~------~~~~p~~~~~~~~~~~~  448 (448)
                      ..|.++|+.        ++.-++++      ..+.|.+...+.++.||
T Consensus       267 ~~vlv~T~~--------~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR  306 (337)
T 2z0m_A          267 YDMLITTDV--------ASRGLDIPLVEKVINFDAPQDLRTYIHRIGR  306 (337)
T ss_dssp             CSEEEECHH--------HHTTCCCCCBSEEEESSCCSSHHHHHHHHTT
T ss_pred             CcEEEEcCc--------cccCCCccCCCEEEEecCCCCHHHhhHhcCc
Confidence            456666653        22233322      34557777777888887

>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=100.00  E-value=2.1e-37  Score=324.30  Aligned_cols=316  Identities=13%  Similarity=0.128  Sum_probs=242.4

Q ss_pred             cccCCCCHHHHHHHhh-ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCC
Q psy1548          82 FRDFLLKPEILRAIVD-CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGM  160 (448)
Q Consensus        82 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGs  160 (448)
                      +.++++++.+.+.+.+ .|                       |..|+++   |.+      +++.++.|+|+++.+|||+
T Consensus        23 ~~~~~l~~~l~~~L~~~fg-----------------------~~~~rp~---Q~~------~i~~il~g~d~lv~~pTGs   70 (591)
T 2v1x_A           23 KEDFPWSGKVKDILQNVFK-----------------------LEKFRPL---QLE------TINVTMAGKEVFLVMPTGG   70 (591)
T ss_dssp             CSCSTTHHHHHHHHHHTSC-----------------------CCSCCTT---HHH------HHHHHHTTCCEEEECCTTS
T ss_pred             cccCCCCHHHHHHHHHHhC-----------------------CCCCCHH---HHH------HHHHHHcCCCEEEEECCCC
Confidence            4568899999999988 57                       9999998   999      9999999999999999999


Q ss_pred             hhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHH-----hcCCCcE
Q psy1548         161 GKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL-----KTHNPQI  235 (448)
Q Consensus       161 GKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l-----~~~~~~I  235 (448)
                      |||++|++|++..      ..++|||+|+++|+.|+.+.+..+     ++++..+.|+.........+     ..+.++|
T Consensus        71 GKTl~~~lpal~~------~g~~lVisP~~~L~~q~~~~l~~~-----gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~I  139 (591)
T 2v1x_A           71 GKSLCYQLPALCS------DGFTLVICPLISLMEDQLMVLKQL-----GISATMLNASSSKEHVKWVHAEMVNKNSELKL  139 (591)
T ss_dssp             CTTHHHHHHHHTS------SSEEEEECSCHHHHHHHHHHHHHH-----TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCE
T ss_pred             hHHHHHHHHHHHc------CCcEEEEeCHHHHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCE
Confidence            9999999999863      348999999999999999999886     67788888887655443322     2446899


Q ss_pred             EEEcHHHHH------HHHHCCCCcCCCeeEEEecchhHHHhhhh--hHHHHHH--HHHhCCCCCeEEEEeccCCccHHHH
Q psy1548         236 VVGTPGRIL------ALVRNKKLNLSLLKHFILDECDKMLEQLE--MRRDVQE--IFRSSPHTKQVMMFSATLSKEIRPV  305 (448)
Q Consensus       236 lV~Tp~~l~------~~l~~~~~~~~~i~~lViDEah~l~~~~~--~~~~~~~--i~~~l~~~~q~i~~SAT~~~~~~~~  305 (448)
                      +|+||++|.      +.+. ....+.++++|||||||++.+| +  |++.+..  .+....+..|++++|||+++.+...
T Consensus       140 lv~Tpe~L~~~~~~~~~l~-~~~~~~~i~~iViDEAH~is~~-g~dfr~~~~~l~~l~~~~~~~~ii~lSAT~~~~v~~~  217 (591)
T 2v1x_A          140 IYVTPEKIAKSKMFMSRLE-KAYEARRFTRIAVDEVHCCSQW-GHDFRPDYKALGILKRQFPNASLIGLTATATNHVLTD  217 (591)
T ss_dssp             EEECHHHHHSCHHHHHHHH-HHHHTTCEEEEEEETGGGGSTT-CTTCCGGGGGGGHHHHHCTTSEEEEEESSCCHHHHHH
T ss_pred             EEEChhHhhccHHHHHHHH-hhhhccCCcEEEEECccccccc-ccccHHHHHHHHHHHHhCCCCcEEEEecCCCHHHHHH
Confidence            999999874      2222 2345678999999999999987 5  7777665  3444445789999999999998888


Q ss_pred             HHHhcCCCeEEEEcCcccccccceeEEEEEcCc--chHHHHHHHHHhh-CCCCeEEEEECccHHHHHHHHHHHhCCCcEE
Q psy1548         306 CKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKE--NEKNKKLFELLDV-LEFNQVVIFVKSVTRCIALSTLLSEQNFPAV  382 (448)
Q Consensus       306 ~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~--~~k~~~L~~ll~~-~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~  382 (448)
                      +..++..+....+...  ....++...+.....  ..+...+..++.. ..++++||||+|++.|+.++..|++.|+.+.
T Consensus       218 i~~~l~~~~~~~~~~~--~~r~nl~~~v~~~~~~~~~~~~~l~~~l~~~~~~~~~IVf~~sr~~~e~la~~L~~~g~~~~  295 (591)
T 2v1x_A          218 AQKILCIEKCFTFTAS--FNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAG  295 (591)
T ss_dssp             HHHHTTCCSCEEEECC--CCCTTEEEEEEECCSSHHHHHHHHHHHHTTTTTTCEEEEECSSHHHHHHHHHHHHHTTCCEE
T ss_pred             HHHHhCCCCcEEEecC--CCCcccEEEEEeCCCcHHHHHHHHHHHHHHhccCCCeEEEeCcHHHHHHHHHHHHHCCCCEE
Confidence            8877765433333222  233455444443332  3456677777764 3677999999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         383 SIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       383 ~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      .+||+|++++|.++++.|++|+  +.|+++|....+++  ++.+.--+-...+|.+++.+.++.||
T Consensus       296 ~~h~~l~~~~R~~~~~~F~~g~--~~VlVAT~a~~~GI--D~p~V~~VI~~~~p~s~~~y~Qr~GR  357 (591)
T 2v1x_A          296 AYHANLEPEDKTTVHRKWSANE--IQVVVATVAFGMGI--DKPDVRFVIHHSMSKSMENYYQESGR  357 (591)
T ss_dssp             EECTTSCHHHHHHHHHHHHTTS--SSEEEECTTSCTTC--CCSCEEEEEESSCCSSHHHHHHHHTT
T ss_pred             EecCCCCHHHHHHHHHHHHcCC--CeEEEEechhhcCC--CcccccEEEEeCCCCCHHHHHHHhcc
Confidence            9999999999999999999988  46777776533322  12122223445678888888888887

>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=100.00  E-value=2.9e-36  Score=282.16  Aligned_cols=218  Identities=24%  Similarity=0.403  Sum_probs=198.7

Q ss_pred             hccCceeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeee
Q psy1548          69 EVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVL  148 (448)
Q Consensus        69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~  148 (448)
                      .+.+...+.....|.++++++.+++++.+.|                       |..|+++   |.+      +++.++.
T Consensus        18 ~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g-----------------------~~~~~~~---Q~~------~i~~~~~   65 (242)
T 3fe2_A           18 TVRGHNCPKPVLNFYEANFPANVMDVIARQN-----------------------FTEPTAI---QAQ------GWPVALS   65 (242)
T ss_dssp             EEESSCCCCCCSSTTTTTCCHHHHHHHHTTT-----------------------CCSCCHH---HHH------HHHHHHH
T ss_pred             EEeCCCCCCccCCHhhcCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhC
Confidence            3445566667788999999999999999999                       9999999   999      9999999


Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhcc-----CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETT-----DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQK  223 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~-----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~  223 (448)
                      |+|+++++|||+|||++|++|++..+...     ..++++||++||++|+.|+.+.++.+.... ++++..++|+.....
T Consensus        66 g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~-~~~~~~~~g~~~~~~  144 (242)
T 3fe2_A           66 GLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAPKGP  144 (242)
T ss_dssp             TCCEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHHHHT-TCCEEEECTTSCHHH
T ss_pred             CCCEEEECCCcCHHHHHHHHHHHHHHHhccccccCCCCEEEEEeCcHHHHHHHHHHHHHHHhhc-CceEEEEECCCChHH
Confidence            99999999999999999999999987643     346789999999999999999999998887 899999999998887


Q ss_pred             hHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHH
Q psy1548         224 DEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIR  303 (448)
Q Consensus       224 ~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~  303 (448)
                      +...+..+ ++|+|+||+++.+++..+...+.+++++|+||||++.++ +|...+..+++.++++.|+++||||+++.+.
T Consensus       145 ~~~~~~~~-~~I~v~Tp~~l~~~l~~~~~~~~~~~~lViDEah~l~~~-~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~  222 (242)
T 3fe2_A          145 QIRDLERG-VEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDM-GFEPQIRKIVDQIRPDRQTLMWSATWPKEVR  222 (242)
T ss_dssp             HHHHHHHC-CSEEEECHHHHHHHHHHTSCCCTTCCEEEETTHHHHHHT-TCHHHHHHHHTTSCSSCEEEEEESCCCHHHH
T ss_pred             HHHHhcCC-CCEEEECHHHHHHHHHcCCCCcccccEEEEeCHHHHhhh-CcHHHHHHHHHhCCccceEEEEEeecCHHHH
Confidence            77777775 899999999999999888888999999999999999998 9999999999999999999999999999999


Q ss_pred             HHHHHhcCCCeEEEEcCc
Q psy1548         304 PVCKKFMHDPMEVYVDDE  321 (448)
Q Consensus       304 ~~~~~~l~~~~~i~~~~~  321 (448)
                      ++++.++.+|..+.+...
T Consensus       223 ~~~~~~l~~~~~i~~~~~  240 (242)
T 3fe2_A          223 QLAEDFLKDYIHINIGAL  240 (242)
T ss_dssp             HHHHHHCSSCEEEEECC-
T ss_pred             HHHHHHCCCCEEEEecCC
Confidence            999999999999987654

>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=100.00  E-value=5.4e-37  Score=317.83  Aligned_cols=315  Identities=14%  Similarity=0.132  Sum_probs=241.8

Q ss_pred             CCcccCCCCHHHHHHHhh-ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          80 SGFRDFLLKPEILRAIVD-CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      .+|+++++++.+.+.+.+ .|                       |..|++.   |.+      +++.++.|+|+++.+||
T Consensus         2 ~~fe~l~L~~~~~~~l~~~~g-----------------------~~~~r~~---Q~~------~i~~il~g~d~lv~apT   49 (523)
T 1oyw_A            2 AQAEVLNLESGAKQVLQETFG-----------------------YQQFRPG---QEE------IIDTVLSGRDCLVVMPT   49 (523)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTC-----------------------CSSCCTT---HHH------HHHHHHTTCCEEEECSC
T ss_pred             CChhhCCCCHHHHHHHHHHhC-----------------------CCCCCHH---HHH------HHHHHHcCCCEEEECCC
Confidence            478999999999999998 67                       8888888   999      99999999999999999


Q ss_pred             CChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhH---HHHhcCCCcE
Q psy1548         159 GMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE---EYLKTHNPQI  235 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~---~~l~~~~~~I  235 (448)
                      |+|||++|++|++..      ...+||++|+++|+.|+.+.++.+     ++.+..+.++.......   ..+..+.++|
T Consensus        50 GsGKTl~~~lp~l~~------~g~~lvi~P~~aL~~q~~~~l~~~-----gi~~~~l~~~~~~~~~~~~~~~~~~~~~~i  118 (523)
T 1oyw_A           50 GGGKSLCYQIPALLL------NGLTVVVSPLISLMKDQVDQLQAN-----GVAAACLNSTQTREQQLEVMTGCRTGQIRL  118 (523)
T ss_dssp             HHHHHHHHHHHHHHS------SSEEEEECSCHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHHTCCSE
T ss_pred             CcHHHHHHHHHHHHh------CCCEEEECChHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCE
Confidence            999999999999853      247999999999999999888875     67788888877654432   3344556899


Q ss_pred             EEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhh-hhhHHHHHHH---HHhCCCCCeEEEEeccCCccHHHHHHHhc-
Q psy1548         236 VVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQ-LEMRRDVQEI---FRSSPHTKQVMMFSATLSKEIRPVCKKFM-  310 (448)
Q Consensus       236 lV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~-~~~~~~~~~i---~~~l~~~~q~i~~SAT~~~~~~~~~~~~l-  310 (448)
                      +|+||+++........+...+++++|+||||++.+| .+|+..+..+   ...+ ++.+++++|||+++.....+...+ 
T Consensus       119 lv~Tpe~l~~~~~~~~l~~~~~~~vViDEaH~i~~~g~~fr~~~~~l~~l~~~~-~~~~~i~lSAT~~~~~~~~i~~~l~  197 (523)
T 1oyw_A          119 LYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLG  197 (523)
T ss_dssp             EEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTSSCCCHHHHGGGGHHHHC-TTSCEEEEESCCCHHHHHHHHHHHT
T ss_pred             EEECHHHHhChHHHHHHhhCCCCEEEEeCccccCcCCCccHHHHHHHHHHHHhC-CCCCEEEEeCCCCHHHHHHHHHHhC
Confidence            999999985322112233478999999999999887 2376666544   4444 468899999999988665444333 


Q ss_pred             -CCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCC
Q psy1548         311 -HDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMT  389 (448)
Q Consensus       311 -~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~  389 (448)
                       .+|..+. ...   ...++...  ......+...+..++....++++||||+|++.|+.+++.|++.|+.+..+||+|+
T Consensus       198 ~~~~~~~~-~~~---~r~~l~~~--v~~~~~~~~~l~~~l~~~~~~~~IVf~~sr~~~e~l~~~L~~~g~~~~~~h~~l~  271 (523)
T 1oyw_A          198 LNDPLIQI-SSF---DRPNIRYM--LMEKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLE  271 (523)
T ss_dssp             CCSCEEEE-CCC---CCTTEEEE--EEECSSHHHHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSC
T ss_pred             CCCCeEEe-CCC---CCCceEEE--EEeCCCHHHHHHHHHHhcCCCcEEEEeCCHHHHHHHHHHHHHCCCCEEEecCCCC
Confidence             3454433 222   23444333  3334567788888888887889999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         390 QEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       390 ~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      +++|.++++.|++|+  ..|.++|+...+++  ++.+.--+-..++|.++..+.++.||
T Consensus       272 ~~~R~~~~~~f~~g~--~~vlVaT~a~~~Gi--D~p~v~~VI~~~~p~s~~~y~Qr~GR  326 (523)
T 1oyw_A          272 NNVRADVQEKFQRDD--LQIVVATVAFGMGI--NKPNVRFVVHFDIPRNIESYYQETGR  326 (523)
T ss_dssp             HHHHHHHHHHHHTTS--CSEEEECTTSCTTT--CCTTCCEEEESSCCSSHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHcCC--CeEEEEechhhCCC--CccCccEEEEECCCCCHHHHHHHhcc
Confidence            999999999999988  56777877544332  22222223445678888888888887

>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=100.00  E-value=1.7e-35  Score=272.59  Aligned_cols=215  Identities=79%  Similarity=1.228  Sum_probs=189.4

Q ss_pred             cCceeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCc
Q psy1548          71 KGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGM  150 (448)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~  150 (448)
                      .+.+.+.+..+|+++++++.+++++.+.+                       |..|+++   |.+      +++.++.|+
T Consensus         5 ~~~~~~~~~~~f~~~~l~~~l~~~l~~~g-----------------------~~~~~~~---Q~~------~i~~~~~~~   52 (220)
T 1t6n_A            5 KGSYVSIHSSGFRDFLLKPELLRAIVDCG-----------------------FEHPSEV---QHE------CIPQAILGM   52 (220)
T ss_dssp             ---------CCSTTSCCCHHHHHHHHHTT-----------------------CCCCCHH---HHH------HHHHHHTTC
T ss_pred             CCCcccccCCCHhhcCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhCCC
Confidence            45677777889999999999999999999                       9999888   999      999999999


Q ss_pred             ceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhc
Q psy1548         151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKT  230 (448)
Q Consensus       151 ~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~  230 (448)
                      |+++++|||+|||++|++|++..+....++.++||++|+++|+.|+.+.++++....+++++..++|+.....+...+..
T Consensus        53 ~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~  132 (220)
T 1t6n_A           53 DVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKK  132 (220)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHH
T ss_pred             CEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhc
Confidence            99999999999999999999998876666679999999999999999999999887768899999999887777777776


Q ss_pred             CCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhc
Q psy1548         231 HNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFM  310 (448)
Q Consensus       231 ~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l  310 (448)
                      +.++|+|+||+++.+++......+.+++++|+||||++.++.++...+..+++.+++..|++++|||+++.+.++++.++
T Consensus       133 ~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~  212 (220)
T 1t6n_A          133 NCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFM  212 (220)
T ss_dssp             SCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSSHHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTC
T ss_pred             CCCCEEEeCHHHHHHHHHhCCCCcccCCEEEEcCHHHHhcccCcHHHHHHHHHhCCCcCeEEEEEeecCHHHHHHHHHHc
Confidence            66899999999999999988888999999999999999874388999999999999999999999999999999999999


Q ss_pred             CCCeEEE
Q psy1548         311 HDPMEVY  317 (448)
Q Consensus       311 ~~~~~i~  317 (448)
                      .+|..+.
T Consensus       213 ~~p~~i~  219 (220)
T 1t6n_A          213 QDPMEIF  219 (220)
T ss_dssp             SSCEEEE
T ss_pred             CCCeEEe
Confidence            9998764

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=100.00  E-value=1.6e-36  Score=306.11  Aligned_cols=289  Identities=16%  Similarity=0.212  Sum_probs=220.1

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .|+++   |++      +++.++.|+|+++++|||+|||++|++|++...   ..++++||++||++|+.|+.+.++.+.
T Consensus        21 ~~~~~---Q~~------~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~---~~~~~~lil~Pt~~L~~q~~~~~~~~~   88 (414)
T 3oiy_A           21 DLTGY---QRL------WAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA---RKGKKSALVFPTVTLVKQTLERLQKLA   88 (414)
T ss_dssp             CCCHH---HHH------HHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHH---TTTCCEEEEESSHHHHHHHHHHHHHHC
T ss_pred             CCCHH---HHH------HHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHh---cCCCEEEEEECCHHHHHHHHHHHHHHc
Confidence            57777   999      999999999999999999999999999988866   345689999999999999999999988


Q ss_pred             ccCCCceEEEEEcCccc---HHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhh----------
Q psy1548         205 KYMSNIKVGVFFGGLPI---QKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQ----------  271 (448)
Q Consensus       205 ~~~~~~~v~~~~g~~~~---~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~----------  271 (448)
                      . . ++++..++|+.+.   ..+...+..+.++|+|+||+++.+++..  +.+.+++++|+||||++..+          
T Consensus        89 ~-~-~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~--~~~~~~~~iViDEaH~~~~~~~~~d~~l~~  164 (414)
T 3oiy_A           89 D-E-KVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASRNIDTLLMM  164 (414)
T ss_dssp             C-S-SCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH--HTTCCCSEEEESCHHHHHHCHHHHHHHHHH
T ss_pred             c-C-CceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH--hccccccEEEEeChHhhhhccchhhhHHhh
Confidence            7 4 8999999999987   4555666666689999999999887764  56678999999999977642          


Q ss_pred             hhhHHH-HHHHHHhCC-----------CCCeEEEEecc-CCccHH-HHHHHhcCCCeEEEEcCcccccccceeEEEEEcC
Q psy1548         272 LEMRRD-VQEIFRSSP-----------HTKQVMMFSAT-LSKEIR-PVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLK  337 (448)
Q Consensus       272 ~~~~~~-~~~i~~~l~-----------~~~q~i~~SAT-~~~~~~-~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~  337 (448)
                      .+|... +..++..++           +..|++++||| .|..+. .+...++.    +.+... .....++.+.+..+ 
T Consensus       165 ~~~~~~~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~----~~~~~~-~~~~~~i~~~~~~~-  238 (414)
T 3oiy_A          165 VGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRL-VSVARNITHVRISS-  238 (414)
T ss_dssp             TTCCHHHHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHHHS----CCSSCC-CCCCCSEEEEEESS-
T ss_pred             cCCcHHHHHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhHHHHHHHhhc----cCcCcc-ccccccchheeecc-
Confidence            166666 777887776           78899999999 565544 33344333    111112 23456677777655 


Q ss_pred             cchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEE-EEeCCCCHHHHHHHHHHHhcCCCceEEEEe----
Q psy1548         338 ENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAV-SIHRGMTQEERLKKYQEFKDFHKGLAITFA----  412 (448)
Q Consensus       338 ~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~-~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~----  412 (448)
                        ++...+..+++.. ++++||||++++.|+.++..|++.|+.+. .+||+    +|.  ++.|++|+  ..|+++    
T Consensus       239 --~~~~~l~~~l~~~-~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~----~r~--~~~f~~g~--~~vLvat~s~  307 (414)
T 3oiy_A          239 --RSKEKLVELLEIF-RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF----EKN--FEDFKVGK--INILIGVQAY  307 (414)
T ss_dssp             --CCHHHHHHHHHHH-CSSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCH----HHH--HHHHHTTS--CSEEEEECCT
T ss_pred             --CHHHHHHHHHHHc-CCCEEEEECCHHHHHHHHHHHHHcCCceehhhcCc----chH--HHHHhCCC--CeEEEEecCc
Confidence              3455667777663 47999999999999999999999999998 99995    444  99999998  456677    


Q ss_pred             cChhhHHHHHHHHH-HhcCCCCCCC--ccccccccccCC
Q psy1548         413 SDENDAKILNNVQD-RFDVSISELP--DEIDLSTYIEGR  448 (448)
Q Consensus       413 t~~~d~~~l~~i~~-~~~~~~~~~p--~~~~~~~~~~~~  448 (448)
                      |+...+++  ++.+ .-.+-..++|  .+...+.++.||
T Consensus       308 T~~~~~Gi--Dip~~v~~VI~~~~p~~~~~~~y~qr~GR  344 (414)
T 3oiy_A          308 YGKLTRGV--DLPERIKYVIFWGTPSGPDVYTYIQASGR  344 (414)
T ss_dssp             TCCCCCCC--CCTTTCCEEEEESCCTTTCHHHHHHHHGG
T ss_pred             CchhhccC--ccccccCEEEEECCCCCCCHHHHHHHhCc
Confidence            54322221  2222 1123335677  677788888887

>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=100.00  E-value=2.8e-35  Score=283.93  Aligned_cols=206  Identities=28%  Similarity=0.450  Sum_probs=186.6

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeC--cceeeec
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLG--MDILCQA  156 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g--~~vli~a  156 (448)
                      ...|.++++++.+++++...|                       |..|+++   |.+      ++|.++.|  +|+++++
T Consensus        91 ~~~f~~l~l~~~l~~~l~~~g-----------------------~~~pt~i---Q~~------ai~~il~~~~~~~l~~a  138 (300)
T 3fmo_B           91 VKSFEELRLKPQLLQGVYAMG-----------------------FNRPSKI---QEN------ALPLMLAEPPQNLIAQS  138 (300)
T ss_dssp             CCCSGGGTCCHHHHHHHHHTT-----------------------CCSCCHH---HHH------HHHHHTSSSCCCEEEEC
T ss_pred             cCCHhhcCCCHHHHHHHHHcC-----------------------CCCCCHH---HHH------HHHHHHcCCCCeEEEEC
Confidence            467999999999999999999                       9999999   999      99999998  9999999


Q ss_pred             cCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEE
Q psy1548         157 KSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV  236 (448)
Q Consensus       157 pTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~Il  236 (448)
                      |||||||++|++|+++.+.....++++||++||++||.|+++.++.+....+++.+....|+.......    ...++|+
T Consensus       139 ~TGsGKT~a~~lp~l~~l~~~~~~~~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~----~~~~~Il  214 (300)
T 3fmo_B          139 QSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ----KISEQIV  214 (300)
T ss_dssp             CTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTC----CCCCSEE
T ss_pred             CCCCCccHHHHHHHHHhhhccCCCceEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhh----cCCCCEE
Confidence            999999999999999998877777899999999999999999999999877688999998887654332    2348999


Q ss_pred             EEcHHHHHHHHHC-CCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeE
Q psy1548         237 VGTPGRILALVRN-KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPME  315 (448)
Q Consensus       237 V~Tp~~l~~~l~~-~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~  315 (448)
                      |+||++|.+++.+ +.+.++++++|||||||+|++..+|...+..+++.+++.+|+++||||+++.+..+++.++.+|..
T Consensus       215 V~TP~~l~~~l~~~~~~~l~~l~~lVlDEad~l~~~~~~~~~~~~i~~~~~~~~q~i~~SAT~~~~v~~~a~~~l~~p~~  294 (300)
T 3fmo_B          215 IGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNV  294 (300)
T ss_dssp             EECHHHHHHHHTTTCCCCGGGCSEEEETTHHHHHHSTTHHHHHHHHHTTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEE
T ss_pred             EECHHHHHHHHHhcCCCChhhceEEEEeCHHHHhhccCcHHHHHHHHHhCCCCCEEEEEeccCCHHHHHHHHHHCCCCeE
Confidence            9999999999966 667889999999999999998328999999999999999999999999999999999999999999


Q ss_pred             EEEcC
Q psy1548         316 VYVDD  320 (448)
Q Consensus       316 i~~~~  320 (448)
                      |.+..
T Consensus       295 i~~~~  299 (300)
T 3fmo_B          295 IKLKR  299 (300)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            87653

>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=100.00  E-value=3.5e-35  Score=273.95  Aligned_cols=209  Identities=35%  Similarity=0.569  Sum_probs=180.5

Q ss_pred             eccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeec
Q psy1548          77 IHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQA  156 (448)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~a  156 (448)
                      .....|+++++++.+++++.+.|                       |..|+++   |++      +++.++.|+|+++++
T Consensus        27 ~~~~~f~~l~l~~~l~~~l~~~g-----------------------~~~~~~~---Q~~------ai~~i~~~~~~li~a   74 (237)
T 3bor_A           27 EIVDNFDDMNLKESLLRGIYAYG-----------------------FEKPSAI---QQR------AIIPCIKGYDVIAQA   74 (237)
T ss_dssp             CCCCSGGGSCCCHHHHHHHHHHT-----------------------CCSCCHH---HHH------HHHHHHTTCCEEECC
T ss_pred             CccCChhhcCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhCCCCEEEEC
Confidence            34567999999999999999999                       9999988   999      999999999999999


Q ss_pred             cCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEE
Q psy1548         157 KSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV  236 (448)
Q Consensus       157 pTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~Il  236 (448)
                      |||+|||++|++|+++.+.....+.++||++||++|+.|+.+.++.+.... +..+..++|+.....+...+..+.++|+
T Consensus        75 pTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~l~~~~~~Il  153 (237)
T 3bor_A           75 QSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYM-GATCHACIGGTNVRNEMQKLQAEAPHIV  153 (237)
T ss_dssp             CSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTT-TCCEEEECC-------------CCCSEE
T ss_pred             CCCCcHHHHHHHHHHHHHHhcCCCceEEEEECcHHHHHHHHHHHHHHhhhc-CceEEEEECCCchHHHHHHHhcCCCCEE
Confidence            999999999999999988766567799999999999999999999998776 7888889998877766666666668999


Q ss_pred             EEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEE
Q psy1548         237 VGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEV  316 (448)
Q Consensus       237 V~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i  316 (448)
                      |+||+++.+++..+...+.+++++|+||||++.++ ++...+..+++.++...|++++|||+++.+.++++.++.+|..+
T Consensus       154 v~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~-~~~~~l~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~l~~p~~i  232 (237)
T 3bor_A          154 VGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSR-GFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRI  232 (237)
T ss_dssp             EECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHHT-TCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCSSCEEE
T ss_pred             EECHHHHHHHHHhCCcCcccCcEEEECCchHhhcc-CcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHCCCCEEE
Confidence            99999999999988888899999999999999998 99999999999999999999999999999999999999999887


Q ss_pred             EEc
Q psy1548         317 YVD  319 (448)
Q Consensus       317 ~~~  319 (448)
                      .+.
T Consensus       233 ~v~  235 (237)
T 3bor_A          233 LVK  235 (237)
T ss_dssp             C--
T ss_pred             Eec
Confidence            654

>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=100.00  E-value=9.3e-35  Score=264.79  Aligned_cols=203  Identities=30%  Similarity=0.515  Sum_probs=186.8

Q ss_pred             CCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCC
Q psy1548          80 SGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSG  159 (448)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTG  159 (448)
                      ..|+++++++++++.+.+.|                       |..|+++   |++      +++.++.|+|+++++|||
T Consensus         3 ~~f~~~~l~~~l~~~l~~~g-----------------------~~~~~~~---Q~~------~i~~~~~~~~~lv~apTG   50 (206)
T 1vec_A            3 NEFEDYCLKRELLMGIFEMG-----------------------WEKPSPI---QEE------SIPIALSGRDILARAKNG   50 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTT-----------------------CCSCCHH---HHH------HHHHHHTTCCEEEECCSS
T ss_pred             CChhhcCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHccCCCEEEECCCC
Confidence            46999999999999999999                       9999888   999      999999999999999999


Q ss_pred             ChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEc
Q psy1548         160 MGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGT  239 (448)
Q Consensus       160 sGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~T  239 (448)
                      +|||++|++|++..+.....++++||++|+++|+.|+.+.++.+....++.++..++|+.....+...+.. .++|+|+|
T Consensus        51 sGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~-~~~i~v~T  129 (206)
T 1vec_A           51 TGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDD-TVHVVIAT  129 (206)
T ss_dssp             STTHHHHHHHHHHHCCTTSCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTS-CCSEEEEC
T ss_pred             CchHHHHHHHHHHHhcccCCCeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcCC-CCCEEEeC
Confidence            99999999999998876666779999999999999999999999887767899999999887766666555 48999999


Q ss_pred             HHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEE
Q psy1548         240 PGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEV  316 (448)
Q Consensus       240 p~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i  316 (448)
                      |+++.+++..+...+.+++++|+||||++.+. ++...+..++..+++..|++++|||+++.+.++++.++.+|..+
T Consensus       130 ~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~-~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i  205 (206)
T 1vec_A          130 PGRILDLIKKGVAKVDHVQMIVLDEADKLLSQ-DFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             HHHHHHHHHTTCSCCTTCCEEEEETHHHHTST-TTHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             HHHHHHHHHcCCcCcccCCEEEEEChHHhHhh-CcHHHHHHHHHhCCccceEEEEEeeCCHHHHHHHHHHcCCCeEe
Confidence            99999999988888999999999999999997 99999999999999999999999999999999999999999765

>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=100.00  E-value=6.4e-35  Score=270.35  Aligned_cols=208  Identities=27%  Similarity=0.467  Sum_probs=182.7

Q ss_pred             eeeeccCCccc-CCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcce
Q psy1548          74 YVSIHSSGFRD-FLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDI  152 (448)
Q Consensus        74 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~v  152 (448)
                      ..+.....|.+ +++++++++++.+.|                       |..|+++   |++      +++.++.|+|+
T Consensus        13 ~~p~p~~~f~~~~~l~~~l~~~l~~~g-----------------------~~~~~~~---Q~~------~i~~~~~~~~~   60 (228)
T 3iuy_A           13 LIPKPTCRFKDAFQQYPDLLKSIIRVG-----------------------ILKPTPI---QSQ------AWPIILQGIDL   60 (228)
T ss_dssp             CCCCCCCSHHHHHTTCHHHHHHHHHHT-----------------------CCSCCHH---HHH------HHHHHHTTCCE
T ss_pred             cCCCChhhHhhhhccCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhCCCCE
Confidence            45556677888 799999999999999                       9999999   999      99999999999


Q ss_pred             eeeccCCChhHHHHHHHHHHhhhcc------CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHH
Q psy1548         153 LCQAKSGMGKTAVFVLATLQQLETT------DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE  226 (448)
Q Consensus       153 li~apTGsGKT~~~~l~~l~~l~~~------~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~  226 (448)
                      ++++|||+|||++|++|++..+...      ..++++||++||++|+.|+.+.++.+.. . ++++..++|+.....+..
T Consensus        61 l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~-~-~~~~~~~~~~~~~~~~~~  138 (228)
T 3iuy_A           61 IVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYSY-K-GLKSICIYGGRNRNGQIE  138 (228)
T ss_dssp             EEECCTTSCHHHHHHHHHHHHHC---------CCCSEEEECSSHHHHHHHHHHHHHHCC-T-TCCEEEECC------CHH
T ss_pred             EEECCCCChHHHHHHHHHHHHHHhccchhhccCCCcEEEEeCCHHHHHHHHHHHHHhcc-c-CceEEEEECCCChHHHHH
Confidence            9999999999999999999877532      2567899999999999999999999863 2 788999999988777777


Q ss_pred             HHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHH
Q psy1548         227 YLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVC  306 (448)
Q Consensus       227 ~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~  306 (448)
                      .+..+ ++|+|+||+++.+++......+.+++++|+||||++.++ +|...+..++..++++.|++++|||+++.+.+++
T Consensus       139 ~~~~~-~~iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~~~~-~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~  216 (228)
T 3iuy_A          139 DISKG-VDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDM-EFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLA  216 (228)
T ss_dssp             HHHSC-CSEEEECHHHHHHHHHTTCCCCTTCCEEEECCHHHHHHT-TCHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHH
T ss_pred             HhcCC-CCEEEECHHHHHHHHHcCCcCcccceEEEEECHHHHhcc-chHHHHHHHHHhCCcCCeEEEEEeeCCHHHHHHH
Confidence            77765 899999999999999988888999999999999999998 9999999999999999999999999999999999


Q ss_pred             HHhcCCCeEEE
Q psy1548         307 KKFMHDPMEVY  317 (448)
Q Consensus       307 ~~~l~~~~~i~  317 (448)
                      ..++.+|..+.
T Consensus       217 ~~~l~~p~~i~  227 (228)
T 3iuy_A          217 LSYLKDPMIVY  227 (228)
T ss_dssp             HTTCSSCEEEE
T ss_pred             HHHCCCCEEEe
Confidence            99999998775

>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=100.00  E-value=8.1e-35  Score=270.19  Aligned_cols=210  Identities=32%  Similarity=0.500  Sum_probs=186.1

Q ss_pred             eeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCccee
Q psy1548          74 YVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDIL  153 (448)
Q Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vl  153 (448)
                      ..+.....|+++++++.+++.+.+.|                       |..|+++   |++      +++.++.|+|++
T Consensus        18 ~~~~~~~~f~~l~l~~~l~~~l~~~g-----------------------~~~~~~~---Q~~------~i~~~~~~~~~l   65 (230)
T 2oxc_A           18 VLLAEPADFESLLLSRPVLEGLRAAG-----------------------FERPSPV---QLK------AIPLGRCGLDLI   65 (230)
T ss_dssp             ------CCGGGGTCCHHHHHHHHHTT-----------------------CCSCCHH---HHH------HHHHHHTTCCEE
T ss_pred             CCCCCCCCHhhcCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhCCCCEE
Confidence            34445568999999999999999999                       9999988   999      999999999999


Q ss_pred             eeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCC
Q psy1548         154 CQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNP  233 (448)
Q Consensus       154 i~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~  233 (448)
                      +++|||+|||++|++|++..+.....+.++||++||++|+.|+.+.++.+....+++++..+.|+.....+...+.  .+
T Consensus        66 ~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~--~~  143 (230)
T 2oxc_A           66 VQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLK--KC  143 (230)
T ss_dssp             EECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHTT--SC
T ss_pred             EECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhcc--CC
Confidence            9999999999999999999887666677999999999999999999999987766889999999987666555543  38


Q ss_pred             cEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhh-hHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCC
Q psy1548         234 QIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLE-MRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHD  312 (448)
Q Consensus       234 ~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~-~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~  312 (448)
                      +|+|+||+++.+++..+.+.+.+++++|+||||++.++ + |...+..+++.+++..|++++|||+++.+.+++..++.+
T Consensus       144 ~Iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~~~~-~~~~~~~~~i~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~  222 (230)
T 2oxc_A          144 HIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEE-GSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRD  222 (230)
T ss_dssp             SEEEECHHHHHHHHHTTSSCGGGCCEEEESSHHHHHST-TSSHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHHTTTCSS
T ss_pred             CEEEECHHHHHHHHhcCCcccccCCEEEeCCchHhhcC-cchHHHHHHHHHhCCCCCeEEEEEeccCHHHHHHHHHHcCC
Confidence            99999999999999988888899999999999999987 7 999999999999999999999999999999999999999


Q ss_pred             CeEEEE
Q psy1548         313 PMEVYV  318 (448)
Q Consensus       313 ~~~i~~  318 (448)
                      |..+.+
T Consensus       223 p~~i~~  228 (230)
T 2oxc_A          223 PTFVRL  228 (230)
T ss_dssp             CEEECC
T ss_pred             CeEEEc
Confidence            987754

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=100.00  E-value=8.3e-35  Score=267.96  Aligned_cols=207  Identities=31%  Similarity=0.520  Sum_probs=185.4

Q ss_pred             CCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCC
Q psy1548          80 SGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSG  159 (448)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTG  159 (448)
                      ..|+++++++.+++++.+.|                       |..|+++   |++      +++.++.|+|+++++|||
T Consensus         4 ~~f~~~~l~~~l~~~l~~~g-----------------------~~~~~~~---Q~~------~i~~~~~~~~~lv~a~TG   51 (219)
T 1q0u_A            4 TQFTRFPFQPFIIEAIKTLR-----------------------FYKPTEI---QER------IIPGALRGESMVGQSQTG   51 (219)
T ss_dssp             CCGGGSCCCHHHHHHHHHTT-----------------------CCSCCHH---HHH------HHHHHHHTCCEEEECCSS
T ss_pred             CCHhhCCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhCCCCEEEECCCC
Confidence            56999999999999999999                       9999888   999      999999999999999999


Q ss_pred             ChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCC---CceEEEEEcCcccHHhHHHHhcCCCcEE
Q psy1548         160 MGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS---NIKVGVFFGGLPIQKDEEYLKTHNPQIV  236 (448)
Q Consensus       160 sGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~---~~~v~~~~g~~~~~~~~~~l~~~~~~Il  236 (448)
                      +|||++|++|+++.+.....+.++||++||++|+.|+.+.++++....+   ++++..++|+.........+.. .++|+
T Consensus        52 sGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~-~~~Ii  130 (219)
T 1q0u_A           52 TGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNV-QPHIV  130 (219)
T ss_dssp             HHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSS-CCSEE
T ss_pred             ChHHHHHHHHHHHHHHhCcCCceEEEEcCcHHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHcCC-CCCEE
Confidence            9999999999999987666677999999999999999999999987653   4788888888765554433333 48999


Q ss_pred             EEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEE
Q psy1548         237 VGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEV  316 (448)
Q Consensus       237 V~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i  316 (448)
                      |+||+++.+++..+...+.+++++|+||||++.++ ++...+..++..+++..|++++|||+++++.++++.++.+|..+
T Consensus       131 v~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~-~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~~  209 (219)
T 1q0u_A          131 IGTPGRINDFIREQALDVHTAHILVVDEADLMLDM-GFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFV  209 (219)
T ss_dssp             EECHHHHHHHHHTTCCCGGGCCEEEECSHHHHHHT-TCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEE
T ss_pred             EeCHHHHHHHHHcCCCCcCcceEEEEcCchHHhhh-ChHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHcCCCeEE
Confidence            99999999999988888899999999999999998 99999999999999999999999999999999999999999988


Q ss_pred             EEcC
Q psy1548         317 YVDD  320 (448)
Q Consensus       317 ~~~~  320 (448)
                      .+..
T Consensus       210 ~~~~  213 (219)
T 1q0u_A          210 HVLE  213 (219)
T ss_dssp             ECC-
T ss_pred             Eeec
Confidence            6543

>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=100.00  E-value=2.4e-34  Score=270.23  Aligned_cols=205  Identities=29%  Similarity=0.523  Sum_probs=188.0

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      ...|+++++++.+++++...|                       |..|+++   |++      +++.++.|+++++++||
T Consensus        42 ~~~f~~l~l~~~l~~~l~~~g-----------------------~~~~~~~---Q~~------~i~~i~~~~~~lv~a~T   89 (249)
T 3ber_A           42 TKTFKDLGVTDVLCEACDQLG-----------------------WTKPTKI---QIE------AIPLALQGRDIIGLAET   89 (249)
T ss_dssp             HCCTGGGTCCHHHHHHHHHTT-----------------------CCSCCHH---HHH------HHHHHHTTCCEEEECCT
T ss_pred             cCCHHHcCCCHHHHHHHHHcC-----------------------CCCCCHH---HHH------HHHHHhCCCCEEEEcCC
Confidence            356999999999999999999                       9999988   999      99999999999999999


Q ss_pred             CChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEE
Q psy1548         159 GMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVG  238 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~  238 (448)
                      |+|||++|++|+++.+.....+.++||++||++|+.|+.+.++++.... ++++..++|+.....+...+..+ ++|+|+
T Consensus        90 GsGKT~~~~~~il~~l~~~~~~~~~lil~Ptr~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~-~~I~v~  167 (249)
T 3ber_A           90 GSGKTGAFALPILNALLETPQRLFALVLTPTRELAFQISEQFEALGSSI-GVQSAVIVGGIDSMSQSLALAKK-PHIIIA  167 (249)
T ss_dssp             TSCHHHHHHHHHHHHHHHSCCSSCEEEECSSHHHHHHHHHHHHHHHGGG-TCCEEEECTTSCHHHHHHHHHTC-CSEEEE
T ss_pred             CCCchhHhHHHHHHHHhcCCCCceEEEEeCCHHHHHHHHHHHHHHhccC-CeeEEEEECCCChHHHHHHhcCC-CCEEEE
Confidence            9999999999999988777777799999999999999999999998877 88999999998877666666554 899999


Q ss_pred             cHHHHHHHHHC-CCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEE
Q psy1548         239 TPGRILALVRN-KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVY  317 (448)
Q Consensus       239 Tp~~l~~~l~~-~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~  317 (448)
                      ||+++.+++.. +.+.+.+++++|+||||++.++ +|...+..++..+++..|+++||||+++.+.++++.++.+|..+.
T Consensus       168 Tp~~l~~~l~~~~~~~l~~~~~lViDEah~l~~~-~~~~~l~~i~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~p~~i~  246 (249)
T 3ber_A          168 TPGRLIDHLENTKGFNLRALKYLVMDEADRILNM-DFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCA  246 (249)
T ss_dssp             CHHHHHHHHHHSTTCCCTTCCEEEECSHHHHHHT-TCHHHHHHHHHSSCSSSEEEEEESSCCHHHHHHHHHHCSSCEEEE
T ss_pred             CHHHHHHHHHcCCCcCccccCEEEEcChhhhhcc-ChHHHHHHHHHhCCCCCeEEEEeccCCHHHHHHHHHHCCCCEEEE
Confidence            99999998875 5567899999999999999998 999999999999999999999999999999999999999998876


Q ss_pred             E
Q psy1548         318 V  318 (448)
Q Consensus       318 ~  318 (448)
                      +
T Consensus       247 v  247 (249)
T 3ber_A          247 V  247 (249)
T ss_dssp             C
T ss_pred             e
Confidence            5

>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=100.00  E-value=7.3e-35  Score=274.36  Aligned_cols=219  Identities=28%  Similarity=0.449  Sum_probs=186.5

Q ss_pred             ccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeecc
Q psy1548          78 HSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAK  157 (448)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~ap  157 (448)
                      ....|.++++++.+++++...|                       |..|+++   |.+      +++.++.|+|+++++|
T Consensus        21 ~~~~f~~l~l~~~l~~~l~~~g-----------------------~~~~~~~---Q~~------~i~~i~~~~~~l~~a~   68 (253)
T 1wrb_A           21 VIENFDELKLDPTIRNNILLAS-----------------------YQRPTPI---QKN------AIPAILEHRDIMACAQ   68 (253)
T ss_dssp             CCCSSGGGSCCCSTTTTTTTTT-----------------------CCSCCHH---HHH------HHHHHHTTCCEEEECC
T ss_pred             ccCCHhhCCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhCCCCEEEECC
Confidence            3457999999999999999999                       9999988   999      9999999999999999


Q ss_pred             CCChhHHHHHHHHHHhhhccC---------CCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHH
Q psy1548         158 SGMGKTAVFVLATLQQLETTD---------SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL  228 (448)
Q Consensus       158 TGsGKT~~~~l~~l~~l~~~~---------~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l  228 (448)
                      ||+|||++|++|++..+....         .++++||++||++|+.|+.+.++.+.... ++++..++|+.....+...+
T Consensus        69 TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~  147 (253)
T 1wrb_A           69 TGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNT-PLRSCVVYGGADTHSQIREV  147 (253)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCSHHHHHHH
T ss_pred             CCChHHHHHHHHHHHHHHhhccccccccccCCceEEEEECCHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHh
Confidence            999999999999998875432         34689999999999999999999998776 78899999998877777666


Q ss_pred             hcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHh--CCC--CCeEEEEeccCCccHHH
Q psy1548         229 KTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRS--SPH--TKQVMMFSATLSKEIRP  304 (448)
Q Consensus       229 ~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~--l~~--~~q~i~~SAT~~~~~~~  304 (448)
                      ..+ ++|+|+||+++.+++......+.+++++|+||||++.++ +|+..+..++..  ++.  ..|++++|||+++++.+
T Consensus       148 ~~~-~~Ivv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~-~~~~~~~~i~~~~~~~~~~~~q~l~~SAT~~~~~~~  225 (253)
T 1wrb_A          148 QMG-CHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDM-GFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQK  225 (253)
T ss_dssp             SSC-CSEEEECHHHHHHHHHTTSBCCTTCCEEEEETHHHHHHT-TCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHH
T ss_pred             CCC-CCEEEECHHHHHHHHHcCCCChhhCCEEEEeCHHHHHhC-chHHHHHHHHhhccCCCCCCcEEEEEEEeCCHHHHH
Confidence            654 899999999999999988888999999999999999998 999999999985  444  68999999999999999


Q ss_pred             HHHHhcCCCeEEEEcCcccccccceeEE
Q psy1548         305 VCKKFMHDPMEVYVDDEAKLTLHGLQQH  332 (448)
Q Consensus       305 ~~~~~l~~~~~i~~~~~~~~~~~~i~~~  332 (448)
                      +++.++.+|..+.+... .....+++|+
T Consensus       226 ~~~~~l~~~~~i~~~~~-~~~~~~i~q~  252 (253)
T 1wrb_A          226 LAADFLYNYIFMTVGRV-GSTSDSIKQE  252 (253)
T ss_dssp             HHHHHCSSCEEEEEC-------------
T ss_pred             HHHHHcCCCEEEEECCC-CCCcCCceec
Confidence            99999999999988766 3455566654

>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=100.00  E-value=5.3e-34  Score=263.29  Aligned_cols=210  Identities=35%  Similarity=0.556  Sum_probs=181.5

Q ss_pred             eeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeee
Q psy1548          76 SIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQ  155 (448)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~  155 (448)
                      +.....|.++++++.+++.+.+.|                       |..|+++   |++      +++.++.|+|++++
T Consensus        10 ~~~~~~f~~l~l~~~l~~~l~~~g-----------------------~~~~~~~---Q~~------~i~~~~~~~~~lv~   57 (224)
T 1qde_A           10 DKVVYKFDDMELDENLLRGVFGYG-----------------------FEEPSAI---QQR------AIMPIIEGHDVLAQ   57 (224)
T ss_dssp             CCCCCCGGGGTCCHHHHHHHHHHT-----------------------CCSCCHH---HHH------HHHHHHTTCCEEEE
T ss_pred             CcccCChhhcCCCHHHHHHHHHCC-----------------------CCCCcHH---HHH------HHHHHhcCCCEEEE
Confidence            334567999999999999999999                       9999888   999      99999999999999


Q ss_pred             ccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcE
Q psy1548         156 AKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQI  235 (448)
Q Consensus       156 apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~I  235 (448)
                      +|||+|||++|++|+++.+.....+.++||++|+++|+.|+.+.++.+.... ++++..+.|+.....+...+..  ++|
T Consensus        58 ~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~--~~i  134 (224)
T 1qde_A           58 AQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRD--AQI  134 (224)
T ss_dssp             CCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTS-CCCEEEECC----------CTT--CSE
T ss_pred             CCCCCcHHHHHHHHHHHHHhccCCCceEEEEECCHHHHHHHHHHHHHHhccc-CceEEEEeCCcchHHHHhcCCC--CCE
Confidence            9999999999999999988776677899999999999999999999998877 8899999998876655544443  799


Q ss_pred             EEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeE
Q psy1548         236 VVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPME  315 (448)
Q Consensus       236 lV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~  315 (448)
                      +|+||+++.+++..+...+.+++++|+||||++.++ ++...+..++..+++..|++++|||+++.+.++++.++.+|..
T Consensus       135 iv~Tp~~l~~~~~~~~~~~~~~~~iViDEah~~~~~-~~~~~l~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~p~~  213 (224)
T 1qde_A          135 VVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSS-GFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVR  213 (224)
T ss_dssp             EEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHT-TCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEE
T ss_pred             EEECHHHHHHHHHhCCcchhhCcEEEEcChhHHhhh-hhHHHHHHHHHhCCccCeEEEEEeecCHHHHHHHHHHCCCCEE
Confidence            999999999999988888999999999999999998 9999999999999999999999999999999999999999998


Q ss_pred             EEEcCc
Q psy1548         316 VYVDDE  321 (448)
Q Consensus       316 i~~~~~  321 (448)
                      +.+...
T Consensus       214 i~~~~~  219 (224)
T 1qde_A          214 ILVKKD  219 (224)
T ss_dssp             EC----
T ss_pred             EEecCC
Confidence            876544

>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=100.00  E-value=9e-35  Score=322.78  Aligned_cols=262  Identities=19%  Similarity=0.198  Sum_probs=209.2

Q ss_pred             CCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhc
Q psy1548         126 PEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK  205 (448)
Q Consensus       126 p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  205 (448)
                      |..+++||++      +++.+..|++++++||||||||++|.+|++..+..   +.+++|++||++|+.|+++.+..+..
T Consensus       182 ~f~ltp~Q~~------AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~---g~rvlvl~PtraLa~Q~~~~l~~~~~  252 (1108)
T 3l9o_A          182 PFTLDPFQDT------AISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN---KQRVIYTSPIKALSNQKYRELLAEFG  252 (1108)
T ss_dssp             SSCCCHHHHH------HHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHT---TCEEEEEESSHHHHHHHHHHHHHHTS
T ss_pred             CCCCCHHHHH------HHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhc---CCeEEEEcCcHHHHHHHHHHHHHHhC
Confidence            4445555999      99999999999999999999999999999988743   45899999999999999999998763


Q ss_pred             cCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhC
Q psy1548         206 YMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSS  285 (448)
Q Consensus       206 ~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l  285 (448)
                           .++.++|+....        ..++|+|+||++|.+++..+...+.++++|||||||++.++ ++...+..++..+
T Consensus       253 -----~VglltGd~~~~--------~~~~IlV~Tpe~L~~~L~~~~~~l~~l~lVVIDEaH~l~d~-~rg~~~e~ii~~l  318 (1108)
T 3l9o_A          253 -----DVGLMTGDITIN--------PDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDK-ERGVVWEETIILL  318 (1108)
T ss_dssp             -----SEEEECSSCBCC--------CSCSEEEEEHHHHHHHHHHCSSHHHHEEEEEEETGGGTTSH-HHHHHHHHHHHHS
T ss_pred             -----CccEEeCccccC--------CCCCEEEeChHHHHHHHHcCccccccCCEEEEhhhhhcccc-chHHHHHHHHHhc
Confidence                 577888887643        24899999999999999888777899999999999999998 9999999999999


Q ss_pred             CCCCeEEEEeccCCcc--HHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCc-------------------------
Q psy1548         286 PHTKQVMMFSATLSKE--IRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKE-------------------------  338 (448)
Q Consensus       286 ~~~~q~i~~SAT~~~~--~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~-------------------------  338 (448)
                      ++..|+++||||+++.  +..++......|..+.....   .+..+.++++....                         
T Consensus       319 ~~~~qvl~lSATipn~~e~a~~l~~~~~~~~~vi~~~~---rp~pl~~~~~~~~~~~~~~~vd~~~~~~~~~~~~~~~~l  395 (1108)
T 3l9o_A          319 PDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNF---RPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASI  395 (1108)
T ss_dssp             CTTSEEEEEECSCSSCHHHHHHHHHHTCSCEEEEEECC---CSSCEEEEEEETTSSCCEEEEETTTEECHHHHHHHHTTC
T ss_pred             CCCceEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCC---CcccceEEEeecCCcceeeeeccccchhhhhHHHHHHHH
Confidence            9999999999999875  44666666667766655433   12233333322110                         


Q ss_pred             ------------------------------chHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCc--------
Q psy1548         339 ------------------------------NEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFP--------  380 (448)
Q Consensus       339 ------------------------------~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~--------  380 (448)
                                                    ..+...+...+.....+++||||++++.|+.++..|...++.        
T Consensus       396 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~l~~~~~~~vIVF~~sr~~~e~la~~L~~~~~~~~~e~~~i  475 (1108)
T 3l9o_A          396 SNQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEAL  475 (1108)
T ss_dssp             -----------------------------CHHHHHHHHHHHHHTTCCCEEEEESCHHHHHHHHHHTCSHHHHCC----CH
T ss_pred             HhhhcccccccccccccccccccccccccchhHHHHHHHHHHhcCCCCEEEEeCcHHHHHHHHHHHHhccCCCHHHHHHH
Confidence                                          122333444455556679999999999999999998764332        


Q ss_pred             -------------------------------EEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         381 -------------------------------AVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       381 -------------------------------~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                                                     +..+||+|++.+|..+++.|++|.  +.|+|+|+.
T Consensus       476 ~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gV~~~Hg~l~~~~R~~v~~~F~~G~--ikVLVAT~v  539 (1108)
T 3l9o_A          476 TKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGF--LKVLFATET  539 (1108)
T ss_dssp             HHHGGGSCTHHHHHTTCCHHHHHHTHHHHHTEEEECSCSCHHHHHHHHHHHHHTC--CCEEEEESC
T ss_pred             HHHHHHHHhhcchhhhhhhhHHHHHHhhhcCeeeecCCCCHHHHHHHHHHHhCCC--CeEEEECcH
Confidence                                           799999999999999999999988  567777764

>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=100.00  E-value=8.7e-34  Score=268.42  Aligned_cols=201  Identities=24%  Similarity=0.403  Sum_probs=178.0

Q ss_pred             cCCcccCC--CCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeec
Q psy1548          79 SSGFRDFL--LKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQA  156 (448)
Q Consensus        79 ~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~a  156 (448)
                      ...|.+++  +++++++++.+.|                       |..|+++   |.+      +++.++.|+|+++++
T Consensus        51 ~~~f~~l~~~l~~~l~~~l~~~g-----------------------~~~~~~~---Q~~------~i~~~~~~~~~lv~a   98 (262)
T 3ly5_A           51 DTSFASLCNLVNENTLKAIKEMG-----------------------FTNMTEI---QHK------SIRPLLEGRDLLAAA   98 (262)
T ss_dssp             GGCC-----CCCHHHHHHHHHTT-----------------------CCBCCHH---HHH------HHHHHHHTCCCEECC
T ss_pred             cCChhHhccccCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhCCCcEEEEc
Confidence            35677777  9999999999999                       9999999   999      999999999999999


Q ss_pred             cCCChhHHHHHHHHHHhhhcc----CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCC
Q psy1548         157 KSGMGKTAVFVLATLQQLETT----DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHN  232 (448)
Q Consensus       157 pTGsGKT~~~~l~~l~~l~~~----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~  232 (448)
                      |||+|||++|++|+++.+...    ..+.++||++||++|+.|+.+.++++.... +..+..++|+.....+...+..+ 
T Consensus        99 ~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~-  176 (262)
T 3ly5_A           99 KTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHH-VHTYGLIMGGSNRSAEAQKLGNG-  176 (262)
T ss_dssp             CTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHHHHHHHHHHHTTTC-CSCEEEECSSSCHHHHHHHHHHC-
T ss_pred             cCCCCchHHHHHHHHHHHHhccccccCCceEEEEeCCHHHHHHHHHHHHHHHhhc-CceEEEEECCCCHHHHHHHhcCC-
Confidence            999999999999999887642    235689999999999999999999998877 78999999998877777777666 


Q ss_pred             CcEEEEcHHHHHHHHHCC-CCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcC
Q psy1548         233 PQIVVGTPGRILALVRNK-KLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMH  311 (448)
Q Consensus       233 ~~IlV~Tp~~l~~~l~~~-~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~  311 (448)
                      ++|+|+||+++.+++... ...+.+++++|+||||++.++ +|...+..+++.++..+|+++||||+++++.++++.+++
T Consensus       177 ~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lViDEah~l~~~-~~~~~l~~i~~~~~~~~q~l~~SAT~~~~v~~~~~~~l~  255 (262)
T 3ly5_A          177 INIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDV-GFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLK  255 (262)
T ss_dssp             CSEEEECHHHHHHHHHHCTTCCCTTCCEEEECSHHHHHHT-TCHHHHHHHHHHSCSSSEEEEECSSCCHHHHHHHHHHCS
T ss_pred             CCEEEEcHHHHHHHHHccCCcccccCCEEEEcChHHHhhh-hHHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHcC
Confidence            899999999999888664 467899999999999999998 999999999999999999999999999999999999887


Q ss_pred             CCe
Q psy1548         312 DPM  314 (448)
Q Consensus       312 ~~~  314 (448)
                      ++.
T Consensus       256 ~~~  258 (262)
T 3ly5_A          256 KEP  258 (262)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>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=100.00  E-value=1.8e-34  Score=310.75  Aligned_cols=283  Identities=14%  Similarity=0.164  Sum_probs=221.8

Q ss_pred             CcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccccee-eeeCcceeeeccCC
Q psy1548          81 GFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK-AVLGMDILCQAKSG  159 (448)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~-~~~g~~vli~apTG  159 (448)
                      .|.++++++.+.+++.+.|                       |..|+++   |.+      +++. +..|+++++++|||
T Consensus         2 ~f~~l~l~~~~~~~l~~~g-----------------------~~~l~~~---Q~~------~i~~~~~~~~~~lv~apTG   49 (720)
T 2zj8_A            2 RVDELRVDERIKSTLKERG-----------------------IESFYPP---QAE------ALKSGILEGKNALISIPTA   49 (720)
T ss_dssp             BGGGCCSCHHHHHHHHHTT-----------------------CCBCCHH---HHH------HHTTTGGGTCEEEEECCGG
T ss_pred             cHhhcCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhcCCCcEEEEcCCc
Confidence            5899999999999999999                       9999998   999      9998 78899999999999


Q ss_pred             ChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEc
Q psy1548         160 MGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGT  239 (448)
Q Consensus       160 sGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~T  239 (448)
                      ||||++|.+|++..+...  +.+++|++|+++|+.|+.+.++++.. + +++++.++|+.......  +  +.++|+|+|
T Consensus        50 sGKT~~~~l~il~~~~~~--~~~~l~i~P~raLa~q~~~~~~~l~~-~-g~~v~~~~G~~~~~~~~--~--~~~~Iiv~T  121 (720)
T 2zj8_A           50 SGKTLIAEIAMVHRILTQ--GGKAVYIVPLKALAEEKFQEFQDWEK-I-GLRVAMATGDYDSKDEW--L--GKYDIIIAT  121 (720)
T ss_dssp             GCHHHHHHHHHHHHHHHH--CSEEEEECSSGGGHHHHHHHTGGGGG-G-TCCEEEECSCSSCCCGG--G--GGCSEEEEC
T ss_pred             cHHHHHHHHHHHHHHHhC--CCEEEEEcCcHHHHHHHHHHHHHHHh-c-CCEEEEecCCCCccccc--c--CCCCEEEEC
Confidence            999999999999877533  35899999999999999999976654 3 78999999987654331  1  237999999


Q ss_pred             HHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEc
Q psy1548         240 PGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVD  319 (448)
Q Consensus       240 p~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~  319 (448)
                      |+++..++......+++++++|+||+|++.++ ++...+..++..++...|++++|||+++ ..++..++ ..+. +.. 
T Consensus       122 pe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~-~r~~~~~~ll~~l~~~~~ii~lSATl~n-~~~~~~~l-~~~~-~~~-  196 (720)
T 2zj8_A          122 AEKFDSLLRHGSSWIKDVKILVADEIHLIGSR-DRGATLEVILAHMLGKAQIIGLSATIGN-PEELAEWL-NAEL-IVS-  196 (720)
T ss_dssp             HHHHHHHHHHTCTTGGGEEEEEEETGGGGGCT-TTHHHHHHHHHHHBTTBEEEEEECCCSC-HHHHHHHT-TEEE-EEC-
T ss_pred             HHHHHHHHHcChhhhhcCCEEEEECCcccCCC-cccHHHHHHHHHhhcCCeEEEEcCCcCC-HHHHHHHh-CCcc-cCC-
Confidence            99999998887777899999999999999887 8888999998888778999999999986 35555544 3211 111 


Q ss_pred             CcccccccceeEEEE------EcC-----cchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhC-----------
Q psy1548         320 DEAKLTLHGLQQHYV------KLK-----ENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQ-----------  377 (448)
Q Consensus       320 ~~~~~~~~~i~~~~~------~~~-----~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~-----------  377 (448)
                       .  ..+..+...+.      ...     ...+...+.+.+..  ++++||||++++.|+.++..|.+.           
T Consensus       197 -~--~rp~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~  271 (720)
T 2zj8_A          197 -D--WRPVKLRRGVFYQGFVTWEDGSIDRFSSWEELVYDAIRK--KKGALIFVNMRRKAERVALELSKKVKSLLTKPEIR  271 (720)
T ss_dssp             -C--CCSSEEEEEEEETTEEEETTSCEEECSSTTHHHHHHHHT--TCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHH
T ss_pred             -C--CCCCcceEEEEeCCeeeccccchhhhhHHHHHHHHHHhC--CCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHH
Confidence             1  01112222111      111     23345555555543  579999999999999999998753           


Q ss_pred             -------C---------------CcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         378 -------N---------------FPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       378 -------g---------------~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                             +               ..+.++||+|++++|..+++.|++|+  +.|.++|+.
T Consensus       272 ~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~f~~g~--~~vlvaT~~  329 (720)
T 2zj8_A          272 ALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGI--IKAVVATPT  329 (720)
T ss_dssp             HHHHHHHTSCSCHHHHHHHHHHTTTEEEECTTSCHHHHHHHHHHHHTTS--SCEEEECST
T ss_pred             HHHHHHHHHhcccchHHHHHHHhcCeeeecCCCCHHHHHHHHHHHHCCC--CeEEEECcH
Confidence                   1               24899999999999999999999987  466667664

>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=100.00  E-value=3.1e-33  Score=254.78  Aligned_cols=201  Identities=33%  Similarity=0.521  Sum_probs=182.1

Q ss_pred             CcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCC
Q psy1548          81 GFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGM  160 (448)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGs  160 (448)
                      .|+++++++.+++.+.+.+                       |..|+++   |++      +++.++.|+++++++|||+
T Consensus         2 ~f~~~~l~~~l~~~l~~~~-----------------------~~~~~~~---Q~~------~i~~~~~~~~~li~~~TGs   49 (207)
T 2gxq_A            2 EFKDFPLKPEILEALHGRG-----------------------LTTPTPI---QAA------ALPLALEGKDLIGQARTGT   49 (207)
T ss_dssp             CGGGSCCCHHHHHHHHHTT-----------------------CCSCCHH---HHH------HHHHHHTTCCEEEECCTTS
T ss_pred             ChhhcCCCHHHHHHHHHcC-----------------------CCCCCHH---HHH------HHHHHcCCCCEEEECCCCC
Confidence            5899999999999999999                       9999988   999      9999999999999999999


Q ss_pred             hhHHHHHHHHHHhhhcc---CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEE
Q psy1548         161 GKTAVFVLATLQQLETT---DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVV  237 (448)
Q Consensus       161 GKT~~~~l~~l~~l~~~---~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV  237 (448)
                      |||++|++|++..+...   ..++++||++|+++|+.|+.+.++.+..   ++++..++|+.....+...+..+ ++|+|
T Consensus        50 GKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~-~~i~v  125 (207)
T 2gxq_A           50 GKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAP---HLKVVAVYGGTGYGKQKEALLRG-ADAVV  125 (207)
T ss_dssp             CHHHHHHHHHHHHCCCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHCT---TSCEEEECSSSCSHHHHHHHHHC-CSEEE
T ss_pred             hHHHHHHHHHHHHHhhccccCCCCcEEEEECCHHHHHHHHHHHHHHhh---cceEEEEECCCChHHHHHHhhCC-CCEEE
Confidence            99999999999987542   3457899999999999999999999875   46788889988777666666654 89999


Q ss_pred             EcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEE
Q psy1548         238 GTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVY  317 (448)
Q Consensus       238 ~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~  317 (448)
                      +||+++.+++..+...+.+++++|+||||++.++ ++...+..++..+++..|++++|||+++.+.++++.++.+|..+.
T Consensus       126 ~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~-~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~  204 (207)
T 2gxq_A          126 ATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSM-GFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLIN  204 (207)
T ss_dssp             ECHHHHHHHHHHTSSCCTTCSEEEEESHHHHHHT-TCHHHHHHHHHTSCTTSEEEEECSSCCHHHHHHHHHHCSSCEEEE
T ss_pred             ECHHHHHHHHHcCCcchhhceEEEEEChhHhhcc-chHHHHHHHHHhCCccCeEEEEEEecCHHHHHHHHHHcCCCeEEE
Confidence            9999999999888888999999999999999998 999999999999999999999999999999999999999998876


Q ss_pred             E
Q psy1548         318 V  318 (448)
Q Consensus       318 ~  318 (448)
                      +
T Consensus       205 ~  205 (207)
T 2gxq_A          205 V  205 (207)
T ss_dssp             C
T ss_pred             c
Confidence            4

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=100.00  E-value=1.6e-33  Score=303.21  Aligned_cols=283  Identities=17%  Similarity=0.165  Sum_probs=220.1

Q ss_pred             CCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccccee-eeeCcceeeeccC
Q psy1548          80 SGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK-AVLGMDILCQAKS  158 (448)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~-~~~g~~vli~apT  158 (448)
                      ..|.++++++.+.+++.+.|                       |..|+++   |.+      +++. +..|+++++++||
T Consensus         8 ~~~~~l~l~~~~~~~l~~~g-----------------------~~~l~~~---Q~~------~i~~~~~~~~~~lv~apT   55 (715)
T 2va8_A            8 MPIEDLKLPSNVIEIIKKRG-----------------------IKKLNPP---QTE------AVKKGLLEGNRLLLTSPT   55 (715)
T ss_dssp             CBGGGSSSCHHHHHHHHTTS-----------------------CCBCCHH---HHH------HHHTTTTTTCCEEEECCT
T ss_pred             CcHHHcCCCHHHHHHHHhCC-----------------------CCCCCHH---HHH------HHHHHhcCCCcEEEEcCC
Confidence            56999999999999999999                       9999998   999      9988 7789999999999


Q ss_pred             CChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEE
Q psy1548         159 GMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVG  238 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~  238 (448)
                      |||||+++.+|++..+...  +.+++|++|+++|+.|+.+.++.+.. . +++++..+|+.......  +.  .++|+|+
T Consensus        56 GsGKT~~~~l~il~~~~~~--~~~il~i~P~r~La~q~~~~~~~~~~-~-g~~v~~~~G~~~~~~~~--~~--~~~Iiv~  127 (715)
T 2va8_A           56 GSGKTLIAEMGIISFLLKN--GGKAIYVTPLRALTNEKYLTFKDWEL-I-GFKVAMTSGDYDTDDAW--LK--NYDIIIT  127 (715)
T ss_dssp             TSCHHHHHHHHHHHHHHHS--CSEEEEECSCHHHHHHHHHHHGGGGG-G-TCCEEECCSCSSSCCGG--GG--GCSEEEE
T ss_pred             CCcHHHHHHHHHHHHHHHC--CCeEEEEeCcHHHHHHHHHHHHHhhc-C-CCEEEEEeCCCCCchhh--cC--CCCEEEE
Confidence            9999999999999876533  45899999999999999999865543 3 78999999987654431  22  3799999


Q ss_pred             cHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEE
Q psy1548         239 TPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV  318 (448)
Q Consensus       239 Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~  318 (448)
                      ||+++..++..+...+++++++|+||+|.+.++ .+...+..++..++ ..|++++|||+++ ..++..++. .+. +..
T Consensus       128 Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~-~~~~~l~~i~~~~~-~~~ii~lSATl~n-~~~~~~~l~-~~~-~~~  202 (715)
T 2va8_A          128 TYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDP-ERGPVVESVTIRAK-RRNLLALSATISN-YKQIAKWLG-AEP-VAT  202 (715)
T ss_dssp             CHHHHHHHHHHCCGGGGGEEEEEECSGGGGGCT-TTHHHHHHHHHHHH-TSEEEEEESCCTT-HHHHHHHHT-CEE-EEC
T ss_pred             cHHHHHHHHhCChhHhhccCEEEEechhhcCCc-ccchHHHHHHHhcc-cCcEEEEcCCCCC-HHHHHHHhC-CCc-cCC
Confidence            999999999887777899999999999998876 78888888887776 7899999999986 355555443 221 111


Q ss_pred             cCcccccccceeEE------------EEEcC--------cchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCC
Q psy1548         319 DDEAKLTLHGLQQH------------YVKLK--------ENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQN  378 (448)
Q Consensus       319 ~~~~~~~~~~i~~~------------~~~~~--------~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g  378 (448)
                      ..    .+..+...            .....        ...+...+.+.+.  .++++||||++++.|+.++..|.+..
T Consensus       203 ~~----r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~LVF~~s~~~~~~~a~~L~~~~  276 (715)
T 2va8_A          203 NW----RPVPLIEGVIYPERKKKEYNVIFKDNTTKKVHGDDAIIAYTLDSLS--KNGQVLVFRNSRKMAESTALKIANYM  276 (715)
T ss_dssp             CC----CSSCEEEEEEEECSSTTEEEEEETTSCEEEEESSSHHHHHHHHHHT--TTCCEEEECSSHHHHHHHHHHHHHTT
T ss_pred             CC----CCCCceEEEEecCCcccceeeecCcchhhhcccchHHHHHHHHHHh--cCCCEEEEECCHHHHHHHHHHHHHHH
Confidence            00    01111111            11111        2345555555554  46799999999999999999998642


Q ss_pred             ------------------------------------CcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         379 ------------------------------------FPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       379 ------------------------------------~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                                                          ..+.++||+|++++|..+++.|++|+  +.|.++|+.
T Consensus       277 ~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~r~~v~~~f~~g~--~~vlvaT~~  347 (715)
T 2va8_A          277 NFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAYHHAGLSKALRDLIEEGFRQRK--IKVIVATPT  347 (715)
T ss_dssp             TSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTEEEECTTSCHHHHHHHHHHHHTTC--SCEEEECGG
T ss_pred             hhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCEEEECCCCCHHHHHHHHHHHHcCC--CeEEEEChH
Confidence                                                24899999999999999999999987  455565553

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=100.00  E-value=3.3e-33  Score=260.21  Aligned_cols=206  Identities=27%  Similarity=0.491  Sum_probs=182.8

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      ...|.++++++.+++.+.+.+                       |..|+++   |.+      +++.++.|+|+++++||
T Consensus        24 ~~~f~~~~l~~~l~~~l~~~~-----------------------~~~~~~~---Q~~------~i~~~~~~~~~li~a~T   71 (236)
T 2pl3_A           24 ITRFSDFPLSKKTLKGLQEAQ-----------------------YRLVTEI---QKQ------TIGLALQGKDVLGAAKT   71 (236)
T ss_dssp             CSBGGGSCCCHHHHHHHHHTT-----------------------CCBCCHH---HHH------HHHHHHTTCCEEEECCT
T ss_pred             cCCHhhcCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHhCCCCEEEEeCC
Confidence            457999999999999999999                       9999998   999      99999999999999999


Q ss_pred             CChhHHHHHHHHHHhhhcc----CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCc
Q psy1548         159 GMGKTAVFVLATLQQLETT----DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQ  234 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~  234 (448)
                      |+|||++|++|+++.+...    ..+.++||++||++|+.|+.+.++.+.... ++++..++|+.....+...+.  .++
T Consensus        72 GsGKT~~~~~~~l~~l~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~--~~~  148 (236)
T 2pl3_A           72 GSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNH-DFSAGLIIGGKDLKHEAERIN--NIN  148 (236)
T ss_dssp             TSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHHHHHHHHHHHTTTS-SCCEEEECCC--CHHHHHHHT--TCS
T ss_pred             CCcHHHHHHHHHHHHHHhhcccccCCceEEEEeCCHHHHHHHHHHHHHHhCCC-CeeEEEEECCCCHHHHHHhCC--CCC
Confidence            9999999999999887532    245689999999999999999999998776 789999999987766655553  489


Q ss_pred             EEEEcHHHHHHHHHCC-CCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCC
Q psy1548         235 IVVGTPGRILALVRNK-KLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDP  313 (448)
Q Consensus       235 IlV~Tp~~l~~~l~~~-~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~  313 (448)
                      |+|+||+++.+++... .+.+.+++++|+||||++.++ ++...+..++..+++..|++++|||+++.+.++++.++.+|
T Consensus       149 iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~~~~~-~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p  227 (236)
T 2pl3_A          149 ILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDM-GFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNP  227 (236)
T ss_dssp             EEEECHHHHHHHHHHCSSCCCTTCCEEEETTHHHHHHT-TTHHHHHHHHHTSCTTSEEEEEESSCCHHHHHHHHHSCSSC
T ss_pred             EEEECHHHHHHHHHhcCCcccccccEEEEeChHHHhcC-CcHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHhCCCC
Confidence            9999999999988664 567889999999999999998 99999999999999999999999999999999999999999


Q ss_pred             eEEEEcC
Q psy1548         314 MEVYVDD  320 (448)
Q Consensus       314 ~~i~~~~  320 (448)
                      ..+.+..
T Consensus       228 ~~i~~~~  234 (236)
T 2pl3_A          228 EYVWVHE  234 (236)
T ss_dssp             EEEECCC
T ss_pred             EEEEeCC
Confidence            9887643

>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=100.00  E-value=1.9e-33  Score=293.63  Aligned_cols=306  Identities=19%  Similarity=0.219  Sum_probs=186.8

Q ss_pred             hhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCC--CeEEEEeeccHHHHHHHHHHHHHhhccC
Q psy1548         130 DTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDS--NVYVLVMCHTRELAFQISKEYERFSKYM  207 (448)
Q Consensus       130 ~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~--~~~~lil~Pt~~L~~q~~~~~~~~~~~~  207 (448)
                      ++||.+      +++.++.|+++++++|||+|||++|++|+++.+...+.  +.++||++||++|+.|+.+.++++....
T Consensus         9 ~~~Q~~------~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~   82 (556)
T 4a2p_A            9 RSYQIE------LAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQ   82 (556)
T ss_dssp             CHHHHH------HHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGG
T ss_pred             CHHHHH------HHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhccc
Confidence            444999      99999999999999999999999999999998866442  5689999999999999999999998877


Q ss_pred             CCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCC-cCCCeeEEEecchhHHHhhhhhHHH-HHHHHHh-
Q psy1548         208 SNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKL-NLSLLKHFILDECDKMLEQLEMRRD-VQEIFRS-  284 (448)
Q Consensus       208 ~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~-~~~~i~~lViDEah~l~~~~~~~~~-~~~i~~~-  284 (448)
                       ++++..++|+.....+...+..+ ++|+|+||+++.+++..+.+ .+.+++++|+||||++.++ +.... +...+.. 
T Consensus        83 -~~~~~~~~g~~~~~~~~~~~~~~-~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~-~~~~~~~~~~~~~~  159 (556)
T 4a2p_A           83 -GYSVQGISGENFSNVSVEKVIED-SDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGN-HPYNVLMTRYLEQK  159 (556)
T ss_dssp             -TCCEEECCCC-----CHHHHHHH-CSEEEECHHHHHHHHHSSSCCCSTTCSEEEEETGGGCSTT-SHHHHHHHHHHHHH
T ss_pred             -CceEEEEeCCCCcchhHHHhhCC-CCEEEECHHHHHHHHHhCcccccccCCEEEEECCcccCCc-chHHHHHHHHHHhh
Confidence             89999999998766665555554 89999999999999998877 7899999999999999876 43333 2233322 


Q ss_pred             ---CCCCCeEEEEeccCCcc-----------HHHHHHH------------------hcCCCeEEEEcCccccccc-----
Q psy1548         285 ---SPHTKQVMMFSATLSKE-----------IRPVCKK------------------FMHDPMEVYVDDEAKLTLH-----  327 (448)
Q Consensus       285 ---l~~~~q~i~~SAT~~~~-----------~~~~~~~------------------~l~~~~~i~~~~~~~~~~~-----  327 (448)
                         .++..|++++|||++..           +..+...                  +...|..............     
T Consensus       160 ~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~i~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  239 (556)
T 4a2p_A          160 FNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAII  239 (556)
T ss_dssp             HCC---CCEEEEEESCCCCTTCSSHHHHHHHHHHHHHHHTCSEEECCCTTHHHHHHHTCCCCEEEEECCCCSCCHHHHHH
T ss_pred             hcccCCCCeEEEEeCCcccCchhhHHHHHHHHHHHHHhcCCeEecchhcchHHHHhcCCCCceEEEEcCCCcCChHHHHH
Confidence               14568999999998531           1112121                  2222222111000000000     


Q ss_pred             ---------------ceeEEEE----------------------------------------------------------
Q psy1548         328 ---------------GLQQHYV----------------------------------------------------------  334 (448)
Q Consensus       328 ---------------~i~~~~~----------------------------------------------------------  334 (448)
                                     .+.....                                                          
T Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  319 (556)
T 4a2p_A          240 SNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALIISE  319 (556)
T ss_dssp             HHHHHHHHHHHHHHCC---------CCCSSHHHHHHHHHHHHHHHHC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhhhhhcccccccchhhHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence                           0000000                                                          


Q ss_pred             -----------------------------------------------EcCcchHHHHHHHHHhh----CCCCeEEEEECc
Q psy1548         335 -----------------------------------------------KLKENEKNKKLFELLDV----LEFNQVVIFVKS  363 (448)
Q Consensus       335 -----------------------------------------------~~~~~~k~~~L~~ll~~----~~~~~~IIF~~s  363 (448)
                                                                     ......|...|..++..    ..+.++||||++
T Consensus       320 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~~l~~~~~~~~~~k~lVF~~~  399 (556)
T 4a2p_A          320 DARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKT  399 (556)
T ss_dssp             HSCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTHHHHHHHHHCSSSCCHHHHHHHHHHHHHHHHCTTCCEEEEESS
T ss_pred             hhhHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhhHHHHhhhhccCCCCCChHHHHHHHHHHHHhcCCCCceEEEEEcc
Confidence                                                           00013466666666654    456799999999


Q ss_pred             cHHHHHHHHHHHhC------------CCcEEEEeCCCCHHHHHHHHHHHhc-CCCceEEEEecChhhHHHHHHHHHHhcC
Q psy1548         364 VTRCIALSTLLSEQ------------NFPAVSIHRGMTQEERLKKYQEFKD-FHKGLAITFASDENDAKILNNVQDRFDV  430 (448)
Q Consensus       364 ~~~a~~l~~~L~~~------------g~~~~~lh~~~~~~eR~~~l~~F~~-g~~g~~I~~~t~~~d~~~l~~i~~~~~~  430 (448)
                      +..++.+++.|++.            |.....+||+|++++|.++++.|++ |+  +.|+++|+...+++  ++.+.-.+
T Consensus       400 ~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~--~~vLvaT~~~~~Gi--Dip~v~~V  475 (556)
T 4a2p_A          400 RALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKD--NRLLIATSVADEGI--DIVQCNLV  475 (556)
T ss_dssp             HHHHHHHHHHHTTCSGGGSCCEEC--------------------------------CCEEEEEC-------------CEE
T ss_pred             HHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhcccCc--eEEEEEcCchhcCC--CchhCCEE
Confidence            99999999999876            5566677889999999999999999 77  45778888766665  77777777


Q ss_pred             CCCCCCccccccccccCC
Q psy1548         431 SISELPDEIDLSTYIEGR  448 (448)
Q Consensus       431 ~~~~~p~~~~~~~~~~~~  448 (448)
                      -..++|.+...+.++.||
T Consensus       476 I~~d~p~s~~~~~Qr~GR  493 (556)
T 4a2p_A          476 VLYEYSGNVTKMIQVRGR  493 (556)
T ss_dssp             EEETCCSCHHHHHHC---
T ss_pred             EEeCCCCCHHHHHHhcCC
Confidence            788889999999999998

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=100.00  E-value=1.7e-34  Score=310.10  Aligned_cols=311  Identities=19%  Similarity=0.229  Sum_probs=197.6

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCC--CeEEEEeeccHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDS--NVYVLVMCHTRELAFQISKEY  200 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~--~~~~lil~Pt~~L~~q~~~~~  200 (448)
                      |..|+++   |.+      +++.++.|+|+++++|||+|||++|++|+++.+...+.  +.++||++||++|+.|+.+.+
T Consensus        11 ~~~lr~~---Q~~------~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~~   81 (696)
T 2ykg_A           11 PFKPRNY---QLE------LALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVF   81 (696)
T ss_dssp             --CCCHH---HHH------HHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHHH
T ss_pred             CCCccHH---HHH------HHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHHH
Confidence            7777777   999      99999999999999999999999999999988765432  258999999999999999999


Q ss_pred             HHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCC-cCCCeeEEEecchhHHHhhhhhHHHHH
Q psy1548         201 ERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKL-NLSLLKHFILDECDKMLEQLEMRRDVQ  279 (448)
Q Consensus       201 ~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~-~~~~i~~lViDEah~l~~~~~~~~~~~  279 (448)
                      +++.... ++++..++|+.....+...+..+ ++|+|+||++|.+.+..+.+ .+.+++++|+||||++.+...+...+.
T Consensus        82 ~~~~~~~-~~~v~~~~g~~~~~~~~~~~~~~-~~Iiv~Tp~~L~~~l~~~~~~~l~~~~~vViDEaH~~~~~~~~~~i~~  159 (696)
T 2ykg_A           82 SKYFERH-GYRVTGISGATAENVPVEQIVEN-NDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMF  159 (696)
T ss_dssp             HHHTTTT-TCCEEEECSSSCSSSCHHHHHHT-CSEEEECHHHHHHHHHTTSSCCGGGCSEEEEETGGGCSTTCHHHHHHH
T ss_pred             HHHhccC-CceEEEEeCCccccccHHHhccC-CCEEEECHHHHHHHHhcCcccccccccEEEEeCCCcccCcccHHHHHH
Confidence            9998766 88999999998766665555554 89999999999999998776 789999999999999876533443333


Q ss_pred             HHHHh-----CCCCCeEEEEeccCCc-------c-HHHHH---------------------HHhcCCCeEEEEcCccccc
Q psy1548         280 EIFRS-----SPHTKQVMMFSATLSK-------E-IRPVC---------------------KKFMHDPMEVYVDDEAKLT  325 (448)
Q Consensus       280 ~i~~~-----l~~~~q~i~~SAT~~~-------~-~~~~~---------------------~~~l~~~~~i~~~~~~~~~  325 (448)
                      ..+..     .++..+++++|||+..       + ...+.                     ..+...|............
T Consensus       160 ~~l~~~~~~~~~~~~~il~LTATp~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~~l~~~~~~p~~~~~~~~~~~~  239 (696)
T 2ykg_A          160 NYLDQKLGGSSGPLPQVIGLTASVGVGDAKTTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRIS  239 (696)
T ss_dssp             HHHHHHHTTCCSCCCEEEEEESCCCCSSCCSHHHHHHHHHHHHHHTTCCEEECCCTTHHHHHHHSCCCEEEEEECCCCSC
T ss_pred             HHHHHhhcccCCCCCeEEEEeCccccCccccHHHHHHHHHHHHHhcCCceEeecccchHHHHhhcCCCceeEEecCcccC
Confidence            33332     2467899999999861       1 11111                     1122223222111000000


Q ss_pred             --------------------------------------------------------------------------------
Q psy1548         326 --------------------------------------------------------------------------------  325 (448)
Q Consensus       326 --------------------------------------------------------------------------------  325 (448)
                                                                                                      
T Consensus       240 ~~fs~~~~~l~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~  319 (696)
T 2ykg_A          240 DKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKY  319 (696)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHSTTGGGSSSCCSCCSSSHHHHHHHHHHHHTSCC------CCHHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHHHHHHhhcccchhhhHHHHHHHHHHHHHHHH
Confidence                                                                                            


Q ss_pred             ------------------------------ccceeEEEEE-------------c---CcchHHHHHHHHHhhC----CCC
Q psy1548         326 ------------------------------LHGLQQHYVK-------------L---KENEKNKKLFELLDVL----EFN  355 (448)
Q Consensus       326 ------------------------------~~~i~~~~~~-------------~---~~~~k~~~L~~ll~~~----~~~  355 (448)
                                                    ...+.+.+..             .   ....|...|..++...    +++
T Consensus       320 ~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~k~~~L~~ll~~~~~~~~~~  399 (696)
T 2ykg_A          320 NDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPET  399 (696)
T ss_dssp             HHHHHHHHHSCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHTTHHHHHHHHHCGGGCCHHHHHHHHHHHHHHTTCTTC
T ss_pred             hHHHhccchhhHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhccCCCC
Confidence                                          0000000000             0   1345777788887654    567


Q ss_pred             eEEEEECccHHHHHHHHHHHhCC----CcEEEE--------eCCCCHHHHHHHHHHHhc-CCCceEEEEecChhhHHHHH
Q psy1548         356 QVVIFVKSVTRCIALSTLLSEQN----FPAVSI--------HRGMTQEERLKKYQEFKD-FHKGLAITFASDENDAKILN  422 (448)
Q Consensus       356 ~~IIF~~s~~~a~~l~~~L~~~g----~~~~~l--------h~~~~~~eR~~~l~~F~~-g~~g~~I~~~t~~~d~~~l~  422 (448)
                      ++||||+++..|+.+++.|++.|    +++..+        ||+|++++|.+++++|++ |+.  .|+++|+...+++  
T Consensus       400 ~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~--~vLVaT~v~~~Gi--  475 (696)
T 2ykg_A          400 ITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDH--NILIATSVADEGI--  475 (696)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC-----------------------------CC--SCSEEEESSCCC---
T ss_pred             cEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCc--cEEEEechhhcCC--
Confidence            99999999999999999999988    888888        559999999999999998 874  3455555434443  


Q ss_pred             HHHHHhcCCCCCCCccccccccccCC
Q psy1548         423 NVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       423 ~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      ++.+.--+-..++|.+...+.++.||
T Consensus       476 Dip~v~~VI~~d~p~s~~~~~Qr~GR  501 (696)
T 2ykg_A          476 DIAQCNLVILYEYVGNVIKMIQTRGR  501 (696)
T ss_dssp             --CCCSEEEEESCC--CCCC------
T ss_pred             cCccCCEEEEeCCCCCHHHHHHhhcc
Confidence            34333334556788888899999998

>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=100.00  E-value=2.7e-33  Score=262.33  Aligned_cols=218  Identities=24%  Similarity=0.406  Sum_probs=183.3

Q ss_pred             cCceeeeccCCcccC----CCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceee
Q psy1548          71 KGAYVSIHSSGFRDF----LLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKA  146 (448)
Q Consensus        71 ~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~  146 (448)
                      .+...+.+...|+++    ++++.+++.+.+.|                       |..|+++   |.+      +++.+
T Consensus        16 ~~~~~p~~~~~f~~l~~~~~l~~~l~~~l~~~g-----------------------~~~~~~~---Q~~------~i~~~   63 (245)
T 3dkp_A           16 QGTDLPDPIATFQQLDQEYKINSRLLQNILDAG-----------------------FQMPTPI---QMQ------AIPVM   63 (245)
T ss_dssp             ESSSCCCCCSSHHHHHHHHCCCHHHHHHHHHTT-----------------------CCSCCHH---HHH------HHHHH
T ss_pred             cCCCCCCcccCHHHhhhccCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHH
Confidence            344455556678776    89999999999999                       9999999   999      99999


Q ss_pred             eeCcceeeeccCCChhHHHHHHHHHHhhhcc-CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhH
Q psy1548         147 VLGMDILCQAKSGMGKTAVFVLATLQQLETT-DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDE  225 (448)
Q Consensus       147 ~~g~~vli~apTGsGKT~~~~l~~l~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~  225 (448)
                      +.|+|+++++|||+|||++|++|++..+... ..+.++||++||++|+.|+.+.++.+.... ++++..+.|+.......
T Consensus        64 ~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~  142 (245)
T 3dkp_A           64 LHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGT-GFRIHMIHKAAVAAKKF  142 (245)
T ss_dssp             HTTCCEEEECCTTSCHHHHHHHHHHHHHCSCCSSSCCEEEECSSHHHHHHHHHHHHHHTTTS-CCCEECCCHHHHHHTTT
T ss_pred             hCCCCEEEECCCCCcHHHHHHHHHHHHHhhcccCCceEEEEeCCHHHHHHHHHHHHHHhccc-CceEEEEecCccHHHHh
Confidence            9999999999999999999999999988642 356689999999999999999999998877 78888777765433332


Q ss_pred             HHHhcCCCcEEEEcHHHHHHHHHCC--CCcCCCeeEEEecchhHHHhh--hhhHHHHHHHHHhC-CCCCeEEEEeccCCc
Q psy1548         226 EYLKTHNPQIVVGTPGRILALVRNK--KLNLSLLKHFILDECDKMLEQ--LEMRRDVQEIFRSS-PHTKQVMMFSATLSK  300 (448)
Q Consensus       226 ~~l~~~~~~IlV~Tp~~l~~~l~~~--~~~~~~i~~lViDEah~l~~~--~~~~~~~~~i~~~l-~~~~q~i~~SAT~~~  300 (448)
                      .......++|+|+||+++.+++...  ...+.+++++|+||||++.++  .++...+..++..+ ++..|+++||||+++
T Consensus       143 ~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~SAT~~~  222 (245)
T 3dkp_A          143 GPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAY  222 (245)
T ss_dssp             STTSCCCCCEEEECHHHHHHHHHSSSCSCCCTTCCEEEESSHHHHHHHC--CHHHHHHHHHHHCCCTTCEEEEEESSCCH
T ss_pred             hhhhcCCCCEEEECHHHHHHHHHhCCCCcccccCcEEEEeChHHhcccccccHHHHHHHHHHhcCCCCcEEEEEeccCCH
Confidence            2223345899999999999999876  567899999999999999884  27888999888776 457899999999999


Q ss_pred             cHHHHHHHhcCCCeEEEEcCc
Q psy1548         301 EIRPVCKKFMHDPMEVYVDDE  321 (448)
Q Consensus       301 ~~~~~~~~~l~~~~~i~~~~~  321 (448)
                      ++.++++.++.+|..+.+...
T Consensus       223 ~v~~~~~~~l~~p~~i~~~~~  243 (245)
T 3dkp_A          223 DVEQWCKLNLDNVISVSIGAR  243 (245)
T ss_dssp             HHHHHHHHHSSSCEEEEECC-
T ss_pred             HHHHHHHHhCCCCEEEEeCCC
Confidence            999999999999999887654

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=100.00  E-value=4.2e-33  Score=290.74  Aligned_cols=306  Identities=18%  Similarity=0.206  Sum_probs=198.4

Q ss_pred             chhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCC--CeEEEEeeccHHHHHHHHHHHHHhhcc
Q psy1548         129 SDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDS--NVYVLVMCHTRELAFQISKEYERFSKY  206 (448)
Q Consensus       129 ~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~--~~~~lil~Pt~~L~~q~~~~~~~~~~~  206 (448)
                      .++||.+      +++.++.|+++++++|||+|||++|++|+++.+.....  +.++||++||++|+.|+.+.++++...
T Consensus         5 ~~~~Q~~------~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~   78 (555)
T 3tbk_A            5 PRNYQLE------LALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFER   78 (555)
T ss_dssp             CCHHHHH------HHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHT
T ss_pred             CcHHHHH------HHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhcc
Confidence            4555999      99999999999999999999999999999998866542  568999999999999999999999887


Q ss_pred             CCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCC-cCCCeeEEEecchhHHHhhhhhHHHHHHHHHhC
Q psy1548         207 MSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKL-NLSLLKHFILDECDKMLEQLEMRRDVQEIFRSS  285 (448)
Q Consensus       207 ~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~-~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l  285 (448)
                      . ++++..++|+.....+...+..+ ++|+|+||+++.+++..+.+ .+.+++++|+||||++.+...+...+...+...
T Consensus        79 ~-~~~~~~~~g~~~~~~~~~~~~~~-~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~  156 (555)
T 3tbk_A           79 L-GYNIASISGATSDSVSVQHIIED-NDIIILTPQILVNNLNNGAIPSLSVFTLMIFDECHNTSKNHPYNQIMFRYLDHK  156 (555)
T ss_dssp             T-TCCEEEECTTTGGGSCHHHHHHH-CSEEEECHHHHHHHHHTSSSCCGGGCSEEEETTGGGCSTTCHHHHHHHHHHHHH
T ss_pred             C-CcEEEEEcCCCcchhhHHHHhcC-CCEEEECHHHHHHHHhcCcccccccCCEEEEECccccCCcchHHHHHHHHHHhh
Confidence            7 89999999998776665555554 89999999999999988777 789999999999999987623333333333332


Q ss_pred             -----CCCCeEEEEeccCCcc-----------HHHHHHHhcCCCeEEEEcCcc------cccccceeEEEEE--------
Q psy1548         286 -----PHTKQVMMFSATLSKE-----------IRPVCKKFMHDPMEVYVDDEA------KLTLHGLQQHYVK--------  335 (448)
Q Consensus       286 -----~~~~q~i~~SAT~~~~-----------~~~~~~~~l~~~~~i~~~~~~------~~~~~~i~~~~~~--------  335 (448)
                           .+..|++++|||++..           +..+.. .+..+. +......      .............        
T Consensus       157 ~~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~~~~l~~-~l~~~~-~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~  234 (555)
T 3tbk_A          157 LGESRDPLPQVVGLTASVGVGDAKTAEEAMQHICKLCA-ALDASV-IATVRDNVAELEQVVYKPQKISRKVASRTSNTFK  234 (555)
T ss_dssp             TSSCCSCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHH-HTTCSE-EECCCSCHHHHHTTCCCCCEEEEECCCCSCCHHH
T ss_pred             hccccCCCCeEEEEecCcccCccccHHHHHHHHHHHHH-hcCCee-eeccccCHHHHHhhcCCCceEEEEecCcccChHH
Confidence                 2557999999998542           111111 111111 1110000      0000000000000        


Q ss_pred             --------------------------------------------------------------------------------
Q psy1548         336 --------------------------------------------------------------------------------  335 (448)
Q Consensus       336 --------------------------------------------------------------------------------  335 (448)
                                                                                                      
T Consensus       235 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  314 (555)
T 3tbk_A          235 CIISQLMKETEKLAKDVSEELGKLFQIQNREFGTQKYEQWIVGVHKACSVFQMADKEEESRVCKALFLYTSHLRKYNDAL  314 (555)
T ss_dssp             HHHHHHHHHHHHHHHTSCHHHHGGGGCCSCCSSSHHHHHHHHHHHHHHHTCCCSSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhhhhcccccccchhhhHHHHHHHHHhhhhhccchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence                                                                                            


Q ss_pred             ----------------------------------------------------cCcchHHHHHHHHHhh----CCCCeEEE
Q psy1548         336 ----------------------------------------------------LKENEKNKKLFELLDV----LEFNQVVI  359 (448)
Q Consensus       336 ----------------------------------------------------~~~~~k~~~L~~ll~~----~~~~~~II  359 (448)
                                                                          .....|...|.+++..    ...+++||
T Consensus       315 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~k~lV  394 (555)
T 3tbk_A          315 IISEDAQMTDALNYLKAFFHDVREAAFDETERELTRRFEEKLEELEKVSRDPSNENPKLRDLYLVLQEEYHLKPETKTIL  394 (555)
T ss_dssp             HHHHHSCHHHHHHHHHHHHHHHCC-----HHHHHHHHHHTTHHHHHHHHHCGGGCCHHHHHHHHHHHHHHHHCTTCCEEE
T ss_pred             hhhhhhhHHHHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhccCCCcCCHHHHHHHHHHHHHhccCCCceEEE
Confidence                                                                0013466666666654    35689999


Q ss_pred             EECccHHHHHHHHHHHhCC------------CcEEEEeCCCCHHHHHHHHHHHhc-CCCceEEEEecChhhHHHHHHHHH
Q psy1548         360 FVKSVTRCIALSTLLSEQN------------FPAVSIHRGMTQEERLKKYQEFKD-FHKGLAITFASDENDAKILNNVQD  426 (448)
Q Consensus       360 F~~s~~~a~~l~~~L~~~g------------~~~~~lh~~~~~~eR~~~l~~F~~-g~~g~~I~~~t~~~d~~~l~~i~~  426 (448)
                      ||+++..++.++..|++.|            .....+||+|++++|.++++.|++ |+.  .|+++|+...+++  ++..
T Consensus       395 F~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~--~vLvaT~~~~~Gl--Dlp~  470 (555)
T 3tbk_A          395 FVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDN--NILIATSVADEGI--DIAE  470 (555)
T ss_dssp             ECSSHHHHHHHHHHHHHCGGGTTCCEEECCC--------------------------CC--SEEEECCCTTCCE--ETTS
T ss_pred             EeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHhcCCCe--eEEEEcchhhcCC--cccc
Confidence            9999999999999999863            345556679999999999999999 773  5667776543333  3333


Q ss_pred             HhcCCCCCCCccccccccccCC
Q psy1548         427 RFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       427 ~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      .-.+-..++|.+...+.++.||
T Consensus       471 v~~VI~~d~p~s~~~~~Qr~GR  492 (555)
T 3tbk_A          471 CNLVILYEYVGNVIKMIQTRGR  492 (555)
T ss_dssp             CSEEEEESCCSSCCCEECSSCC
T ss_pred             CCEEEEeCCCCCHHHHHHhcCc
Confidence            3335566778899999999998

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=100.00  E-value=8.9e-33  Score=304.32  Aligned_cols=263  Identities=20%  Similarity=0.201  Sum_probs=206.9

Q ss_pred             CCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhc
Q psy1548         126 PEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK  205 (448)
Q Consensus       126 p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  205 (448)
                      |..+++||.+      +++.+..|+++++++|||+|||++|.+|++..+..   +.++||++|+++|+.|+++.+..+..
T Consensus        84 ~f~L~~~Q~e------ai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~---g~rvL~l~PtkaLa~Q~~~~l~~~~~  154 (1010)
T 2xgj_A           84 PFTLDPFQDT------AISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN---KQRVIYTSPIKALSNQKYRELLAEFG  154 (1010)
T ss_dssp             SSCCCHHHHH------HHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHT---TCEEEEEESSHHHHHHHHHHHHHHHS
T ss_pred             CCCCCHHHHH------HHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhcc---CCeEEEECChHHHHHHHHHHHHHHhC
Confidence            3345556999      99999999999999999999999999999887743   45899999999999999999998763


Q ss_pred             cCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhC
Q psy1548         206 YMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSS  285 (448)
Q Consensus       206 ~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l  285 (448)
                           +++.++|+.....        .++|+|+||++|.+++.++...+.+++++||||||++.++ ++...+..++..+
T Consensus       155 -----~vglltGd~~~~~--------~~~IvV~Tpe~L~~~L~~~~~~l~~l~lVViDEaH~l~d~-~rg~~~e~il~~l  220 (1010)
T 2xgj_A          155 -----DVGLMTGDITINP--------DAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDK-ERGVVWEETIILL  220 (1010)
T ss_dssp             -----CEEEECSSCEECT--------TCSEEEEEHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCT-TTHHHHHHHHHHS
T ss_pred             -----CEEEEeCCCccCC--------CCCEEEEcHHHHHHHHHcCcchhhcCCEEEEechhhhccc-chhHHHHHHHHhc
Confidence                 6788888876542        3789999999999999887778899999999999999987 8888999999999


Q ss_pred             CCCCeEEEEeccCCccH--HHHHHHhcCCCeEEEEcCcccccccceeEEEEEcC---------c----------------
Q psy1548         286 PHTKQVMMFSATLSKEI--RPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLK---------E----------------  338 (448)
Q Consensus       286 ~~~~q~i~~SAT~~~~~--~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~---------~----------------  338 (448)
                      ++..|++++|||+++..  ..++......+..+.....   .+..+.++++...         .                
T Consensus       221 ~~~~~il~LSATi~n~~e~a~~l~~~~~~~~~vi~~~~---rp~pl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  297 (1010)
T 2xgj_A          221 PDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNF---RPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASI  297 (1010)
T ss_dssp             CTTCEEEEEECCCTTHHHHHHHHHHHHTSCEEEEEECC---CSSCEEEEEEETTSSCCEEEECTTCCBCHHHHHHHHHTC
T ss_pred             CCCCeEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCC---CcccceEEEEecCCcceeeeeccccccchHHHHHHHHHH
Confidence            99999999999998752  2334444455666554433   1233444443311         0                


Q ss_pred             ------------------------------chHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCc--------
Q psy1548         339 ------------------------------NEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFP--------  380 (448)
Q Consensus       339 ------------------------------~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~--------  380 (448)
                                                    ......+...+......++||||+++..|+.++..|.+.++.        
T Consensus       298 ~~~~~~~~~~~~~~g~~~~~~k~~~~~~~~~~~l~~l~~~l~~~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i  377 (1010)
T 2xgj_A          298 SNQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEAL  377 (1010)
T ss_dssp             C------------------------------CHHHHHHHHHHHHTCCSEEEEESSHHHHHHHHHTTTTSCCCCHHHHHHH
T ss_pred             hhhhcccccccccccccccccccccccccchHHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCChHHHHHH
Confidence                                          111223444444445568999999999999999999875543        


Q ss_pred             -------------------------------EEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChh
Q psy1548         381 -------------------------------AVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDEN  416 (448)
Q Consensus       381 -------------------------------~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~  416 (448)
                                                     +..+||+|++.+|..+++.|++|.  +.|+++|+..
T Consensus       378 ~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gI~~~Hggl~~~eR~~ve~~F~~G~--ikVLVAT~~l  442 (1010)
T 2xgj_A          378 TKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGF--LKVLFATETF  442 (1010)
T ss_dssp             HHHHHHHHTTSCGGGTTCHHHHHHHHHHHHTEEEESTTSCHHHHHHHHHHHHTTC--CSEEEEEGGG
T ss_pred             HHHHHHHHHhcchhhhcchhHHHHHHHHhCCeeEECCCCCHHHHHHHHHHHhcCC--CcEEEEehHh
Confidence                                           789999999999999999999987  5677777653

>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=100.00  E-value=5.2e-33  Score=298.48  Aligned_cols=282  Identities=15%  Similarity=0.161  Sum_probs=215.2

Q ss_pred             CcccCC--CCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          81 GFRDFL--LKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        81 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      .|++++  +++.+.+++.+.|                       |..|+++   |.+      +++.+..|+++++++||
T Consensus         2 ~f~~l~~~l~~~~~~~l~~~g-----------------------~~~l~~~---Q~~------~i~~i~~~~~~lv~apT   49 (702)
T 2p6r_A            2 KVEELAESISSYAVGILKEEG-----------------------IEELFPP---QAE------AVEKVFSGKNLLLAMPT   49 (702)
T ss_dssp             CSHHHHHHHHHHHHHHHHCC--------------------------CCCCC---CHH------HHHHHTTCSCEEEECSS
T ss_pred             chhhhhhccCHHHHHHHHhCC-----------------------CCCCCHH---HHH------HHHHHhCCCcEEEEcCC
Confidence            577888  9999999999999                       9999999   999      99999999999999999


Q ss_pred             CChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEE
Q psy1548         159 GMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVG  238 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~  238 (448)
                      |||||++|.+|++..+..   +.+++|++|+++|+.|+.+.++.+.. . +++++.++|+.......  +  +.++|+|+
T Consensus        50 GsGKT~~~~l~il~~~~~---~~~~l~i~P~r~La~q~~~~~~~~~~-~-g~~v~~~~G~~~~~~~~--~--~~~~Iiv~  120 (702)
T 2p6r_A           50 AAGKTLLAEMAMVREAIK---GGKSLYVVPLRALAGEKYESFKKWEK-I-GLRIGISTGDYESRDEH--L--GDCDIIVT  120 (702)
T ss_dssp             HHHHHHHHHHHHHHHHHT---TCCEEEEESSHHHHHHHHHHHTTTTT-T-TCCEEEECSSCBCCSSC--S--TTCSEEEE
T ss_pred             ccHHHHHHHHHHHHHHHh---CCcEEEEeCcHHHHHHHHHHHHHHHh-c-CCEEEEEeCCCCcchhh--c--cCCCEEEE
Confidence            999999999999987653   45899999999999999999865543 3 78999999987654431  1  24899999


Q ss_pred             cHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhC---CCCCeEEEEeccCCccHHHHHHHhcCCCeE
Q psy1548         239 TPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSS---PHTKQVMMFSATLSKEIRPVCKKFMHDPME  315 (448)
Q Consensus       239 Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l---~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~  315 (448)
                      ||+++..++.+....+++++++|+||+|.+.++ ++...+..++..+   .+..|++++|||+++ ..++..++ ..+. 
T Consensus       121 Tpe~l~~~l~~~~~~l~~~~~vIiDE~H~l~~~-~r~~~~~~ll~~l~~~~~~~~ii~lSATl~n-~~~~~~~l-~~~~-  196 (702)
T 2p6r_A          121 TSEKADSLIRNRASWIKAVSCLVVDEIHLLDSE-KRGATLEILVTKMRRMNKALRVIGLSATAPN-VTEIAEWL-DADY-  196 (702)
T ss_dssp             EHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCT-TTHHHHHHHHHHHHHHCTTCEEEEEECCCTT-HHHHHHHT-TCEE-
T ss_pred             CHHHHHHHHHcChhHHhhcCEEEEeeeeecCCC-CcccHHHHHHHHHHhcCcCceEEEECCCcCC-HHHHHHHh-CCCc-
Confidence            999999999987777899999999999999886 7777777766554   578999999999986 45555544 3221 


Q ss_pred             EEEcCcccccccceeEEEE------EcCc-------chHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhC-----
Q psy1548         316 VYVDDEAKLTLHGLQQHYV------KLKE-------NEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQ-----  377 (448)
Q Consensus       316 i~~~~~~~~~~~~i~~~~~------~~~~-------~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~-----  377 (448)
                      +....    .+..+...+.      ....       ..+...+.+.+.  .++++||||++++.|+.++..|.+.     
T Consensus       197 ~~~~~----r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~  270 (702)
T 2p6r_A          197 YVSDW----RPVPLVEGVLCEGTLELFDGAFSTSRRVKFEELVEECVA--ENGGVLVFESTRRGAEKTAVKLSAITAKYV  270 (702)
T ss_dssp             EECCC----CSSCEEEEEECSSEEEEEETTEEEEEECCHHHHHHHHHH--TTCCEEEECSSHHHHHHHHHHHHHHHHTTC
T ss_pred             ccCCC----CCccceEEEeeCCeeeccCcchhhhhhhhHHHHHHHHHh--cCCCEEEEcCCHHHHHHHHHHHHHHHHhhc
Confidence            11111    1111221111      0111       115566666654  4679999999999999999998753     


Q ss_pred             -------------------------CCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         378 -------------------------NFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       378 -------------------------g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                                               +..+.++||+|++++|..+++.|++|+  +.|.++|+.
T Consensus       271 ~~~~~~~~i~~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~f~~g~--~~vlvaT~~  331 (702)
T 2p6r_A          271 ENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGN--IKVVVATPT  331 (702)
T ss_dssp             CCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHHTTS--CCEEEECST
T ss_pred             ChHHHHHHHHhhccccccHHHHHHHhcCeEEecCCCCHHHHHHHHHHHHCCC--CeEEEECcH
Confidence                                     235788999999999999999999987  466666664

>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=99.98  E-value=2e-32  Score=297.73  Aligned_cols=311  Identities=18%  Similarity=0.199  Sum_probs=191.7

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCC--CeEEEEeeccHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDS--NVYVLVMCHTRELAFQISKEY  200 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~--~~~~lil~Pt~~L~~q~~~~~  200 (448)
                      +..|+++   |.+      +++.++.|+++++++|||+|||++|++|++..+...+.  +.++|||+|+++|+.|+.+.+
T Consensus       246 ~~~l~~~---Q~~------~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~~L~~Q~~~~~  316 (797)
T 4a2q_A          246 TKKARSY---QIE------LAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVF  316 (797)
T ss_dssp             --CCCHH---HHH------HHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHH
T ss_pred             CCCCCHH---HHH------HHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHH
Confidence            5556665   999      99999999999999999999999999999998866532  568999999999999999999


Q ss_pred             HHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCC-cCCCeeEEEecchhHHHhhhhhHHHHH
Q psy1548         201 ERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKL-NLSLLKHFILDECDKMLEQLEMRRDVQ  279 (448)
Q Consensus       201 ~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~-~~~~i~~lViDEah~l~~~~~~~~~~~  279 (448)
                      +++.... ++++..++|+.....+...+..+ ++|+|+||+++.+.+..+.+ .+.++++||+||||++.....+...+.
T Consensus       317 ~~~~~~~-~~~v~~~~g~~~~~~~~~~~~~~-~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEaH~~~~~~~~~~i~~  394 (797)
T 4a2q_A          317 KHHFERQ-GYSVQGISGENFSNVSVEKVIED-SDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMT  394 (797)
T ss_dssp             HHHHGGG-TCCEEEECCC-----CHHHHHHT-CSEEEECHHHHHHHHHSSSCCCGGGCSEEEETTGGGCSTTSHHHHHHH
T ss_pred             HHhcccC-CceEEEEeCCcchhhhHHHhhCC-CCEEEEchHHHHHHHHhccccccccCCEEEEECccccCCCccHHHHHH
Confidence            9998877 89999999998776666666554 89999999999999988777 789999999999999877523333333


Q ss_pred             HHHHh----CCCCCeEEEEeccCCc-----------cHHHHHH------------------HhcCCCeEEEEcCcccccc
Q psy1548         280 EIFRS----SPHTKQVMMFSATLSK-----------EIRPVCK------------------KFMHDPMEVYVDDEAKLTL  326 (448)
Q Consensus       280 ~i~~~----l~~~~q~i~~SAT~~~-----------~~~~~~~------------------~~l~~~~~i~~~~~~~~~~  326 (448)
                      .++..    ..+..|++++|||++.           .+..++.                  .++..|.............
T Consensus       395 ~~~~~~~~~~~~~~~~l~lSATp~~~~~~~~~~~~~~i~~l~~~L~~~~i~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~  474 (797)
T 4a2q_A          395 RYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHN  474 (797)
T ss_dssp             HHHHHHHTTCCCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHHTCSEEECCCTTHHHHHHHSCCCCCEEEECCCCSCC
T ss_pred             HHHHHhhccCCCCCeEEEEcCCccccccccHHHHHHHHHHHHHhcCCcEEecccccHHHHHHhcCCCceEEEecCCCCCc
Confidence            33332    2556899999999852           1222221                  1222222111100000000


Q ss_pred             c-----------------------c---eeEEEE-------E--------------------------------------
Q psy1548         327 H-----------------------G---LQQHYV-------K--------------------------------------  335 (448)
Q Consensus       327 ~-----------------------~---i~~~~~-------~--------------------------------------  335 (448)
                      .                       .   +....+       +                                      
T Consensus       475 ~~~~~~~~l~~~i~~~~~~~~~l~~l~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~  554 (797)
T 4a2q_A          475 PFAAIISNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYND  554 (797)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC------------CCSSHHHHHHHHHHHHHHHHCCCSSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhHHhhhhccccccchhHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHH
Confidence            0                       0   000000       0                                      


Q ss_pred             ------------------------------------------------------cCcchHHHHHHHHHhh----CCCCeE
Q psy1548         336 ------------------------------------------------------LKENEKNKKLFELLDV----LEFNQV  357 (448)
Q Consensus       336 ------------------------------------------------------~~~~~k~~~L~~ll~~----~~~~~~  357 (448)
                                                                            .....|...|..++..    ..+.++
T Consensus       555 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~lL~~~~~~~~~~kv  634 (797)
T 4a2q_A          555 ALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRT  634 (797)
T ss_dssp             HHHHHHHSCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHTTHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHHCSSCCE
T ss_pred             HHhhhccccHHHHHHHHHHHHHHHhccCccHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHHHhccCCCCeE
Confidence                                                                  0013366666666654    456899


Q ss_pred             EEEECccHHHHHHHHHHHhC------------CCcEEEEeCCCCHHHHHHHHHHHhc-CCCceEEEEecChhhHHHHHHH
Q psy1548         358 VIFVKSVTRCIALSTLLSEQ------------NFPAVSIHRGMTQEERLKKYQEFKD-FHKGLAITFASDENDAKILNNV  424 (448)
Q Consensus       358 IIF~~s~~~a~~l~~~L~~~------------g~~~~~lh~~~~~~eR~~~l~~F~~-g~~g~~I~~~t~~~d~~~l~~i  424 (448)
                      ||||+++..++.++..|++.            |..+..+||+|++.+|.++++.|++ |+  +.|+++|+....++  ++
T Consensus       635 LIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~~~g~--~~vLVaT~~~~~GI--Dl  710 (797)
T 4a2q_A          635 LLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKD--NRLLIATSVADEGI--DI  710 (797)
T ss_dssp             EEEESSHHHHHHHHHHHHTCSTTCSCCCEEC----------------------------C--CSEEEEECC---------
T ss_pred             EEEECcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhhccCC--ceEEEEcCchhcCC--Cc
Confidence            99999999999999999873            6667788999999999999999999 77  45778887655555  55


Q ss_pred             HHHhcCCCCCCCccccccccccCC
Q psy1548         425 QDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       425 ~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      ...-.+-..+.|.+...+.++.||
T Consensus       711 p~v~~VI~yd~p~s~~~~iQr~GR  734 (797)
T 4a2q_A          711 VQCNLVVLYEYSGNVTKMIQVRGR  734 (797)
T ss_dssp             CCCSEEEEESCCSCHHHHHTC---
T ss_pred             hhCCEEEEeCCCCCHHHHHHhcCC
Confidence            555556667788888888899988

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.98  E-value=3.4e-32  Score=299.67  Aligned_cols=264  Identities=16%  Similarity=0.189  Sum_probs=208.0

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .|..++++|.+      +++.++.|+++++++|||+|||++|++|+...+.   .+.++||++|+++|+.|+++.+..+.
T Consensus        36 ~~f~l~~~Q~~------aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~---~g~~vlvl~PtraLa~Q~~~~l~~~~  106 (997)
T 4a4z_A           36 WPFELDTFQKE------AVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHR---NMTKTIYTSPIKALSNQKFRDFKETF  106 (997)
T ss_dssp             CSSCCCHHHHH------HHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHH---TTCEEEEEESCGGGHHHHHHHHHTTC
T ss_pred             CCCCCCHHHHH------HHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHh---cCCeEEEEeCCHHHHHHHHHHHHHHc
Confidence            44556777999      9999999999999999999999999999887653   34589999999999999998888765


Q ss_pred             ccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHh
Q psy1548         205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRS  284 (448)
Q Consensus       205 ~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~  284 (448)
                      .   +++++.++|+.....        .++|+|+||++|.+++......+.++++||+||||++.++ ++...+..++..
T Consensus       107 ~---~~~v~~l~G~~~~~~--------~~~IlV~Tpe~L~~~l~~~~~~l~~l~lvViDEaH~l~d~-~~g~~~e~ii~~  174 (997)
T 4a4z_A          107 D---DVNIGLITGDVQINP--------DANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQ-DRGVVWEEVIIM  174 (997)
T ss_dssp             -----CCEEEECSSCEECT--------TSSEEEEEHHHHHHHHHHTCSGGGGEEEEEECCTTCCCTT-CTTCCHHHHHHH
T ss_pred             C---CCeEEEEeCCCccCC--------CCCEEEECHHHHHHHHHhCchhhcCCCEEEEECccccccc-chHHHHHHHHHh
Confidence            3   678899999876432        3799999999999999887777899999999999999998 899999999999


Q ss_pred             CCCCCeEEEEeccCCccHHHHHHHhc---CCCeEEEEcCcccccccceeEEE----------------------------
Q psy1548         285 SPHTKQVMMFSATLSKEIRPVCKKFM---HDPMEVYVDDEAKLTLHGLQQHY----------------------------  333 (448)
Q Consensus       285 l~~~~q~i~~SAT~~~~~~~~~~~~l---~~~~~i~~~~~~~~~~~~i~~~~----------------------------  333 (448)
                      +++..|++++|||+++.. ++..++.   ..+..+.....   .+..+.+++                            
T Consensus       175 l~~~v~iIlLSAT~~n~~-ef~~~l~~~~~~~~~vi~~~~---r~~pl~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l  250 (997)
T 4a4z_A          175 LPQHVKFILLSATVPNTY-EFANWIGRTKQKNIYVISTPK---RPVPLEINIWAKKELIPVINQNSEFLEANFRKHKEIL  250 (997)
T ss_dssp             SCTTCEEEEEECCCTTHH-HHHHHHHHHHTCCEEEEECSS---CSSCEEEEEEETTEEEEEECTTCCBCHHHHHHHHHHH
T ss_pred             cccCCCEEEEcCCCCChH-HHHHHHhcccCCceEEEecCC---CCccceEEEecCCcchhcccchhhhhHHHHHHHHHHh
Confidence            999999999999998653 4444432   12222222111   011111111                            


Q ss_pred             -----------------------------------------------------------------EEcCcchHHHHHHHH
Q psy1548         334 -----------------------------------------------------------------VKLKENEKNKKLFEL  348 (448)
Q Consensus       334 -----------------------------------------------------------------~~~~~~~k~~~L~~l  348 (448)
                                                                                       .......+...+...
T Consensus       251 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rg~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~  330 (997)
T 4a4z_A          251 NGESAKGAPSKTDNGRGGSTARGGRGGSNTRDGRGGRGNSTRGGANRGGSRGAGAIGSNKRKFFTQDGPSKKTWPEIVNY  330 (997)
T ss_dssp             C-----------------------------------------------------------------CCCCTTHHHHHHHH
T ss_pred             hccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhHHHHHHHH
Confidence                                                                             111233456677778


Q ss_pred             HhhCCCCeEEEEECccHHHHHHHHHHHhCCC---------------------------------------cEEEEeCCCC
Q psy1548         349 LDVLEFNQVVIFVKSVTRCIALSTLLSEQNF---------------------------------------PAVSIHRGMT  389 (448)
Q Consensus       349 l~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~---------------------------------------~~~~lh~~~~  389 (448)
                      +......++||||++++.|+.++..|.+.|+                                       .+..+||+|+
T Consensus       331 l~~~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gi~~~H~gl~  410 (997)
T 4a4z_A          331 LRKRELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERGIAVHHGGLL  410 (997)
T ss_dssp             HHHTTCCSEEEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHHHTTTEEEECTTSC
T ss_pred             HHhCCCCCEEEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHhhcCeeeecCCCC
Confidence            8877778999999999999999999987766                                       4799999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         390 QEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       390 ~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                      +.+|..+++.|++|.  +.|+|+|..
T Consensus       411 ~~~R~~v~~~F~~G~--~kVLvAT~~  434 (997)
T 4a4z_A          411 PIVKELIEILFSKGF--IKVLFATET  434 (997)
T ss_dssp             HHHHHHHHHHHHTTC--CSEEEECTH
T ss_pred             HHHHHHHHHHHHCCC--CcEEEEchH
Confidence            999999999999988  577888774

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.97  E-value=1.5e-32  Score=304.83  Aligned_cols=255  Identities=16%  Similarity=0.203  Sum_probs=206.1

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      | .|+++   |++      ++|.++.|+|++++||||||||++|++|++..+   ..++++||++||++|+.|+.+.++.
T Consensus        77 f-~pt~i---Q~~------ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~---~~~~~~Lil~PtreLa~Q~~~~l~~  143 (1104)
T 4ddu_A           77 K-DLTGY---QRL------WAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA---RKGKKSALVFPTVTLVKQTLERLQK  143 (1104)
T ss_dssp             S-CCCHH---HHH------HHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHH---TTTCCEEEEESSHHHHHHHHHHHHT
T ss_pred             C-CCCHH---HHH------HHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHH---hcCCeEEEEechHHHHHHHHHHHHH
Confidence            5 58888   999      999999999999999999999999888888776   3456899999999999999999999


Q ss_pred             hhccCCCceEEEEEcCccc---HHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHH----------
Q psy1548         203 FSKYMSNIKVGVFFGGLPI---QKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKML----------  269 (448)
Q Consensus       203 ~~~~~~~~~v~~~~g~~~~---~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~----------  269 (448)
                      +. .. ++++..++|+.+.   ..+...+..+.++|+|+||++|.+++..  +.+.++++||+||||++.          
T Consensus       144 l~-~~-~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~--l~~~~l~~lViDEaH~l~~~~r~~Dr~L  219 (1104)
T 4ddu_A          144 LA-DE-KVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASRNIDTLL  219 (1104)
T ss_dssp             TS-CT-TSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH--HHTSCCSEEEESCHHHHTTSSHHHHHHH
T ss_pred             hh-CC-CCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh--hcccCcCEEEEeCCCccccccccchhhh
Confidence            77 44 8999999999987   5666777776799999999999887764  667899999999997654          


Q ss_pred             h-hhhhHHH-HHHHHHhCC-----------CCCeEEEEecc-CCccHH-HHHHHhcCCCeEEEEcCcccccccceeEEEE
Q psy1548         270 E-QLEMRRD-VQEIFRSSP-----------HTKQVMMFSAT-LSKEIR-PVCKKFMHDPMEVYVDDEAKLTLHGLQQHYV  334 (448)
Q Consensus       270 ~-~~~~~~~-~~~i~~~l~-----------~~~q~i~~SAT-~~~~~~-~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~  334 (448)
                      + + +|... +..+++.++           ...|+++|||| .|..+. .+...++.    +.+... .....++.+.+.
T Consensus       220 ~~~-gf~~~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l~----i~v~~~-~~~~~~i~~~~~  293 (1104)
T 4ddu_A          220 MMV-GIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRL-VSVARNITHVRI  293 (1104)
T ss_dssp             HTS-SCCHHHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHTC----CCCCBC-CCCCCCEEEEEE
T ss_pred             Hhc-CCCHHHHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhccee----EEeccC-CCCcCCceeEEE
Confidence            4 5 77777 888888877           78999999999 565554 23444433    222222 345667888877


Q ss_pred             EcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEE-EEeCCCCHHHHHHHHHHHhcCCCceEEEEe
Q psy1548         335 KLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAV-SIHRGMTQEERLKKYQEFKDFHKGLAITFA  412 (448)
Q Consensus       335 ~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~-~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~  412 (448)
                      .+   +|...|..++... ++++||||++++.|+.++..|++.|+++. .+||.     |.+ ++.|++|+.  .|+++
T Consensus       294 ~~---~k~~~L~~ll~~~-~~~~LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg~-----rr~-l~~F~~G~~--~VLVa  360 (1104)
T 4ddu_A          294 SS---RSKEKLVELLEIF-RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF-----EKN-FEDFKVGKI--NILIG  360 (1104)
T ss_dssp             SC---CCHHHHHHHHHHH-CSSEEEEESSSHHHHHHHHHHHHTTCCEEESSSSH-----HHH-HHHHHHTSC--SEEEE
T ss_pred             ec---CHHHHHHHHHHhc-CCCEEEEECcHHHHHHHHHHHHhCCCCeeeEecCc-----HHH-HHHHHCCCC--CEEEE
Confidence            66   3556667777663 47999999999999999999999999998 99992     555 999999984  55666

>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=99.97  E-value=2.9e-31  Score=271.31  Aligned_cols=304  Identities=16%  Similarity=0.180  Sum_probs=214.7

Q ss_pred             CchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccC
Q psy1548         128 DSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYM  207 (448)
Q Consensus       128 ~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  207 (448)
                      .+++||.+      +++.++.+ ++++.+|||+|||++++++++..+.  ..+.++||++|+++|+.|+.+.+.++.+..
T Consensus         9 ~l~~~Q~~------~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~--~~~~~~liv~P~~~L~~q~~~~~~~~~~~~   79 (494)
T 1wp9_A            9 QPRIYQEV------IYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLT--KYGGKVLMLAPTKPLVLQHAESFRRLFNLP   79 (494)
T ss_dssp             CCCHHHHH------HHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHH--HSCSCEEEECSSHHHHHHHHHHHHHHBCSC
T ss_pred             CccHHHHH------HHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHh--cCCCeEEEEECCHHHHHHHHHHHHHHhCcc
Confidence            34666999      99999988 9999999999999999999988765  234589999999999999999999987543


Q ss_pred             CCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCC
Q psy1548         208 SNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPH  287 (448)
Q Consensus       208 ~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~  287 (448)
                       ..++..+.|+............  ++|+|+||+.+...+..+.+.+.+++++|+||||++.+. .....+...+....+
T Consensus        80 -~~~v~~~~g~~~~~~~~~~~~~--~~ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~-~~~~~~~~~~~~~~~  155 (494)
T 1wp9_A           80 -PEKIVALTGEKSPEERSKAWAR--AKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGN-YAYVFIAREYKRQAK  155 (494)
T ss_dssp             -GGGEEEECSCSCHHHHHHHHHH--CSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTT-CHHHHHHHHHHHHCS
T ss_pred             -hhheEEeeCCcchhhhhhhccC--CCEEEecHHHHHHHHhcCCcchhhceEEEEECCcccCCC-CcHHHHHHHHHhcCC
Confidence             5688899988775544333332  799999999999999888888899999999999998765 444455555555567


Q ss_pred             CCeEEEEeccCCcc---HHHHHHHhcCCCeEEEEcCcccc----cccceeEEEEE-------------------------
Q psy1548         288 TKQVMMFSATLSKE---IRPVCKKFMHDPMEVYVDDEAKL----TLHGLQQHYVK-------------------------  335 (448)
Q Consensus       288 ~~q~i~~SAT~~~~---~~~~~~~~l~~~~~i~~~~~~~~----~~~~i~~~~~~-------------------------  335 (448)
                      ..+++++|||+...   +..+...+...+..+........    ...........                         
T Consensus       156 ~~~~l~lTaTp~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  235 (494)
T 1wp9_A          156 NPLVIGLTASPGSTPEKIMEVINNLGIEHIEYRSENSPDVRPYVKGIRFEWVRVDLPEIYKEVRKLLREMLRDALKPLAE  235 (494)
T ss_dssp             SCCEEEEESCSCSSHHHHHHHHHHTTCCEEEECCTTSTTTGGGCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEecCCCCCcHHHHHHHHhcChheeeccCCCcHHHHHhcCCCceeEEecCCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence            78999999999754   33344333222111111000000    00000000000                         


Q ss_pred             --------------------------------------------------------------------------------
Q psy1548         336 --------------------------------------------------------------------------------  335 (448)
Q Consensus       336 --------------------------------------------------------------------------------  335 (448)
                                                                                                      
T Consensus       236 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  315 (494)
T 1wp9_A          236 TGLLESSSPDIPKKEVLRAGQIINEEMAKGNHDLRGLLLYHAMALKLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKA  315 (494)
T ss_dssp             HTSSSCCCTTSCHHHHHHHHHHHHHHHTTTCCSTTTHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTCCHH
T ss_pred             hccccccCCCcchhHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHHHhhccccchh
Confidence                                                                                            


Q ss_pred             -----------------------cCcchHHHHHHHHHhh----CCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeC--
Q psy1548         336 -----------------------LKENEKNKKLFELLDV----LEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHR--  386 (448)
Q Consensus       336 -----------------------~~~~~k~~~L~~ll~~----~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~--  386 (448)
                                             .....|...+.+++..    ..++++||||+++..++.+++.|++.|+++..+||  
T Consensus       316 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~  395 (494)
T 1wp9_A          316 SKEIFSDKRMKKAISLLVQAKEIGLDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQA  395 (494)
T ss_dssp             HHHHHTSHHHHHHHHHHHHHHHHTCSCHHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSS
T ss_pred             hhhhhhhHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhccCCCCeEEEEEccHHHHHHHHHHHHHcCCCcEEEeccc
Confidence                                   0233466777777766    46789999999999999999999999999999999  


Q ss_pred             ------CCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         387 ------GMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       387 ------~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                            +|+..+|.++++.|++|+  ..|+++|+....++  ++...-.+-..+.|.+...+.++.||
T Consensus       396 ~~~~~~~~~~~~r~~~~~~F~~~~--~~vLv~T~~~~~Gl--dl~~~~~Vi~~d~~~~~~~~~Qr~GR  459 (494)
T 1wp9_A          396 SKENDRGLSQREQKLILDEFARGE--FNVLVATSVGEEGL--DVPEVDLVVFYEPVPSAIRSIQRRGR  459 (494)
T ss_dssp             CC-------CCHHHHHHHHHHHTS--CSEEEECGGGGGGG--GSTTCCEEEESSCCHHHHHHHHHHTT
T ss_pred             cccccccCCHHHHHHHHHHHhcCC--ceEEEECCccccCC--CchhCCEEEEeCCCCCHHHHHHHHhh
Confidence                  999999999999999988  45666665433332  23222223344556556666777776

>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=99.97  E-value=3.7e-32  Score=286.33  Aligned_cols=301  Identities=19%  Similarity=0.220  Sum_probs=223.4

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      | .|+++   |..      ++|.++.|+  |..++||+|||++|.+|++.....   +..++||+||++||.|+.+++..
T Consensus        82 ~-~pt~V---Q~~------~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL~---g~~vlVltptreLA~qd~e~~~~  146 (844)
T 1tf5_A           82 M-FPFKV---QLM------GGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALT---GKGVHVVTVNEYLASRDAEQMGK  146 (844)
T ss_dssp             C-CCCHH---HHH------HHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTT---SSCEEEEESSHHHHHHHHHHHHH
T ss_pred             C-CCcHH---HHH------hhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHc---CCCEEEEeCCHHHHHHHHHHHHH
Confidence            8 99999   999      999999999  999999999999999999854332   45799999999999999999999


Q ss_pred             hhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHH-HHHHHCC------CCcCCCeeEEEecchhHHH-hh---
Q psy1548         203 FSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRI-LALVRNK------KLNLSLLKHFILDECDKML-EQ---  271 (448)
Q Consensus       203 ~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l-~~~l~~~------~~~~~~i~~lViDEah~l~-~~---  271 (448)
                      +...+ ++++++++||.+...+...  . .++|+||||++| .+++...      .+.++.+.++|+||||.|+ +.   
T Consensus       147 l~~~l-gl~v~~i~gg~~~~~r~~~--~-~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mLiDea~t  222 (844)
T 1tf5_A          147 IFEFL-GLTVGLNLNSMSKDEKREA--Y-AADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEART  222 (844)
T ss_dssp             HHHHT-TCCEEECCTTSCHHHHHHH--H-HSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTC
T ss_pred             HHhhc-CCeEEEEeCCCCHHHHHHh--c-CCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhhhhcccc
Confidence            99998 9999999999875544333  2 389999999999 6666532      3567899999999999998 43   


Q ss_pred             -----------hhhHHHHHHHHHhCC---------CCCeEE-----------------EEeccCCcc---HHHHH--HHh
Q psy1548         272 -----------LEMRRDVQEIFRSSP---------HTKQVM-----------------MFSATLSKE---IRPVC--KKF  309 (448)
Q Consensus       272 -----------~~~~~~~~~i~~~l~---------~~~q~i-----------------~~SAT~~~~---~~~~~--~~~  309 (448)
                                 .+|...+..++..++         +.+|++                 ++|||++..   +...+  ..+
T Consensus       223 plIisg~~~~~~~~~~~i~~iv~~l~~~~~y~vd~k~rq~~lt~~g~~~~e~~~~i~~Lfsat~~~~~~~i~~al~A~~l  302 (844)
T 1tf5_A          223 PLIISGQAAKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVA  302 (844)
T ss_dssp             EEEEEEEEECCCHHHHHHHHHHTTCCSSSSBCCCSSSCCCCBCHHHHHHHHHHTTCSCTTSGGGHHHHHHHHHHHHHHHT
T ss_pred             chhhcCCcccchhHHHHHHHHHHhCcccccceeccccceEEecHHHHHHHHHHhCccccCCCccchhHHHHHHHHHHHHH
Confidence                       037889999999997         367887                 899998643   32222  222


Q ss_pred             cC-CC--e-----EEEEcCcc----------------------------ccccccee-----------------------
Q psy1548         310 MH-DP--M-----EVYVDDEA----------------------------KLTLHGLQ-----------------------  330 (448)
Q Consensus       310 l~-~~--~-----~i~~~~~~----------------------------~~~~~~i~-----------------------  330 (448)
                      +. ++  +     .+.++...                            ..+..++.                       
T Consensus       303 ~~~d~dYiv~dg~v~ivDe~tgr~m~grr~sdGLhqaieake~v~I~~e~~t~a~It~q~~fr~y~kl~GmTGTa~te~~  382 (844)
T 1tf5_A          303 MQKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMTGTAKTEEE  382 (844)
T ss_dssp             CCBTTTEEEETTEEEEBCTTTCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEEEHHHHHTTSSEEEEEESCCGGGHH
T ss_pred             hhcCCceEEecCeeEEeecccccccCCCccchhhHHHHhhcccceecccccccceeeHHHHHHHHhhhccCCcccchhHH
Confidence            22 11  1     11111000                            00000111                       


Q ss_pred             ------------------------EEEEEcCcchHHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhCCCcEEEE
Q psy1548         331 ------------------------QHYVKLKENEKNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSI  384 (448)
Q Consensus       331 ------------------------~~~~~~~~~~k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~l  384 (448)
                                              +.++.+...+|...+...+...  .+.++||||+|++.++.|+..|++.|+++..+
T Consensus       383 e~~~iY~l~vv~IPtn~p~~r~d~~d~v~~~~~~K~~al~~~i~~~~~~~~pvLVft~s~~~se~Ls~~L~~~gi~~~vL  462 (844)
T 1tf5_A          383 EFRNIYNMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVL  462 (844)
T ss_dssp             HHHHHHCCCEEECCCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEE
T ss_pred             HHHHHhCCceEEecCCCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEe
Confidence                                    1245566778999998887642  45689999999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHH--------HHhcCCCCCCCccccccccccCC
Q psy1548         385 HRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQ--------DRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       385 h~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~--------~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      ||++.+.+|..+.+.|+.   | .|+++|+-.-+++  +|.        ..+.+-..++|.+...+.++.||
T Consensus       463 hg~~~~rEr~ii~~ag~~---g-~VlIATdmAgRG~--DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~GR  528 (844)
T 1tf5_A          463 NAKNHEREAQIIEEAGQK---G-AVTIATNMAGRGT--DIKLGEGVKELGGLAVVGTERHESRRIDNQLRGR  528 (844)
T ss_dssp             CSSCHHHHHHHHTTTTST---T-CEEEEETTSSTTC--CCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTT
T ss_pred             eCCccHHHHHHHHHcCCC---C-eEEEeCCccccCc--CccccchhhhcCCcEEEEecCCCCHHHHHhhcCc
Confidence            999988888766655544   3 5788887443332  333        33456677889988888888887

>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=99.97  E-value=2.1e-31  Score=293.16  Aligned_cols=311  Identities=18%  Similarity=0.204  Sum_probs=189.9

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCC--CeEEEEeeccHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDS--NVYVLVMCHTRELAFQISKEY  200 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~--~~~~lil~Pt~~L~~q~~~~~  200 (448)
                      +..|+++   |.+      +++.++.|+++++++|||+|||++|++|++..+.....  +.++|||+|+++|+.|+.+.+
T Consensus       246 ~~~~r~~---Q~~------ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~  316 (936)
T 4a2w_A          246 TKKARSY---QIE------LAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVF  316 (936)
T ss_dssp             --CCCHH---HHH------HHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHH
T ss_pred             CCCCCHH---HHH------HHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHH
Confidence            4455555   999      99999999999999999999999999999988765431  568999999999999999999


Q ss_pred             HHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCC-cCCCeeEEEecchhHHHhhhhhHHHHH
Q psy1548         201 ERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKL-NLSLLKHFILDECDKMLEQLEMRRDVQ  279 (448)
Q Consensus       201 ~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~-~~~~i~~lViDEah~l~~~~~~~~~~~  279 (448)
                      +++.... ++++..++|+.....+...+..+ ++|+|+||++|.+.+..+.+ .+.++++||+||||++.....+...+.
T Consensus       317 ~~~~~~~-~~~v~~~~G~~~~~~~~~~~~~~-~~IvI~Tp~~L~~~l~~~~~~~l~~~~liViDEaH~~~~~~~~~~i~~  394 (936)
T 4a2w_A          317 KHHFERQ-GYSVQGISGENFSNVSVEKVIED-SDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMT  394 (936)
T ss_dssp             HHHHHTT-TCCEEEECCC-----CCHHHHHH-CSEEEECHHHHHHHHHSSSCCCGGGCSEEEEETGGGCSTTCHHHHHHH
T ss_pred             HHHhccc-CceEEEEECCcchhhHHHHhccC-CCEEEecHHHHHHHHHcCccccccCCCEEEEECccccCCCccHHHHHH
Confidence            9998876 89999999998766554444443 89999999999999988776 788999999999999877623333333


Q ss_pred             HHHHh----CCCCCeEEEEeccCCc-----------cHHHHH------------------HHhcCCCeEEEEcCcccccc
Q psy1548         280 EIFRS----SPHTKQVMMFSATLSK-----------EIRPVC------------------KKFMHDPMEVYVDDEAKLTL  326 (448)
Q Consensus       280 ~i~~~----l~~~~q~i~~SAT~~~-----------~~~~~~------------------~~~l~~~~~i~~~~~~~~~~  326 (448)
                      .++..    ..+..|++++|||++.           .+..++                  ..+...|.............
T Consensus       395 ~~~~~~~~~~~~~~~~l~LSATp~~~~~~~l~~~~~~i~~L~~~L~~~~i~~~~~~~~~l~~~~~~p~~~~~~~~~~~~~  474 (936)
T 4a2w_A          395 RYLEQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHN  474 (936)
T ss_dssp             HHHHHHHTTCSCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHHTCSEEECCCSSHHHHHHHSCCCCEEEEECCCCSCC
T ss_pred             HHHHHhhccCCCcCeEEEecCCcccccchhHHHHHHHHHHHHHhcCCceeecccccHHHHHHhccCCcceEEecccccCc
Confidence            33332    2456899999999852           111222                  12222332222111100000


Q ss_pred             -----------------------cc---eeEEEEE---------------------------------------------
Q psy1548         327 -----------------------HG---LQQHYVK---------------------------------------------  335 (448)
Q Consensus       327 -----------------------~~---i~~~~~~---------------------------------------------  335 (448)
                                             ..   +....+.                                             
T Consensus       475 ~~~~~l~~l~~~i~~~~~~~l~~~~l~~~~~~~~g~~~y~~~l~~l~k~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~~~  554 (936)
T 4a2w_A          475 PFAAIISNLMSETEALMRTIAYVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYND  554 (936)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC------------CCSSHHHHHHHHHHHHHHHHCCCSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhhhhhccccccchHHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHH
Confidence                                   00   0000000                                             


Q ss_pred             ------------------------------------------------------cCcchHHHHHHHHHhh----CCCCeE
Q psy1548         336 ------------------------------------------------------LKENEKNKKLFELLDV----LEFNQV  357 (448)
Q Consensus       336 ------------------------------------------------------~~~~~k~~~L~~ll~~----~~~~~~  357 (448)
                                                                            .....|...|..++..    ..+.++
T Consensus       555 al~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~e~~l~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~lL~~~~~~~~~~rv  634 (936)
T 4a2w_A          555 ALIISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRT  634 (936)
T ss_dssp             HHHHHHHSCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTSTTCCCHHHHHHHHHHHHTTTSCTTCCE
T ss_pred             HHhhhcchhHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHhhhccCCCCHHHHHHHHHHHHHhccCCCCeE
Confidence                                                                  0013356666667765    346799


Q ss_pred             EEEECccHHHHHHHHHHHhC------------CCcEEEEeCCCCHHHHHHHHHHHhc-CCCceEEEEecChhhHHHHHHH
Q psy1548         358 VIFVKSVTRCIALSTLLSEQ------------NFPAVSIHRGMTQEERLKKYQEFKD-FHKGLAITFASDENDAKILNNV  424 (448)
Q Consensus       358 IIF~~s~~~a~~l~~~L~~~------------g~~~~~lh~~~~~~eR~~~l~~F~~-g~~g~~I~~~t~~~d~~~l~~i  424 (448)
                      ||||+++..++.++..|++.            |..+..+||+|++.+|.+++++|++ |+  +.|+++|+...+++  ++
T Consensus       635 LIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr~~g~--~~VLVaT~~~~eGI--Dl  710 (936)
T 4a2w_A          635 LLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKD--NRLLIATSVADEGI--DI  710 (936)
T ss_dssp             EEEESSHHHHHHHHHHHHHCSTTSSCCCEEC----------------------------C--CSEEEEECC--------C
T ss_pred             EEEeCCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhhccCC--eeEEEEeCchhcCC--cc
Confidence            99999999999999999986            6667778999999999999999999 77  45777877655554  44


Q ss_pred             HHHhcCCCCCCCccccccccccCC
Q psy1548         425 QDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       425 ~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      ...--+-+.+.|.+...+.++.||
T Consensus       711 p~v~~VI~yD~p~s~~~~iQr~GR  734 (936)
T 4a2w_A          711 VQCNLVVLYEYSGNVTKMIQVRGR  734 (936)
T ss_dssp             CCCSEEEEESCCSCSHHHHCC---
T ss_pred             hhCCEEEEeCCCCCHHHHHHhcCC
Confidence            444445566778888888888888

>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=99.97  E-value=1.8e-32  Score=304.27  Aligned_cols=252  Identities=15%  Similarity=0.247  Sum_probs=201.2

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      |. | ++   |++      ++|.++.|+|+++++|||||||+ |.+|++..+..  .++++||++||++|+.|+.+.++.
T Consensus        56 ~~-p-~i---Q~~------ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~--~~~~~lil~PtreLa~Q~~~~l~~  121 (1054)
T 1gku_B           56 EP-R-AI---QKM------WAKRILRKESFAATAPTGVGKTS-FGLAMSLFLAL--KGKRCYVIFPTSLLVIQAAETIRK  121 (1054)
T ss_dssp             SC-C-HH---HHH------HHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHT--TSCCEEEEESCHHHHHHHHHHHHH
T ss_pred             CC-H-HH---HHH------HHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhh--cCCeEEEEeccHHHHHHHHHHHHH
Confidence            77 7 77   999      99999999999999999999998 88999887654  356899999999999999999999


Q ss_pred             hhccCCCc----eEEEEEcCcccHHhH---HHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhH
Q psy1548         203 FSKYMSNI----KVGVFFGGLPIQKDE---EYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMR  275 (448)
Q Consensus       203 ~~~~~~~~----~v~~~~g~~~~~~~~---~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~  275 (448)
                      +.... ++    ++..++|+.+...+.   ..+..  ++|+|+||++|.+++.+    +++++++|+||||+|+++   .
T Consensus       122 l~~~~-~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~--~~IlV~TP~~L~~~l~~----L~~l~~lViDEah~~l~~---~  191 (1054)
T 1gku_B          122 YAEKA-GVGTENLIGYYHGRIPKREKENFMQNLRN--FKIVITTTQFLSKHYRE----LGHFDFIFVDDVDAILKA---S  191 (1054)
T ss_dssp             HHTTT-CCSGGGSEEECCSSCCSHHHHHHHHSGGG--CSEEEEEHHHHHHCSTT----SCCCSEEEESCHHHHHTS---T
T ss_pred             HHhhc-CCCccceEEEEeCCCChhhHHHHHhhccC--CCEEEEcHHHHHHHHHH----hccCCEEEEeChhhhhhc---c
Confidence            99877 77    899999998876642   23333  89999999999987765    668999999999999874   4


Q ss_pred             HHHHHHHHhC-----------CCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHH
Q psy1548         276 RDVQEIFRSS-----------PHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKK  344 (448)
Q Consensus       276 ~~~~~i~~~l-----------~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~  344 (448)
                      ..+..++..+           +...|++++|||++.. ..+...++.++..+.+... .....++.+.+.   ..+|...
T Consensus       192 ~~~~~i~~~lgf~~~~~~~~~~~~~q~~l~SAT~t~~-~~~~~~~~~~~~~i~v~~~-~~~~~~i~~~~~---~~~k~~~  266 (1054)
T 1gku_B          192 KNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAK-KGKKAELFRQLLNFDIGSS-RITVRNVEDVAV---NDESIST  266 (1054)
T ss_dssp             HHHHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSC-CCTTHHHHHHHHCCCCSCC-EECCCCEEEEEE---SCCCTTT
T ss_pred             ccHHHHHHHhCcchhhhhhhcccCCceEEEEecCCCc-hhHHHHHhhcceEEEccCc-ccCcCCceEEEe---chhHHHH
Confidence            5666666665           3567899999999887 5444444433333333333 334556777666   3556677


Q ss_pred             HHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEe
Q psy1548         345 LFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFA  412 (448)
Q Consensus       345 L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~  412 (448)
                      |..+++.. ++++||||++++.|+.++..|++. +++..+||+|     .++++.|++|+.  .|+++
T Consensus       267 L~~ll~~~-~~~~LVF~~t~~~a~~l~~~L~~~-~~v~~lhg~~-----~~~l~~F~~G~~--~VLVa  325 (1054)
T 1gku_B          267 LSSILEKL-GTGGIIYARTGEEAEEIYESLKNK-FRIGIVTATK-----KGDYEKFVEGEI--DHLIG  325 (1054)
T ss_dssp             THHHHTTS-CSCEEEEESSHHHHHHHHHTTTTS-SCEEECTTSS-----SHHHHHHHHTSC--SEEEE
T ss_pred             HHHHHhhc-CCCEEEEEcCHHHHHHHHHHHhhc-cCeeEEeccH-----HHHHHHHHcCCC--cEEEE
Confidence            77888766 478999999999999999999998 9999999998     378999999985  45555

>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=99.97  E-value=5.3e-31  Score=276.86  Aligned_cols=301  Identities=19%  Similarity=0.184  Sum_probs=198.7

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .|+++   |..      ++|.++.|+  +..++||+|||++|++|++.....   +.+++|++||++||.|+.+.+..+.
T Consensus        74 ~p~~V---Q~~------~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l~---g~~vlVltPTreLA~Q~~e~~~~l~  139 (853)
T 2fsf_A           74 RHFDV---QLL------GGMVLNERC--IAEMRTGEGKTLTATLPAYLNALT---GKGVHVVTVNDYLAQRDAENNRPLF  139 (853)
T ss_dssp             CCCHH---HHH------HHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTT---SSCCEEEESSHHHHHHHHHHHHHHH
T ss_pred             CCChH---HHh------hcccccCCe--eeeecCCchHHHHHHHHHHHHHHc---CCcEEEEcCCHHHHHHHHHHHHHHH
Confidence            79999   999      999999998  999999999999999999865432   4579999999999999999999999


Q ss_pred             ccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHH-HHHHHCC------CCcCCCeeEEEecchhHHHhh------
Q psy1548         205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRI-LALVRNK------KLNLSLLKHFILDECDKMLEQ------  271 (448)
Q Consensus       205 ~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l-~~~l~~~------~~~~~~i~~lViDEah~l~~~------  271 (448)
                      ..+ ++++++++||.+...  ..+..+ ++|+||||+++ .++++.+      .+.++++.++|+||||.|+..      
T Consensus       140 ~~l-gl~v~~i~GG~~~~~--r~~~~~-~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~mLiD~a~tpL  215 (853)
T 2fsf_A          140 EFL-GLTVGINLPGMPAPA--KREAYA-ADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSILIDEARTPL  215 (853)
T ss_dssp             HHT-TCCEEECCTTCCHHH--HHHHHH-SSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHHHTTTTTTCEE
T ss_pred             Hhc-CCeEEEEeCCCCHHH--HHHhcC-CCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHHHHHhcCcccc
Confidence            998 999999999987543  333333 89999999999 7887654      256789999999999999832      


Q ss_pred             ---------hhhHHHHHHHHHhCCC--------------------CCeEE------------------------EEeccC
Q psy1548         272 ---------LEMRRDVQEIFRSSPH--------------------TKQVM------------------------MFSATL  298 (448)
Q Consensus       272 ---------~~~~~~~~~i~~~l~~--------------------~~q~i------------------------~~SAT~  298 (448)
                               .++...+..++..+++                    .+|++                        ++|||+
T Consensus       216 IiSg~~~~~~~~y~~i~~iv~~L~~~~~~~~~~~~~~~dy~vdek~rqv~lte~g~~~~e~~l~~~~l~~~~~~Lfsat~  295 (853)
T 2fsf_A          216 IISGPAEDSSEMYKRVNKIIPHLIRQEKEDSETFQGEGHFSVDEKSRQVNLTERGLVLIEELLVKEGIMDEGESLYSPAN  295 (853)
T ss_dssp             EEEEC---------------------------------------------------------------------------
T ss_pred             cccCCCccchhHHHHHHHHHHhchhhhccccccccccccceeccccceEEEcHHHHHHHHHHHHhCCcccccccccCccc
Confidence                     1367788888888864                    45654                        899997


Q ss_pred             CccHHHH---H--HHhcC--------CC-----------------------------eEEEEcCcccccccceeE-----
Q psy1548         299 SKEIRPV---C--KKFMH--------DP-----------------------------MEVYVDDEAKLTLHGLQQ-----  331 (448)
Q Consensus       299 ~~~~~~~---~--~~~l~--------~~-----------------------------~~i~~~~~~~~~~~~i~~-----  331 (448)
                      +.-...+   +  ..++.        ++                             ..+.+... ..+..+|.+     
T Consensus       296 ~~~~~~i~~al~A~~l~~~d~dYiV~d~~vviVde~tgR~m~grr~sdGLhQaieake~v~I~~e-~~tla~It~qnyfr  374 (853)
T 2fsf_A          296 IMLMHHVTAALRAHALFTRDVDYIVKDGEVIIVDEHTGRTMQGRRWSDGLHQAVEAKEGVQIQNE-NQTLASITFQNYFR  374 (853)
T ss_dssp             -------------------------------------------------------------CCCC-CEEEEEEEHHHHHT
T ss_pred             chHHHHHHHHHHHHHHhhcCccceeecCcEEEEecccCcccCCCccchhhhHHHHhcccceeccc-ccccceeehHHHHh
Confidence            6421111   1  11111        11                             11222221 112222221     


Q ss_pred             ------------------------------------------EEEEcCcchHHHHHHHHHhh--CCCCeEEEEECccHHH
Q psy1548         332 ------------------------------------------HYVKLKENEKNKKLFELLDV--LEFNQVVIFVKSVTRC  367 (448)
Q Consensus       332 ------------------------------------------~~~~~~~~~k~~~L~~ll~~--~~~~~~IIF~~s~~~a  367 (448)
                                                                .++.+...+|...+...+..  ..+.++||||+|++.+
T Consensus       375 ~Y~kl~GmTGTa~te~~ef~~iY~l~vv~IPtn~p~~R~d~~d~v~~~~~~K~~al~~~i~~~~~~gqpvLVft~sie~s  454 (853)
T 2fsf_A          375 LYEKLAGMTGTADTEAFEFSSIYKLDTVVVPTNRPMIRKDLPDLVYMTEAEKIQAIIEDIKERTAKGQPVLVGTISIEKS  454 (853)
T ss_dssp             TSSEEEEEECTTCCCHHHHHHHHCCEEEECCCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHTTTCCEEEEESSHHHH
T ss_pred             hhhhhhcCCCCchhHHHHHHHHhCCcEEEcCCCCCceeecCCcEEEeCHHHHHHHHHHHHHHHhcCCCCEEEEECcHHHH
Confidence                                                      23556778899999988854  3466899999999999


Q ss_pred             HHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChh----hHHHH----------------------
Q psy1548         368 IALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDEN----DAKIL----------------------  421 (448)
Q Consensus       368 ~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~----d~~~l----------------------  421 (448)
                      +.|+..|++.|+++..+||++.+.+|..+.+.|+.|    .|+++|+-.    |....                      
T Consensus       455 e~Ls~~L~~~gi~~~vLnak~~~rEa~iia~agr~G----~VtIATnmAgRGtDI~l~gn~~~~~~~~~~~~~~~~~~~~  530 (853)
T 2fsf_A          455 ELVSNELTKAGIKHNVLNAKFHANEAAIVAQAGYPA----AVTIATNMAGRGTDIVLGGSWQAEVAALENPTAEQIEKIK  530 (853)
T ss_dssp             HHHHHHHHHTTCCCEECCTTCHHHHHHHHHTTTSTT----CEEEEESCCSSCSCCCTTCCHHHHHHHCSSCCSSHHHHHH
T ss_pred             HHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC----eEEEecccccCCcCccCCCchHhhhhhcccchhHHHHHHH
Confidence            999999999999999999999988888888888776    366666521    21110                      


Q ss_pred             ---HH-HHHH-----hcCCCCCCCccccccccccCC
Q psy1548         422 ---NN-VQDR-----FDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       422 ---~~-i~~~-----~~~~~~~~p~~~~~~~~~~~~  448 (448)
                         .. =+..     +.+-..++|++...+.++.||
T Consensus       531 ~~~~~~~~~V~~~GGl~VI~te~pes~riy~qr~GR  566 (853)
T 2fsf_A          531 ADWQVRHDAVLEAGGLHIIGTERHESRRIDNQLRGR  566 (853)
T ss_dssp             HHHHHHHHHHHHTTSEEEEESSCCSSHHHHHHHHTT
T ss_pred             HHhhhhhhHHHhcCCcEEEEccCCCCHHHHHhhccc
Confidence               00 0112     467788999998888888887

>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=99.97  E-value=6.3e-30  Score=293.40  Aligned_cols=273  Identities=20%  Similarity=0.282  Sum_probs=204.2

Q ss_pred             ccCCCCchhhhhhhccccccceeee-eCcceeeeccCCChhHHHHHHHHHHhhhcc--------CCCeEEEEeeccHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAV-LGMDILCQAKSGMGKTAVFVLATLQQLETT--------DSNVYVLVMCHTRELA  193 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~-~g~~vli~apTGsGKT~~~~l~~l~~l~~~--------~~~~~~lil~Pt~~L~  193 (448)
                      |..++++   |.+      ++|.++ .++|++++||||||||++|.+|+++.+...        ..+.++||++|+++|+
T Consensus        77 ~~~ln~i---Qs~------~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~kALa  147 (1724)
T 4f92_B           77 FKTLNRI---QSK------LYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLV  147 (1724)
T ss_dssp             CSBCCHH---HHH------THHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSSHHHH
T ss_pred             CCCCCHH---HHH------HHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCHHHHH
Confidence            7888899   999      999877 478999999999999999999999988542        2456899999999999


Q ss_pred             HHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCC--CcCCCeeEEEecchhHHHhh
Q psy1548         194 FQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK--LNLSLLKHFILDECDKMLEQ  271 (448)
Q Consensus       194 ~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~--~~~~~i~~lViDEah~l~~~  271 (448)
                      .|+++.+.+..... +++|..++|+.+.....  .  ..++|+|+||+++..++++..  ..+++++++|+||+|.+.+ 
T Consensus       148 ~e~~~~l~~~~~~~-gi~V~~~tGd~~~~~~~--~--~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l~d-  221 (1724)
T 4f92_B          148 QEMVGSFGKRLATY-GITVAELTGDHQLCKEE--I--SATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHD-  221 (1724)
T ss_dssp             HHHHHHHHHHHTTT-TCCEEECCSSCSSCCTT--G--GGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGGGS-
T ss_pred             HHHHHHHHHHHhhC-CCEEEEEECCCCCCccc--c--CCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchhcCC-
Confidence            99999999888777 89999999998754432  1  238999999999977776543  2478999999999996654 


Q ss_pred             hhhHHHHHHHHH-------hCCCCCeEEEEeccCCccHHHHHHHhcCCCe-EEEEcCcccccccceeEEEEEcCcchH--
Q psy1548         272 LEMRRDVQEIFR-------SSPHTKQVMMFSATLSKEIRPVCKKFMHDPM-EVYVDDEAKLTLHGLQQHYVKLKENEK--  341 (448)
Q Consensus       272 ~~~~~~~~~i~~-------~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~-~i~~~~~~~~~~~~i~~~~~~~~~~~k--  341 (448)
                       +.+..++.++.       .+++..|+|++|||+|+ ..++++++..++. .+..... ...+..+.+.++.......  
T Consensus       222 -~RG~~lE~~l~rl~~~~~~~~~~~riI~LSATl~N-~~dvA~wL~~~~~~~~~~~~~-~~RPvpL~~~~~~~~~~~~~~  298 (1724)
T 4f92_B          222 -DRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPN-YEDVATFLRVDPAKGLFYFDN-SFRPVPLEQTYVGITEKKAIK  298 (1724)
T ss_dssp             -TTHHHHHHHHHHHHHHHHHHTCCCEEEEEECSCTT-HHHHHHHTTCCHHHHEEECCG-GGCSSCEEEECCEECCCCHHH
T ss_pred             -ccHHHHHHHHHHHHHHHHhCCCCCcEEEEecccCC-HHHHHHHhCCCCCCCeEEECC-CCccCccEEEEeccCCcchhh
Confidence             55555555443       45788999999999986 4566665544321 1112122 2344567776665554322  


Q ss_pred             -HH----HHHHHHhh-CCCCeEEEEECccHHHHHHHHHHHhC-------------------------------------C
Q psy1548         342 -NK----KLFELLDV-LEFNQVVIFVKSVTRCIALSTLLSEQ-------------------------------------N  378 (448)
Q Consensus       342 -~~----~L~~ll~~-~~~~~~IIF~~s~~~a~~l~~~L~~~-------------------------------------g  378 (448)
                       ..    .+...+.. ...+++||||+|++.|+.+|+.|.+.                                     .
T Consensus       299 ~~~~~~~~~~~~v~~~~~~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~  378 (1724)
T 4f92_B          299 RFQIMNEIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLP  378 (1724)
T ss_dssp             HHHHHHHHHHHHHTTCCSSCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTT
T ss_pred             hhHHHHHHHHHHHHHHhcCCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhh
Confidence             22    22233332 34678999999999999999888531                                     1


Q ss_pred             CcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         379 FPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       379 ~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                      ..+.++||||++++|..+.+.|++|.  +.|.+||+.
T Consensus       379 ~Gva~HHagL~~~~R~~vE~~F~~G~--i~vlvaTsT  413 (1724)
T 4f92_B          379 YGFAIHHAGMTRVDRTLVEDLFADKH--IQVLVSTAT  413 (1724)
T ss_dssp             TTEEEECSSSCTHHHHHHHHHHHTTC--CCEEEECHH
T ss_pred             cCEEEEcCCCCHHHHHHHHHHHHCCC--CeEEEEcch
Confidence            23889999999999999999999998  567777664

>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=99.97  E-value=1.5e-29  Score=290.30  Aligned_cols=286  Identities=17%  Similarity=0.177  Sum_probs=210.6

Q ss_pred             CCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeee-CcceeeeccCCChhHH
Q psy1548          86 LLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVL-GMDILCQAKSGMGKTA  164 (448)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~-g~~vli~apTGsGKT~  164 (448)
                      .+++...+.+...+                       |..++++   |.+      +++.++. ++|++++||||||||+
T Consensus       910 ~L~~~~~e~l~~~~-----------------------f~~fnpi---Q~q------~~~~l~~~~~nvlv~APTGSGKTl  957 (1724)
T 4f92_B          910 ALRNSAFESLYQDK-----------------------FPFFNPI---QTQ------VFNTVYNSDDNVFVGAPTGSGKTI  957 (1724)
T ss_dssp             GSCCHHHHTTTTTT-----------------------CSBCCHH---HHH------HHHHHHSCCSCEEEECCTTSCCHH
T ss_pred             cccCHHHHHHHHhc-----------------------CCCCCHH---HHH------HHHHHhcCCCcEEEEeCCCCCchH
Confidence            35567777887777                       8999999   999      9999865 5789999999999999


Q ss_pred             HHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH-hhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHH
Q psy1548         165 VFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER-FSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRI  243 (448)
Q Consensus       165 ~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~-~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l  243 (448)
                      +|.+|++..+...+ +.++||++|+++|+.|+++.+++ +.... +++++.++|+.....  ..+..  ++|+|+||+++
T Consensus       958 iaelail~~l~~~~-~~kavyi~P~raLa~q~~~~~~~~f~~~~-g~~V~~ltGd~~~~~--~~~~~--~~IiV~TPEkl 1031 (1724)
T 4f92_B          958 CAEFAILRMLLQSS-EGRCVYITPMEALAEQVYMDWYEKFQDRL-NKKVVLLTGETSTDL--KLLGK--GNIIISTPEKW 1031 (1724)
T ss_dssp             HHHHHHHHHHHHCT-TCCEEEECSCHHHHHHHHHHHHHHHTTTS-CCCEEECCSCHHHHH--HHHHH--CSEEEECHHHH
T ss_pred             HHHHHHHHHHHhCC-CCEEEEEcChHHHHHHHHHHHHHHhchhc-CCEEEEEECCCCcch--hhcCC--CCEEEECHHHH
Confidence            99999999887654 34899999999999999998875 55555 889999999875332  22332  79999999999


Q ss_pred             HHHHHCC--CCcCCCeeEEEecchhHHHhhhhhHHHHHHHH-------HhCCCCCeEEEEeccCCccHHHHHHHhcCCCe
Q psy1548         244 LALVRNK--KLNLSLLKHFILDECDKMLEQLEMRRDVQEIF-------RSSPHTKQVMMFSATLSKEIRPVCKKFMHDPM  314 (448)
Q Consensus       244 ~~~l~~~--~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~-------~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~  314 (448)
                      ..++++.  ...+++++++|+||+|.+.+  ..+..++.++       ..+++..|+|++|||+++ ..++.+++...+.
T Consensus      1032 d~llr~~~~~~~l~~v~lvViDE~H~l~d--~rg~~le~il~rl~~i~~~~~~~~riI~lSATl~N-~~dla~WL~~~~~ 1108 (1724)
T 4f92_B         1032 DILSRRWKQRKNVQNINLFVVDEVHLIGG--ENGPVLEVICSRMRYISSQIERPIRIVALSSSLSN-AKDVAHWLGCSAT 1108 (1724)
T ss_dssp             HHHHTTTTTCHHHHSCSEEEECCGGGGGS--TTHHHHHHHHHHHHHHHHTTSSCCEEEEEESCBTT-HHHHHHHHTCCST
T ss_pred             HHHHhCcccccccceeeEEEeechhhcCC--CCCccHHHHHHHHHHHHhhcCCCceEEEEeCCCCC-HHHHHHHhCCCCC
Confidence            8888653  23478999999999998765  3444444443       345678999999999986 4677776654443


Q ss_pred             EEEEcCcccccccceeEEEEEcCcchHH-------HHHHHHH-hhCCCCeEEEEECccHHHHHHHHHHHhC---------
Q psy1548         315 EVYVDDEAKLTLHGLQQHYVKLKENEKN-------KKLFELL-DVLEFNQVVIFVKSVTRCIALSTLLSEQ---------  377 (448)
Q Consensus       315 ~i~~~~~~~~~~~~i~~~~~~~~~~~k~-------~~L~~ll-~~~~~~~~IIF~~s~~~a~~l~~~L~~~---------  377 (448)
                      .+..... ...+..++.++.........       ..+...+ +....+++||||+|++.|+.+|..|...         
T Consensus      1109 ~~~~~~~-~~RPvpL~~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~ 1187 (1724)
T 4f92_B         1109 STFNFHP-NVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQR 1187 (1724)
T ss_dssp             TEEECCG-GGCSSCEEEEEEEECCCSHHHHHHTTHHHHHHHHHHHCSSSCEEEEESSHHHHHHHHHHHHHHHHHTTCTTT
T ss_pred             CeEEeCC-CCCCCCeEEEEEeccCCCchhhhhhhcchHHHHHHHhcCCCCeeeeCCCHHHHHHHHHHHHHHHhhccchhh
Confidence            3332222 23344555555444432221       1222333 3345679999999999999988776421         


Q ss_pred             -------------------------CCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         378 -------------------------NFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       378 -------------------------g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                                               ...+.++||||++++|..+.+.|++|.  +.|++||+.
T Consensus      1188 ~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~hHagL~~~~R~~VE~lF~~G~--i~VLvaT~t 1248 (1724)
T 4f92_B         1188 FLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGA--IQVVVASRS 1248 (1724)
T ss_dssp             TBCSCHHHHHHHHTTCCCHHHHHHHHTTEEEECTTSCHHHHHHHHHHHHHTS--BCEEEEEGG
T ss_pred             hhcccHHHHHHHHhhcccHHHHHHHhCCEEEECCCCCHHHHHHHHHHHHCCC--CeEEEEChH
Confidence                                     224899999999999999999999998  566777664

>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=99.97  E-value=4.3e-32  Score=291.48  Aligned_cols=308  Identities=20%  Similarity=0.232  Sum_probs=199.1

Q ss_pred             CchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccC---CCeEEEEeeccHHHHHHH-HHHHHHh
Q psy1548         128 DSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTD---SNVYVLVMCHTRELAFQI-SKEYERF  203 (448)
Q Consensus       128 ~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~---~~~~~lil~Pt~~L~~q~-~~~~~~~  203 (448)
                      .+++||.+      +++.++.|+++++.+|||+|||++|++|++..+....   .+.++||++|+++|+.|+ .+.++++
T Consensus         7 ~l~~~Q~~------~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~   80 (699)
T 4gl2_A            7 QLRPYQME------VAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPF   80 (699)
T ss_dssp             CCCHHHHH------HHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHH
T ss_pred             CccHHHHH------HHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHH
Confidence            44566999      9999999999999999999999999999998775432   235899999999999999 9999998


Q ss_pred             hccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHH------HCCCCcCCCeeEEEecchhHHHhhhhhHHH
Q psy1548         204 SKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALV------RNKKLNLSLLKHFILDECDKMLEQLEMRRD  277 (448)
Q Consensus       204 ~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l------~~~~~~~~~i~~lViDEah~l~~~~~~~~~  277 (448)
                      ...  ++++..++|+.........+... ++|+|+||++|.+.+      ....+.+.++++||+||||++.....+...
T Consensus        81 ~~~--~~~v~~~~g~~~~~~~~~~~~~~-~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~~~~~~~~~~i  157 (699)
T 4gl2_A           81 LKK--WYRVIGLSGDTQLKISFPEVVKS-CDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNI  157 (699)
T ss_dssp             HTT--TSCEEEEC----CCCCHHHHHHS-CSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGGCBTTBSSCSH
T ss_pred             cCc--CceEEEEeCCcchhhHHHhhhcC-CCEEEECHHHHHHHHhccccccccceecccCcEEEEECccccCccchHHHH
Confidence            854  48899999998766555555443 899999999999988      445577889999999999987553122222


Q ss_pred             HHHHHHh----C---------CCCCeEEEEeccCCcc-----------HHHHHHHhc------------------CCCeE
Q psy1548         278 VQEIFRS----S---------PHTKQVMMFSATLSKE-----------IRPVCKKFM------------------HDPME  315 (448)
Q Consensus       278 ~~~i~~~----l---------~~~~q~i~~SAT~~~~-----------~~~~~~~~l------------------~~~~~  315 (448)
                      +...+..    .         .+..|++++|||++..           +..++..+.                  ..|..
T Consensus       158 ~~~~l~~~~~~~~~~~~~~~~~~~~~il~lTATp~~~~~~~~~~~~~~i~~l~~~l~~~~i~~~~~~~~~l~~~~~~p~~  237 (699)
T 4gl2_A          158 MRHYLMQKLKNNRLKKENKPVIPLPQILGLTASPGVGGATKQAKAEEHILKLCANLDAFTIKTVKENLDQLKNQIQEPCK  237 (699)
T ss_dssp             HHHHHHHHHHHHHHHC----CCCCCEEEEECSCCCCCSCCSHHHHHHHHHHHHHHHTCSCCCCCCTTHHHHHHHSCCCEE
T ss_pred             HHHHHHhhhcccccccccccCCCCCEEEEecccccccccccHHHHHHHHHHHHhhcCCCEEEeecCchHHHhhhcCCCce
Confidence            2222211    1         1567999999999862           222222221                  12211


Q ss_pred             EEEcCccccccc----------------ce---eE---------------------------------------------
Q psy1548         316 VYVDDEAKLTLH----------------GL---QQ---------------------------------------------  331 (448)
Q Consensus       316 i~~~~~~~~~~~----------------~i---~~---------------------------------------------  331 (448)
                      ............                .+   ..                                             
T Consensus       238 ~~~~~~~~~~~~~~~~l~~l~~~i~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  317 (699)
T 4gl2_A          238 KFAIADATREDPFKEKLLEIMTRIQTYCQMSPMSDFGTQPYEQWAIQMEKKAAKEGNRKERVCAEHLRKYNEALQINDTI  317 (699)
T ss_dssp             EEEEEC-----CHHHHHHHHHHHHHHHHTCCCCSCSSSHHHHHHHHHHHHHHHHHTCTTTHHHHHHHHHHHHHHHHHHHS
T ss_pred             EEEEcccccCChHHHHHHHHHHHHHHHhccCcchhccchHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHH
Confidence            111000000000                00   00                                             


Q ss_pred             -----------------------------EEEEcC--------------------------cchHHHHHHHHHhh----C
Q psy1548         332 -----------------------------HYVKLK--------------------------ENEKNKKLFELLDV----L  352 (448)
Q Consensus       332 -----------------------------~~~~~~--------------------------~~~k~~~L~~ll~~----~  352 (448)
                                                   ......                          ...|...|..++..    .
T Consensus       318 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~k~~~L~~~L~~~~~~~  397 (699)
T 4gl2_A          318 RMIDAYTHLETFYNEEKDKKFAVIEDDLKKPLKLDETDRFLMTLFFENNKMLKRLAENPEYENEKLTKLRNTIMEQYTRT  397 (699)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHC------------CCHHHHHHHHHHHHHHHHHHHHHTCCC----CSSCSHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHhhhccccccccccccccchhHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHhcC
Confidence                                         000000                          01111222223322    2


Q ss_pred             C-CCeEEEEECccHHHHHHHHHHHhC------CCcEEEEeCC--------CCHHHHHHHHHHHhcCCCceEEEEecChhh
Q psy1548         353 E-FNQVVIFVKSVTRCIALSTLLSEQ------NFPAVSIHRG--------MTQEERLKKYQEFKDFHKGLAITFASDEND  417 (448)
Q Consensus       353 ~-~~~~IIF~~s~~~a~~l~~~L~~~------g~~~~~lh~~--------~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d  417 (448)
                      + ++++||||+++..++.+++.|++.      |+++..+||+        |++.+|.++++.|++|+  ..|+++|+...
T Consensus       398 ~~~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~--~~VLVaT~~~~  475 (699)
T 4gl2_A          398 EESARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGK--INLLIATTVAE  475 (699)
T ss_dssp             SSCCCEEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC-----CCSEEECSCC
T ss_pred             CCCCcEEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCC--CcEEEEccccc
Confidence            3 689999999999999999999987      8999999999        99999999999999988  45666666543


Q ss_pred             HHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         418 AKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       418 ~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      +++  ++.+.--+-..++|.+...+.++.||
T Consensus       476 ~GI--Dip~v~~VI~~d~p~s~~~~~Qr~GR  504 (699)
T 4gl2_A          476 EGL--DIKECNIVIRYGLVTNEIAMVQARGR  504 (699)
T ss_dssp             TTS--CCCSCCCCEEESCCCCHHHHHHHHTT
T ss_pred             cCC--ccccCCEEEEeCCCCCHHHHHHHcCC
Confidence            333  33333334456678777788888887

>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=99.96  E-value=1.6e-29  Score=265.93  Aligned_cols=269  Identities=19%  Similarity=0.184  Sum_probs=205.7

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      + .|+++   |..      ++|.++.|+  |+.++||+|||++|.+|++.....   +..++||+||++||.|..+++..
T Consensus       110 ~-rP~~V---Q~~------~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~---g~~v~VvTpTreLA~Qdae~m~~  174 (922)
T 1nkt_A          110 Q-RPFDV---QVM------GAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALA---GNGVHIVTVNDYLAKRDSEWMGR  174 (922)
T ss_dssp             C-CCCHH---HHH------HHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTT---TSCEEEEESSHHHHHHHHHHHHH
T ss_pred             C-CCCHH---HHH------HHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHh---CCCeEEEeCCHHHHHHHHHHHHH
Confidence            6 89999   999      999999998  999999999999999999754332   34799999999999999999999


Q ss_pred             hhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHH-HHHHHCC------CCcCCCeeEEEecchhHHHhh----
Q psy1548         203 FSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRI-LALVRNK------KLNLSLLKHFILDECDKMLEQ----  271 (448)
Q Consensus       203 ~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l-~~~l~~~------~~~~~~i~~lViDEah~l~~~----  271 (448)
                      +...+ ++++++++||.+.......  . .++|+||||++| .+++..+      .+.++.+.++|+||||.|+..    
T Consensus       175 l~~~l-GLsv~~i~gg~~~~~r~~~--y-~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmLiDeart  250 (922)
T 1nkt_A          175 VHRFL-GLQVGVILATMTPDERRVA--Y-NADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDEART  250 (922)
T ss_dssp             HHHHT-TCCEEECCTTCCHHHHHHH--H-HSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHHTTGGGS
T ss_pred             HHhhc-CCeEEEEeCCCCHHHHHHh--c-CCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHHHhcCcc
Confidence            99998 9999999999875433322  2 389999999999 7777653      456788999999999999842    


Q ss_pred             -----------hhhHHHHHHHHHhCC---------CCCeEE-----------------EEeccCCccHHHH---H--HHh
Q psy1548         272 -----------LEMRRDVQEIFRSSP---------HTKQVM-----------------MFSATLSKEIRPV---C--KKF  309 (448)
Q Consensus       272 -----------~~~~~~~~~i~~~l~---------~~~q~i-----------------~~SAT~~~~~~~~---~--~~~  309 (448)
                                 .+|...+..++..++         +.+|++                 ++|||++.-...+   +  ..+
T Consensus       251 PLiiSg~~~~~~~~y~~i~~iv~~L~~~~dy~vDek~rqv~Lte~G~~~~e~~l~i~~Lfsat~~~l~~~i~~aL~A~~l  330 (922)
T 1nkt_A          251 PLIISGPADGASNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGIDNLYEAANSPLVSYLNNALKAKEL  330 (922)
T ss_dssp             CEEEEEECCCCHHHHHHHHHHHHHSCBTTTEEEETTTTEEEECHHHHHHHHHHHTCSSTTCSTTCCHHHHHHHHHHHHHH
T ss_pred             ceeecCCCCcchhHHHHHHHHHHhCcccccceeccCcceEEecHhHHHHHHHHhCCccccCCcchhHHHHHHHHHHHHHH
Confidence                       268899999999998         678998                 8999987533222   1  122


Q ss_pred             cC--------CCeEEEEcCcc----------------------------ccccccee-----------------------
Q psy1548         310 MH--------DPMEVYVDDEA----------------------------KLTLHGLQ-----------------------  330 (448)
Q Consensus       310 l~--------~~~~i~~~~~~----------------------------~~~~~~i~-----------------------  330 (448)
                      +.        ++..+.++...                            ..+..+|.                       
T Consensus       331 ~~~d~dYiV~dg~vviVDe~TGR~m~grr~sdGLHQaieaKe~V~I~~e~~TlatIt~Qnyfr~Y~kL~GMTGTa~te~~  410 (922)
T 1nkt_A          331 FSRDKDYIVRDGEVLIVDEFTGRVLIGRRYNEGMHQAIEAKEHVEIKAENQTLATITLQNYFRLYDKLAGMTGTAQTEAA  410 (922)
T ss_dssp             CCBTTTEEECSSCEEEBCSSSCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEECHHHHHTTSSEEEEEESCCGGGHH
T ss_pred             hhcccceeeecCceEEEecccCcccCCccccchhhHHHhccccccccccccccceeehHHHHHhhhhhhccccCchhHHH
Confidence            22        12222222100                            00111111                       


Q ss_pred             ------------------------EEEEEcCcchHHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhCCCcEEEE
Q psy1548         331 ------------------------QHYVKLKENEKNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSI  384 (448)
Q Consensus       331 ------------------------~~~~~~~~~~k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~l  384 (448)
                                              ..++.+...+|...+...+...  .+.++||||+|++.++.|+..|++.|+++..+
T Consensus       411 Ef~~iY~l~vv~IPtn~p~~R~d~~d~v~~t~~~K~~al~~~i~~~~~~gqpvLVft~Sie~sE~Ls~~L~~~Gi~~~vL  490 (922)
T 1nkt_A          411 ELHEIYKLGVVSIPTNMPMIREDQSDLIYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVL  490 (922)
T ss_dssp             HHHHHHCCEEEECCCSSCCCCEECCCEEESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEE
T ss_pred             HHHHHhCCCeEEeCCCCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhcCCcEEEEECCHHHHHHHHHHHHHCCCCEEEe
Confidence                                    1235566778999888887543  45689999999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHhcCCCceEEEEecC
Q psy1548         385 HRGMTQEERLKKYQEFKDFHKGLAITFASD  414 (448)
Q Consensus       385 h~~~~~~eR~~~l~~F~~g~~g~~I~~~t~  414 (448)
                      ||++.+.+|..+.+.|+.|.    |+++|+
T Consensus       491 nak~~~rEa~iia~agr~G~----VtIATn  516 (922)
T 1nkt_A          491 NAKYHEQEATIIAVAGRRGG----VTVATN  516 (922)
T ss_dssp             CSSCHHHHHHHHHTTTSTTC----EEEEET
T ss_pred             cCChhHHHHHHHHhcCCCCe----EEEecc
Confidence            99998888877777777654    555555

>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=99.96  E-value=1.5e-28  Score=274.53  Aligned_cols=258  Identities=14%  Similarity=0.107  Sum_probs=194.2

Q ss_pred             hhhhhhhccccccceeeee----Cc--ceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         130 DTYLHRVARAGRFGTKAVL----GM--DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       130 ~~yQ~~~~~~~~~~~~~~~----g~--~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      .++|.+      +++.++.    |+  |+++++|||+|||++|+++++..+.   .+.+++|++||++|+.|+++.+.++
T Consensus       605 t~~Q~~------ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~---~g~~vlvlvPt~~La~Q~~~~~~~~  675 (1151)
T 2eyq_A          605 TPDQAQ------AINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD---NHKQVAVLVPTTLLAQQHYDNFRDR  675 (1151)
T ss_dssp             CHHHHH------HHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT---TTCEEEEECSSHHHHHHHHHHHHHH
T ss_pred             CHHHHH------HHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHH---hCCeEEEEechHHHHHHHHHHHHHH
Confidence            444999      9998886    66  9999999999999999999887654   3459999999999999999999988


Q ss_pred             hccCCCceEEEEEcCcccHHh---HHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHH
Q psy1548         204 SKYMSNIKVGVFFGGLPIQKD---EEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQE  280 (448)
Q Consensus       204 ~~~~~~~~v~~~~g~~~~~~~---~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~  280 (448)
                      .... ++++..+.|.......   ...+..+.++|+|+||+.+.     +.+.+++++++|+||+|++..      ....
T Consensus       676 ~~~~-~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~-----~~~~~~~l~lvIiDEaH~~g~------~~~~  743 (1151)
T 2eyq_A          676 FANW-PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-----SDVKFKDLGLLIVDEEHRFGV------RHKE  743 (1151)
T ss_dssp             STTT-TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-----SCCCCSSEEEEEEESGGGSCH------HHHH
T ss_pred             hhcC-CCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHh-----CCccccccceEEEechHhcCh------HHHH
Confidence            7766 7888888876654433   34456667999999997653     346689999999999998533      2344


Q ss_pred             HHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEE
Q psy1548         281 IFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIF  360 (448)
Q Consensus       281 i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF  360 (448)
                      .++.++...++++||||+++....+....+.++..+...+.   ....+..++...........+...+  ..+++++||
T Consensus       744 ~l~~l~~~~~vl~lSATp~p~~l~~~~~~~~~~~~i~~~~~---~r~~i~~~~~~~~~~~i~~~il~~l--~~g~qvlvf  818 (1151)
T 2eyq_A          744 RIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPPA---RRLAVKTFVREYDSMVVREAILREI--LRGGQVYYL  818 (1151)
T ss_dssp             HHHHHHTTSEEEEEESSCCCHHHHHHHTTTSEEEECCCCCC---BCBCEEEEEEECCHHHHHHHHHHHH--TTTCEEEEE
T ss_pred             HHHHhcCCCCEEEEcCCCChhhHHHHHhcCCCceEEecCCC---CccccEEEEecCCHHHHHHHHHHHH--hcCCeEEEE
Confidence            45555677899999999988776666665555443332222   2234555544443322222222222  246899999


Q ss_pred             ECccHHHHHHHHHHHhC--CCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         361 VKSVTRCIALSTLLSEQ--NFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       361 ~~s~~~a~~l~~~L~~~--g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                      |++++.++.+++.|++.  +..+..+||+|++.+|.+++++|++|+  ..|+++|+.
T Consensus       819 ~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~~F~~g~--~~VLVaT~v  873 (1151)
T 2eyq_A          819 YNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQR--FNVLVCTTI  873 (1151)
T ss_dssp             CCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTS--CCEEEESST
T ss_pred             ECCHHHHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHHHHcCC--CcEEEECCc
Confidence            99999999999999987  889999999999999999999999987  467777764

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.96  E-value=7.1e-29  Score=256.83  Aligned_cols=295  Identities=16%  Similarity=0.158  Sum_probs=199.8

Q ss_pred             CchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccC
Q psy1548         128 DSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYM  207 (448)
Q Consensus       128 ~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  207 (448)
                      ..++||.+      +++.++.++++++++|||+|||++|+.++...+...  +.++|||+|+++|+.|+.+.++++....
T Consensus       113 ~l~~~Q~~------ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~--~~~vlvl~P~~~L~~Q~~~~~~~~~~~~  184 (510)
T 2oca_A          113 EPHWYQKD------AVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY--EGKILIIVPTTALTTQMADDFVDYRLFS  184 (510)
T ss_dssp             CCCHHHHH------HHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHC--SSEEEEEESSHHHHHHHHHHHHHTTSSC
T ss_pred             CCCHHHHH------HHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCC--CCeEEEEECcHHHHHHHHHHHHHhhcCC
Confidence            34555999      999999999999999999999999999988876533  3489999999999999999999886554


Q ss_pred             CCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCC
Q psy1548         208 SNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPH  287 (448)
Q Consensus       208 ~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~  287 (448)
                       +.++..+.|+.....+    ..+.++|+|+||+.+..   .....+.+++++|+||||++..     ..+..+++.+++
T Consensus       185 -~~~v~~~~~~~~~~~~----~~~~~~I~i~T~~~l~~---~~~~~~~~~~liIiDE~H~~~~-----~~~~~il~~~~~  251 (510)
T 2oca_A          185 -HAMIKKIGGGASKDDK----YKNDAPVVVGTWQTVVK---QPKEWFSQFGMMMNDECHLATG-----KSISSIISGLNN  251 (510)
T ss_dssp             -GGGEEECGGGCCTTGG----GCTTCSEEEEEHHHHTT---SCGGGGGGEEEEEEETGGGCCH-----HHHHHHGGGCTT
T ss_pred             -ccceEEEecCCccccc----cccCCcEEEEeHHHHhh---chhhhhhcCCEEEEECCcCCCc-----ccHHHHHHhccc
Confidence             6788888888765544    23358999999997543   3445678899999999998755     346677788888


Q ss_pred             CCeEEEEeccCCccHHHHHH-HhcCCCeEEEEcCc-----ccccccceeEEEEEcC---------------------cch
Q psy1548         288 TKQVMMFSATLSKEIRPVCK-KFMHDPMEVYVDDE-----AKLTLHGLQQHYVKLK---------------------ENE  340 (448)
Q Consensus       288 ~~q~i~~SAT~~~~~~~~~~-~~l~~~~~i~~~~~-----~~~~~~~i~~~~~~~~---------------------~~~  340 (448)
                      ..+++++|||+++....... ..+.++..+.....     .......+.......+                     ...
T Consensus       252 ~~~~l~lSATp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  331 (510)
T 2oca_A          252 CMFKFGLSGSLRDGKANIMQYVGMFGEIFKPVTTSKLMEDGQVTELKINSIFLRYPDEFTTKLKGKTYQEEIKIITGLSK  331 (510)
T ss_dssp             CCEEEEEESCGGGCSSCHHHHHHHHCSEECCCCCC---------CCEEEEEEEECCHHHHHHHTTCCHHHHHHHHHTCHH
T ss_pred             CcEEEEEEeCCCCCcccHHHhHHhhCCeEEeeCHHHHhhCCcCCCceEEEEeecCChHHhccccccchHHHHHHHhccHH
Confidence            88999999999766433211 11223332222111     0111112222222221                     112


Q ss_pred             HHHHHHHHHhhC---CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEec-Chh
Q psy1548         341 KNKKLFELLDVL---EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFAS-DEN  416 (448)
Q Consensus       341 k~~~L~~ll~~~---~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t-~~~  416 (448)
                      +...+.+++...   .++++||||+ .++++.+++.|.+.+.++..+||+|++.+|.++++.|++|+  ..|+++| +.-
T Consensus       332 ~~~~l~~~l~~~~~~~~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~--~~vLv~T~~~~  408 (510)
T 2oca_A          332 RNKWIAKLAIKLAQKDENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGK--GIIIVASYGVF  408 (510)
T ss_dssp             HHHHHHHHHHHHHTTTCEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCC--SCEEEEEHHHH
T ss_pred             HHHHHHHHHHHHHhcCCCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCC--CCEEEEEcChh
Confidence            344455555443   3345566665 88999999999999889999999999999999999999987  4577777 421


Q ss_pred             hHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         417 DAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       417 d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      ..++  ++.+.--+-+...|.+...+.|+.||
T Consensus       409 ~~Gi--Dip~v~~vi~~~~~~s~~~~~Q~~GR  438 (510)
T 2oca_A          409 STGI--SVKNLHHVVLAHGVKSKIIVLQTIGR  438 (510)
T ss_dssp             HHSC--CCCSEEEEEESSCCCSCCHHHHHHHH
T ss_pred             hccc--ccccCcEEEEeCCCCCHHHHHHHHhc
Confidence            1111  11111112233445555556666665

>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=99.95  E-value=2e-27  Score=248.24  Aligned_cols=226  Identities=17%  Similarity=0.158  Sum_probs=165.9

Q ss_pred             cceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCccc
Q psy1548         142 FGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPI  221 (448)
Q Consensus       142 ~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~  221 (448)
                      +++.+..+++++++||||||||++|.+|+++.      +.+++|++||++||.|+.+.+.+..    +..+...+|+...
T Consensus       225 i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~~------g~~vLVl~PTReLA~Qia~~l~~~~----g~~vg~~vG~~~~  294 (666)
T 3o8b_A          225 PPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQ------GYKVLVLNPSVAATLGFGAYMSKAH----GIDPNIRTGVRTI  294 (666)
T ss_dssp             CCCCCSSCEEEEEECCTTSCTTTHHHHHHHHT------TCCEEEEESCHHHHHHHHHHHHHHH----SCCCEEECSSCEE
T ss_pred             HHHHHHcCCeEEEEeCCchhHHHHHHHHHHHC------CCeEEEEcchHHHHHHHHHHHHHHh----CCCeeEEECcEec
Confidence            55556678999999999999999999998862      4589999999999999988776654    4566677777542


Q ss_pred             HHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCe--EEEEeccCC
Q psy1548         222 QKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQ--VMMFSATLS  299 (448)
Q Consensus       222 ~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q--~i~~SAT~~  299 (448)
                              ...++|+|+||++|   +....+.+++++++||||||+ ++. ++...+..+++.++...|  ++++|||++
T Consensus       295 --------~~~~~IlV~TPGrL---l~~~~l~l~~l~~lVlDEAH~-l~~-~~~~~l~~Il~~l~~~~~~llil~SAT~~  361 (666)
T 3o8b_A          295 --------TTGAPVTYSTYGKF---LADGGCSGGAYDIIICDECHS-TDS-TTILGIGTVLDQAETAGARLVVLATATPP  361 (666)
T ss_dssp             --------CCCCSEEEEEHHHH---HHTTSCCTTSCSEEEETTTTC-CSH-HHHHHHHHHHHHTTTTTCSEEEEEESSCT
T ss_pred             --------cCCCCEEEECcHHH---HhCCCcccCcccEEEEccchh-cCc-cHHHHHHHHHHhhhhcCCceEEEECCCCC
Confidence                    23489999999997   466778889999999999975 455 888889999999987666  788899998


Q ss_pred             ccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCC
Q psy1548         300 KEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNF  379 (448)
Q Consensus       300 ~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~  379 (448)
                      ..+.      ...|....+....   ...+ .   .......       ++....+++||||++++.|+.+++.|++.|+
T Consensus       362 ~~i~------~~~p~i~~v~~~~---~~~i-~---~~~~~~~-------l~~~~~~~vLVFv~Tr~~ae~la~~L~~~g~  421 (666)
T 3o8b_A          362 GSVT------VPHPNIEEVALSN---TGEI-P---FYGKAIP-------IEAIRGGRHLIFCHSKKKCDELAAKLSGLGI  421 (666)
T ss_dssp             TCCC------CCCTTEEEEECBS---CSSE-E---ETTEEEC-------GGGSSSSEEEEECSCHHHHHHHHHHHHTTTC
T ss_pred             cccc------cCCcceEEEeecc---cchh-H---HHHhhhh-------hhhccCCcEEEEeCCHHHHHHHHHHHHhCCC
Confidence            7522      1222221111110   0001 0   0111100       2334578999999999999999999999999


Q ss_pred             cEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHH
Q psy1548         380 PAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAK  419 (448)
Q Consensus       380 ~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~  419 (448)
                      ++..+||+|++++       |+++  +..|+++|+-.+++
T Consensus       422 ~v~~lHG~l~q~e-------r~~~--~~~VLVATdVaerG  452 (666)
T 3o8b_A          422 NAVAYYRGLDVSV-------IPTI--GDVVVVATDALMTG  452 (666)
T ss_dssp             CEEEECTTSCGGG-------SCSS--SCEEEEECTTHHHH
T ss_pred             cEEEecCCCCHHH-------HHhC--CCcEEEECChHHcc
Confidence            9999999999875       3443  34889988864433

>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=99.95  E-value=4.5e-29  Score=267.06  Aligned_cols=259  Identities=20%  Similarity=0.228  Sum_probs=182.3

Q ss_pred             CCCCchhhhhhhccccccceeeeeC------cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHH
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLG------MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK  198 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g------~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~  198 (448)
                      .|++.   |++      +++.++.+      +++++++|||||||++|++|++..+..   +.+++|++||++|+.|+++
T Consensus       368 ~lt~~---Q~~------ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~---g~qvlvlaPtr~La~Q~~~  435 (780)
T 1gm5_A          368 KLTNA---QKR------AHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA---GFQTAFMVPTSILAIQHYR  435 (780)
T ss_dssp             CCCHH---HHH------HHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH---TSCEEEECSCHHHHHHHHH
T ss_pred             CCCHH---HHH------HHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHHHHHH
Confidence            45555   999      99988875      599999999999999999999988754   3589999999999999999


Q ss_pred             HHHHhhccCCCceEEEEEcCcccHHh---HHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhH
Q psy1548         199 EYERFSKYMSNIKVGVFFGGLPIQKD---EEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMR  275 (448)
Q Consensus       199 ~~~~~~~~~~~~~v~~~~g~~~~~~~---~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~  275 (448)
                      .++++.... ++++..++|+......   ...+..+.++|+|+||+.+.+     ...+.+++++|+||+|++...  . 
T Consensus       436 ~l~~~~~~~-gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~~~~~~l~lVVIDEaHr~g~~--q-  506 (780)
T 1gm5_A          436 RTVESFSKF-NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-----DVHFKNLGLVIIDEQHRFGVK--Q-  506 (780)
T ss_dssp             HHHHHHTCS-SCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-----CCCCSCCCEEEEESCCCC-------
T ss_pred             HHHHHhhhc-CceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh-----hhhccCCceEEecccchhhHH--H-
Confidence            999998877 8999999999876543   344566679999999987754     456889999999999986332  1 


Q ss_pred             HHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHh-hC-C
Q psy1548         276 RDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLD-VL-E  353 (448)
Q Consensus       276 ~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~-~~-~  353 (448)
                         ...+.......++++||||+.+......  +..+.....++.. ......+...+  .... +...+...+. .. .
T Consensus       507 ---r~~l~~~~~~~~vL~mSATp~p~tl~~~--~~g~~~~s~i~~~-p~~r~~i~~~~--~~~~-~~~~l~~~i~~~l~~  577 (780)
T 1gm5_A          507 ---REALMNKGKMVDTLVMSATPIPRSMALA--FYGDLDVTVIDEM-PPGRKEVQTML--VPMD-RVNEVYEFVRQEVMR  577 (780)
T ss_dssp             ----CCCCSSSSCCCEEEEESSCCCHHHHHH--HTCCSSCEEECCC-CSSCCCCEECC--CCSS-THHHHHHHHHHHTTT
T ss_pred             ---HHHHHHhCCCCCEEEEeCCCCHHHHHHH--HhCCcceeeeecc-CCCCcceEEEE--eccc-hHHHHHHHHHHHHhc
Confidence               1222233456899999999877644433  2332221112111 01112232222  2222 2333444443 22 4


Q ss_pred             CCeEEEEECcc--------HHHHHHHHHHHh---CCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         354 FNQVVIFVKSV--------TRCIALSTLLSE---QNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       354 ~~~~IIF~~s~--------~~a~~l~~~L~~---~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                      +++++|||++.        ..++.+++.|++   .++.+..+||+|++++|..+++.|++|+  ..|+++|+-
T Consensus       578 g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~--~~ILVaT~v  648 (780)
T 1gm5_A          578 GGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGR--YDILVSTTV  648 (780)
T ss_dssp             SCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTS--SSBCCCSSC
T ss_pred             CCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCC--CeEEEECCC
Confidence            67899999976        457889999988   4789999999999999999999999988  345555553

>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=99.94  E-value=2.2e-28  Score=256.92  Aligned_cols=243  Identities=12%  Similarity=0.087  Sum_probs=176.7

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      ...|.++   |+.      ++|.++.|+|+++++|||||||++|++|+++.+..  .+.++||++||++|+.|+.+.+..
T Consensus       169 ~~~~lpi---q~~------~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~--~~~~vLvl~PtreLa~Qi~~~l~~  237 (618)
T 2whx_A          169 ERIGEPD---YEV------DEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALK--RRLRTLILAPTRVVAAEMEEALRG  237 (618)
T ss_dssp             CCCCCCC---CCC------CGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTTT
T ss_pred             cccCCCc---ccc------CHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHh--CCCeEEEEcChHHHHHHHHHHhcC
Confidence            4678899   988      89999999999999999999999999999988765  346899999999999998877652


Q ss_pred             hhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHH
Q psy1548         203 FSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIF  282 (448)
Q Consensus       203 ~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~  282 (448)
                             ..+. +.+.. ..    ........+.++|.+.+...+... ..+.++++||+||||++ +. ++...+..+.
T Consensus       238 -------~~v~-~~~~~-l~----~~~tp~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~-~~~~~~~~i~  301 (618)
T 2whx_A          238 -------LPIR-YQTPA-VK----SDHTGREIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DP-CSVAARGYIS  301 (618)
T ss_dssp             -------SCEE-ECCTT-SS----CCCCSSSCEEEEEHHHHHHHHHHC-SSCCCCSEEEEESTTCC-SH-HHHHHHHHHH
T ss_pred             -------Ccee-Eeccc-ce----eccCCCceEEEEChHHHHHHHhcc-ccccCCeEEEEECCCCC-Cc-cHHHHHHHHH
Confidence                   2232 11111 00    001112357778888887665544 34789999999999998 54 7777888777


Q ss_pred             HhCC-CCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEE
Q psy1548         283 RSSP-HTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFV  361 (448)
Q Consensus       283 ~~l~-~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~  361 (448)
                      ..++ ++.|+++||||++..+..+..   .++..+.+....              +.. +...+...+.. ..+++||||
T Consensus       302 ~~l~~~~~q~il~SAT~~~~~~~~~~---~~~~~~~v~~~~--------------~~~-~~~~ll~~l~~-~~~~~LVF~  362 (618)
T 2whx_A          302 TRVEMGEAAAIFMTATPPGSTDPFPQ---SNSPIEDIEREI--------------PER-SWNTGFDWITD-YQGKTVWFV  362 (618)
T ss_dssp             HHHHHTSCEEEEECSSCTTCCCSSCC---CSSCEEEEECCC--------------CSS-CCSSSCHHHHH-CCSCEEEEC
T ss_pred             HHhcccCccEEEEECCCchhhhhhhc---cCCceeeecccC--------------CHH-HHHHHHHHHHh-CCCCEEEEE
Confidence            7765 678999999999887543322   234333332210              100 01112222322 257999999


Q ss_pred             CccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhh
Q psy1548         362 KSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDEND  417 (448)
Q Consensus       362 ~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d  417 (448)
                      +|++.|+.+++.|++.|+++..+||+    +|.+++++|++|+  ..|+++|+...
T Consensus       363 ~s~~~a~~l~~~L~~~g~~v~~lhg~----~R~~~l~~F~~g~--~~VLVaTdv~~  412 (618)
T 2whx_A          363 PSIKAGNDIANCLRKSGKRVIQLSRK----TFDTEYPKTKLTD--WDFVVTTDISE  412 (618)
T ss_dssp             SSHHHHHHHHHHHHHTTCCEEEECTT----THHHHTTHHHHSC--CSEEEECGGGG
T ss_pred             CChhHHHHHHHHHHHcCCcEEEEChH----HHHHHHHhhcCCC--cEEEEECcHHH
Confidence            99999999999999999999999985    7889999999987  56778877533

>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=99.94  E-value=9.6e-27  Score=250.35  Aligned_cols=284  Identities=12%  Similarity=0.120  Sum_probs=198.5

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeee-Ccceeeecc
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVL-GMDILCQAK  157 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~-g~~vli~ap  157 (448)
                      ...|.++++++.+.+.+...+                        ..|..+   |++      +++.++. |++++++||
T Consensus        71 ~~~f~~~~l~~~~~~~l~~r~------------------------~lP~~~---q~~------~i~~~l~~~~~vii~gp  117 (773)
T 2xau_A           71 INPFTGREFTPKYVDILKIRR------------------------ELPVHA---QRD------EFLKLYQNNQIMVFVGE  117 (773)
T ss_dssp             BCTTTCSBCCHHHHHHHHHHT------------------------TSGGGG---GHH------HHHHHHHHCSEEEEECC
T ss_pred             CCCccccCCCHHHHHHHHHhh------------------------cCChHH---HHH------HHHHHHhCCCeEEEECC
Confidence            457999999999999998765                        468888   888      8888776 568999999


Q ss_pred             CCChhHHHHHHHHHHhhh--ccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcE
Q psy1548         158 SGMGKTAVFVLATLQQLE--TTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQI  235 (448)
Q Consensus       158 TGsGKT~~~~l~~l~~l~--~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~I  235 (448)
                      ||+|||+  ++|++....  ....+.++++++|+++|+.|+.+.+........+..++.-......       .....+|
T Consensus       118 TGSGKTt--llp~ll~~~~~~~~~g~~ilvl~P~r~La~q~~~~l~~~~~~~v~~~vG~~i~~~~~-------~~~~~~I  188 (773)
T 2xau_A          118 TGSGKTT--QIPQFVLFDEMPHLENTQVACTQPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFENK-------TSNKTIL  188 (773)
T ss_dssp             TTSSHHH--HHHHHHHHHHCGGGGTCEEEEEESCHHHHHHHHHHHHHHTTCCBTTTEEEEETTEEE-------CCTTCSE
T ss_pred             CCCCHHH--HHHHHHHHhccccCCCceEEecCchHHHHHHHHHHHHHHhCCchhheecceeccccc-------cCCCCCE
Confidence            9999998  456552221  1122567999999999999998766554321112233322111110       1124789


Q ss_pred             EEEcHHHHHHHHHCCCCcCCCeeEEEecchhH-HHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCe
Q psy1548         236 VVGTPGRILALVRNKKLNLSLLKHFILDECDK-MLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPM  314 (448)
Q Consensus       236 lV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~-l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~  314 (448)
                      +++||+++.+.+... ..+.++++||+||+|. .++.......+..+.... +..|++++|||++.  ..+.. ++.++.
T Consensus       189 ~v~T~G~l~r~l~~~-~~l~~~~~lIlDEah~R~ld~d~~~~~l~~l~~~~-~~~~iIl~SAT~~~--~~l~~-~~~~~~  263 (773)
T 2xau_A          189 KYMTDGMLLREAMED-HDLSRYSCIILDEAHERTLATDILMGLLKQVVKRR-PDLKIIIMSATLDA--EKFQR-YFNDAP  263 (773)
T ss_dssp             EEEEHHHHHHHHHHS-TTCTTEEEEEECSGGGCCHHHHHHHHHHHHHHHHC-TTCEEEEEESCSCC--HHHHH-HTTSCC
T ss_pred             EEECHHHHHHHHhhC-ccccCCCEEEecCccccccchHHHHHHHHHHHHhC-CCceEEEEeccccH--HHHHH-HhcCCC
Confidence            999999999877654 3488999999999996 555312334455555444 57899999999964  34444 444444


Q ss_pred             EEEEcCcccccccceeEEEEEcCcchHHH----HHHHHHhhCCCCeEEEEECccHHHHHHHHHHHh-----------CCC
Q psy1548         315 EVYVDDEAKLTLHGLQQHYVKLKENEKNK----KLFELLDVLEFNQVVIFVKSVTRCIALSTLLSE-----------QNF  379 (448)
Q Consensus       315 ~i~~~~~~~~~~~~i~~~~~~~~~~~k~~----~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~-----------~g~  379 (448)
                      .+.+...    ...+.++|......++..    .+..+......+++||||+++++++.+++.|++           .++
T Consensus       264 vi~v~gr----~~pv~~~~~~~~~~~~~~~~l~~l~~~~~~~~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~  339 (773)
T 2xau_A          264 LLAVPGR----TYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPL  339 (773)
T ss_dssp             EEECCCC----CCCEEEECCSSCCSCHHHHHHHHHHHHHHHSCSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCE
T ss_pred             cccccCc----ccceEEEEecCCchhHHHHHHHHHHHHHHhcCCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCe
Confidence            4444332    234666665555544432    333344444678999999999999999999985           578


Q ss_pred             cEEEEeCCCCHHHHHHHHHHHh-----cCCCceEEEEecCh
Q psy1548         380 PAVSIHRGMTQEERLKKYQEFK-----DFHKGLAITFASDE  415 (448)
Q Consensus       380 ~~~~lh~~~~~~eR~~~l~~F~-----~g~~g~~I~~~t~~  415 (448)
                      .+..+||+|++++|.++++.|+     +|.  ..|.++|+.
T Consensus       340 ~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~--~kVlVAT~i  378 (773)
T 2xau_A          340 SVYPLYGSLPPHQQQRIFEPAPESHNGRPG--RKVVISTNI  378 (773)
T ss_dssp             EEEEECTTCCHHHHGGGGSCCCCCSSSSCC--EEEEEECTH
T ss_pred             EEEEeCCCCCHHHHHHHHhhcccccCCCCc--eEEEEeCcH
Confidence            8999999999999999999998     654  678888875

>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=99.94  E-value=1.8e-27  Score=242.26  Aligned_cols=241  Identities=12%  Similarity=0.111  Sum_probs=167.2

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcce-eeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDI-LCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYE  201 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~v-li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  201 (448)
                      +..|+++   | +      ++|.++.|+++ ++++|||||||++|++|++..+..  .+.++||++||++|+.|+.+.+.
T Consensus         2 ~~q~~~i---q-~------~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~--~~~~~lvl~Ptr~La~Q~~~~l~   69 (451)
T 2jlq_A            2 SAMGEPD---Y-E------VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALL--RRLRTLILAPTRVVAAEMEEALR   69 (451)
T ss_dssp             CCCCSCC---C-C------CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTT
T ss_pred             CCCCCCc---H-H------HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHh--cCCcEEEECCCHHHHHHHHHHhc
Confidence            6678887   6 6      68999999887 999999999999999999987654  34689999999999999888764


Q ss_pred             HhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHH
Q psy1548         202 RFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEI  281 (448)
Q Consensus       202 ~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i  281 (448)
                             +..+....+....      .......|.++|++.+...+.+. ..+.+++++|+||||++ +. .+...+..+
T Consensus        70 -------g~~v~~~~~~~~~------~~~~~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~-~~~~~~~~~  133 (451)
T 2jlq_A           70 -------GLPIRYQTPAVKS------DHTGREIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DP-CSVAARGYI  133 (451)
T ss_dssp             -------TSCEEECCTTCSC------CCCSSCCEEEEEHHHHHHHHHHC-SCCCCCSEEEEETTTCC-SH-HHHHHHHHH
T ss_pred             -------Cceeeeeeccccc------cCCCCceEEEEChHHHHHHhhCc-ccccCCCEEEEeCCccC-Cc-chHHHHHHH
Confidence                   2333221111100      01123579999999998777644 45789999999999977 33 333333322


Q ss_pred             HH-hCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEE
Q psy1548         282 FR-SSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIF  360 (448)
Q Consensus       282 ~~-~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF  360 (448)
                      .. ..+++.|+++||||++.....+   +..++..+.....  .....    +         ..+...+... .+++|||
T Consensus       134 ~~~~~~~~~~~i~~SAT~~~~~~~~---~~~~~~~~~~~~~--~p~~~----~---------~~~~~~l~~~-~~~~lVF  194 (451)
T 2jlq_A          134 STRVEMGEAAAIFMTATPPGSTDPF---PQSNSPIEDIERE--IPERS----W---------NTGFDWITDY-QGKTVWF  194 (451)
T ss_dssp             HHHHHTTSCEEEEECSSCTTCCCSS---CCCSSCEEEEECC--CCSSC----C---------SSSCHHHHHC-CSCEEEE
T ss_pred             HHhhcCCCceEEEEccCCCccchhh---hcCCCceEecCcc--CCchh----h---------HHHHHHHHhC-CCCEEEE
Confidence            22 2356789999999998764332   2334443333211  00000    0         0112223332 5689999


Q ss_pred             ECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChh
Q psy1548         361 VKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDEN  416 (448)
Q Consensus       361 ~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~  416 (448)
                      |+++++|+.+++.|++.|+.+..+||++.    .++++.|++|+  ..|+++|+-.
T Consensus       195 ~~s~~~a~~l~~~L~~~g~~~~~lh~~~~----~~~~~~f~~g~--~~vLVaT~v~  244 (451)
T 2jlq_A          195 VPSIKAGNDIANCLRKSGKRVIQLSRKTF----DTEYPKTKLTD--WDFVVTTDIS  244 (451)
T ss_dssp             CSSHHHHHHHHHHHHTTTCCEEEECTTTH----HHHGGGGGSSC--CSEEEECGGG
T ss_pred             cCCHHHHHHHHHHHHHcCCeEEECCHHHH----HHHHHhhccCC--ceEEEECCHH
Confidence            99999999999999999999999999864    57999999988  4677777653

>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=99.93  E-value=3.1e-28  Score=249.58  Aligned_cols=239  Identities=17%  Similarity=0.166  Sum_probs=174.4

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .+..+++||.+      +++.++.++++++++|||+|||++|+.++...      +.++||++|+++|+.|+.+.+.+| 
T Consensus        90 ~~~~l~~~Q~~------ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~------~~~~Lvl~P~~~L~~Q~~~~~~~~-  156 (472)
T 2fwr_A           90 AEISLRDYQEK------ALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIF-  156 (472)
T ss_dssp             CCCCBCHHHHH------HHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH------CSCEEEEESSHHHHHHHHHHGGGG-
T ss_pred             CCCCcCHHHHH------HHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc------CCCEEEEECCHHHHHHHHHHHHhC-
Confidence            35567788999      99999999999999999999999999988764      358999999999999998888884 


Q ss_pred             ccCCCce-EEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHH
Q psy1548         205 KYMSNIK-VGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFR  283 (448)
Q Consensus       205 ~~~~~~~-v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~  283 (448)
                          +++ +..+.|+...          ..+|+|+||+.+...+..   ...+++++|+||||++.+. .+..    ++.
T Consensus       157 ----~~~~v~~~~g~~~~----------~~~Ivv~T~~~l~~~~~~---~~~~~~liIvDEaH~~~~~-~~~~----~~~  214 (472)
T 2fwr_A          157 ----GEEYVGEFSGRIKE----------LKPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPAE-SYVQ----IAQ  214 (472)
T ss_dssp             ----CGGGEEEBSSSCBC----------CCSEEEEEHHHHHHTHHH---HTTTCSEEEEETGGGTTST-TTHH----HHH
T ss_pred             ----CCcceEEECCCcCC----------cCCEEEEEcHHHHHHHHH---hcCCCCEEEEECCcCCCCh-HHHH----HHH
Confidence                566 7787777642          368999999998776542   1245889999999999876 6553    444


Q ss_pred             hCCCCCeEEEEeccCCc-------------------cHHHHHHHhcCCCeEE--EEcCccc--c----------------
Q psy1548         284 SSPHTKQVMMFSATLSK-------------------EIRPVCKKFMHDPMEV--YVDDEAK--L----------------  324 (448)
Q Consensus       284 ~l~~~~q~i~~SAT~~~-------------------~~~~~~~~~l~~~~~i--~~~~~~~--~----------------  324 (448)
                      .+ +..+++++|||+..                   ...++...++..+...  .+.....  .                
T Consensus       215 ~~-~~~~~l~lSATp~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  293 (472)
T 2fwr_A          215 MS-IAPFRLGLTATFEREDGRHEILKEVVGGKVFELFPDSLAGKHLAKYTIKRIFVPLAEDERVEYEKREKVYKQFLRAR  293 (472)
T ss_dssp             TC-CCSEEEEEESCCCCTTSGGGSHHHHTCCEEEECCHHHHTSCCCCSEEECCEEECCCHHHHHHTTTTTHHHHSCSSSC
T ss_pred             hc-CCCeEEEEecCccCCCCHHHHHHHHhCCeEeecCHHHHhcCcCCCeEEEEEEcCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            44 45789999999873                   2333323333322211  1110000  0                


Q ss_pred             -----cccceeEEE---------------------EEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCC
Q psy1548         325 -----TLHGLQQHY---------------------VKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQN  378 (448)
Q Consensus       325 -----~~~~i~~~~---------------------~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g  378 (448)
                           ....+.+.+                     +.+....|...+.+++....++++||||++...++.+++.|.   
T Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~k~lvF~~~~~~~~~l~~~l~---  370 (472)
T 2fwr_A          294 GITLRRAEDFNKIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKDKIIIFTRHNELVYRISKVFL---  370 (472)
T ss_dssp             CCTTTCCSSSTTTTTTTCCSSSSSTTTHHHHHHHHHHHSCSHHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHTT---
T ss_pred             CccccchhhHHHHHHHhccCHHHHHHHHHHHHHHHHhhcChHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHHHhC---
Confidence                 000000000                     012234577888899988888899999999999999999984   


Q ss_pred             CcEEEEeCCCCHHHHHHHHHHHhcCC
Q psy1548         379 FPAVSIHRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       379 ~~~~~lh~~~~~~eR~~~l~~F~~g~  404 (448)
                        +..+||+++..+|.++++.|++|+
T Consensus       371 --~~~~~g~~~~~~R~~~~~~F~~g~  394 (472)
T 2fwr_A          371 --IPAITHRTSREEREEILEGFRTGR  394 (472)
T ss_dssp             --CCBCCSSSCSHHHHTHHHHHHHSS
T ss_pred             --cceeeCCCCHHHHHHHHHHHhCCC
Confidence              567999999999999999999988

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.93  E-value=2e-27  Score=251.32  Aligned_cols=241  Identities=14%  Similarity=0.151  Sum_probs=159.8

Q ss_pred             CCCCchhhhh-----hhccccccceeee------eCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHH
Q psy1548         125 MPEDSDTYLH-----RVARAGRFGTKAV------LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELA  193 (448)
Q Consensus       125 ~p~~~~~yQ~-----~~~~~~~~~~~~~------~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~  193 (448)
                      .|+++   |+     +      ++|.++      .|+|+++++|||||||++|++|+++.+..  .+.+++|++||++|+
T Consensus       215 ~pt~I---Q~~~r~~~------aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~--~~~~~lilaPTr~La  283 (673)
T 2wv9_A          215 YVSAI---VQGERVEE------PVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQ--KRLRTAVLAPTRVVA  283 (673)
T ss_dssp             EEEEE---ECC-------------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHH--TTCCEEEEESSHHHH
T ss_pred             ccCce---eecccccc------chHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHh--CCCcEEEEccHHHHH
Confidence            78999   99     8      999988      89999999999999999999999987654  346899999999999


Q ss_pred             HHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhh
Q psy1548         194 FQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLE  273 (448)
Q Consensus       194 ~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~  273 (448)
                      .|+++.++.+.     +.  ...+..  .    .......-+-+.+.+.+...+... ..+++++++|+||||++ +. .
T Consensus       284 ~Q~~~~l~~~~-----i~--~~~~~l--~----~v~tp~~ll~~l~~~~l~~~l~~~-~~l~~l~lvViDEaH~~-~~-~  347 (673)
T 2wv9_A          284 AEMAEALRGLP-----VR--YLTPAV--Q----REHSGNEIVDVMCHATLTHRLMSP-LRVPNYNLFVMDEAHFT-DP-A  347 (673)
T ss_dssp             HHHHHHTTTSC-----CE--ECCC---------CCCCSCCCEEEEEHHHHHHHHHSS-SCCCCCSEEEEESTTCC-CH-H
T ss_pred             HHHHHHHhcCC-----ee--eecccc--c----ccCCHHHHHHHHHhhhhHHHHhcc-cccccceEEEEeCCccc-Cc-c
Confidence            99988776542     21  111100  0    000001124444555555544443 56889999999999988 22 2


Q ss_pred             hHHHHHHHHHhC-CCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhC
Q psy1548         274 MRRDVQEIFRSS-PHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVL  352 (448)
Q Consensus       274 ~~~~~~~i~~~l-~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~  352 (448)
                      +...+..+...+ +...|+++||||++..+..+...  ..|.. .+..              ..+...+...+ ..+.. 
T Consensus       348 ~~~~~~~l~~~~~~~~~~vl~~SAT~~~~i~~~~~~--~~~i~-~v~~--------------~~~~~~~~~~l-~~l~~-  408 (673)
T 2wv9_A          348 SIAARGYIATRVEAGEAAAIFMTATPPGTSDPFPDT--NSPVH-DVSS--------------EIPDRAWSSGF-EWITD-  408 (673)
T ss_dssp             HHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCCC--SSCEE-EEEC--------------CCCSSCCSSCC-HHHHS-
T ss_pred             HHHHHHHHHHhccccCCcEEEEcCCCChhhhhhccc--CCceE-EEee--------------ecCHHHHHHHH-HHHHh-
Confidence            223333333333 36789999999998774432221  11211 1100              01111111112 22222 


Q ss_pred             CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhh
Q psy1548         353 EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDEND  417 (448)
Q Consensus       353 ~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d  417 (448)
                      .++++||||++++.|+.+++.|++.|+++..+||+    +|.++++.|++|+  ..|+++|+...
T Consensus       409 ~~~~~lVF~~s~~~~e~la~~L~~~g~~v~~lHg~----eR~~v~~~F~~g~--~~VLVaTdv~e  467 (673)
T 2wv9_A          409 YAGKTVWFVASVKMSNEIAQCLQRAGKRVIQLNRK----SYDTEYPKCKNGD--WDFVITTDISE  467 (673)
T ss_dssp             CCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECSS----SHHHHGGGGGTCC--CSEEEECGGGG
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHhCCCeEEEeChH----HHHHHHHHHHCCC--ceEEEECchhh
Confidence            46799999999999999999999999999999994    8999999999987  56777877533

>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=99.93  E-value=1.4e-28  Score=249.41  Aligned_cols=220  Identities=14%  Similarity=0.161  Sum_probs=140.6

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHh
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD  224 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~  224 (448)
                      .+++|+|+++++|||||||++|++|+++.+...  +.+++|++||++|+.|+++.++.+       .+....+..     
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~--~~~~lil~Ptr~La~Q~~~~l~~~-------~v~~~~~~~-----   69 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARR--RLRTLVLAPTRVVLSEMKEAFHGL-------DVKFHTQAF-----   69 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTTTS-------CEEEESSCC-----
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhc--CCeEEEEcchHHHHHHHHHHHhcC-------CeEEecccc-----
Confidence            456799999999999999999999999876543  468999999999999998877643       222111110     


Q ss_pred             HHHHhcCCCcEEEEcHHHHH---------HHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhC-CCCCeEEEE
Q psy1548         225 EEYLKTHNPQIVVGTPGRIL---------ALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSS-PHTKQVMMF  294 (448)
Q Consensus       225 ~~~l~~~~~~IlV~Tp~~l~---------~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l-~~~~q~i~~  294 (448)
                                -.++||+++.         ..+. ....+++++++|+||+|++ +. ++...+..+.... +...|+++|
T Consensus        70 ----------~~v~Tp~~l~~~l~~~~l~~~~~-~~~~~~~l~~vViDEah~~-~~-~~~~~~~~~~~~~~~~~~~~l~~  136 (440)
T 1yks_A           70 ----------SAHGSGREVIDAMCHATLTYRML-EPTRVVNWEVIIMDEAHFL-DP-ASIAARGWAAHRARANESATILM  136 (440)
T ss_dssp             ----------CCCCCSSCCEEEEEHHHHHHHHT-SSSCCCCCSEEEETTTTCC-SH-HHHHHHHHHHHHHHTTSCEEEEE
T ss_pred             ----------eeccCCccceeeecccchhHhhh-CcccccCccEEEEECcccc-Cc-chHHHHHHHHHHhccCCceEEEE
Confidence                      0255554432         2222 2345789999999999998 32 3433333333322 367899999


Q ss_pred             eccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHH
Q psy1548         295 SATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLL  374 (448)
Q Consensus       295 SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L  374 (448)
                      |||+++.+..+...  ..+....               ...++...+...+..+.+  .++++||||++++.|+.+++.|
T Consensus       137 SAT~~~~~~~~~~~--~~~~~~~---------------~~~~~~~~~~~~~~~l~~--~~~~~lVF~~s~~~a~~l~~~L  197 (440)
T 1yks_A          137 TATPPGTSDEFPHS--NGEIEDV---------------QTDIPSEPWNTGHDWILA--DKRPTAWFLPSIRAANVMAASL  197 (440)
T ss_dssp             CSSCTTCCCSSCCC--SSCEEEE---------------ECCCCSSCCSSSCHHHHH--CCSCEEEECSCHHHHHHHHHHH
T ss_pred             eCCCCchhhhhhhc--CCCeeEe---------------eeccChHHHHHHHHHHHh--cCCCEEEEeCCHHHHHHHHHHH
Confidence            99998775433221  1111110               011111111111222222  2579999999999999999999


Q ss_pred             HhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChh
Q psy1548         375 SEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDEN  416 (448)
Q Consensus       375 ~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~  416 (448)
                      ++.|+++..+||    ++|.++++.|++|+  ..|+++|+..
T Consensus       198 ~~~~~~v~~lhg----~~R~~~~~~F~~g~--~~vLVaT~v~  233 (440)
T 1yks_A          198 RKAGKSVVVLNR----KTFEREYPTIKQKK--PDFILATDIA  233 (440)
T ss_dssp             HHTTCCEEECCS----SSCC--------CC--CSEEEESSST
T ss_pred             HHcCCCEEEecc----hhHHHHHhhhcCCC--ceEEEECChh
Confidence            999999999999    46899999999987  5677777753

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.92  E-value=2.8e-26  Score=241.54  Aligned_cols=294  Identities=15%  Similarity=0.184  Sum_probs=161.8

Q ss_pred             Cchhhhhhhccccccceeeee----C-cceeeeccCCChhHHHHHHHHHHhhhccC-------CCeEEEEeeccHHHHHH
Q psy1548         128 DSDTYLHRVARAGRFGTKAVL----G-MDILCQAKSGMGKTAVFVLATLQQLETTD-------SNVYVLVMCHTRELAFQ  195 (448)
Q Consensus       128 ~~~~yQ~~~~~~~~~~~~~~~----g-~~vli~apTGsGKT~~~~l~~l~~l~~~~-------~~~~~lil~Pt~~L~~q  195 (448)
                      ..++||.+      +++.++.    | +++++++|||+|||++++..+ ..+....       .+.++|||+|+++|+.|
T Consensus       178 ~lr~~Q~~------ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~-~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q  250 (590)
T 3h1t_A          178 SPRYYQQI------AINRAVQSVLQGKKRSLITMATGTGKTVVAFQIS-WKLWSARWNRTGDYRKPRILFLADRNVLVDD  250 (590)
T ss_dssp             -CCHHHHH------HHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHH-HHHHHTTCCSSCSSSCCCEEEEEC-------
T ss_pred             CchHHHHH------HHHHHHHHHhcCCCceEEEecCCCChHHHHHHHH-HHHHhcccccccccCCCeEEEEeCCHHHHHH
Confidence            56777999      8887775    4 679999999999999965444 4443332       56799999999999999


Q ss_pred             HH-HHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHC----CCCcCCCeeEEEecchhHHHh
Q psy1548         196 IS-KEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRN----KKLNLSLLKHFILDECDKMLE  270 (448)
Q Consensus       196 ~~-~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~----~~~~~~~i~~lViDEah~l~~  270 (448)
                      +. +.++.+.     ..+..+.++.         .....+|+|+||+++......    ..+...++++||+||||++..
T Consensus       251 ~~~~~~~~~~-----~~~~~~~~~~---------~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~  316 (590)
T 3h1t_A          251 PKDKTFTPFG-----DARHKIEGGK---------VVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSA  316 (590)
T ss_dssp             ----CCTTTC-----SSEEECCC-----------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC----
T ss_pred             HHHHHHHhcc-----hhhhhhhccC---------CCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccc
Confidence            88 6666553     2333333221         122479999999999887642    234567789999999999866


Q ss_pred             hhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCc----cccccccee----------------
Q psy1548         271 QLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDE----AKLTLHGLQ----------------  330 (448)
Q Consensus       271 ~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~----~~~~~~~i~----------------  330 (448)
                      .  ....+..++..++ ..++++||||+..........++..+.....-..    ....+..+.                
T Consensus       317 ~--~~~~~~~il~~~~-~~~~l~lTATP~~~~~~~~~~~f~~~~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~  393 (590)
T 3h1t_A          317 R--DNSNWREILEYFE-PAFQIGMTATPLREDNRDTYRYFGNPIYTYSLRQGIDDGFLAPYRVHRVISEVDAAGWRPSKG  393 (590)
T ss_dssp             -------CHHHHHHST-TSEEEEEESSCSCTTTHHHHHHSCSCSEEECHHHHHHHTSSCCEEEEEEEETTCC--------
T ss_pred             c--chHHHHHHHHhCC-cceEEEeccccccccchhHHHHcCCceEecCHHHHhhCCccCCcEEEEeeeeeeccccccccc
Confidence            3  2355677777775 4679999999875433333333333322110000    000000000                


Q ss_pred             ----------EEEEEcCc-------chHHH----HHHHHHhh-CCCCeEEEEECccHHHHHHHHHHHhCCC--------c
Q psy1548         331 ----------QHYVKLKE-------NEKNK----KLFELLDV-LEFNQVVIFVKSVTRCIALSTLLSEQNF--------P  380 (448)
Q Consensus       331 ----------~~~~~~~~-------~~k~~----~L~~ll~~-~~~~~~IIF~~s~~~a~~l~~~L~~~g~--------~  380 (448)
                                ........       ..+..    .+...+.. ...+++||||+++.+|+.+++.|++.+.        .
T Consensus       394 ~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~i~~~l~~~l~~~~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~  473 (590)
T 3h1t_A          394 DVDRFGREIPDGEYQTKDFERVIALKARTDAFAKHLTDFMKRTDRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDY  473 (590)
T ss_dssp             ---------------CCSHHHHHHHHHTHHHHHHHHHHHHHHHCTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTS
T ss_pred             cccccccccccccCCHHHhhhHhcChHHHHHHHHHHHHHHHhcCCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCe
Confidence                      00000000       01111    23333433 3457999999999999999999987543        2


Q ss_pred             EEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecC-hhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         381 AVSIHRGMTQEERLKKYQEFKDFHKGLAITFASD-ENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       381 ~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~-~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      +..+||+++. +|.+++++|++|+....+.++|+ --..++  ++...-.+-+...|.+...+.||.||
T Consensus       474 ~~~i~g~~~~-~r~~~l~~F~~~~~~~~~ilvtt~~l~~Gi--Dip~v~~Vi~~~~~~s~~~~~Q~iGR  539 (590)
T 3h1t_A          474 VARVTSEEGK-IGKGHLSRFQELETSTPVILTTSQLLTTGV--DAPTCKNVVLARVVNSMSEFKQIVGR  539 (590)
T ss_dssp             EEECSSTTHH-HHHHHHHHHHCTTCCCCCEEEESSTTTTTC--CCTTEEEEEEESCCCCHHHHHHHHTT
T ss_pred             EEEEeCCChH-HHHHHHHHHhCCCCCCCEEEEECChhhcCc--cchheeEEEEEecCCChHHHHHHHhh
Confidence            7889999764 79999999999886544444443 211211  11111112233445666667777777

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.92  E-value=2.6e-25  Score=224.97  Aligned_cols=225  Identities=12%  Similarity=0.130  Sum_probs=152.2

Q ss_pred             eCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEY  227 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~  227 (448)
                      +|+++++++|||||||++|++|+++.+..  .+.+++|++||++|+.|+.+.+.       +..+....|+...      
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~--~g~~~lvl~Pt~~La~Q~~~~~~-------~~~v~~~~~~~~~------   65 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVK--KRLRTVILAPTRVVASEMYEALR-------GEPIRYMTPAVQS------   65 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTT-------TSCEEEC------------
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHh--CCCCEEEECcHHHHHHHHHHHhC-------CCeEEEEecCccc------
Confidence            47899999999999999999999966543  34589999999999999877664       3455554444211      


Q ss_pred             HhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHh-CCCCCeEEEEeccCCccHHHHH
Q psy1548         228 LKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRS-SPHTKQVMMFSATLSKEIRPVC  306 (448)
Q Consensus       228 l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~-l~~~~q~i~~SAT~~~~~~~~~  306 (448)
                      .......+.+.|.+.+...+.. ...+.+++++|+||+|++ +. .+......+... .+...|+++||||+++.+..+.
T Consensus        66 ~~~~~~~~~~~~~~~l~~~l~~-~~~~~~l~~vViDEaH~~-~~-~~~~~~~~l~~~~~~~~~~~l~~SAT~~~~~~~~~  142 (431)
T 2v6i_A           66 ERTGNEIVDFMCHSTFTMKLLQ-GVRVPNYNLYIMDEAHFL-DP-ASVAARGYIETRVSMGDAGAIFMTATPPGTTEAFP  142 (431)
T ss_dssp             ---CCCSEEEEEHHHHHHHHHH-TCCCCCCSEEEEESTTCC-SH-HHHHHHHHHHHHHHTTSCEEEEEESSCTTCCCSSC
T ss_pred             cCCCCceEEEEchHHHHHHHhc-CccccCCCEEEEeCCccC-Cc-cHHHHHHHHHHHhhCCCCcEEEEeCCCCcchhhhc
Confidence            1111245777888888766555 455889999999999987 32 333333333333 2568899999999987643221


Q ss_pred             HHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeC
Q psy1548         307 KKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHR  386 (448)
Q Consensus       307 ~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~  386 (448)
                      ..  ..|.. ....              ..+. .+...+...+... .+++||||+++++|+.+++.|++.|+.+..+||
T Consensus       143 ~~--~~~i~-~~~~--------------~~~~-~~~~~~~~~l~~~-~~~~lVF~~~~~~~~~l~~~L~~~~~~v~~lhg  203 (431)
T 2v6i_A          143 PS--NSPII-DEET--------------RIPD-KAWNSGYEWITEF-DGRTVWFVHSIKQGAEIGTCLQKAGKKVLYLNR  203 (431)
T ss_dssp             CC--SSCCE-EEEC--------------CCCS-SCCSSCCHHHHSC-SSCEEEECSSHHHHHHHHHHHHHTTCCEEEEST
T ss_pred             CC--CCcee-eccc--------------cCCH-HHHHHHHHHHHcC-CCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCC
Confidence            11  11111 1100              0111 1111223334433 568999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         387 GMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       387 ~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                      +    +|.+++++|++|+  ..|+++|+-
T Consensus       204 ~----~r~~~~~~f~~g~--~~vLVaT~v  226 (431)
T 2v6i_A          204 K----TFESEYPKCKSEK--WDFVITTDI  226 (431)
T ss_dssp             T----THHHHTTHHHHSC--CSEEEECGG
T ss_pred             c----cHHHHHHhhcCCC--CeEEEECch
Confidence            7    6789999999997  567777775

>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=99.92  E-value=1.3e-25  Score=228.89  Aligned_cols=252  Identities=13%  Similarity=0.133  Sum_probs=167.8

Q ss_pred             cceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCccc
Q psy1548         142 FGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPI  221 (448)
Q Consensus       142 ~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~  221 (448)
                      ....+..|+++++++|||||||++|++|+++.+..  .+.++||++||++|+.|+.+.+..       ..+....+....
T Consensus        14 ~~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~--~~~~~lvl~Ptr~La~Q~~~~l~g-------~~v~~~~~~~~~   84 (459)
T 2z83_A           14 SPNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQ--QRLRTAVLAPTRVVAAEMAEALRG-------LPVRYQTSAVQR   84 (459)
T ss_dssp             -CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHH--TTCCEEEEECSHHHHHHHHHHTTT-------SCEEECC-----
T ss_pred             HHHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHh--CCCcEEEECchHHHHHHHHHHhcC-------ceEeEEeccccc
Confidence            33445668999999999999999999999987754  346899999999999998887762       222211111100


Q ss_pred             HHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhH-----HHhhhhhHHHHHHHHHhCCCCCeEEEEec
Q psy1548         222 QKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDK-----MLEQLEMRRDVQEIFRSSPHTKQVMMFSA  296 (448)
Q Consensus       222 ~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~-----l~~~~~~~~~~~~i~~~l~~~~q~i~~SA  296 (448)
                      .      ......+.++|.+.+...+... ..++++++||+||||+     ++.. ++.....     .++..|+++|||
T Consensus        85 ~------~t~~~~i~~~~~~~l~~~l~~~-~~l~~~~~iViDEaH~~~~~~~~~~-~~~~~~~-----~~~~~~~il~SA  151 (459)
T 2z83_A           85 E------HQGNEIVDVMCHATLTHRLMSP-NRVPNYNLFVMDEAHFTDPASIAAR-GYIATKV-----ELGEAAAIFMTA  151 (459)
T ss_dssp             ---------CCCSEEEEEHHHHHHHHHSC-C-CCCCSEEEESSTTCCSHHHHHHH-HHHHHHH-----HTTSCEEEEECS
T ss_pred             C------CCCCcEEEEEchHHHHHHhhcc-ccccCCcEEEEECCccCCchhhHHH-HHHHHHh-----ccCCccEEEEEc
Confidence            0      1112457788988887766654 4578999999999998     4443 4433322     236789999999


Q ss_pred             cCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHh
Q psy1548         297 TLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSE  376 (448)
Q Consensus       297 T~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~  376 (448)
                      |++..+..+...  ..|.......               .+. .+...+..++... .+++||||++++.|+.+++.|++
T Consensus       152 T~~~~~~~~~~~--~~pi~~~~~~---------------~~~-~~~~~~~~~l~~~-~~~~LVF~~s~~~~~~l~~~L~~  212 (459)
T 2z83_A          152 TPPGTTDPFPDS--NAPIHDLQDE---------------IPD-RAWSSGYEWITEY-AGKTVWFVASVKMGNEIAMCLQR  212 (459)
T ss_dssp             SCTTCCCSSCCC--SSCEEEEECC---------------CCS-SCCSSCCHHHHHC-CSCEEEECSCHHHHHHHHHHHHH
T ss_pred             CCCcchhhhccC--CCCeEEeccc---------------CCc-chhHHHHHHHHhc-CCCEEEEeCChHHHHHHHHHHHh
Confidence            999775333221  2333221110               000 0001112223333 57999999999999999999999


Q ss_pred             CCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCC------------------------
Q psy1548         377 QNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSI------------------------  432 (448)
Q Consensus       377 ~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~------------------------  432 (448)
                      .|+.+..+||+    +|.++++.|++|+  ..|+++|+....+        ++++.                        
T Consensus       213 ~g~~v~~lh~~----~R~~~~~~f~~g~--~~iLVaT~v~~~G--------iDip~~~VI~~G~~~~~~~~~~~~~~~~~  278 (459)
T 2z83_A          213 AGKKVIQLNRK----SYDTEYPKCKNGD--WDFVITTDISEMG--------ANFGASRVIDCRKSVKPTILEEGEGRVIL  278 (459)
T ss_dssp             TTCCEEEESTT----CCCCCGGGSSSCC--CSEEEESSCC-----------CCCSCSEEEECCEECCEEEECSSSCEEEE
T ss_pred             cCCcEEecCHH----HHHHHHhhccCCC--ceEEEECChHHhC--------eecCCCEEEECCccccccccccccccccc
Confidence            99999999995    7889999999987  5677888754333        33332                        


Q ss_pred             -CCCCccccccccccCC
Q psy1548         433 -SELPDEIDLSTYIEGR  448 (448)
Q Consensus       433 -~~~p~~~~~~~~~~~~  448 (448)
                       .+.|.+...+.++.||
T Consensus       279 ~~d~p~s~~~~~QR~GR  295 (459)
T 2z83_A          279 GNPSPITSASAAQRRGR  295 (459)
T ss_dssp             CSCEECCHHHHHHHHTT
T ss_pred             ccCCCCCHHHHHHhccc
Confidence             3467777778888887

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.90  E-value=5.3e-24  Score=224.61  Aligned_cols=231  Identities=15%  Similarity=0.092  Sum_probs=163.3

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHh
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD  224 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~  224 (448)
                      ..+.|++++++||||||||+.    ++..+...+   ..+|++||++||.|+++.+...     ++++..++|+......
T Consensus       151 r~l~rk~vlv~apTGSGKT~~----al~~l~~~~---~gl~l~PtR~LA~Qi~~~l~~~-----g~~v~lltG~~~~iv~  218 (677)
T 3rc3_A          151 RAMQRKIIFHSGPTNSGKTYH----AIQKYFSAK---SGVYCGPLKLLAHEIFEKSNAA-----GVPCDLVTGEERVTVQ  218 (677)
T ss_dssp             HTSCCEEEEEECCTTSSHHHH----HHHHHHHSS---SEEEEESSHHHHHHHHHHHHHT-----TCCEEEECSSCEECCS
T ss_pred             HhcCCCEEEEEcCCCCCHHHH----HHHHHHhcC---CeEEEeCHHHHHHHHHHHHHhc-----CCcEEEEECCeeEEec
Confidence            456789999999999999983    333333332   3599999999999999998775     6788888888654110


Q ss_pred             HHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCC-CCCeEEEEeccCCccHH
Q psy1548         225 EEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSP-HTKQVMMFSATLSKEIR  303 (448)
Q Consensus       225 ~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~-~~~q~i~~SAT~~~~~~  303 (448)
                         -.....+++++|++.+.        ....++++||||||++.+. ++...+..++..++ ...+++++|||. +.+.
T Consensus       219 ---TpGr~~~il~~T~e~~~--------l~~~v~lvVIDEaH~l~d~-~~g~~~~~~l~~l~~~~i~il~~SAT~-~~i~  285 (677)
T 3rc3_A          219 ---PNGKQASHVSCTVEMCS--------VTTPYEVAVIDEIQMIRDP-ARGWAWTRALLGLCAEEVHLCGEPAAI-DLVM  285 (677)
T ss_dssp             ---TTCCCCSEEEEEGGGCC--------SSSCEEEEEECSGGGGGCT-TTHHHHHHHHHHCCEEEEEEEECGGGH-HHHH
T ss_pred             ---CCCcccceeEecHhHhh--------hcccCCEEEEecceecCCc-cchHHHHHHHHccCccceEEEeccchH-HHHH
Confidence               00012578888886532        2467899999999999887 89999999988887 678999999995 3344


Q ss_pred             HHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEE
Q psy1548         304 PVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVS  383 (448)
Q Consensus       304 ~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~  383 (448)
                      .+.... ..+..+.....    ......    ...     .+ ..+.... ...||||+++++++.+++.|++.|+.+..
T Consensus       286 ~l~~~~-~~~~~v~~~~r----~~~l~~----~~~-----~l-~~l~~~~-~g~iIf~~s~~~ie~la~~L~~~g~~v~~  349 (677)
T 3rc3_A          286 ELMYTT-GEEVEVRDYKR----LTPISV----LDH-----AL-ESLDNLR-PGDCIVCFSKNDIYSVSRQIEIRGLESAV  349 (677)
T ss_dssp             HHHHHH-TCCEEEEECCC----SSCEEE----CSS-----CC-CSGGGCC-TTEEEECSSHHHHHHHHHHHHHTTCCCEE
T ss_pred             HHHHhc-CCceEEEEeee----cchHHH----HHH-----HH-HHHHhcC-CCCEEEEcCHHHHHHHHHHHHhcCCCeee
Confidence            444433 33443322111    011100    000     00 1122223 34589999999999999999999999999


Q ss_pred             EeCCCCHHHHHHHHHHHhcCCCceEEEEecChh
Q psy1548         384 IHRGMTQEERLKKYQEFKDFHKGLAITFASDEN  416 (448)
Q Consensus       384 lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~  416 (448)
                      +||+|++++|.++++.|++++....|.++|+..
T Consensus       350 lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi~  382 (677)
T 3rc3_A          350 IYGSLPPGTKLAQAKKFNDPNDPCKILVATDAI  382 (677)
T ss_dssp             ECTTSCHHHHHHHHHHHHCTTSSCCEEEECGGG
T ss_pred             eeccCCHHHHHHHHHHHHccCCCeEEEEeCcHH
Confidence            999999999999999999944446788887753

>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=99.89  E-value=3e-23  Score=214.08  Aligned_cols=295  Identities=15%  Similarity=0.172  Sum_probs=184.1

Q ss_pred             CCchhhhhhhccccccceee----eeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         127 EDSDTYLHRVARAGRFGTKA----VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       127 ~~~~~yQ~~~~~~~~~~~~~----~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      ..+++||.+      +++.+    ..|+++++..+||+|||++++. ++..+.......++|||||+ .|+.|+.+.+++
T Consensus        36 ~~L~~~Q~~------~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~-~i~~~~~~~~~~~~LIv~P~-~l~~qw~~e~~~  107 (500)
T 1z63_A           36 ANLRPYQIK------GFSWMRFMNKLGFGICLADDMGLGKTLQTIA-VFSDAKKENELTPSLVICPL-SVLKNWEEELSK  107 (500)
T ss_dssp             SCCCHHHHH------HHHHHHHHHHTTCCEEECCCTTSCHHHHHHH-HHHHHHHTTCCSSEEEEECS-TTHHHHHHHHHH
T ss_pred             ccchHHHHH------HHHHHHHHhhCCCCEEEEeCCCCcHHHHHHH-HHHHHHhcCCCCCEEEEccH-HHHHHHHHHHHH
Confidence            446888999      77655    3478999999999999998654 44444433444589999995 688999999999


Q ss_pred             hhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHH
Q psy1548         203 FSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIF  282 (448)
Q Consensus       203 ~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~  282 (448)
                      +..   +.++..+.|+....      ....++|+|+|++.+.....   +....++++|+||||++.+. .  ......+
T Consensus       108 ~~~---~~~v~~~~g~~~~~------~~~~~~ivi~t~~~l~~~~~---l~~~~~~~vIvDEaH~~kn~-~--~~~~~~l  172 (500)
T 1z63_A          108 FAP---HLRFAVFHEDRSKI------KLEDYDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKNP-Q--TKIFKAV  172 (500)
T ss_dssp             HCT---TSCEEECSSSTTSC------CGGGSSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSCT-T--SHHHHHH
T ss_pred             HCC---CceEEEEecCchhc------cccCCcEEEeeHHHHhccch---hcCCCcCEEEEeCccccCCH-h--HHHHHHH
Confidence            873   56777766665321      11237899999999865433   33456789999999998654 2  2233444


Q ss_pred             HhCCCCCeEEEEeccCCc-cHHHH---H---------------------------------HHhcCCCeEEEEcCcc---
Q psy1548         283 RSSPHTKQVMMFSATLSK-EIRPV---C---------------------------------KKFMHDPMEVYVDDEA---  322 (448)
Q Consensus       283 ~~l~~~~q~i~~SAT~~~-~~~~~---~---------------------------------~~~l~~~~~i~~~~~~---  322 (448)
                      ..++ ..+.+++|||+.. ...++   +                                 ..++ .|..+......   
T Consensus       173 ~~l~-~~~~l~LTaTP~~n~~~el~~ll~~l~p~~~~~~~~f~~~~~~~~~~~~~~~~~~l~~~l-~~~~lrr~k~~~~~  250 (500)
T 1z63_A          173 KELK-SKYRIALTGTPIENKVDDLWSIMTFLNPGLLGSYSEFKSKFATPIKKGDNMAKEELKAII-SPFILRRTKYDKAI  250 (500)
T ss_dssp             HTSC-EEEEEEECSSCSTTCHHHHHHHHHHHSTTTTCCHHHHHTTTHHHHHTTCHHHHHHHHHHH-TTTEECCCTTCHHH
T ss_pred             Hhhc-cCcEEEEecCCCCCCHHHHHHHHHHhCCCcCCCHHHHHHHhccccccccHHHHHHHHHHH-hhHeeeecccccch
Confidence            4453 4568999999743 22221   1                                 1111 12222111100   


Q ss_pred             cccccceeEEEEEcC---------------------------------------------------------cchHHHHH
Q psy1548         323 KLTLHGLQQHYVKLK---------------------------------------------------------ENEKNKKL  345 (448)
Q Consensus       323 ~~~~~~i~~~~~~~~---------------------------------------------------------~~~k~~~L  345 (448)
                      ....+......+.++                                                         ...|...+
T Consensus       251 ~~~lp~~~~~~v~~~l~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lr~~~~~p~l~~~~~~~~~~s~K~~~l  330 (500)
T 1z63_A          251 INDLPDKIETNVYCNLTPEQAAMYKAEVENLFNNIDSVTGIKRKGMILSTLLKLKQIVDHPALLKGGEQSVRRSGKMIRT  330 (500)
T ss_dssp             HTTSCSEEEEEEEECCCHHHHHHHHHHHHHHTTTTTTCCTHHHHHHHHHHHHHHHHHTTCTHHHHCSCCCSTTCHHHHHH
T ss_pred             hhcCCCCeEEEEEcCCCHHHHHHHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhCCHHHhcCccchhhcchhHHHH
Confidence            001111111111111                                                         12355555


Q ss_pred             HHHHhhC--CCCeEEEEECccHHHHHHHHHHHhC-CCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHH
Q psy1548         346 FELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQ-NFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILN  422 (448)
Q Consensus       346 ~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~-g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~  422 (448)
                      .+++...  .+.++||||++...++.++..|.+. |+++..+||+++..+|.+++++|+++.....+.++++....++  
T Consensus       331 ~~~l~~~~~~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~~~~~Gl--  408 (500)
T 1z63_A          331 MEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGI--  408 (500)
T ss_dssp             HHHHHHHHTTTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECCCC-CCC--
T ss_pred             HHHHHHHHccCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEecccccCCC--
Confidence            6666543  5679999999999999999999885 9999999999999999999999999853323444444322221  


Q ss_pred             HHHHHhcCCCCCCCccccccccccCC
Q psy1548         423 NVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       423 ~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      ++...-.+-+.+.|-+...+.|+.||
T Consensus       409 nl~~~~~vi~~d~~~~~~~~~Q~~gR  434 (500)
T 1z63_A          409 NLTSANRVIHFDRWWNPAVEDQATDR  434 (500)
T ss_dssp             CCTTCSEEEESSCCSCC---CHHHHT
T ss_pred             chhhCCEEEEeCCCCCcchHHHHHHH
Confidence            22222223445556666667777776

>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=99.88  E-value=1e-23  Score=232.53  Aligned_cols=310  Identities=17%  Similarity=0.135  Sum_probs=196.5

Q ss_pred             CCCCchhhhhhhccccccceeeee--CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVL--GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~--g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      .+..+++||.+      ++..++.  +.++|++++||+|||++++..+...+..+. ..++|||||+ .|+.|+...+.+
T Consensus       150 ~~~~LrpyQ~e------av~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g~-~~rvLIVvP~-sLl~Qw~~E~~~  221 (968)
T 3dmq_A          150 QRTSLIPHQLN------IAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGA-AERVLIIVPE-TLQHQWLVEMLR  221 (968)
T ss_dssp             CSSCCCHHHHH------HHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTSS-CCCEEEECCT-TTHHHHHHHHHH
T ss_pred             CCCCCcHHHHH------HHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhCC-CCeEEEEeCH-HHHHHHHHHHHH
Confidence            34556788999      7766665  458999999999999998777766654443 3479999999 999999988866


Q ss_pred             hhccCCCceEEEEEcCcccHHhHHH-HhcCCCcEEEEcHHHHHHHHHC-CCCcCCCeeEEEecchhHHHhhhh-hHHHHH
Q psy1548         203 FSKYMSNIKVGVFFGGLPIQKDEEY-LKTHNPQIVVGTPGRILALVRN-KKLNLSLLKHFILDECDKMLEQLE-MRRDVQ  279 (448)
Q Consensus       203 ~~~~~~~~~v~~~~g~~~~~~~~~~-l~~~~~~IlV~Tp~~l~~~l~~-~~~~~~~i~~lViDEah~l~~~~~-~~~~~~  279 (448)
                      ..    ++++..+.|+......... ......+|+|+|++.+...... ..+...+++++|+||||++..... ....+.
T Consensus       222 ~f----~l~v~v~~~~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~dlVIvDEAH~~kn~~~~~s~~~~  297 (968)
T 3dmq_A          222 RF----NLRFALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQ  297 (968)
T ss_dssp             HS----CCCCEECCHHHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCCCEEEECCSSCCCCBTTBCCHHHH
T ss_pred             Hh----CCCEEEEccchhhhhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCCCEEEehhhHhhcCCCCcchHHHH
Confidence            55    4555555443321110000 0111368999999987532111 113345788999999999864311 111122


Q ss_pred             HHHHhCCCCCeEEEEeccCCc----cHHHHHHHhcCC-------------------------------------------
Q psy1548         280 EIFRSSPHTKQVMMFSATLSK----EIRPVCKKFMHD-------------------------------------------  312 (448)
Q Consensus       280 ~i~~~l~~~~q~i~~SAT~~~----~~~~~~~~~l~~-------------------------------------------  312 (448)
                      .+........+++++|||+..    ++..++......                                           
T Consensus       298 ~l~~L~~~~~~~L~LTATPi~n~~~el~sll~~L~p~~~~~~~~f~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~L~~~l  377 (968)
T 3dmq_A          298 AIEQLAEHVPGVLLLTATPEQLGMESHFARLRLLDPNRFHDFAQFVEEQKNYCPVADAVAMLLAGNKLSNDELNMLGEMI  377 (968)
T ss_dssp             HHHHHHTTCSSEEESCSSCSSSCSSCTHHHHHHHCTTTCSSTHHHHHHHHHHHHHHHHHHTTTTSCCCCGGGTTSSTTTT
T ss_pred             HHHHHhhcCCcEEEEEcCCccCCHHHHHHHHHhcCccccCCHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHh
Confidence            222222244568999999732    111111110000                                           


Q ss_pred             -------------------------------------CeEEEEcCc--ccccccceeEEE--------------------
Q psy1548         313 -------------------------------------PMEVYVDDE--AKLTLHGLQQHY--------------------  333 (448)
Q Consensus       313 -------------------------------------~~~i~~~~~--~~~~~~~i~~~~--------------------  333 (448)
                                                           ...+.....  ............                    
T Consensus       378 ~~~~~~~l~~~~~~~~~~~~~~~~~~i~~lld~~g~~~~l~r~~r~~i~~~p~r~~~~~~l~~~~~~~~~~~~~~~~~~~  457 (968)
T 3dmq_A          378 GEQDIEPLLQAANSDSEDAQSARQELVSMLMDRHGTSRVLFRNTRNGVKGFPKRELHTIKLPLPTQYQTAIKVSGIMGAR  457 (968)
T ss_dssp             CTTCSSTTGGGTCCCSSCSTTTHHHHHHHHGGGCTTTTTEECCCTTTCCCCCCCCCCEEEECCCHHHHHHHHHHHHTTCC
T ss_pred             cchhhHHHHhcccchhhhhHHHHHHHHHHHHHhhCcchhhhhhhhhhhcccChhheEeeecCCCHHHHHHHHHHhhhhhh
Confidence                                                 000000000  000000000000                    


Q ss_pred             -------------------------EEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHh-CCCcEEEEeCC
Q psy1548         334 -------------------------VKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSE-QNFPAVSIHRG  387 (448)
Q Consensus       334 -------------------------~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~-~g~~~~~lh~~  387 (448)
                                               ..+....|...|..++....++++||||+++..++.++..|++ .|+++..+||+
T Consensus       458 ~~~~~~~~~~l~pe~~~~~l~~~~~~~~~~~~K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~~~lhG~  537 (968)
T 3dmq_A          458 KSAEDRARDMLYPERIYQEFEGDNATWWNFDPRVEWLMGYLTSHRSQKVLVICAKAATALQLEQVLREREGIRAAVFHEG  537 (968)
T ss_dssp             SSGGGGTHHHHCSGGGTTTTTSSSCCTTTTSHHHHHHHHHHHHTSSSCCCEECSSTHHHHHHHHHHHTTTCCCEEEECTT
T ss_pred             hhhHHHHhhhcChHHHHHHhhhhhhcccCccHHHHHHHHHHHhCCCCCEEEEeCcHHHHHHHHHHHHHHcCCcEEEEeCC
Confidence                                     1223446889999999888888999999999999999999995 59999999999


Q ss_pred             CCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         388 MTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       388 ~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      |++.+|.++++.|++|+.++.|+++|+....++  ++...-.+-+.+.|.+...+.++.||
T Consensus       538 ~~~~~R~~~l~~F~~g~~~~~vLvaT~v~~~Gl--Dl~~~~~VI~~d~p~~~~~~~Q~~GR  596 (968)
T 3dmq_A          538 MSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGR--NFQFASHMVMFDLPFNPDLLEQRIGR  596 (968)
T ss_dssp             SCTTHHHHHHHHHHSTTSSCEEEECSCCTTCSS--CCTTCCEEECSSCCSSHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHhCCCCcccEEEecchhhcCC--CcccCcEEEEecCCCCHHHHHHHhhc
Confidence            999999999999999987788888886533332  33333334456667667777777776

>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=99.88  E-value=4.1e-23  Score=188.61  Aligned_cols=160  Identities=20%  Similarity=0.243  Sum_probs=116.2

Q ss_pred             CchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhcc---CCCeEEEEeeccHHHHHH-HHHHHHHh
Q psy1548         128 DSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETT---DSNVYVLVMCHTRELAFQ-ISKEYERF  203 (448)
Q Consensus       128 ~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~---~~~~~~lil~Pt~~L~~q-~~~~~~~~  203 (448)
                      ..++||.+      +++.++.|+++++.+|||+|||++++++++..+...   ..+.++||++|+++|+.| +.+.+..+
T Consensus        33 ~l~~~Q~~------~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~~~~  106 (216)
T 3b6e_A           33 QLRPYQME------VAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPF  106 (216)
T ss_dssp             CCCHHHHH------HHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTHHHH
T ss_pred             CchHHHHH------HHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHHHHH
Confidence            34555999      999999999999999999999999999998776442   235689999999999999 77888888


Q ss_pred             hccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCC------CcCCCeeEEEecchhHHHhhhhhHHH
Q psy1548         204 SKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK------LNLSLLKHFILDECDKMLEQLEMRRD  277 (448)
Q Consensus       204 ~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~------~~~~~i~~lViDEah~l~~~~~~~~~  277 (448)
                      ...  ++++..+.|+.........+... ++|+|+||+++...+....      ..+.+++++|+||||++.+. ++...
T Consensus       107 ~~~--~~~v~~~~g~~~~~~~~~~~~~~-~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~~~~-~~~~~  182 (216)
T 3b6e_A          107 LKK--WYRVIGLSGDTQLKISFPEVVKS-CDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKE-AVYNN  182 (216)
T ss_dssp             HTT--TSCEEECCC---CCCCHHHHHHH-CSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC--------CHHH
T ss_pred             hcc--CceEEEEeCCcccchhHHhhccC-CCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchhhccC-CcHHH
Confidence            754  57888888887655544444443 7999999999999887643      56788999999999999775 45444


Q ss_pred             HH-HHHHhC-------------CCCCeEEEEecc
Q psy1548         278 VQ-EIFRSS-------------PHTKQVMMFSAT  297 (448)
Q Consensus       278 ~~-~i~~~l-------------~~~~q~i~~SAT  297 (448)
                      +. .++...             .+..+++++|||
T Consensus       183 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          183 IMRHYLMQKLKNNRLKKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCCCCCCEEEEEECC
T ss_pred             HHHHHHHHhcccccccccccCCCCcceEEEeecC
Confidence            43 322211             156799999998

>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=99.87  E-value=1e-21  Score=182.40  Aligned_cols=169  Identities=15%  Similarity=0.218  Sum_probs=126.4

Q ss_pred             CCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCC--CeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         127 EDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDS--NVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       127 ~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~--~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .++..+|.+      +++.+..|+++++.||||||||.++.++++........  +.++++++|+++|+.|+.+.+....
T Consensus        60 ~p~~~~q~~------~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~  133 (235)
T 3llm_A           60 LPVKKFESE------ILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFER  133 (235)
T ss_dssp             SGGGGGHHH------HHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTT
T ss_pred             CChHHHHHH------HHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHh
Confidence            345666999      99999999999999999999999999998886654432  4589999999999999988877655


Q ss_pred             ccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHH-HhhhhhH-HHHHHHH
Q psy1548         205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM-LEQLEMR-RDVQEIF  282 (448)
Q Consensus       205 ~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l-~~~~~~~-~~~~~i~  282 (448)
                      ....+..++.-......      .....++|+|+||+++.+++..   .+++++++|+||||.+ ++. ++. ..+..++
T Consensus       134 ~~~~~~~~g~~~~~~~~------~~~~~~~Ivv~Tpg~l~~~l~~---~l~~~~~lVlDEah~~~~~~-~~~~~~l~~i~  203 (235)
T 3llm_A          134 GEEPGKSCGYSVRFESI------LPRPHASIMFCTVGVLLRKLEA---GIRGISHVIVDEIHERDINT-DFLLVVLRDVV  203 (235)
T ss_dssp             TCCTTSSEEEEETTEEE------CCCSSSEEEEEEHHHHHHHHHH---CCTTCCEEEECCTTSCCHHH-HHHHHHHHHHH
T ss_pred             ccccCceEEEeechhhc------cCCCCCeEEEECHHHHHHHHHh---hhcCCcEEEEECCccCCcch-HHHHHHHHHHH
Confidence            43224444433222111      1112478999999999999876   3789999999999986 565 666 4666666


Q ss_pred             HhCCCCCeEEEEeccCCccHHHHHHHhcCCCe
Q psy1548         283 RSSPHTKQVMMFSATLSKEIRPVCKKFMHDPM  314 (448)
Q Consensus       283 ~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~  314 (448)
                      ... ++.|+++||||++.+.  +.+.+...|.
T Consensus       204 ~~~-~~~~~il~SAT~~~~~--~~~~~~~~pv  232 (235)
T 3llm_A          204 QAY-PEVRIVLMSATIDTSM--FCEYFFNCPI  232 (235)
T ss_dssp             HHC-TTSEEEEEECSSCCHH--HHHHTTSCCC
T ss_pred             hhC-CCCeEEEEecCCCHHH--HHHHcCCCCE
Confidence            665 4789999999999775  5555555554

>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=99.86  E-value=3.4e-21  Score=211.41  Aligned_cols=153  Identities=19%  Similarity=0.186  Sum_probs=113.5

Q ss_pred             chhhhhhhccccccceeeee--------------CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHH
Q psy1548         129 SDTYLHRVARAGRFGTKAVL--------------GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAF  194 (448)
Q Consensus       129 ~~~yQ~~~~~~~~~~~~~~~--------------g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~  194 (448)
                      .++||.+      +++.++.              +++++++++||||||+++ ++++..+...+...++|||+|+++|+.
T Consensus       272 ~R~~Q~~------AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~~~~~~rvLvlvpr~eL~~  344 (1038)
T 2w00_A          272 MRPYQIA------ATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATELDFIDKVFFVVDRKDLDY  344 (1038)
T ss_dssp             CCHHHHH------HHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTTCTTCCEEEEEECGGGCCH
T ss_pred             CCHHHHH------HHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHhcCCCceEEEEeCcHHHHH
Confidence            4566999      8877664              378999999999999997 666665544344469999999999999


Q ss_pred             HHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCC--CcCCCeeEEEecchhHHHhhh
Q psy1548         195 QISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKK--LNLSLLKHFILDECDKMLEQL  272 (448)
Q Consensus       195 q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~--~~~~~i~~lViDEah~l~~~~  272 (448)
                      |+.+.+..+....       +.++.+.......+....++|+|+||+++..++....  ..+....+||+||||++... 
T Consensus       345 Q~~~~f~~f~~~~-------v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~~~~~~lvIiDEAHrs~~~-  416 (1038)
T 2w00_A          345 QTMKEYQRFSPDS-------VNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQFG-  416 (1038)
T ss_dssp             HHHHHHHTTSTTC-------SSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGGGGSCEEEEEESCCTTHHH-
T ss_pred             HHHHHHHHhcccc-------cccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccchhccccccEEEEEccchhcch-
Confidence            9999998876421       1244444445555554458999999999998876432  23567889999999997653 


Q ss_pred             hhHHHHHHHHHhCCCCCeEEEEeccCCc
Q psy1548         273 EMRRDVQEIFRSSPHTKQVMMFSATLSK  300 (448)
Q Consensus       273 ~~~~~~~~i~~~l~~~~q~i~~SAT~~~  300 (448)
                      +   .+..+...+| +.++++||||+..
T Consensus       417 ~---~~~~I~~~~p-~a~~lgfTATP~~  440 (1038)
T 2w00_A          417 E---AQKNLKKKFK-RYYQFGFTGTPIF  440 (1038)
T ss_dssp             H---HHHHHHHHCS-SEEEEEEESSCCC
T ss_pred             H---HHHHHHHhCC-cccEEEEeCCccc
Confidence            3   3455666675 4789999999864

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.85  E-value=4.1e-20  Score=194.20  Aligned_cols=128  Identities=23%  Similarity=0.168  Sum_probs=109.5

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      + .|+++   |..      ++|.++.|+  +.+++||+|||++|.+|++.....   +.+++|++||++||.|.++.+..
T Consensus        78 ~-~Pt~V---Q~~------~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~---G~qv~VvTPTreLA~Qdae~m~~  142 (997)
T 2ipc_A           78 M-RHFDV---QLI------GGAVLHEGK--IAEMKTGEGKTLVATLAVALNALT---GKGVHVVTVNDYLARRDAEWMGP  142 (997)
T ss_dssp             C-CCCHH---HHH------HHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTT---CSCCEEEESSHHHHHHHHHHHHH
T ss_pred             C-CCcHH---HHh------hcccccCCc--eeeccCCCchHHHHHHHHHHHHHh---CCCEEEEeCCHHHHHHHHHHHHH
Confidence            7 89999   999      999999998  999999999999999999644332   34799999999999999999999


Q ss_pred             hhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHH-HHHHHCC------CCcCC---CeeEEEecchhHHH
Q psy1548         203 FSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRI-LALVRNK------KLNLS---LLKHFILDECDKML  269 (448)
Q Consensus       203 ~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l-~~~l~~~------~~~~~---~i~~lViDEah~l~  269 (448)
                      +...+ ++++++++|+.+.....  ...+ ++|+||||+++ .+++..+      .+.++   .+.++|+||+|.|+
T Consensus       143 l~~~l-GLsv~~i~Gg~~~~~r~--~ay~-~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDsmL  215 (997)
T 2ipc_A          143 VYRGL-GLSVGVIQHASTPAERR--KAYL-ADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSIL  215 (997)
T ss_dssp             HHHTT-TCCEEECCTTCCHHHHH--HHHT-SSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHHHT
T ss_pred             HHHhc-CCeEEEEeCCCCHHHHH--HHcC-CCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHHHH
Confidence            99998 99999999998744333  2233 89999999999 7888755      24567   89999999999987

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.84  E-value=4.1e-21  Score=208.49  Aligned_cols=272  Identities=14%  Similarity=0.125  Sum_probs=177.4

Q ss_pred             CCchhhhhhhccccccceeee----eCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         127 EDSDTYLHRVARAGRFGTKAV----LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       127 ~~~~~yQ~~~~~~~~~~~~~~----~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      ..+++||.+      ++..+.    .|++.|++.+||+|||+.++..+...+........+||||| ..|+.|+.+.+.+
T Consensus       235 ~~Lr~yQ~e------gv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P-~sll~qW~~E~~~  307 (800)
T 3mwy_W          235 GELRDFQLT------GINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVP-LSTMPAWLDTFEK  307 (800)
T ss_dssp             SCCCTHHHH------HHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECC-TTTHHHHHHHHHH
T ss_pred             CCcCHHHHH------HHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEEC-chHHHHHHHHHHH
Confidence            457899999      776554    68999999999999999876665554444444457999999 6788999999998


Q ss_pred             hhccCCCceEEEEEcCcccHHhHHHH-----------hcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhh
Q psy1548         203 FSKYMSNIKVGVFFGGLPIQKDEEYL-----------KTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQ  271 (448)
Q Consensus       203 ~~~~~~~~~v~~~~g~~~~~~~~~~l-----------~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~  271 (448)
                      +.   |++++.++.|+..........           ....++|+|+|++.+......  +....+++||+||||++-..
T Consensus       308 ~~---p~~~v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~--l~~~~w~~vIvDEaH~lkn~  382 (800)
T 3mwy_W          308 WA---PDLNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAE--LGSIKWQFMAVDEAHRLKNA  382 (800)
T ss_dssp             HS---TTCCEEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHH--HHTSEEEEEEETTGGGGCCS
T ss_pred             HC---CCceEEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHH--HhcCCcceeehhhhhhhcCc
Confidence            87   477888888776544332221           123478999999998654321  22235789999999988442


Q ss_pred             hhhHHHHHHHHHhCCCCCeEEEEeccCC-cc---HHHHHHHhcCC-----------------------------CeEEEE
Q psy1548         272 LEMRRDVQEIFRSSPHTKQVMMFSATLS-KE---IRPVCKKFMHD-----------------------------PMEVYV  318 (448)
Q Consensus       272 ~~~~~~~~~i~~~l~~~~q~i~~SAT~~-~~---~~~~~~~~l~~-----------------------------~~~i~~  318 (448)
                         .......+..++ ....+++|||+- +.   +..++..+...                             |..+.-
T Consensus       383 ---~s~~~~~l~~l~-~~~rl~LTgTPiqN~l~el~~ll~fL~p~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~p~~lRR  458 (800)
T 3mwy_W          383 ---ESSLYESLNSFK-VANRMLITGTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRR  458 (800)
T ss_dssp             ---SSHHHHHHTTSE-EEEEEEECSCCCSSCSHHHHHHHHHHCSCCC---------CCTTHHHHHHHHHHHTTGGGEEEC
T ss_pred             ---hhHHHHHHHHhh-hccEEEeeCCcCCCCHHHHHHHHHHhCccccCchhhhcccccchhHHHHHHHHHHHHhHHHhhh
Confidence               223333444443 345688999962 22   22222222111                             111110


Q ss_pred             cCcc-cccccceeEEEEEcC------------------------------------------------------------
Q psy1548         319 DDEA-KLTLHGLQQHYVKLK------------------------------------------------------------  337 (448)
Q Consensus       319 ~~~~-~~~~~~i~~~~~~~~------------------------------------------------------------  337 (448)
                      .... ....+......+.+.                                                            
T Consensus       459 ~k~dv~~~LP~k~~~~v~v~ls~~q~~~Y~~i~~~~~~~l~~~~~~~~~~~l~~l~~Lrk~~~hp~l~~~~~~~~~~~~~  538 (800)
T 3mwy_W          459 LKKDVEKSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLFDNAEERVLQKFG  538 (800)
T ss_dssp             CGGGGTTTSCCEEEEEEEECCCHHHHHHHHHHHHHCCC----------CTHHHHHHHHHHHHHCGGGSSSHHHHHCCCC-
T ss_pred             hHHhhhhccCCcEEEEEEeCCCHHHHHHHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHhcChhhhcchHHHHHHhcc
Confidence            0000 000011111111110                                                            


Q ss_pred             ---------------cchHHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHH
Q psy1548         338 ---------------ENEKNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEF  400 (448)
Q Consensus       338 ---------------~~~k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F  400 (448)
                                     ...|...|..++...  .+.++||||.....++.|...|...|+++..+||+++..+|.++++.|
T Consensus       539 ~~~~~~~~~~~~l~~~s~K~~~L~~lL~~~~~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F  618 (800)
T 3mwy_W          539 DGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHF  618 (800)
T ss_dssp             ---CCSHHHHHHHHHTCHHHHHHHHHHHHHTTTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTT
T ss_pred             cccccHHHHHHHhhhcChHHHHHHHHHHHHhhCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHh
Confidence                           123566667777654  456999999999999999999999999999999999999999999999


Q ss_pred             hcCCCceEEEEecC
Q psy1548         401 KDFHKGLAITFASD  414 (448)
Q Consensus       401 ~~g~~g~~I~~~t~  414 (448)
                      +++..+.-+.++++
T Consensus       619 ~~~~~~~~v~LlSt  632 (800)
T 3mwy_W          619 NSPDSNDFVFLLST  632 (800)
T ss_dssp             SSTTCSCCCEEEEH
T ss_pred             hCCCCCceEEEEec
Confidence            99876543444433

>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=99.83  E-value=2.4e-20  Score=178.00  Aligned_cols=153  Identities=15%  Similarity=0.203  Sum_probs=120.8

Q ss_pred             chhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCC
Q psy1548         129 SDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS  208 (448)
Q Consensus       129 ~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  208 (448)
                      .++||.+      +++.++.+++.++++|||+|||++++.++...+...  ..++||++|+++|+.|+.+.++++.... 
T Consensus       114 l~~~Q~~------ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~--~~~~lil~Pt~~L~~q~~~~l~~~~~~~-  184 (282)
T 1rif_A          114 PHWYQKD------AVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY--EGKILIIVPTTALTTQMADDFVDYRLFS-  184 (282)
T ss_dssp             CCHHHHH------HHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHC--SSEEEEECSSHHHHHHHHHHHHHHTSCC-
T ss_pred             ccHHHHH------HHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcC--CCeEEEEECCHHHHHHHHHHHHHhcccc-
Confidence            3445999      999888888899999999999999988887766532  3389999999999999999999987654 


Q ss_pred             CceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCC
Q psy1548         209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHT  288 (448)
Q Consensus       209 ~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~  288 (448)
                      ...+..++++.....    ......+|+|+||+.+..   .....+.+++++|+||||++..     ..+..++..+...
T Consensus       185 ~~~~~~~~~~~~~~~----~~~~~~~I~v~T~~~l~~---~~~~~~~~~~~vIiDEaH~~~~-----~~~~~il~~~~~~  252 (282)
T 1rif_A          185 HAMIKKIGGGASKDD----KYKNDAPVVVGTWQTVVK---QPKEWFSQFGMMMNDECHLATG-----KSISSIISGLNNC  252 (282)
T ss_dssp             GGGEEECSTTCSSTT----CCCTTCSEEEECHHHHTT---SCGGGGGGEEEEEEETGGGCCH-----HHHHHHTTTCTTC
T ss_pred             cceEEEEeCCCcchh----hhccCCcEEEEchHHHHh---hHHHHHhhCCEEEEECCccCCc-----ccHHHHHHHhhcC
Confidence            677888888765432    111247999999987643   2334568899999999998864     2567777888778


Q ss_pred             CeEEEEeccCCccH
Q psy1548         289 KQVMMFSATLSKEI  302 (448)
Q Consensus       289 ~q~i~~SAT~~~~~  302 (448)
                      .+++++|||+++..
T Consensus       253 ~~~l~lSATp~~~~  266 (282)
T 1rif_A          253 MFKFGLSGSLRDGK  266 (282)
T ss_dssp             CEEEEECSSCCTTS
T ss_pred             CeEEEEeCCCCCcc
Confidence            99999999998754

>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=99.82  E-value=4e-19  Score=188.29  Aligned_cols=272  Identities=13%  Similarity=0.072  Sum_probs=167.8

Q ss_pred             Cchhhhhhhccccccceee---------eeCcceeeeccCCChhHHHHHHHHHHhhhccC----CCeEEEEeeccHHHHH
Q psy1548         128 DSDTYLHRVARAGRFGTKA---------VLGMDILCQAKSGMGKTAVFVLATLQQLETTD----SNVYVLVMCHTRELAF  194 (448)
Q Consensus       128 ~~~~yQ~~~~~~~~~~~~~---------~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~----~~~~~lil~Pt~~L~~  194 (448)
                      .+++||.+      ++..+         ..++..|+..+||+|||+.++..+...+...+    ...++|||||+ .|+.
T Consensus        55 ~LrpyQ~~------gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~~~~~p~~~~~LiV~P~-sll~  127 (644)
T 1z3i_X           55 VLRPHQRE------GVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVR  127 (644)
T ss_dssp             TCCHHHHH------HHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHH
T ss_pred             cccHHHHH------HHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHhCccccCCCCcEEEEecH-HHHH
Confidence            46788999      66554         34578999999999999998766665544332    23469999997 7889


Q ss_pred             HHHHHHHHhhccCCCceEEEEEcCcccHHh--HHHHhc-----CCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhH
Q psy1548         195 QISKEYERFSKYMSNIKVGVFFGGLPIQKD--EEYLKT-----HNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDK  267 (448)
Q Consensus       195 q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~--~~~l~~-----~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~  267 (448)
                      |+.+++.++...  .+.+..+.++......  ......     ...+|+|+|++.+....  ..+....++++|+||||+
T Consensus       128 qW~~E~~~~~~~--~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~--~~l~~~~~~~vI~DEaH~  203 (644)
T 1z3i_X          128 NWYNEVGKWLGG--RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHA--EVLHKGKVGLVICDEGHR  203 (644)
T ss_dssp             HHHHHHHHHHGG--GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHT--TTTTTSCCCEEEETTGGG
T ss_pred             HHHHHHHHHcCC--CeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhH--HHhhcCCccEEEEECcee
Confidence            999999998754  3566666666432211  111111     13689999999987543  334445678999999998


Q ss_pred             HHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCcc----HHHHH---------------HHhc------------------
Q psy1548         268 MLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKE----IRPVC---------------KKFM------------------  310 (448)
Q Consensus       268 l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~----~~~~~---------------~~~l------------------  310 (448)
                      +-+. . ...... +..++ ....+++|||+-.+    +..++               +.|.                  
T Consensus       204 ikn~-~-~~~~~a-l~~l~-~~~rl~LTgTPiqN~l~El~sll~fl~p~~l~~~~~F~~~f~~pi~~~~~~~~~~~~~~~  279 (644)
T 1z3i_X          204 LKNS-D-NQTYLA-LNSMN-AQRRVLISGTPIQNDLLEYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDADASDKDRAA  279 (644)
T ss_dssp             CCTT-C-HHHHHH-HHHHC-CSEEEEECSSCSGGGGGGCHHHHHHHHHHHHCCHHHHHHHTHHHHHHHHSTTCCSHHHHH
T ss_pred             cCCh-h-hHHHHH-HHhcc-cCcEEEEecCcccCCHHHHHHHHHhhCCCcCCCHHHHHHhhcchhhhcCCcCCCHHHHHH
Confidence            8553 1 222222 23333 45679999996321    11000               0000                  


Q ss_pred             -----------CCCeEEEEcCcc-cccccceeEEEEEc------------------------------------------
Q psy1548         311 -----------HDPMEVYVDDEA-KLTLHGLQQHYVKL------------------------------------------  336 (448)
Q Consensus       311 -----------~~~~~i~~~~~~-~~~~~~i~~~~~~~------------------------------------------  336 (448)
                                 -.|..+.-.... ....+......+.+                                          
T Consensus       280 ~~~~~~~L~~~l~~~~lRR~k~~v~~~LP~k~~~~v~~~ls~~q~~lY~~~~~~~~~~~~~~~g~~~~~~l~~l~~Lrk~  359 (644)
T 1z3i_X          280 GEQKLQELISIVNRCLIRRTSDILSKYLPVKIEQVVCCNLTPLQKELYKLFLKQAKPVESLQTGKISVSSLSSITSLKKL  359 (644)
T ss_dssp             HHHHHHHHHHHHHHHEECCCGGGGGGTSCCEEEEEEEECCCHHHHHHHHHHHHHHCGGGSSCTTCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhhHHhHhhhCCCceEEEEEeCCCHHHHHHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHH
Confidence                       000000000000 00000000111110                                          


Q ss_pred             ------------------------------------CcchHHHHHHHHHhh---CCCCeEEEEECccHHHHHHHHHHHhC
Q psy1548         337 ------------------------------------KENEKNKKLFELLDV---LEFNQVVIFVKSVTRCIALSTLLSEQ  377 (448)
Q Consensus       337 ------------------------------------~~~~k~~~L~~ll~~---~~~~~~IIF~~s~~~a~~l~~~L~~~  377 (448)
                                                          ....|...+..++..   ..+.++||||++...++.+...|...
T Consensus       360 c~hp~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~K~~~l~~ll~~~~~~~~~k~lIFs~~~~~~~~l~~~l~~~  439 (644)
T 1z3i_X          360 CNHPALIYEKCLTGEEGFDGALDLFPQNYSTKAVEPQLSGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNR  439 (644)
T ss_dssp             HHCTHHHHHHHHHTCTTCTTGGGTSCSSCCSSSCCGGGSHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHhcccchhhhHHhhccccccccccCcccChHHHHHHHHHHHHhhcCCCEEEEEEccHHHHHHHHHHHHHC
Confidence                                                012344445454443   24679999999999999999999999


Q ss_pred             CCcEEEEeCCCCHHHHHHHHHHHhcCCCce-EEEEecC
Q psy1548         378 NFPAVSIHRGMTQEERLKKYQEFKDFHKGL-AITFASD  414 (448)
Q Consensus       378 g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~-~I~~~t~  414 (448)
                      |+.+..+||+++..+|.+++++|+++..+. .+++.+.
T Consensus       440 g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st~  477 (644)
T 1z3i_X          440 RYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSSK  477 (644)
T ss_dssp             TCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGG
T ss_pred             CCCEEEEeCCCCHHHHHHHHHHhcCCCCCcEEEEEecc
Confidence            999999999999999999999999988654 3444443

>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=99.81  E-value=4.3e-19  Score=183.42  Aligned_cols=296  Identities=16%  Similarity=0.141  Sum_probs=203.1

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .|..+   |..      ..-.+..|+  |....||+|||+++.+|++-....   |..+.|++|+..||.|-.+++..+.
T Consensus        75 r~~dv---Qli------gg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~---G~~vhVvT~ndyLA~rdae~m~~l~  140 (822)
T 3jux_A           75 RPFDV---QVM------GGIALHEGK--VAEMKTGEGKTLAATMPIYLNALI---GKGVHLVTVNDYLARRDALWMGPVY  140 (822)
T ss_dssp             CCCHH---HHH------HHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTT---SSCEEEEESSHHHHHHHHHHHHHHH
T ss_pred             CCcHH---HHH------HHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhc---CCceEEEeccHHHHHhHHHHHHHHH
Confidence            57778   888      555556666  899999999999999998754433   3469999999999999999999999


Q ss_pred             ccCCCceEEEEEcC--------------------------------------------------cccHHhHHHHhcCCCc
Q psy1548         205 KYMSNIKVGVFFGG--------------------------------------------------LPIQKDEEYLKTHNPQ  234 (448)
Q Consensus       205 ~~~~~~~v~~~~g~--------------------------------------------------~~~~~~~~~l~~~~~~  234 (448)
                      ..+ ++++++++..                                                  .+........   .++
T Consensus       141 ~~L-glsvg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~err~aY---~~D  216 (822)
T 3jux_A          141 LFL-GLRVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEITRKEAY---LCD  216 (822)
T ss_dssp             HHT-TCCEEEEETTTEEEEEEESSHHHHHHHHHTTCCSSCTTCCSSSCCGGGSCHHHHTTTCEECCBCCHHHHH---HSS
T ss_pred             HHh-CCEEEEEcCCCcccccccccchhhhhhhcccccccccccccccccccccccccchhccccCCHHHHHHHh---cCC
Confidence            999 9999999982                                                  1111222222   269


Q ss_pred             EEEEcHHHH-HHHHHCC------CCcCCCeeEEEecchhHHHhh---------------hhhHHHHHHHHHhC-------
Q psy1548         235 IVVGTPGRI-LALVRNK------KLNLSLLKHFILDECDKMLEQ---------------LEMRRDVQEIFRSS-------  285 (448)
Q Consensus       235 IlV~Tp~~l-~~~l~~~------~~~~~~i~~lViDEah~l~~~---------------~~~~~~~~~i~~~l-------  285 (448)
                      |.+||..-+ .++|+.+      ..-...+.+.|+||+|.++=+               ......+..+.+.+       
T Consensus       217 ItYgTn~EfgFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiLIDeArtPLiISg~~~~~~~~y~~~~~~v~~l~~~~dy~  296 (822)
T 3jux_A          217 VTYGTNNEFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVLIDEARTPLIISGPSKESPSVYRRFAQIAKKFVKDKDFT  296 (822)
T ss_dssp             EEEEEHHHHHHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHHTTGGGSCEEEECCCCSCHHHHHHHHHHTTSSCBTTTEE
T ss_pred             CEEccCcchhhHhHHhhccCCHHHhccCCCCeEEEecccceeecCCCCCceeeCCCCCccHHHHHHHHHHHhcCcCCcEE
Confidence            999999887 3455432      223466789999999977532               00111111111100       


Q ss_pred             -------------------------------------------------CCC----------------------------
Q psy1548         286 -------------------------------------------------PHT----------------------------  288 (448)
Q Consensus       286 -------------------------------------------------~~~----------------------------  288 (448)
                                                                       ..+                            
T Consensus       297 vdek~~~v~lTe~G~~~~E~~l~i~nly~~~n~~l~~~i~~AL~A~~l~~~d~dYiV~dg~V~iVDe~TGR~m~grr~s~  376 (822)
T 3jux_A          297 VDEKARTIILTEEGVAKAEKIIGVENLYDPGNVSLLYHLINALKALHLFKKDVDYVVMNGEVIIVDEFTGRLLPGRRYSG  376 (822)
T ss_dssp             ECCSSSCEEECHHHHHHHHHHHTCSCTTSGGGHHHHHHHHHHHHHHHHSTTTSSEEEETTEEEECSSSSCSCCCSCCCGG
T ss_pred             EEcccCeEEECHHHHHHHHHHhCCccccchhhhHHHHHHHHHHHHHHHHcCCCcEEEECCEEEEEECCCCcCCCCCcCch
Confidence                                                             000                            


Q ss_pred             ---------------------------------CeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeE-EEE
Q psy1548         289 ---------------------------------KQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQ-HYV  334 (448)
Q Consensus       289 ---------------------------------~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~-~~~  334 (448)
                                                       .++.+||+|+..+..++...|.-+  .+.+...  .....+.+ ..+
T Consensus       377 GLHQaiEaKEgv~i~~e~~tla~IT~Qn~Fr~Y~kL~GMTGTa~te~~Ef~~iY~l~--vv~IPtn--kp~~R~d~~d~v  452 (822)
T 3jux_A          377 GLHQAIEAKEGVPIKEESITYATITFQNYFRMYEKLAGMTGTAKTEESEFVQVYGME--VVVIPTH--KPMIRKDHDDLV  452 (822)
T ss_dssp             GHHHHHHHHHSSCCCCCCCEEEEECHHHHHTTSSEEEEEESSCGGGHHHHHHHSCCC--EEECCCS--SCCCCEECCCEE
T ss_pred             HHHHHHHHHcCCCCCCCcchhHHHHHHHHHHHhhHHeEECCCCchHHHHHHHHhCCe--EEEECCC--CCcceeecCcEE
Confidence                                             257999999988877776666433  3333222  12222222 356


Q ss_pred             EcCcchHHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEe
Q psy1548         335 KLKENEKNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFA  412 (448)
Q Consensus       335 ~~~~~~k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~  412 (448)
                      .....+|...+...+...  .+.++||||+|++.++.++..|++.|+++..+||+..+.+|..+.+.|+.|    .|+++
T Consensus       453 y~t~~eK~~al~~~I~~~~~~gqpVLVFt~S~e~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g----~VtVA  528 (822)
T 3jux_A          453 FRTQKEKYEKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKG----MVTIA  528 (822)
T ss_dssp             ESSHHHHHHHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTT----CEEEE
T ss_pred             EecHHHHHHHHHHHHHHHhhCCCCEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCC----eEEEE
Confidence            677888999998888653  467899999999999999999999999999999996666666666666554    47888


Q ss_pred             cChhhHHHHHHHH--------HHhcCCCCCCCccccccccccCC
Q psy1548         413 SDENDAKILNNVQ--------DRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       413 t~~~d~~~l~~i~--------~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      |+-.-+++  +|.        ..+.+-..++|++...+.++.||
T Consensus       529 TdmAgRGt--DI~lg~~V~~~GglhVInte~Pes~r~y~qriGR  570 (822)
T 3jux_A          529 TNMAGRGT--DIKLGPGVAELGGLCIIGTERHESRRIDNQLRGR  570 (822)
T ss_dssp             ETTTTTTC--CCCCCTTTTTTTSCEEEESSCCSSHHHHHHHHTT
T ss_pred             cchhhCCc--CccCCcchhhcCCCEEEecCCCCCHHHHHHhhCc
Confidence            76432222  221        22345567888888888888887

>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=99.73  E-value=6.6e-18  Score=156.77  Aligned_cols=142  Identities=20%  Similarity=0.151  Sum_probs=108.8

Q ss_pred             cCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         124 DMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       124 ~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      ..+...++||.+      +++.++.++++++++|||+|||.+++.++...      +.+++|++|+++|+.|+.+.+.++
T Consensus        89 ~~~~~l~~~Q~~------ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~------~~~~liv~P~~~L~~q~~~~~~~~  156 (237)
T 2fz4_A           89 DAEISLRDYQEK------ALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIF  156 (237)
T ss_dssp             CCCCCCCHHHHH------HHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS------CSCEEEEESSHHHHHHHHHHHGGG
T ss_pred             cCCCCcCHHHHH------HHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc------CCCEEEEeCCHHHHHHHHHHHHhC
Confidence            334456777999      99888888999999999999999988877653      347999999999999998888873


Q ss_pred             hccCCCce-EEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHH
Q psy1548         204 SKYMSNIK-VGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIF  282 (448)
Q Consensus       204 ~~~~~~~~-v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~  282 (448)
                           +++ +..+.|+...          ..+|+|+|++.+......   ...+++++|+||||++.+. .+.    .++
T Consensus       157 -----~~~~v~~~~g~~~~----------~~~i~v~T~~~l~~~~~~---~~~~~~llIiDEaH~l~~~-~~~----~i~  213 (237)
T 2fz4_A          157 -----GEEYVGEFSGRIKE----------LKPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPAE-SYV----QIA  213 (237)
T ss_dssp             -----CGGGEEEESSSCBC----------CCSEEEEEHHHHHHTHHH---HTTTCSEEEEECSSCCCTT-THH----HHH
T ss_pred             -----CCCeEEEEeCCCCC----------cCCEEEEeHHHHHhhHHH---hcccCCEEEEECCccCCCh-HHH----HHH
Confidence                 566 7777776532          368999999998765542   1245889999999998765 443    344


Q ss_pred             HhCCCCCeEEEEeccCCcc
Q psy1548         283 RSSPHTKQVMMFSATLSKE  301 (448)
Q Consensus       283 ~~l~~~~q~i~~SAT~~~~  301 (448)
                      ..++ ..+++++|||+++.
T Consensus       214 ~~~~-~~~~l~LSATp~r~  231 (237)
T 2fz4_A          214 QMSI-APFRLGLTATFERE  231 (237)
T ss_dssp             HTCC-CSEEEEEEESCC--
T ss_pred             Hhcc-CCEEEEEecCCCCC
Confidence            5554 67889999998754

>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=99.62  E-value=1.8e-15  Score=160.29  Aligned_cols=73  Identities=15%  Similarity=0.142  Sum_probs=59.0

Q ss_pred             hHHHHHHHHHhh-C-CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecC
Q psy1548         340 EKNKKLFELLDV-L-EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASD  414 (448)
Q Consensus       340 ~k~~~L~~ll~~-~-~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~  414 (448)
                      .+...+...+.. . .+.++||||+|+..|+.+++.|.+.|+++..+||+|++.+|.++++.|++|+.  .|+++|+
T Consensus       423 ~~~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~--~VLvaT~  497 (664)
T 1c4o_A          423 NQILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHY--DCLVGIN  497 (664)
T ss_dssp             THHHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSC--SEEEESC
T ss_pred             chHHHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCc--eEEEccC
Confidence            344444444432 2 46799999999999999999999999999999999999999999999999883  4555544

>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=99.60  E-value=1.6e-14  Score=127.04  Aligned_cols=123  Identities=81%  Similarity=1.231  Sum_probs=106.3

Q ss_pred             ccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC-
Q psy1548         326 LHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH-  404 (448)
Q Consensus       326 ~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~-  404 (448)
                      +.++.|+++.++..+|...|..+++....+++||||+++..|+.++..|.+.|+++..+||+|++.+|..+++.|++|+ 
T Consensus         3 ~~~i~q~~~~~~~~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~   82 (172)
T 1t5i_A            3 LHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQR   82 (172)
T ss_dssp             --CCEEEEEECCGGGHHHHHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSC
T ss_pred             cCCeEEEEEECChHHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCCC
Confidence            4679999999999999999999999988889999999999999999999999999999999999999999999999988 


Q ss_pred             ---------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCCCCCCCccc
Q psy1548         405 ---------------------------------------------KGLAITFASDENDAKILNNVQDRFDVSISELPDEI  439 (448)
Q Consensus       405 ---------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~  439 (448)
                                                                   .|.+++|+++.++...++.+++.++..+.++|.++
T Consensus        83 ~vLvaT~~~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  162 (172)
T 1t5i_A           83 RILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEI  162 (172)
T ss_dssp             SEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEECC---
T ss_pred             cEEEECCchhcCcchhhCCEEEEECCCCCHHHHHHHhcccccCCCCcEEEEEEcChhHHHHHHHHHHHHhcchhhCChhh
Confidence                                                         78999999988788999999999999999999999


Q ss_pred             cccccccCC
Q psy1548         440 DLSTYIEGR  448 (448)
Q Consensus       440 ~~~~~~~~~  448 (448)
                      +...+++++
T Consensus       163 ~~~~~~~~~  171 (172)
T 1t5i_A          163 DISSYIEQT  171 (172)
T ss_dssp             ------CCC
T ss_pred             chhhccccc
Confidence            988777653

>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=99.56  E-value=2.2e-13  Score=144.34  Aligned_cols=109  Identities=14%  Similarity=0.081  Sum_probs=72.8

Q ss_pred             CCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHh-hC-CCCeEEEEECcc
Q psy1548         287 HTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLD-VL-EFNQVVIFVKSV  364 (448)
Q Consensus       287 ~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~-~~-~~~~~IIF~~s~  364 (448)
                      ...|++++|||+++.....    ............ ....+.   ..+ .....+...+...+. .. .+.++||||+|+
T Consensus       385 ~~~q~i~~SAT~~~~~~~~----~~~~~~~~~r~~-~l~~p~---i~v-~~~~~~~~~Ll~~l~~~~~~~~~vlVf~~t~  455 (661)
T 2d7d_A          385 HMHNIVYVSATPGPYEIEH----TDEMVEQIIRPT-GLLDPL---IDV-RPIEGQIDDLIGEIQARIERNERVLVTTLTK  455 (661)
T ss_dssp             TCSEEEEECSSCCHHHHHH----CSSCEEECCCTT-CCCCCE---EEE-ECSTTHHHHHHHHHHHHHTTTCEEEEECSSH
T ss_pred             cCCCEEEEecCCChhHHHh----hhCeeeeeeccc-CCCCCe---EEE-ecccchHHHHHHHHHHHHhcCCeEEEEECCH
Confidence            4679999999987653222    111122211111 011111   111 122234444444443 22 467999999999


Q ss_pred             HHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC
Q psy1548         365 TRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       365 ~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~  404 (448)
                      ..|+.+++.|++.|+++..+||+|++.+|.++++.|++|+
T Consensus       456 ~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~  495 (661)
T 2d7d_A          456 KMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGK  495 (661)
T ss_dssp             HHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCC
Confidence            9999999999999999999999999999999999999997

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.53  E-value=6.2e-15  Score=153.47  Aligned_cols=131  Identities=13%  Similarity=0.119  Sum_probs=97.0

Q ss_pred             hhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCC
Q psy1548         130 DTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  209 (448)
Q Consensus       130 ~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  209 (448)
                      +++|.++.++  ....+..|+++++++|||+|||++|++|++..      +.+++|++||++|+.|+.+.+..+.... +
T Consensus         5 r~~Q~~~~~~--v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~~------~~~v~i~~pt~~l~~q~~~~~~~l~~~~-~   75 (551)
T 3crv_A            5 RDWQEKLKDK--VIEGLRNNFLVALNAPTGSGKTLFSLLVSLEV------KPKVLFVVRTHNEFYPIYRDLTKIREKR-N   75 (551)
T ss_dssp             CHHHHHHHHH--HHHHHHTTCEEEEECCTTSSHHHHHHHHHHHH------CSEEEEEESSGGGHHHHHHHHTTCCCSS-C
T ss_pred             CHHHHHHHHH--HHHHHHcCCcEEEECCCCccHHHHHHHHHHhC------CCeEEEEcCCHHHHHHHHHHHHHHhhhc-C
Confidence            4449984442  23455678999999999999999999999982      4589999999999999999999987776 7


Q ss_pred             ceEEEEEcCccc---------------------------------HHhHH------------------HHhcCCCcEEEE
Q psy1548         210 IKVGVFFGGLPI---------------------------------QKDEE------------------YLKTHNPQIVVG  238 (448)
Q Consensus       210 ~~v~~~~g~~~~---------------------------------~~~~~------------------~l~~~~~~IlV~  238 (448)
                      +++..+.|....                                 .....                  .... .++|+|+
T Consensus        76 ~~~~~l~gr~~~c~~~~~~~~~~~~~c~~c~~~~~~~~~g~~~~~~~~~~~~~~~G~~~~~Cpy~~ar~~~~-~adIVV~  154 (551)
T 3crv_A           76 ITFSFLVGKPSSCLYAEKGAESEDIPCKYCELKGSIVEVKTDDSPLSLVKKLKKDGLQDKFCPYYSLLNSLY-KADVIAL  154 (551)
T ss_dssp             CCEEECCCHHHHCTTBCTTCCGGGCCGGGCTTTTCCCCCCCCSCHHHHHHHHHHHHHHHTCCHHHHHHHHGG-GCSEEEE
T ss_pred             ccEEEEccccccCcCchhcCCCcccccCCCCCccccccccccCCHHHHHHHHHHcCCcCCcCccHHHHhhhh-cCCEEEe
Confidence            888777663221                                 11111                  1112 3799999


Q ss_pred             cHHHHHHHHHCCCCcC-CCeeEEEecchhHHHh
Q psy1548         239 TPGRILALVRNKKLNL-SLLKHFILDECDKMLE  270 (448)
Q Consensus       239 Tp~~l~~~l~~~~~~~-~~i~~lViDEah~l~~  270 (448)
                      |+..+.+...+..+.+ ....++||||||.+.+
T Consensus       155 ~~~~l~~~~~~~~~~~~~~~~~vIiDEAHnl~d  187 (551)
T 3crv_A          155 TYPYFFIDRYREFIDIDLREYMIVIDEAHNLDK  187 (551)
T ss_dssp             ETHHHHCHHHHTTSCCCSTTEEEEETTGGGGGG
T ss_pred             CchHhcCHHHHHhcCCCcCCeEEEEecccchHH
Confidence            9999988654433332 4667899999998876

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.48  E-value=2.7e-13  Score=121.30  Aligned_cols=133  Identities=23%  Similarity=0.281  Sum_probs=105.4

Q ss_pred             HHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeC
Q psy1548         307 KKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHR  386 (448)
Q Consensus       307 ~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~  386 (448)
                      ..++.+|..+.+... .....++.|.+..++...|...|.+++... ++++||||+++..++.++..|+..|+.+..+||
T Consensus         9 ~~~~~~p~~i~v~~~-~~~~~~i~q~~~~~~~~~K~~~L~~~l~~~-~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg   86 (191)
T 2p6n_A            9 SGVDLGTENLYFQSM-GAASLDVIQEVEYVKEEAKMVYLLECLQKT-PPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHG   86 (191)
T ss_dssp             --------------------CCSEEEEEECCGGGHHHHHHHHHTTS-CSCEEEECSCHHHHHHHHHHHHHHTCCEEEECT
T ss_pred             ccccCCCEEEEECCC-CCCCcCceEEEEEcChHHHHHHHHHHHHhC-CCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeC
Confidence            357788988888766 456789999999999999999999999875 458999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHhcCC----------------------------------------------CceEEEEecChhhHHH
Q psy1548         387 GMTQEERLKKYQEFKDFH----------------------------------------------KGLAITFASDENDAKI  420 (448)
Q Consensus       387 ~~~~~eR~~~l~~F~~g~----------------------------------------------~g~~I~~~t~~~d~~~  420 (448)
                      +|++.+|.++++.|++|+                                              .|.+++|++..++..+
T Consensus        87 ~~~~~~R~~~l~~F~~g~~~vLvaT~~~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~g~~g~~i~l~~~~~~~~~  166 (191)
T 2p6n_A           87 GKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESV  166 (191)
T ss_dssp             TSCHHHHHHHHHHHHHTSCSEEEECHHHHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC---CCEEEEEECTTSCHHH
T ss_pred             CCCHHHHHHHHHHHhcCCCEEEEEcCchhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccCCCCcEEEEEEcCchhHHH
Confidence            999999999999999998                                              7899999998767889


Q ss_pred             HHHHHHHhcCCCCCCCccccc
Q psy1548         421 LNNVQDRFDVSISELPDEIDL  441 (448)
Q Consensus       421 l~~i~~~~~~~~~~~p~~~~~  441 (448)
                      ++.+++.++...+++|.++..
T Consensus       167 ~~~l~~~l~~~~~~~p~~l~~  187 (191)
T 2p6n_A          167 LMDLKALLLEAKQKVPPVLQV  187 (191)
T ss_dssp             HHHHHHHHHHTTCCCCHHHHS
T ss_pred             HHHHHHHHHHccCcCCHHHHh
Confidence            999999999999999988643

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=99.42  E-value=2.8e-12  Score=111.54  Aligned_cols=112  Identities=25%  Similarity=0.443  Sum_probs=102.3

Q ss_pred             ccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcC
Q psy1548         324 LTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDF  403 (448)
Q Consensus       324 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g  403 (448)
                      ....++.|+++.++..+|...|.+++....++++||||+++..++.+++.|.+.|+.+..+||+|++.+|..+++.|++|
T Consensus         5 ~~~~~i~~~~~~~~~~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g   84 (163)
T 2hjv_A            5 LTTRNIEHAVIQVREENKFSLLKDVLMTENPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRG   84 (163)
T ss_dssp             -CCCCEEEEEEECCGGGHHHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             cCcccceEEEEECChHHHHHHHHHHHHhcCCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHcC
Confidence            35677999999999999999999999988888999999999999999999999999999999999999999999999999


Q ss_pred             C----------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCCCCCCC
Q psy1548         404 H----------------------------------------------KGLAITFASDENDAKILNNVQDRFDVSISELP  436 (448)
Q Consensus       404 ~----------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p  436 (448)
                      +                                              .|.+++|++.. +...++.+++.++.++.+++
T Consensus        85 ~~~vlv~T~~~~~Gld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~g~~g~~~~~~~~~-~~~~~~~i~~~~~~~~~~~~  162 (163)
T 2hjv_A           85 EYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAF-EKRFLADIEEYIGFEIQKIE  162 (163)
T ss_dssp             SCSEEEECGGGTTTCCCSCCSEEEESSCCSSHHHHHHHTTTSSCTTCCEEEEEEECGG-GHHHHHHHHHHHTSCCEECC
T ss_pred             CCeEEEECChhhcCCchhcCCEEEEeCCCCCHHHHHHhccccCcCCCCceEEEEecHH-HHHHHHHHHHHHCCCcCccC
Confidence            8                                              68899999876 78899999999998887654

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=99.42  E-value=2.8e-12  Score=111.77  Aligned_cols=113  Identities=32%  Similarity=0.542  Sum_probs=102.6

Q ss_pred             cceeEEEEEcCcch-HHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC-
Q psy1548         327 HGLQQHYVKLKENE-KNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH-  404 (448)
Q Consensus       327 ~~i~~~~~~~~~~~-k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~-  404 (448)
                      .+++|+|+.++..+ |...|.++++...++++||||+++..|+.++..|++.|+.+..+||+|++.+|.++++.|++|+ 
T Consensus         2 ~~i~~~~~~~~~~~~K~~~l~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~   81 (165)
T 1fuk_A            2 EGIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSS   81 (165)
T ss_dssp             --CEEEEEEEESGGGHHHHHHHHHHHTTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSC
T ss_pred             CCcEEEEEECCcchhHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHcCCC
Confidence            46889999988877 9999999999988899999999999999999999999999999999999999999999999997 


Q ss_pred             ---------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCCCCCCCccc
Q psy1548         405 ---------------------------------------------KGLAITFASDENDAKILNNVQDRFDVSISELPDEI  439 (448)
Q Consensus       405 ---------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~  439 (448)
                                                                   .|.++++++.. +...+..+++.++..+.++|.++
T Consensus        82 ~vlv~T~~~~~G~d~~~~~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~  160 (165)
T 1fuk_A           82 RILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNE-DVGAMRELEKFYSTQIEELPSDI  160 (165)
T ss_dssp             SEEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETT-THHHHHHHHHHSSCCCEECCSCC
T ss_pred             EEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEEcch-HHHHHHHHHHHHccCccccCccH
Confidence                                                         68899999876 78899999999999999999775


Q ss_pred             c
Q psy1548         440 D  440 (448)
Q Consensus       440 ~  440 (448)
                      .
T Consensus       161 ~  161 (165)
T 1fuk_A          161 A  161 (165)
T ss_dssp             T
T ss_pred             H
Confidence            3

>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=99.39  E-value=5.9e-12  Score=110.85  Aligned_cols=114  Identities=26%  Similarity=0.394  Sum_probs=104.2

Q ss_pred             ccccceeEEEEEcCcch-HHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhc
Q psy1548         324 LTLHGLQQHYVKLKENE-KNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKD  402 (448)
Q Consensus       324 ~~~~~i~~~~~~~~~~~-k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~  402 (448)
                      .++.++.|+|+.++..+ |...|..+++....+++||||+++..|+.++..|.+.|+.+..+||+|++.+|..+++.|++
T Consensus         3 ~~~~~i~q~~~~~~~~~~K~~~L~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~f~~   82 (175)
T 2rb4_A            3 LTLNNIRQYYVLCEHRKDKYQALCNIYGSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRD   82 (175)
T ss_dssp             CCBCCEEEEEEECSSHHHHHHHHHHHHTTSCCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHT
T ss_pred             CccCCceEEEEEcCChHhHHHHHHHHHHhCCCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHHc
Confidence            35678999999998765 99999999998888899999999999999999999999999999999999999999999999


Q ss_pred             CC----------------------------------------------------CceEEEEecChhhHHHHHHHHHHhcC
Q psy1548         403 FH----------------------------------------------------KGLAITFASDENDAKILNNVQDRFDV  430 (448)
Q Consensus       403 g~----------------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~  430 (448)
                      |+                                                    .|.+++|++.. +...++.+++.++.
T Consensus        83 g~~~vLvaT~~~~~Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR~g~~g~~~~~~~~~-~~~~~~~i~~~~~~  161 (175)
T 2rb4_A           83 GKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEVD-ELPSLMKIQDHFNS  161 (175)
T ss_dssp             TSCSEEEECCSCCTTTCCTTEEEEEESSCCC--CCSCCHHHHHHHHCBC----CCEEEEEEECGG-GHHHHHHHHHHHTC
T ss_pred             CCCeEEEEecchhcCCCcccCCEEEEeCCCCCccccCCHHHHHHHhcccccCCCCceEEEEEccc-hHHHHHHHHHHhcC
Confidence            87                                                    67889999876 68899999999999


Q ss_pred             CCCCCCcc
Q psy1548         431 SISELPDE  438 (448)
Q Consensus       431 ~~~~~p~~  438 (448)
                      .+.++|..
T Consensus       162 ~~~~~~~~  169 (175)
T 2rb4_A          162 SIKQLNAE  169 (175)
T ss_dssp             CCEEECSS
T ss_pred             cccccCCc
Confidence            99888765

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.38  E-value=2e-13  Score=141.57  Aligned_cols=128  Identities=17%  Similarity=0.119  Sum_probs=84.9

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .|++.   |.++.++  ..+.+..|+++++.+|||+|||++|++|++..      +.+++|++||++|+.|+.+.+..+ 
T Consensus         7 ~~r~~---Q~~~~~~--v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~------~~~~~~~~~t~~l~~q~~~~~~~l-   74 (540)
T 2vl7_A            7 QLRQW---QAEKLGE--AINALKHGKTLLLNAKPGLGKTVFVEVLGMQL------KKKVLIFTRTHSQLDSIYKNAKLL-   74 (540)
T ss_dssp             --CCH---HHHHHHH--HHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH------TCEEEEEESCHHHHHHHHHHHGGG-
T ss_pred             CCCHH---HHHHHHH--HHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC------CCcEEEEcCCHHHHHHHHHHHHhc-
Confidence            56666   9993332  23445678999999999999999999999764      458999999999999999887774 


Q ss_pred             ccCCCceEEEEEcCccc--------HH------------------------hHHH---------------HhcCCCcEEE
Q psy1548         205 KYMSNIKVGVFFGGLPI--------QK------------------------DEEY---------------LKTHNPQIVV  237 (448)
Q Consensus       205 ~~~~~~~v~~~~g~~~~--------~~------------------------~~~~---------------l~~~~~~IlV  237 (448)
                          ++++..+.|....        ..                        .+..               ... .++|+|
T Consensus        75 ----~~~~~~l~gr~~lC~~~~~~~~~~~~~c~~c~~~~~~~~~gd~~~~~~~~~~~~~~~~Cpy~~~r~~~~-~adiVV  149 (540)
T 2vl7_A           75 ----GLKTGFLIGKSASCIYAQGDEEPDEINCSKCRLKDKIKTIEDKEPSKLIEEFKDAVDYCPYYSLRANLK-DKDVIA  149 (540)
T ss_dssp             ----TCCEEEC---------------------------------------------------------CTTGG-GCSEEE
T ss_pred             ----CCcEEEecCCccccCCchhcccccccCCCCCCchhcccccccCCcHHHHHHHhhhcCCChHHHHHHHhh-cCCEEE
Confidence                3344433332100        00                        0000               011 369999


Q ss_pred             EcHHHHHHHHHCCCC-------cCCCeeEEEecchhHHH
Q psy1548         238 GTPGRILALVRNKKL-------NLSLLKHFILDECDKML  269 (448)
Q Consensus       238 ~Tp~~l~~~l~~~~~-------~~~~i~~lViDEah~l~  269 (448)
                      +|+..+.+....+.+       .+....++||||||.+.
T Consensus       150 ~n~~~l~~~~~~~~~~~~~~~~~~~~~~~vIiDEAHnl~  188 (540)
T 2vl7_A          150 MTYPYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNLL  188 (540)
T ss_dssp             EETHHHHSHHHHHHHSCSSTTSCCGGGEEEEETTGGGGG
T ss_pred             EChHHhcCHHHHHhhCcccccccCcCCCEEEEEccccHH
Confidence            999999874432221       23567899999999883

>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=99.33  E-value=5.3e-12  Score=112.23  Aligned_cols=117  Identities=22%  Similarity=0.359  Sum_probs=98.5

Q ss_pred             ccccceeEEEEEcCcchHHHHHHHHHhhC-CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhc
Q psy1548         324 LTLHGLQQHYVKLKENEKNKKLFELLDVL-EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKD  402 (448)
Q Consensus       324 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~-~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~  402 (448)
                      ....++.|.++.++..+|...|.++++.. .++++||||+++..|+.++..|+..|+.+..+||+|++.+|..+++.|++
T Consensus        15 ~~~~~i~q~~~~v~~~~K~~~L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f~~   94 (185)
T 2jgn_A           15 STSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRS   94 (185)
T ss_dssp             -CCTTEEEEEEECCGGGHHHHHHHHHHHC-CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHHHH
T ss_pred             CCCCCceEEEEEeCcHHHHHHHHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHHHc
Confidence            45678999999999999999999999887 56799999999999999999999999999999999999999999999999


Q ss_pred             CC----------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCCCCCCC
Q psy1548         403 FH----------------------------------------------KGLAITFASDENDAKILNNVQDRFDVSISELP  436 (448)
Q Consensus       403 g~----------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p  436 (448)
                      |+                                              .|.+++|++.. +...++.+++.++...+++|
T Consensus        95 g~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g~~g~~~~~~~~~-~~~~~~~l~~~l~~~~~~~~  173 (185)
T 2jgn_A           95 GKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNER-NINITKDLLDLLVEAKQEVP  173 (185)
T ss_dssp             TSSSEEEEEC------CCCSBSEEEESSCCSSHHHHHHHHTTBCCTTSCEEEEEEECGG-GGGGHHHHHHHHHHTTCCCC
T ss_pred             CCCeEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHccccCCCCCCcEEEEEEchh-hHHHHHHHHHHHHhccCCCC
Confidence            98                                              68899999876 78888999999999999999


Q ss_pred             ccccc
Q psy1548         437 DEIDL  441 (448)
Q Consensus       437 ~~~~~  441 (448)
                      .++..
T Consensus       174 ~~l~~  178 (185)
T 2jgn_A          174 SWLEN  178 (185)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            88653

>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=98.80  E-value=2.2e-12  Score=113.06  Aligned_cols=118  Identities=21%  Similarity=0.280  Sum_probs=100.6

Q ss_pred             cceeEEEEEcCc-chHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCC
Q psy1548         327 HGLQQHYVKLKE-NEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHK  405 (448)
Q Consensus       327 ~~i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~  405 (448)
                      .++.|+++.++. ..|...|..+++...++++||||+++..|+.++..|++.|+.+..+||+|++.+|..+++.|++|+ 
T Consensus         2 ~~i~~~~~~~~~~~~k~~~l~~ll~~~~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~~~f~~g~-   80 (170)
T 2yjt_D            2 KKIHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGR-   80 (170)
Confidence            357788888888 889999999998877789999999999999999999999999999999999999999999999987 


Q ss_pred             ceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         406 GLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       406 g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                       ..|+++|+....++  ++...-.+-..++|.+...+.++.||
T Consensus        81 -~~vLvaT~~~~~Gi--d~~~~~~Vi~~~~p~~~~~~~qr~GR  120 (170)
T 2yjt_D           81 -VNVLVATDVAARGI--DIPDVSHVFNFDMPRSGDTYLHRIGR  120 (170)
Confidence             45777776544444  55555556677889888889999987

>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=99.17  E-value=2e-10  Score=104.32  Aligned_cols=110  Identities=14%  Similarity=0.207  Sum_probs=99.2

Q ss_pred             ceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC---
Q psy1548         328 GLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH---  404 (448)
Q Consensus       328 ~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~---  404 (448)
                      .+.+.++.++...|...|..++....++++||||+++..++.++..|.+.|+.+..+||+|++.+|.++++.|++|+   
T Consensus         5 ~~~~~~~~~~~~~k~~~l~~ll~~~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~v   84 (212)
T 3eaq_A            5 TYEEEAVPAPVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRV   84 (212)
T ss_dssp             CBCCEEEECCTTSHHHHHHHHHHHHCCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCE
T ss_pred             ceeeeEEeCCHHHHHHHHHHHHHhCCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeE
Confidence            35567778888999999999999888899999999999999999999999999999999999999999999999998   


Q ss_pred             -------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCCCCCCCcc
Q psy1548         405 -------------------------------------------KGLAITFASDENDAKILNNVQDRFDVSISELPDE  438 (448)
Q Consensus       405 -------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~  438 (448)
                                                                 .|.+++|++.. +...++.+++.++..+..++..
T Consensus        85 lvaT~~~~~Gidi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g~~g~~~~l~~~~-~~~~~~~i~~~~~~~~~~~~~~  160 (212)
T 3eaq_A           85 LVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYGPR-ERRDVEALERAVGRRFKRVNPP  160 (212)
T ss_dssp             EEECTTTTCSSSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC--BEEEEEECGG-GHHHHHHHHHHHSSCCEECCCC
T ss_pred             EEecChhhcCCCCccCcEEEECCCCcCHHHHHHHhcccCCCCCCCeEEEEEchh-HHHHHHHHHHHhcCcCeecCCC
Confidence                                                       78999999876 7889999999999888877543

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=99.16  E-value=2.2e-10  Score=109.40  Aligned_cols=110  Identities=15%  Similarity=0.211  Sum_probs=100.8

Q ss_pred             ceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC---
Q psy1548         328 GLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH---  404 (448)
Q Consensus       328 ~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~---  404 (448)
                      .+.++++.++..+|...|..+++...++++||||++++.++.++..|.+.|+.+..+||+|++.+|..+++.|++|+   
T Consensus         2 ~v~~~~i~~~~~~K~~~L~~ll~~~~~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~f~~g~~~v   81 (300)
T 3i32_A            2 TYEEEAVPAPVRGRLEVLSDLLYVASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRV   81 (300)
T ss_dssp             CSEEEEEECCSSSHHHHHHHHHHHHCCSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHHHHHTSCCE
T ss_pred             ceEEEEEECCHHHHHHHHHHHHHhcCCCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhcCCceE
Confidence            46789999999999999999999888899999999999999999999999999999999999999999999999998   


Q ss_pred             -------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCCCCCCCcc
Q psy1548         405 -------------------------------------------KGLAITFASDENDAKILNNVQDRFDVSISELPDE  438 (448)
Q Consensus       405 -------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~  438 (448)
                                                                 .|.+++|++.. +...++.+++.++..+..++..
T Consensus        82 LVaT~va~~Gidi~~v~~VI~~d~p~s~~~y~Qr~GRagR~g~~G~~i~l~~~~-e~~~~~~ie~~~~~~~~~~~~~  157 (300)
T 3i32_A           82 LVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYGPR-ERRDVEALERAVGRRFKRVNPP  157 (300)
T ss_dssp             EEECSTTTCSTTCCCCSEEEESSCCSSTTHHHHHHTCCC-----CEEEEEECSS-THHHHHHHHHHHTCCCEECCCC
T ss_pred             EEEechhhcCccccceeEEEEcCCCCCHHHHHHHccCcCcCCCCceEEEEeChH-HHHHHHHHHHHhCCcceEeCCC
Confidence                                                       78999999887 7889999999999888776543

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=98.79  E-value=2.7e-09  Score=112.05  Aligned_cols=84  Identities=20%  Similarity=0.219  Sum_probs=67.7

Q ss_pred             hhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCC
Q psy1548         130 DTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  209 (448)
Q Consensus       130 ~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  209 (448)
                      +++|.++..+  ....+..|+++++.||||+|||++|++|++..+...  +.+++|++||++|+.|+.+.+..+.... +
T Consensus         5 R~~Q~~~~~~--v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~--~~kvli~t~T~~l~~Qi~~el~~l~~~~-~   79 (620)
T 4a15_A            5 RQYQVEAIDF--LRSSLQKSYGVALESPTGSGKTIMALKSALQYSSER--KLKVLYLVRTNSQEEQVIKELRSLSSTM-K   79 (620)
T ss_dssp             CHHHHHHHHH--HHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHH--TCEEEEEESSHHHHHHHHHHHHHHHHHS-C
T ss_pred             CHHHHHHHHH--HHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhc--CCeEEEECCCHHHHHHHHHHHHHHhhcc-C
Confidence            3448884442  335566899999999999999999999999887543  3589999999999999999999998765 6


Q ss_pred             ceEEEEEcC
Q psy1548         210 IKVGVFFGG  218 (448)
Q Consensus       210 ~~v~~~~g~  218 (448)
                      +++..+.|+
T Consensus        80 ~~~~~l~gr   88 (620)
T 4a15_A           80 IRAIPMQGR   88 (620)
T ss_dssp             CCEEECCCH
T ss_pred             eEEEEEECC
Confidence            777766653

>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=98.74  E-value=9.3e-09  Score=107.86  Aligned_cols=143  Identities=17%  Similarity=0.235  Sum_probs=89.8

Q ss_pred             hhhhccccccceeeeeCcceeeeccCCChhH--HHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCc
Q psy1548         133 LHRVARAGRFGTKAVLGMDILCQAKSGMGKT--AVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI  210 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~g~~vli~apTGsGKT--~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~  210 (448)
                      |+.      +++.++.++.++++|++|+|||  ++++++.+..+... .+.++++++||..++.++.+.+..+...+ ++
T Consensus       154 Q~~------Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~-~~~~vll~APTg~AA~~L~e~~~~~~~~l-~l  225 (608)
T 1w36_D          154 QKV------AAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADG-ERCRIRLAAPTGKAAARLTESLGKALRQL-PL  225 (608)
T ss_dssp             HHH------HHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSS-CCCCEEEEBSSHHHHHHHHHHHTHHHHHS-SC
T ss_pred             HHH------HHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhhc-CCCeEEEEeCChhHHHHHHHHHHHHHhcC-CC
Confidence            999      9999999999999999999999  66777777755322 34689999999999999988877665544 22


Q ss_pred             eEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCe
Q psy1548         211 KVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQ  290 (448)
Q Consensus       211 ~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q  290 (448)
                      ..... ...+  .....+    ..++-.+|+.. . +.........++++|||||+ |++    ...+..++..++...|
T Consensus       226 ~~~~~-~~~~--~~~~Ti----h~ll~~~~~~~-~-~~~~~~~~l~~d~lIIDEAs-ml~----~~~~~~Ll~~l~~~~~  291 (608)
T 1w36_D          226 TDEQK-KRIP--EDASTL----HRLLGAQPGSQ-R-LRHHAGNPLHLDVLVVDEAS-MID----LPMMSRLIDALPDHAR  291 (608)
T ss_dssp             CSCCC-CSCS--CCCBTT----TSCC-------------CTTSCCSCSEEEECSGG-GCB----HHHHHHHHHTCCTTCE
T ss_pred             CHHHH-hccc--hhhhhh----HhhhccCCCch-H-HHhccCCCCCCCEEEEechh-hCC----HHHHHHHHHhCCCCCE
Confidence            11000 0000  000000    11222233321 1 11112223378899999999 544    2456778888999999


Q ss_pred             EEEEecc
Q psy1548         291 VMMFSAT  297 (448)
Q Consensus       291 ~i~~SAT  297 (448)
                      ++++.-.
T Consensus       292 liLvGD~  298 (608)
T 1w36_D          292 VIFLGDR  298 (608)
T ss_dssp             EEEEECT
T ss_pred             EEEEcch
Confidence            9998754

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=98.43  E-value=1.2e-07  Score=89.14  Aligned_cols=111  Identities=14%  Similarity=0.131  Sum_probs=79.1

Q ss_pred             cCcchHHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhC-CCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEe
Q psy1548         336 LKENEKNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQ-NFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFA  412 (448)
Q Consensus       336 ~~~~~k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~-g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~  412 (448)
                      .....|...|.+++...  .+.++||||++...++.+...|.+. |+++..+||++++.+|.++++.|+++...-.++++
T Consensus        92 ~~~s~K~~~L~~ll~~~~~~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~v~L~s  171 (271)
T 1z5z_A           92 VRRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLS  171 (271)
T ss_dssp             STTCHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEE
T ss_pred             cccCHHHHHHHHHHHHHHhCCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCCCEEEEe
Confidence            34567999999988776  6789999999999999999999885 99999999999999999999999998543345555


Q ss_pred             cChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         413 SDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       413 t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      |.....++  ++...-.+-+.++|-+...+.+..||
T Consensus       172 t~~~g~Gl--nl~~a~~VI~~d~~wnp~~~~Q~~gR  205 (271)
T 1z5z_A          172 VKAGGFGI--NLTSANRVIHFDRWWNPAVEDQATDR  205 (271)
T ss_dssp             CCTTCCCC--CCTTCSEEEECSCCSCTTTC------
T ss_pred             hhhhcCCc--CcccCCEEEEECCCCChhHHHHHHHh
Confidence            54332222  22222334455666667677777776

>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=98.37  E-value=1.2e-07  Score=97.76  Aligned_cols=134  Identities=20%  Similarity=0.245  Sum_probs=88.8

Q ss_pred             ccccCCCcee--eeecCceeEEeecCCCccccccccCC-CccccccccccccccchhhhhhhhccCceeeeccCCcccCC
Q psy1548          10 KLSCGSGNVF--LFFRAFIRFSSSFPHSKMADNDDLLD-YEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFL   86 (448)
Q Consensus        10 ~~~~~~~~~~--~~~r~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (448)
                      .+.+..+.++  +|.|+|+.|.+....++.....+++. ........+.......+.........+..+..++.+.....
T Consensus       195 ~l~~~~~~~~~~~~~r~~l~~~v~~~~~~~~~l~~~l~~~~~~~~IVf~~sr~~~e~l~~~L~~~g~~~~~~h~~l~~~~  274 (523)
T 1oyw_A          195 LLGLNDPLIQISSFDRPNIRYMLMEKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNV  274 (523)
T ss_dssp             HHTCCSCEEEECCCCCTTEEEEEEECSSHHHHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHH
T ss_pred             HhCCCCCeEEeCCCCCCceEEEEEeCCCHHHHHHHHHHhcCCCcEEEEeCCHHHHHHHHHHHHHCCCCEEEecCCCCHHH
Confidence            4556666666  89999999998876554322222221 12234556665555555555455445555555555443222


Q ss_pred             CCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548          87 LKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      ...-+........+|+|||+++++|||+++++.|+++..|..+..|.|++|||||..
T Consensus       275 R~~~~~~f~~g~~~vlVaT~a~~~GiD~p~v~~VI~~~~p~s~~~y~Qr~GRaGR~g  331 (523)
T 1oyw_A          275 RADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDG  331 (523)
T ss_dssp             HHHHHHHHHTTSCSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTS
T ss_pred             HHHHHHHHHcCCCeEEEEechhhCCCCccCccEEEEECCCCCHHHHHHHhccccCCC
Confidence            212222223344589999999999999999999999999999999999999999943

>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=98.33  E-value=2.6e-07  Score=96.43  Aligned_cols=133  Identities=18%  Similarity=0.215  Sum_probs=88.1

Q ss_pred             ccccCCCcee--eeecCceeEEeecCCCcccc-ccccCC-----CccccccccccccccchhhhhhhhccCceeeeccCC
Q psy1548          10 KLSCGSGNVF--LFFRAFIRFSSSFPHSKMAD-NDDLLD-----YEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSG   81 (448)
Q Consensus        10 ~~~~~~~~~~--~~~r~~~~~~~~~~~~~~~~-~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (448)
                      .|.++...++  +|.|+|+.|.+........+ .+.+.+     ...+....+.......+.........+..+...+.+
T Consensus       221 ~l~~~~~~~~~~~~~r~nl~~~v~~~~~~~~~~~~~l~~~l~~~~~~~~~IVf~~sr~~~e~la~~L~~~g~~~~~~h~~  300 (591)
T 2v1x_A          221 ILCIEKCFTFTASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHAN  300 (591)
T ss_dssp             HTTCCSCEEEECCCCCTTEEEEEEECCSSHHHHHHHHHHHHTTTTTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTT
T ss_pred             HhCCCCcEEEecCCCCcccEEEEEeCCCcHHHHHHHHHHHHHHhccCCCeEEEeCcHHHHHHHHHHHHHCCCCEEEecCC
Confidence            4555555555  89999999988765432111 122221     133455666665555555555555455555555554


Q ss_pred             cccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          82 FRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ........-+..+.....+|+|||++++||||+++++.|++|..|..++.|.|++|||||.
T Consensus       301 l~~~~R~~~~~~F~~g~~~VlVAT~a~~~GID~p~V~~VI~~~~p~s~~~y~Qr~GRaGR~  361 (591)
T 2v1x_A          301 LEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRD  361 (591)
T ss_dssp             SCHHHHHHHHHHHHTTSSSEEEECTTSCTTCCCSCEEEEEESSCCSSHHHHHHHHTTSCTT
T ss_pred             CCHHHHHHHHHHHHcCCCeEEEEechhhcCCCcccccEEEEeCCCCCHHHHHHHhccCCcC
Confidence            4432222222333344558999999999999999999999999999999999999999994

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*

Probab=97.79  E-value=0.0005  Score=72.40  Aligned_cols=65  Identities=17%  Similarity=0.149  Sum_probs=49.7

Q ss_pred             hhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhcc-CCCeEEEEeeccHHHHHHHHHHHHHhhc
Q psy1548         133 LHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETT-DSNVYVLVMCHTRELAFQISKEYERFSK  205 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~  205 (448)
                      |.+      ++..  .+..++|.|+.|||||.+..--+...+... ....++|++++|+..+.++.+.+..+.+
T Consensus        14 Q~~------av~~--~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~~~   79 (647)
T 3lfu_A           14 QRE------AVAA--PRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLMG   79 (647)
T ss_dssp             HHH------HHTC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHHHC
T ss_pred             HHH------HHhC--CCCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHHHHHHHHHHHHHhc
Confidence            888      6652  367899999999999987655555555432 2335899999999999999999888754

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=97.71  E-value=0.00013  Score=76.58  Aligned_cols=68  Identities=19%  Similarity=0.093  Sum_probs=50.2

Q ss_pred             CchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         128 DSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       128 ~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      .+.+.|.+      ++..++.+.-.+|+||+|+|||.+.. .++..+... .+.++++++||..-+.++.+.+...
T Consensus       180 ~ln~~Q~~------av~~~l~~~~~li~GppGTGKT~~~~-~~i~~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~~  247 (624)
T 2gk6_A          180 DLNHSQVY------AVKTVLQRPLSLIQGPPGTGKTVTSA-TIVYHLARQ-GNGPVLVCAPSNIAVDQLTEKIHQT  247 (624)
T ss_dssp             CCCHHHHH------HHHHHHTCSEEEEECCTTSCHHHHHH-HHHHHHHTS-SSCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             CCCHHHHH------HHHHHhcCCCeEEECCCCCCHHHHHH-HHHHHHHHc-CCCeEEEEeCcHHHHHHHHHHHHhc
Confidence            35666999      77776667778999999999997743 333333322 3458999999999999988777654

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=97.66  E-value=0.00015  Score=78.20  Aligned_cols=68  Identities=13%  Similarity=0.093  Sum_probs=50.2

Q ss_pred             CchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         128 DSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       128 ~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      .+.+.|.+      ++..++.+.-.+|+||.|+|||.+..- ++..+... .+.++++++||..-+.++.+.+...
T Consensus       360 ~Ln~~Q~~------Av~~~l~~~~~lI~GppGTGKT~~i~~-~i~~l~~~-~~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          360 QLNSSQSN------AVSHVLQRPLSLIQGPPGTGKTVTSAT-IVYHLSKI-HKDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             CCCHHHHH------HHHHHTTCSEEEEECSTTSSHHHHHHH-HHHHHHHH-HCCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             cCCHHHHH------HHHHHhcCCCEEEECCCCCCHHHHHHH-HHHHHHhC-CCCeEEEEcCcHHHHHHHHHHHHhh
Confidence            34566999      777776667789999999999976443 33333221 2348999999999999988888764

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=97.55  E-value=0.00031  Score=75.59  Aligned_cols=67  Identities=18%  Similarity=0.071  Sum_probs=49.9

Q ss_pred             chhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         129 SDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       129 ~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      +.+.|.+      ++..++.+.-.+|+||.|+|||.+.. .++..+... .+.++++++||..-+.++.+.+...
T Consensus       357 Ln~~Q~~------Av~~~l~~~~~lI~GppGTGKT~ti~-~~i~~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~~  423 (800)
T 2wjy_A          357 LNHSQVY------AVKTVLQRPLSLIQGPPGTGKTVTSA-TIVYHLARQ-GNGPVLVCAPSNIAVDQLTEKIHQT  423 (800)
T ss_dssp             CCHHHHH------HHHHHHTSSEEEEECCTTSCHHHHHH-HHHHHHHTT-CSSCEEEEESSHHHHHHHHHHHHTT
T ss_pred             CCHHHHH------HHHHhccCCeEEEEcCCCCCHHHHHH-HHHHHHHHc-CCCcEEEEcCcHHHHHHHHHHHHHh
Confidence            4666999      77777777778999999999997643 344443332 3458999999999999988777653

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=97.53  E-value=0.00017  Score=74.79  Aligned_cols=129  Identities=15%  Similarity=0.104  Sum_probs=77.5

Q ss_pred             CCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhc
Q psy1548         126 PEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK  205 (448)
Q Consensus       126 p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  205 (448)
                      +..+.+.|++      ++..++.++.+++.||.|+|||.+. ..++..+..  .+.++++++||...+..+.+...    
T Consensus       187 ~~~L~~~Q~~------Av~~~~~~~~~~I~G~pGTGKTt~i-~~l~~~l~~--~g~~Vl~~ApT~~Aa~~L~e~~~----  253 (574)
T 3e1s_A          187 RKGLSEEQAS------VLDQLAGHRLVVLTGGPGTGKSTTT-KAVADLAES--LGLEVGLCAPTGKAARRLGEVTG----  253 (574)
T ss_dssp             TTTCCHHHHH------HHHHHTTCSEEEEECCTTSCHHHHH-HHHHHHHHH--TTCCEEEEESSHHHHHHHHHHHT----
T ss_pred             cCCCCHHHHH------HHHHHHhCCEEEEEcCCCCCHHHHH-HHHHHHHHh--cCCeEEEecCcHHHHHHhHhhhc----
Confidence            3344566999      8877778889999999999999653 334443333  24579999999988876554321    


Q ss_pred             cCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhC
Q psy1548         206 YMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSS  285 (448)
Q Consensus       206 ~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l  285 (448)
                          .....+          ..+..    .   .|.    ............+++||||++.+..     ..+..+++.+
T Consensus       254 ----~~a~Ti----------h~ll~----~---~~~----~~~~~~~~~~~~dvlIIDEasml~~-----~~~~~Ll~~~  303 (574)
T 3e1s_A          254 ----RTASTV----------HRLLG----Y---GPQ----GFRHNHLEPAPYDLLIVDEVSMMGD-----ALMLSLLAAV  303 (574)
T ss_dssp             ----SCEEEH----------HHHTT----E---ETT----EESCSSSSCCSCSEEEECCGGGCCH-----HHHHHHHTTS
T ss_pred             ----ccHHHH----------HHHHc----C---Ccc----hhhhhhcccccCCEEEEcCccCCCH-----HHHHHHHHhC
Confidence                111000          00000    0   000    0011122234678999999995532     3456677778


Q ss_pred             CCCCeEEEEecc
Q psy1548         286 PHTKQVMMFSAT  297 (448)
Q Consensus       286 ~~~~q~i~~SAT  297 (448)
                      +...+++++.-.
T Consensus       304 ~~~~~lilvGD~  315 (574)
T 3e1s_A          304 PPGARVLLVGDT  315 (574)
T ss_dssp             CTTCEEEEEECT
T ss_pred             cCCCEEEEEecc
Confidence            878888877544

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=97.44  E-value=0.0001  Score=77.75  Aligned_cols=67  Identities=18%  Similarity=0.113  Sum_probs=50.4

Q ss_pred             CchhhhhhhccccccceeeeeCcc-eeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         128 DSDTYLHRVARAGRFGTKAVLGMD-ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       128 ~~~~yQ~~~~~~~~~~~~~~~g~~-vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      .+.+.|.+      |+..++..++ .||+||.|+|||.+..-.+.+.+..   +.++|+++||..-+.++.+.+...
T Consensus       189 ~LN~~Q~~------AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~~l~~~---~~~ILv~a~TN~AvD~i~erL~~~  256 (646)
T 4b3f_X          189 CLDTSQKE------AVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQ---GLKVLCCAPSNIAVDNLVERLALC  256 (646)
T ss_dssp             TCCHHHHH------HHHHHHHCSSEEEEECCTTSCHHHHHHHHHHHHHHT---TCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCCHHHHH------HHHHHhcCCCceEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEcCchHHHHHHHHHHHhc
Confidence            45677999      8877776554 6899999999998755444444432   458999999999998887777653

>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=97.38  E-value=0.00012  Score=65.88  Aligned_cols=45  Identities=44%  Similarity=0.878  Sum_probs=42.3

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      .+|+|||+++++|+|.++++.|++|..|.....|.|.+|||||..
T Consensus        82 ~~vlvaT~~~~~Gidi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~g  126 (212)
T 3eaq_A           82 VRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAG  126 (212)
T ss_dssp             CCEEEECTTTTCSSSCCCBSEEEESSCCSSHHHHHHHHTTBCCCC
T ss_pred             CeEEEecChhhcCCCCccCcEEEECCCCcCHHHHHHHhcccCCCC
Confidence            479999999999999999999999999999999999999999943

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=97.38  E-value=0.00026  Score=71.45  Aligned_cols=131  Identities=12%  Similarity=0.104  Sum_probs=73.8

Q ss_pred             ccCCCCchhhhhhhccccccceeeee----Cc-ceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVL----GM-DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQIS  197 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~----g~-~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~  197 (448)
                      |..+++-   |++      ++..++.    ++ .+++.|+.|+|||.+. ..++..+..... ..+++++||...+..+.
T Consensus        23 ~~~Ln~~---Q~~------av~~~~~~i~~~~~~~li~G~aGTGKT~ll-~~~~~~l~~~~~-~~il~~a~T~~Aa~~l~   91 (459)
T 3upu_A           23 FDDLTEG---QKN------AFNIVMKAIKEKKHHVTINGPAGTGATTLT-KFIIEALISTGE-TGIILAAPTHAAKKILS   91 (459)
T ss_dssp             SSCCCHH---HHH------HHHHHHHHHHSSSCEEEEECCTTSCHHHHH-HHHHHHHHHTTC-CCEEEEESSHHHHHHHH
T ss_pred             cccCCHH---HHH------HHHHHHHHHhcCCCEEEEEeCCCCCHHHHH-HHHHHHHHhcCC-ceEEEecCcHHHHHHHH
Confidence            5556666   999      6655433    23 8999999999999653 344444433322 36899999998776655


Q ss_pred             HHHHHhhccCCCceEEEEEcCcccHHhHHHHhc-----CCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhh
Q psy1548         198 KEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKT-----HNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQL  272 (448)
Q Consensus       198 ~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~-----~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~  272 (448)
                      +.+.        ..+..+.         ..+..     .....+..          .....+...+++|+||++.+..  
T Consensus        92 ~~~~--------~~~~T~h---------~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~iiiDE~~~~~~--  142 (459)
T 3upu_A           92 KLSG--------KEASTIH---------SILKINPVTYEENVLFEQ----------KEVPDLAKCRVLICDEVSMYDR--  142 (459)
T ss_dssp             HHHS--------SCEEEHH---------HHHTEEEEECSSCEEEEE----------CSCCCCSSCSEEEESCGGGCCH--
T ss_pred             hhhc--------cchhhHH---------HHhccCcccccccchhcc----------cccccccCCCEEEEECchhCCH--
Confidence            4331        1111110         00000     00011110          1223356788999999995532  


Q ss_pred             hhHHHHHHHHHhCCCCCeEEEEec
Q psy1548         273 EMRRDVQEIFRSSPHTKQVMMFSA  296 (448)
Q Consensus       273 ~~~~~~~~i~~~l~~~~q~i~~SA  296 (448)
                         ..+..++..++...+++++.-
T Consensus       143 ---~~~~~l~~~~~~~~~~~~vGD  163 (459)
T 3upu_A          143 ---KLFKILLSTIPPWCTIIGIGD  163 (459)
T ss_dssp             ---HHHHHHHHHSCTTCEEEEEEC
T ss_pred             ---HHHHHHHHhccCCCEEEEECC
Confidence               244556666666677776653

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=97.33  E-value=0.00018  Score=63.61  Aligned_cols=45  Identities=40%  Similarity=0.743  Sum_probs=41.8

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ..+|+|+|+++++|+|.++++.|++|+.|.....|.|.+||+||.
T Consensus       104 ~~~vLvaT~~~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~  148 (191)
T 2p6n_A          104 KKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCS  148 (191)
T ss_dssp             SCSEEEECHHHHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC-
T ss_pred             CCEEEEEcCchhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccC
Confidence            348999999999999999999999999999999999999999983

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=97.24  E-value=0.00029  Score=66.87  Aligned_cols=45  Identities=44%  Similarity=0.818  Sum_probs=41.1

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ..+|+|||+++++|+|.++++.|++|..|.....|.|.+|||||.
T Consensus        78 ~~~vLVaT~va~~Gidi~~v~~VI~~d~p~s~~~y~Qr~GRagR~  122 (300)
T 3i32_A           78 EVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRA  122 (300)
T ss_dssp             SCCEEEECSTTTCSTTCCCCSEEEESSCCSSTTHHHHHHTCCC--
T ss_pred             CceEEEEechhhcCccccceeEEEEcCCCCCHHHHHHHccCcCcC
Confidence            357999999999999999999999999999999999999999994

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=97.14  E-value=0.0003  Score=60.28  Aligned_cols=44  Identities=48%  Similarity=0.955  Sum_probs=41.7

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ..|+|+|+++++|+|.++++.|++|+.|.....|.|.+||+||.
T Consensus        86 ~~vlv~T~~~~~Gld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~  129 (163)
T 2hjv_A           86 YRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRA  129 (163)
T ss_dssp             CSEEEECGGGTTTCCCSCCSEEEESSCCSSHHHHHHHTTTSSCT
T ss_pred             CeEEEECChhhcCCchhcCCEEEEeCCCCCHHHHHHhccccCcC
Confidence            47999999999999999999999999999999999999999883

>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=97.14  E-value=0.0003  Score=60.91  Aligned_cols=44  Identities=93%  Similarity=1.376  Sum_probs=41.7

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR  141 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~  141 (448)
                      ...|+|||+++++|+|.++++.|++|+.|.....|.|.+||+||
T Consensus        81 ~~~vLvaT~~~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R  124 (172)
T 1t5i_A           81 QRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR  124 (172)
T ss_dssp             SCSEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTG
T ss_pred             CCcEEEECCchhcCcchhhCCEEEEECCCCCHHHHHHHhccccc
Confidence            34899999999999999999999999999999999999999988

>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=97.14  E-value=0.00055  Score=60.04  Aligned_cols=72  Identities=33%  Similarity=0.507  Sum_probs=44.0

Q ss_pred             cCceeeeccCCcccCCCCHHHHHHH-hhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548          71 KGAYVSIHSSGFRDFLLKPEILRAI-VDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      .+..+...+.+...-.... .++.+ .....|+|+|+++++|+|.+++..|++|+.|.....|.|.+||+||..
T Consensus        69 ~g~~~~~lhg~~~~~~r~~-~~~~f~~g~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~g  141 (185)
T 2jgn_A           69 EGYACTSIHGDRSQRDREE-ALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVG  141 (185)
T ss_dssp             TTCCEEEEC--------CH-HHHHHHHTSSSEEEEEC------CCCSBSEEEESSCCSSHHHHHHHHTTBCCTT
T ss_pred             cCCceEEEeCCCCHHHHHH-HHHHHHcCCCeEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHccccCCCC
Confidence            3433444444444333333 33343 344589999999999999999999999999999999999999999843

>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=97.14  E-value=0.00056  Score=68.48  Aligned_cols=57  Identities=39%  Similarity=0.715  Sum_probs=47.4

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      ..|+|||+++++|+|.++++.|++|+.|.....|-|.+||+||+..   .|..+++..|.
T Consensus       351 ~~vLvaT~v~~rGlDi~~v~~VI~~d~p~~~~~y~qriGR~gR~g~---~G~a~~~~~~~  407 (434)
T 2db3_A          351 MKVLIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGN---NGRATSFFDPE  407 (434)
T ss_dssp             CSEEEECGGGTSSCCCTTCCEEEESSCCSSHHHHHHHHTTSSCTTC---CEEEEEEECTT
T ss_pred             CcEEEEchhhhCCCCcccCCEEEEECCCCCHHHHHHHhcccccCCC---CCEEEEEEecc
Confidence            4899999999999999999999999999999999999999999532   34444444443

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=97.07  E-value=0.00057  Score=58.60  Aligned_cols=43  Identities=47%  Similarity=1.043  Sum_probs=40.3

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR  141 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~  141 (448)
                      .+|+|+|+++++|+|.+++..|++|..|.....|.|.+||+||
T Consensus        81 ~~vlv~T~~~~~G~d~~~~~~Vi~~~~p~~~~~~~qr~GR~gR  123 (165)
T 1fuk_A           81 SRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGR  123 (165)
T ss_dssp             CSEEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-
T ss_pred             CEEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHhccccc
Confidence            4899999999999999999999999999999999999999988

>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=97.05  E-value=0.00043  Score=60.02  Aligned_cols=44  Identities=48%  Similarity=0.940  Sum_probs=39.4

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCC------CCchhhhhhhccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMP------EDSDTYLHRVARAGR  141 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p------~~~~~yQ~~~~~~~~  141 (448)
                      ..+|+|+|+++++|+|.++++.|++|..|      .....|.|.+||+||
T Consensus        84 ~~~vLvaT~~~~~Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR  133 (175)
T 2rb4_A           84 KEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGR  133 (175)
T ss_dssp             SCSEEEECCSCCTTTCCTTEEEEEESSCCC--CCSCCHHHHHHHHCBC--
T ss_pred             CCeEEEEecchhcCCCcccCCEEEEeCCCCCccccCCHHHHHHHhccccc
Confidence            34899999999999999999999999999      888999999999988

>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=96.11  E-value=9.2e-05  Score=64.05  Aligned_cols=44  Identities=52%  Similarity=0.893  Sum_probs=41.2

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR  141 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~  141 (448)
                      ..+|+|+|+++++|+|.++++.|++|+.|.....|.|.+||+||
T Consensus        80 ~~~vLvaT~~~~~Gid~~~~~~Vi~~~~p~~~~~~~qr~GR~~R  123 (170)
T 2yjt_D           80 RVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTAR  123 (170)
Confidence            34799999999999999999999999999999999999999988

>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold, hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4} PDB: 2o0h_A* 2o0k_A*

Probab=96.82  E-value=0.0066  Score=59.38  Aligned_cols=76  Identities=11%  Similarity=0.123  Sum_probs=55.4

Q ss_pred             CCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhc
Q psy1548         126 PEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK  205 (448)
Q Consensus       126 p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  205 (448)
                      |..+.+||..      .+..+...+-+++..+-+.|||.+....++..+... .+..+++++|++..|..+.+.++.+..
T Consensus       161 p~~L~p~Qk~------il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~~-~g~~v~~vA~t~~qA~~vf~~i~~mi~  233 (385)
T 2o0j_A          161 KVQLRDYQRD------MLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN-KDKAVGILAHKGSMSAEVLDRTKQAIE  233 (385)
T ss_dssp             ECCCCHHHHH------HHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHSS-SSCEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHH------HHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHhC-CCCeEEEEeCCHHHHHHHHHHHHHHHH
Confidence            4456777998      443332345689999999999988766666544333 345899999999999988888887776


Q ss_pred             cCC
Q psy1548         206 YMS  208 (448)
Q Consensus       206 ~~~  208 (448)
                      ..|
T Consensus       234 ~~P  236 (385)
T 2o0j_A          234 LLP  236 (385)
T ss_dssp             HSC
T ss_pred             hCh
Confidence            554

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=96.70  E-value=0.0048  Score=61.23  Aligned_cols=108  Identities=19%  Similarity=0.157  Sum_probs=62.5

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHh
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK  229 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~  229 (448)
                      +=.++.|+.|+|||...    .+.+..    ...+|++||++++..+.+.+.+.....                      
T Consensus       162 ~v~~I~G~aGsGKTt~I----~~~~~~----~~~lVlTpT~~aa~~l~~kl~~~~~~~----------------------  211 (446)
T 3vkw_A          162 KVVLVDGVPGCGKTKEI----LSRVNF----EEDLILVPGRQAAEMIRRRANASGIIV----------------------  211 (446)
T ss_dssp             EEEEEEECTTSCHHHHH----HHHCCT----TTCEEEESCHHHHHHHHHHHTTTSCCC----------------------
T ss_pred             cEEEEEcCCCCCHHHHH----HHHhcc----CCeEEEeCCHHHHHHHHHHhhhcCccc----------------------
Confidence            44678999999999753    222221    257999999999988877664321000                      


Q ss_pred             cCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEecc
Q psy1548         230 THNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSAT  297 (448)
Q Consensus       230 ~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT  297 (448)
                        ....-|.|-++++  ++.........+.+|||||-.+ .. +.   +..++...+. .+++++.-+
T Consensus       212 --~~~~~V~T~dsfL--~~~~~~~~~~~d~liiDE~sm~-~~-~~---l~~l~~~~~~-~~vilvGD~  269 (446)
T 3vkw_A          212 --ATKDNVRTVDSFL--MNYGKGARCQFKRLFIDEGLML-HT-GC---VNFLVEMSLC-DIAYVYGDT  269 (446)
T ss_dssp             --CCTTTEEEHHHHH--HTTTSSCCCCCSEEEEETGGGS-CH-HH---HHHHHHHTTC-SEEEEEECT
T ss_pred             --cccceEEEeHHhh--cCCCCCCCCcCCEEEEeCcccC-CH-HH---HHHHHHhCCC-CEEEEecCc
Confidence              0123356766543  2222222234789999999844 43 33   2333444433 566666554

>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=96.64  E-value=0.00095  Score=69.01  Aligned_cols=45  Identities=36%  Similarity=0.576  Sum_probs=42.5

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ...|+|||+++++|+|+++++.|++|..|.....|.|.+|||||.
T Consensus       392 ~~~vLvaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~  436 (563)
T 3i5x_A          392 ESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARS  436 (563)
T ss_dssp             SSEEEEECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCT
T ss_pred             CCCEEEEcchhhcCCCcccCCEEEEECCCCchhhhhhhcCccccC
Confidence            348999999999999999999999999999999999999999994

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=96.61  E-value=0.0014  Score=68.17  Aligned_cols=46  Identities=37%  Similarity=0.611  Sum_probs=42.9

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      ...|+|||+++++|+|+++++.|+++..|.....|.|.+|||||+.
T Consensus       341 ~~~vLVaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~g  386 (579)
T 3sqw_A          341 ESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSG  386 (579)
T ss_dssp             SSEEEEECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCTT
T ss_pred             CCeEEEEcchhhcCCCcccCCEEEEcCCCCCHHHhhhhccccccCC
Confidence            4589999999999999999999999999999999999999999953

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=96.40  E-value=0.0014  Score=64.65  Aligned_cols=45  Identities=47%  Similarity=0.807  Sum_probs=41.9

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ...|+|||+++++|+|.++++.|++|..|.....|.|.+||+||.
T Consensus       326 ~~~vlvaT~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~  370 (417)
T 2i4i_A          326 KSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRV  370 (417)
T ss_dssp             SSCEEEECHHHHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC-
T ss_pred             CCCEEEECChhhcCCCcccCCEEEEEcCCCCHHHHHHhcCccccC
Confidence            458999999999999999999999999999999999999999983

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*

Probab=96.33  E-value=0.024  Score=58.88  Aligned_cols=76  Identities=11%  Similarity=0.125  Sum_probs=56.5

Q ss_pred             CCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhc
Q psy1548         126 PEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK  205 (448)
Q Consensus       126 p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  205 (448)
                      |..+.+||..      .+..+...+-+++..+-|+|||.+....++..+...+ +..++++.|+...|..+...++.+..
T Consensus       161 ~~~l~p~Q~~------i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~~-~~~i~~va~t~~qA~~~~~~i~~~i~  233 (592)
T 3cpe_A          161 KVQLRDYQRD------MLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNK-DKAVGILAHKGSMSAEVLDRTKQAIE  233 (592)
T ss_dssp             BCCCCHHHHH------HHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTSS-SCEEEEEESSHHHHHHHHHHHHHHHT
T ss_pred             cCcCCHHHHH------HHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhCC-CCeEEEEECCHHHHHHHHHHHHHHHH
Confidence            4456777999      4443333567999999999999887655555444433 45899999999999999988888876


Q ss_pred             cCC
Q psy1548         206 YMS  208 (448)
Q Consensus       206 ~~~  208 (448)
                      ..|
T Consensus       234 ~~p  236 (592)
T 3cpe_A          234 LLP  236 (592)
T ss_dssp             TSC
T ss_pred             hCh
Confidence            654

>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=96.21  E-value=0.0028  Score=62.41  Aligned_cols=45  Identities=38%  Similarity=1.006  Sum_probs=42.1

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ..+|+|+|+++++|+|.++++.|++|..|.....|.|.+||+||.
T Consensus       326 ~~~vlv~T~~~~~Gidi~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~  370 (410)
T 2j0s_A          326 ASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRY  370 (410)
T ss_dssp             SSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGG
T ss_pred             CCCEEEECChhhCcCCcccCCEEEEECCCCCHHHHHHhcccccCC
Confidence            358999999999999999999999999999999999999999983

>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=96.18  E-value=0.0027  Score=61.87  Aligned_cols=45  Identities=49%  Similarity=0.985  Sum_probs=41.3

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCCC------Cchhhhhhhcccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMPE------DSDTYLHRVARAGRF  142 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~------~~~~yQ~~~~~~~~~  142 (448)
                      ..+|+|+|+++++|+|.++++.|++|..|.      ....|.|.+|||||.
T Consensus       293 ~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~  343 (395)
T 3pey_A          293 RSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRF  343 (395)
T ss_dssp             SCCEEEECGGGSSSCCCTTEEEEEESSCCBCTTSSBCHHHHHHHHTTSSCT
T ss_pred             CCCEEEECChhhcCCCcccCCEEEEcCCCCCCcCCCCHHHhhHhccccccC
Confidence            347999999999999999999999999998      778999999999993

>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=96.17  E-value=0.0039  Score=60.82  Aligned_cols=44  Identities=93%  Similarity=1.376  Sum_probs=41.7

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR  141 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~  141 (448)
                      ...|+|+|+++++|+|.+.++.|+++..|.....|.|.+||+||
T Consensus       300 ~~~vlv~T~~~~~Gidi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R  343 (391)
T 1xti_A          300 QRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR  343 (391)
T ss_dssp             CCSEEEESCCCSSCBCCTTEEEEEESSCCSSHHHHHHHHCBCSS
T ss_pred             CCcEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHhcccccC
Confidence            34899999999999999999999999999999999999999998

>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=96.16  E-value=0.0036  Score=66.42  Aligned_cols=59  Identities=27%  Similarity=0.374  Sum_probs=49.2

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhH
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKT  163 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT  163 (448)
                      ..|+|||+++++|+|+++++.|++|+.|.....|.|.+||||+      .|..+++..+.++...
T Consensus       465 ~~VLVaT~~~~~GIDip~v~~VI~~d~p~s~~~~~Qr~GRArr------~g~~~~l~~~~~~~~~  523 (699)
T 4gl2_A          465 INLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARA------DESTYVLVAHSGSGVI  523 (699)
T ss_dssp             -CCSEEECSCCTTSCCCSCCCCEEESCCCCHHHHHHHHTTSCS------SSCEEEEEEESSSCSH
T ss_pred             CcEEEEccccccCCccccCCEEEEeCCCCCHHHHHHHcCCCCC------CCceEEEEEeCCchHH
Confidence            3899999999999999999999999999999999999999876      2456666666666533

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=96.12  E-value=0.036  Score=48.77  Aligned_cols=40  Identities=13%  Similarity=0.255  Sum_probs=26.6

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEec
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSA  296 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SA  296 (448)
                      ..-.++||||+|.+..  .....+..++...+....+++.|.
T Consensus       101 ~~~~vliiDe~~~l~~--~~~~~l~~~l~~~~~~~~~i~~~~  140 (226)
T 2chg_A          101 APFKIIFLDEADALTA--DAQAALRRTMEMYSKSCRFILSCN  140 (226)
T ss_dssp             CSCEEEEEETGGGSCH--HHHHHHHHHHHHTTTTEEEEEEES
T ss_pred             cCceEEEEeChhhcCH--HHHHHHHHHHHhcCCCCeEEEEeC
Confidence            4557899999998755  344556666666666666666544

>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=96.02  E-value=0.0029  Score=60.25  Aligned_cols=45  Identities=42%  Similarity=0.832  Sum_probs=42.2

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ..+|+|||+++++|+|.++++.|+++..|.....|.|.+|||||.
T Consensus       266 ~~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~gR~  310 (337)
T 2z0m_A          266 EYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRM  310 (337)
T ss_dssp             SCSEEEECHHHHTTCCCCCBSEEEESSCCSSHHHHHHHHTTBCGG
T ss_pred             CCcEEEEcCccccCCCccCCCEEEEecCCCCHHHhhHhcCccccC
Confidence            348999999999999999999999999999999999999999994

>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=96.01  E-value=0.0036  Score=61.47  Aligned_cols=44  Identities=50%  Similarity=0.984  Sum_probs=39.8

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCC------CCchhhhhhhccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMP------EDSDTYLHRVARAGR  141 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p------~~~~~yQ~~~~~~~~  141 (448)
                      ..+|+|||+++++|+|.++++.|++|..|      .....|.|.+|||||
T Consensus       316 ~~~vlv~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR  365 (412)
T 3fht_A          316 KEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGR  365 (412)
T ss_dssp             SCSEEEECGGGTSSCCCTTEEEEEESSCCBCSSSSBCHHHHHHHHTTSSC
T ss_pred             CCcEEEEcCccccCCCccCCCEEEEECCCCCCCCCcchheeecccCcccC
Confidence            34799999999999999999999999999      456788999999998

>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=95.98  E-value=0.007  Score=63.40  Aligned_cols=47  Identities=30%  Similarity=0.320  Sum_probs=42.2

Q ss_pred             hccceeEeeccccCCcccc--------cceeEeeccCCCCchhhhhhhccccccc
Q psy1548          97 DCWRILVATNLFGRGMDIE--------RVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        97 ~~~~~~~~~~~~~~~~d~~--------~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      ..+.|+|||+++|||+|+.        ....|+++..|...+.|.+.+||+||..
T Consensus       521 ~~g~VtVATdmAgRGtDI~lg~~V~~~GglhVInte~Pes~r~y~qriGRTGRqG  575 (822)
T 3jux_A          521 QKGMVTIATNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQG  575 (822)
T ss_dssp             STTCEEEEETTTTTTCCCCCCTTTTTTTSCEEEESSCCSSHHHHHHHHTTSSCSS
T ss_pred             CCCeEEEEcchhhCCcCccCCcchhhcCCCEEEecCCCCCHHHHHHhhCccccCC
Confidence            3569999999999999997        5569999999999999999999999954

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=95.97  E-value=0.0087  Score=53.94  Aligned_cols=113  Identities=17%  Similarity=0.140  Sum_probs=60.9

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL  228 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l  228 (448)
                      |.=+++.|++|+|||... +-++..+...  +.+++++.|...--     -...+...+ ++.                 
T Consensus        12 G~i~litG~mGsGKTT~l-l~~~~r~~~~--g~kVli~~~~~d~r-----~~~~i~srl-G~~-----------------   65 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAEL-IRRLHRLEYA--DVKYLVFKPKIDTR-----SIRNIQSRT-GTS-----------------   65 (223)
T ss_dssp             CEEEEEECSTTSCHHHHH-HHHHHHHHHT--TCCEEEEEECCCGG-----GCSSCCCCC-CCS-----------------
T ss_pred             cEEEEEECCCCCcHHHHH-HHHHHHHHhc--CCEEEEEEeccCch-----HHHHHHHhc-CCC-----------------
Confidence            566788999999999764 3344443322  34688887765310     000111111 110                 


Q ss_pred             hcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEec
Q psy1548         229 KTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSA  296 (448)
Q Consensus       229 ~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SA  296 (448)
                         ...+.+.+...+...+..... -...++|||||++.+..  .....+..+..   ...++++..-
T Consensus        66 ---~~~~~~~~~~~i~~~i~~~~~-~~~~dvViIDEaQ~l~~--~~ve~l~~L~~---~gi~Vil~Gl  124 (223)
T 2b8t_A           66 ---LPSVEVESAPEILNYIMSNSF-NDETKVIGIDEVQFFDD--RICEVANILAE---NGFVVIISGL  124 (223)
T ss_dssp             ---SCCEEESSTHHHHHHHHSTTS-CTTCCEEEECSGGGSCT--HHHHHHHHHHH---TTCEEEEECC
T ss_pred             ---ccccccCCHHHHHHHHHHHhh-CCCCCEEEEecCccCcH--HHHHHHHHHHh---CCCeEEEEec
Confidence               023445666667776665322 24578999999996432  33333433332   2566666554

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=95.96  E-value=0.0041  Score=61.50  Aligned_cols=46  Identities=26%  Similarity=0.448  Sum_probs=42.4

Q ss_pred             ccceeEe----eccccCCccccc-ceeEeeccCC--CCchhhhhhhccccccc
Q psy1548          98 CWRILVA----TNLFGRGMDIER-VNIVFNYDMP--EDSDTYLHRVARAGRFG  143 (448)
Q Consensus        98 ~~~~~~~----~~~~~~~~d~~~-~~~v~~~~~p--~~~~~yQ~~~~~~~~~~  143 (448)
                      ..+|+||    |+++++|+|.++ ++.|++|..|  .....|.|.+|||||..
T Consensus       297 ~~~vLvat~s~T~~~~~GiDip~~v~~VI~~~~p~~~~~~~y~qr~GR~gR~g  349 (414)
T 3oiy_A          297 KINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRIL  349 (414)
T ss_dssp             SCSEEEEECCTTCCCCCCCCCTTTCCEEEEESCCTTTCHHHHHHHHGGGCCEE
T ss_pred             CCeEEEEecCcCchhhccCccccccCEEEEECCCCCCCHHHHHHHhCccccCC
Confidence            3489999    999999999999 9999999999  89999999999999943

>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=95.95  E-value=0.0051  Score=65.52  Aligned_cols=46  Identities=30%  Similarity=0.317  Sum_probs=42.6

Q ss_pred             ccceeEeeccccCCcccc--------cceeEeeccCCCCchhhhhhhccccccc
Q psy1548          98 CWRILVATNLFGRGMDIE--------RVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~--------~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      .+.|+|||++++||+|.+        .+..|++++.|...+.|-+..||+||+.
T Consensus       480 ~g~VlIATdmAgRG~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~GRTGRqG  533 (844)
T 1tf5_A          480 KGAVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQG  533 (844)
T ss_dssp             TTCEEEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGG
T ss_pred             CCeEEEeCCccccCcCccccchhhhcCCcEEEEecCCCCHHHHHhhcCccccCC
Confidence            368999999999999999        7789999999999999999999999954

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=95.92  E-value=0.013  Score=50.66  Aligned_cols=19  Identities=26%  Similarity=0.385  Sum_probs=16.4

Q ss_pred             eCcceeeeccCCChhHHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~  166 (448)
                      .|+.+++.||+|+|||...
T Consensus        37 ~g~~~~l~G~~G~GKTtL~   55 (180)
T 3ec2_A           37 EGKGLTFVGSPGVGKTHLA   55 (180)
T ss_dssp             GCCEEEECCSSSSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            3788999999999999654

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=95.91  E-value=0.019  Score=50.02  Aligned_cols=39  Identities=15%  Similarity=0.071  Sum_probs=25.6

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR  190 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~  190 (448)
                      |+=.++.||.|+|||...+ -++.....  .+.+++++.|..
T Consensus         3 g~i~vi~G~~gsGKTT~ll-~~~~~~~~--~g~~v~~~~~~~   41 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELL-SFVEIYKL--GKKKVAVFKPKI   41 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHH-HHHHHHHH--TTCEEEEEEEC-
T ss_pred             cEEEEEECCCCCCHHHHHH-HHHHHHHH--CCCeEEEEeecc
Confidence            5567899999999997643 33333322  234788888885

>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=95.91  E-value=0.0048  Score=60.65  Aligned_cols=43  Identities=44%  Similarity=1.029  Sum_probs=36.2

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR  141 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~  141 (448)
                      .+|+|+|+++++|+|.++++.|+++..|.....|.|.+|||||
T Consensus       331 ~~vlv~T~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR  373 (414)
T 3eiq_A          331 SRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGR  373 (414)
T ss_dssp             --CEEECSSCC--CCGGGCSCEEESSCCSSTHHHHHHSCCC--
T ss_pred             CcEEEECCccccCCCccCCCEEEEeCCCCCHHHhhhhcCcccC
Confidence            3799999999999999999999999999999999999999998

>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=95.88  E-value=0.0043  Score=60.82  Aligned_cols=43  Identities=51%  Similarity=1.005  Sum_probs=41.2

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR  141 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~  141 (448)
                      ..|+|+|+++++|+|.++++.|+++..|.....|.|.+|||||
T Consensus       309 ~~vLv~T~~~~~Gidip~~~~Vi~~~~p~s~~~~~Qr~GR~gR  351 (400)
T 1s2m_A          309 VRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGR  351 (400)
T ss_dssp             SSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSC
T ss_pred             CcEEEEcCccccCCCccCCCEEEEeCCCCCHHHHHHhcchhcC
Confidence            4899999999999999999999999999999999999999998

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=95.84  E-value=0.032  Score=53.01  Aligned_cols=25  Identities=8%  Similarity=0.028  Sum_probs=18.9

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhh
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQL  174 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l  174 (448)
                      +.++++.||+|+|||.+.- .++..+
T Consensus        45 ~~~lli~GpPGTGKT~~v~-~v~~~L   69 (318)
T 3te6_A           45 NKLFYITNADDSTKFQLVN-DVMDEL   69 (318)
T ss_dssp             CCEEEEECCCSHHHHHHHH-HHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHH
Confidence            5789999999999997743 344444

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=95.78  E-value=0.018  Score=50.60  Aligned_cols=39  Identities=10%  Similarity=0.084  Sum_probs=26.2

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR  190 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~  190 (448)
                      |+=.++.||+|+|||...+ -++.+...  .+.+++++.|..
T Consensus         8 g~i~v~~G~mgsGKTT~ll-~~a~r~~~--~g~kV~v~k~~~   46 (191)
T 1xx6_A            8 GWVEVIVGPMYSGKSEELI-RRIRRAKI--AKQKIQVFKPEI   46 (191)
T ss_dssp             CEEEEEECSTTSSHHHHHH-HHHHHHHH--TTCCEEEEEEC-
T ss_pred             CEEEEEECCCCCcHHHHHH-HHHHHHHH--CCCEEEEEEecc
Confidence            4556889999999996644 44444332  345789998885

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=95.77  E-value=0.058  Score=52.19  Aligned_cols=19  Identities=37%  Similarity=0.331  Sum_probs=16.1

Q ss_pred             eCcceeeeccCCChhHHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~  166 (448)
                      .+..+++.||+|+|||...
T Consensus        43 ~~~~vll~G~~G~GKT~l~   61 (387)
T 2v1u_A           43 KPSNALLYGLTGTGKTAVA   61 (387)
T ss_dssp             CCCCEEECBCTTSSHHHHH
T ss_pred             CCCcEEEECCCCCCHHHHH
Confidence            3578999999999999764

>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=95.67  E-value=0.003  Score=60.88  Aligned_cols=44  Identities=43%  Similarity=0.955  Sum_probs=41.5

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ..|+|+|+++++|+|.++++.|+++..|.....|.|.+|||||.
T Consensus       289 ~~vlv~T~~~~~Gid~~~~~~Vi~~~~~~s~~~~~Q~~GR~~R~  332 (367)
T 1hv8_A          289 IRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRA  332 (367)
T ss_dssp             SSEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCS
T ss_pred             CeEEEECChhhcCCCcccCCEEEEecCCCCHHHhhhcccccccC
Confidence            47999999999999999999999999999999999999999983

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=95.62  E-value=0.05  Score=51.69  Aligned_cols=36  Identities=19%  Similarity=0.168  Sum_probs=22.4

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC  187 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~  187 (448)
                      +..+++.||+|+|||...- .+...+...  +..++++.
T Consensus        37 ~~~lll~G~~GtGKT~la~-~i~~~~~~~--~~~~~~i~   72 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLLQ-AAGNEAKKR--GYRVIYSS   72 (324)
T ss_dssp             CSSEEEECSSSSSHHHHHH-HHHHHHHHT--TCCEEEEE
T ss_pred             CCeEEEECCCCCcHHHHHH-HHHHHHHHC--CCEEEEEE
Confidence            4689999999999996642 333333322  23455554

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=95.62  E-value=0.0045  Score=65.62  Aligned_cols=44  Identities=30%  Similarity=0.467  Sum_probs=28.3

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ..+|+|||+++++|+|.++++.|++|+.|.....|.|.+|| ||.
T Consensus       461 ~~~vLVaT~v~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-GR~  504 (696)
T 2ykg_A          461 DHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRA  504 (696)
T ss_dssp             CCSCSEEEESSCCC---CCCSEEEEESCC--CCCC----------
T ss_pred             CccEEEEechhhcCCcCccCCEEEEeCCCCCHHHHHHhhcc-CcC
Confidence            45899999999999999999999999999999999999999 984

>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=95.59  E-value=0.0062  Score=62.43  Aligned_cols=52  Identities=29%  Similarity=0.456  Sum_probs=24.6

Q ss_pred             HHHHHHhh--ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          90 EILRAIVD--CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        90 ~~~~~~~~--~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      .+++....  ...|+|||+++++|+|+++++.|++|+.|.....|.|.+|| ||.
T Consensus       443 ~~~~~F~~~g~~~vLvaT~~~~~GiDip~v~~VI~~d~p~s~~~~~Qr~GR-gR~  496 (556)
T 4a2p_A          443 GVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA  496 (556)
T ss_dssp             -----------CCEEEEEC-----------CEEEEETCCSCHHHHHHC-------
T ss_pred             HHHHHhcccCceEEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC
Confidence            34444544  34899999999999999999999999999999999999999 773

>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=95.59  E-value=0.0021  Score=65.04  Aligned_cols=43  Identities=51%  Similarity=1.018  Sum_probs=0.0

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCC------Cchhhhhhhccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPE------DSDTYLHRVARAGR  141 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~------~~~~yQ~~~~~~~~  141 (448)
                      ..|+|||+++++|+|+++++.|++|..|.      .+..|.|.+|||||
T Consensus       384 ~~iLv~T~~~~~GlDip~v~~VI~~d~p~~~~~~~s~~~~~Qr~GRagR  432 (479)
T 3fmp_B          384 EKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGR  432 (479)
T ss_dssp             -------------------------------------------------
T ss_pred             CcEEEEccccccCCccccCCEEEEecCCCCCccCCCHHHHHHHhccccc
Confidence            47999999999999999999999999993      56788999999998

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=95.33  E-value=0.022  Score=50.67  Aligned_cols=40  Identities=10%  Similarity=0.075  Sum_probs=25.5

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE  191 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~  191 (448)
                      |+=.++.++.|+|||...+ -.+.+...  .+.+++++.|...
T Consensus        28 G~l~vitG~MgsGKTT~lL-~~a~r~~~--~g~kVli~k~~~d   67 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELI-RRVRRTQF--AKQHAIVFKPCID   67 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHH-HHHHHHHH--TTCCEEEEECC--
T ss_pred             CEEEEEECCCCCcHHHHHH-HHHHHHHH--CCCEEEEEEeccC
Confidence            4445688999999997644 33333322  2457999998864

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=95.26  E-value=0.035  Score=53.89  Aligned_cols=18  Identities=33%  Similarity=0.303  Sum_probs=15.3

Q ss_pred             CcceeeeccCCChhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~  166 (448)
                      ++.+++.||+|+|||...
T Consensus        45 ~~~vll~G~~G~GKT~la   62 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFVS   62 (384)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            357999999999999764

>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=95.23  E-value=0.12  Score=51.52  Aligned_cols=38  Identities=13%  Similarity=0.218  Sum_probs=23.3

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC  187 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~  187 (448)
                      +..+++.||+|+|||..+. .+...+.....+..++++.
T Consensus       130 ~~~lll~Gp~G~GKTtLa~-aia~~l~~~~~~~~v~~v~  167 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQ-SIGNYVVQNEPDLRVMYIT  167 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHH-HHHHHHHHHCCSSCEEEEE
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHHhCCCCeEEEee
Confidence            5689999999999996643 3333333322233455543

>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=95.23  E-value=0.0079  Score=60.36  Aligned_cols=44  Identities=23%  Similarity=0.413  Sum_probs=40.4

Q ss_pred             cceeEeeccccCCcccccceeEeecc--------------------CCCCchhhhhhhccccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYD--------------------MPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~--------------------~p~~~~~yQ~~~~~~~~~~  143 (448)
                      .+|+|||+++++|+|.++ +.|++|.                    .|.....|.|.+|||||.-
T Consensus       235 ~~vLVaT~v~~~GiDip~-~~VI~~~~~~~~~~d~~~~~~l~~~~~~p~s~~~y~Qr~GRaGR~g  298 (451)
T 2jlq_A          235 WDFVVTTDISEMGANFRA-GRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRNP  298 (451)
T ss_dssp             CSEEEECGGGGSSCCCCC-SEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCCT
T ss_pred             ceEEEECCHHHhCcCCCC-CEEEECCCcccccccccccceeeecccccCCHHHHHHhccccCCCC
Confidence            389999999999999999 9999987                    8888999999999999954

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=95.19  E-value=0.013  Score=49.29  Aligned_cols=19  Identities=26%  Similarity=0.398  Sum_probs=16.7

Q ss_pred             eCcceeeeccCCChhHHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~  166 (448)
                      .|..+++.||+|+|||...
T Consensus        35 ~g~~~~l~G~~G~GKTtL~   53 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLL   53 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            7889999999999999653

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=95.18  E-value=0.0081  Score=61.41  Aligned_cols=50  Identities=30%  Similarity=0.458  Sum_probs=39.8

Q ss_pred             HHHHHhh--ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccc
Q psy1548          91 ILRAIVD--CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR  141 (448)
Q Consensus        91 ~~~~~~~--~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~  141 (448)
                      +++...+  ...|+|||+++++|+|.++++.|++|+.|.....|.|.+|| ||
T Consensus       443 ~~~~F~~~g~~~vLvaT~~~~~GlDlp~v~~VI~~d~p~s~~~~~Qr~GR-gR  494 (555)
T 3tbk_A          443 VLEAFRASGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR-GR  494 (555)
T ss_dssp             ---------CCSEEEECCCTTCCEETTSCSEEEEESCCSSCCCEECSSCC-CT
T ss_pred             HHHHHhcCCCeeEEEEcchhhcCCccccCCEEEEeCCCCCHHHHHHhcCc-Cc
Confidence            4445544  34899999999999999999999999999999999999888 77

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=95.16  E-value=0.015  Score=52.35  Aligned_cols=19  Identities=16%  Similarity=0.020  Sum_probs=16.2

Q ss_pred             eCcceeeeccCCChhHHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~  166 (448)
                      .+..+++.||+|+|||...
T Consensus        51 ~~~~~ll~G~~G~GKT~la   69 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLI   69 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4678999999999999654

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=95.14  E-value=0.21  Score=46.01  Aligned_cols=18  Identities=28%  Similarity=0.311  Sum_probs=15.5

Q ss_pred             CcceeeeccCCChhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~  166 (448)
                      .+.+++.||+|+|||..+
T Consensus        64 ~~~vLl~G~~GtGKT~la   81 (272)
T 1d2n_A           64 LVSVLLEGPPHSGKTALA   81 (272)
T ss_dssp             EEEEEEECSTTSSHHHHH
T ss_pred             CeEEEEECCCCCcHHHHH
Confidence            358999999999999764

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=95.04  E-value=0.058  Score=44.72  Aligned_cols=20  Identities=10%  Similarity=0.144  Sum_probs=17.0

Q ss_pred             eeCcceeeeccCCChhHHHH
Q psy1548         147 VLGMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       147 ~~g~~vli~apTGsGKT~~~  166 (448)
                      ..+.++++.||+|+|||..+
T Consensus        22 ~~~~~vll~G~~GtGKt~lA   41 (145)
T 3n70_A           22 ETDIAVWLYGAPGTGRMTGA   41 (145)
T ss_dssp             TCCSCEEEESSTTSSHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHH
Confidence            35678999999999999764

>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=95.02  E-value=0.012  Score=63.40  Aligned_cols=52  Identities=29%  Similarity=0.456  Sum_probs=28.9

Q ss_pred             HHHHHHhh--ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          90 EILRAIVD--CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        90 ~~~~~~~~--~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      .+++....  ...|+|||+++++|+|+++++.|++|+.|.....|.|.+|| ||.
T Consensus       684 ~~l~~F~~~g~~~vLVaT~~~~~GIDlp~v~~VI~yd~p~s~~~~iQr~GR-GR~  737 (797)
T 4a2q_A          684 GVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA  737 (797)
T ss_dssp             ----------CCSEEEEECC-------CCCSEEEEESCCSCHHHHHTC-------
T ss_pred             HHHHHhhccCCceEEEEcCchhcCCCchhCCEEEEeCCCCCHHHHHHhcCC-CCC
Confidence            34455544  34799999999999999999999999999999999999999 883

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=94.95  E-value=0.052  Score=52.63  Aligned_cols=35  Identities=11%  Similarity=0.151  Sum_probs=21.5

Q ss_pred             ceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee
Q psy1548         151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC  187 (448)
Q Consensus       151 ~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~  187 (448)
                      .+++.||+|+|||... -.+...+.... +..++++.
T Consensus        46 ~~li~G~~G~GKTtl~-~~l~~~~~~~~-~~~~~~i~   80 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTL-RKLWELYKDKT-TARFVYIN   80 (389)
T ss_dssp             EEEEECCTTSSHHHHH-HHHHHHHTTSC-CCEEEEEE
T ss_pred             eEEEECCCCCCHHHHH-HHHHHHHhhhc-CeeEEEEe
Confidence            7999999999999764 33334332221 23455554

>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=94.88  E-value=0.0046  Score=60.29  Aligned_cols=44  Identities=45%  Similarity=1.020  Sum_probs=0.0

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR  141 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~  141 (448)
                      ..+|+|||+++++|+|.++++.|+++..|.....|.|.+||+||
T Consensus       309 ~~~vlv~T~~~~~Gldi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R  352 (394)
T 1fuu_A          309 SSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGR  352 (394)
T ss_dssp             --------------------------------------------
T ss_pred             CCcEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHcCcccC
Confidence            34799999999999999999999999999999999999999988

>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=94.72  E-value=0.012  Score=59.29  Aligned_cols=44  Identities=23%  Similarity=0.400  Sum_probs=36.8

Q ss_pred             cceeEeeccccCCcccccceeEee--------------------ccCCCCchhhhhhhccccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFN--------------------YDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~--------------------~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      .+|+|||+++++|+|+++ +.|++                    |+.|.....|.|.+|||||..
T Consensus       237 ~~iLVaT~v~~~GiDip~-~~VI~~G~~~~~~~~~~~~~~~~~~~d~p~s~~~~~QR~GRaGR~g  300 (459)
T 2z83_A          237 WDFVITTDISEMGANFGA-SRVIDCRKSVKPTILEEGEGRVILGNPSPITSASAAQRRGRVGRNP  300 (459)
T ss_dssp             CSEEEESSCC---CCCSC-SEEEECCEECCEEEECSSSCEEEECSCEECCHHHHHHHHTTSSCCT
T ss_pred             ceEEEECChHHhCeecCC-CEEEECCcccccccccccccccccccCCCCCHHHHHHhccccCCCC
Confidence            489999999999999999 99998                    678999999999999999943

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=94.64  E-value=0.16  Score=47.65  Aligned_cols=19  Identities=26%  Similarity=0.371  Sum_probs=16.3

Q ss_pred             eCcceeeeccCCChhHHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~  166 (448)
                      .+.++++.||+|+|||..+
T Consensus        66 ~~~~vll~G~~GtGKT~la   84 (309)
T 3syl_A           66 PTLHMSFTGNPGTGKTTVA   84 (309)
T ss_dssp             CCCEEEEEECTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            4568999999999999764

>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=94.57  E-value=0.02  Score=60.28  Aligned_cols=54  Identities=28%  Similarity=0.449  Sum_probs=45.6

Q ss_pred             cceeEeeccccCCcccccceeEeeccC-----CCCchhhhhhhccccccceeeeeCcceeeec
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDM-----PEDSDTYLHRVARAGRFGTKAVLGMDILCQA  156 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~-----p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~a  156 (448)
                      ..|+|+|+++++|+|.++++.|++++.     |...+.|-|.+|||||.    ..|+.+++..
T Consensus       496 ~~VLVaT~~l~~GlDip~v~lVi~~d~d~~G~p~s~~~~iQr~GRagR~----~~G~~i~~~~  554 (661)
T 2d7d_A          496 YDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN----AEGRVIMYAD  554 (661)
T ss_dssp             CSEEEESCCCSTTCCCTTEEEEEETTTTCCTTTTSHHHHHHHHHTTTTS----TTCEEEEECS
T ss_pred             eEEEEecchhhCCcccCCCCEEEEeCcccccCCCCHHHHHHHhCcccCC----CCCEEEEEEe
Confidence            479999999999999999999999986     88999999999999994    2455554443

>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=94.51  E-value=0.018  Score=57.27  Aligned_cols=53  Identities=28%  Similarity=0.438  Sum_probs=44.8

Q ss_pred             HHHHHhh-ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548          91 ILRAIVD-CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        91 ~~~~~~~-~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      +++...+ ...|+|+|++.++|+|.+.++.|++|+.|.....|.|.+|||||..
T Consensus       411 ~~~~F~~~~~~vLv~T~~~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~GR~~R~g  464 (494)
T 1wp9_A          411 ILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRHM  464 (494)
T ss_dssp             HHHHHHHTSCSEEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSCC
T ss_pred             HHHHHhcCCceEEEECCccccCCCchhCCEEEEeCCCCCHHHHHHHHhhccCCC
Confidence            3444433 3489999999999999999999999999998888899999999954

>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=94.46  E-value=0.021  Score=62.77  Aligned_cols=52  Identities=29%  Similarity=0.456  Sum_probs=29.8

Q ss_pred             HHHHHHhh--ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          90 EILRAIVD--CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        90 ~~~~~~~~--~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ++++.+..  ...|+|||+++++|+|.++++.|++|+.|.....|.|.+|| ||.
T Consensus       684 ~il~~Fr~~g~~~VLVaT~~~~eGIDlp~v~~VI~yD~p~s~~~~iQr~GR-GR~  737 (936)
T 4a2w_A          684 GVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA  737 (936)
T ss_dssp             ----------CCSEEEEECC------CCCCSEEEEESCCSCSHHHHCC-------
T ss_pred             HHHHHhhccCCeeEEEEeCchhcCCcchhCCEEEEeCCCCCHHHHHHhcCC-CCC
Confidence            34455544  34799999999999999999999999999999999999999 774

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=94.44  E-value=0.14  Score=49.10  Aligned_cols=43  Identities=14%  Similarity=0.329  Sum_probs=29.7

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCC
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLS  299 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~  299 (448)
                      .+.+++++||+|. ++. .....+...+...+.+..+|+.|....
T Consensus       133 ~~~~vlilDE~~~-L~~-~~~~~L~~~le~~~~~~~~Il~t~~~~  175 (354)
T 1sxj_E          133 HRYKCVIINEANS-LTK-DAQAALRRTMEKYSKNIRLIMVCDSMS  175 (354)
T ss_dssp             -CCEEEEEECTTS-SCH-HHHHHHHHHHHHSTTTEEEEEEESCSC
T ss_pred             CCCeEEEEeCccc-cCH-HHHHHHHHHHHhhcCCCEEEEEeCCHH
Confidence            4567999999998 444 556667777777766766666665543

>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=94.43  E-value=0.015  Score=58.15  Aligned_cols=52  Identities=19%  Similarity=0.203  Sum_probs=40.1

Q ss_pred             HHHHHHh-hccceeEeeccccCCcccccceeEee-------------------ccCCCCchhhhhhhcccccc
Q psy1548          90 EILRAIV-DCWRILVATNLFGRGMDIERVNIVFN-------------------YDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        90 ~~~~~~~-~~~~~~~~~~~~~~~~d~~~~~~v~~-------------------~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ..++.+. ...+|+|||+++++|+|.+ ++.|++                   +..|.....|.|.+||+||.
T Consensus       214 ~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~~g~~~~pv~~~~~~~~vi~~~~p~~~~~~~Qr~GR~GR~  285 (440)
T 1yks_A          214 REYPTIKQKKPDFILATDIAEMGANLC-VERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRN  285 (440)
T ss_dssp             --------CCCSEEEESSSTTCCTTCC-CSEEEECCEEEEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCC
T ss_pred             HHHhhhcCCCceEEEECChhheeeccC-ceEEEeCCccceeeecccccceeeccccccCHHHHHHhccccCCC
Confidence            3344443 3458999999999999999 999886                   78899999999999999994

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=94.38  E-value=0.1  Score=49.45  Aligned_cols=42  Identities=14%  Similarity=0.245  Sum_probs=27.0

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEecc
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSAT  297 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT  297 (448)
                      ...+++++||+|.+... .....+..++...+.+.++|+.+..
T Consensus       104 ~~~~vliiDEi~~l~~~-~~~~~L~~~le~~~~~~~iI~~~n~  145 (324)
T 3u61_B          104 GRQKVIVIDEFDRSGLA-ESQRHLRSFMEAYSSNCSIIITANN  145 (324)
T ss_dssp             SCEEEEEEESCCCGGGH-HHHHHHHHHHHHHGGGCEEEEEESS
T ss_pred             CCCeEEEEECCcccCcH-HHHHHHHHHHHhCCCCcEEEEEeCC
Confidence            36688999999988622 3444555555555566677664443

>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=94.37  E-value=0.024  Score=59.72  Aligned_cols=44  Identities=30%  Similarity=0.480  Sum_probs=40.8

Q ss_pred             cceeEeeccccCCcccccceeEeeccC-----CCCchhhhhhhcccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDM-----PEDSDTYLHRVARAGRF  142 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~-----p~~~~~yQ~~~~~~~~~  142 (448)
                      ..|+|+|+++++|+|.++++.|++++.     |.....|-|.+|||||.
T Consensus       490 ~~VLvaT~~l~~GlDip~v~lVI~~d~d~~G~p~s~~~~iQr~GRagR~  538 (664)
T 1c4o_A          490 YDCLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN  538 (664)
T ss_dssp             CSEEEESCCCCTTCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTS
T ss_pred             ceEEEccChhhcCccCCCCCEEEEeCCcccCCCCCHHHHHHHHCccCcC
Confidence            479999999999999999999999986     88889999999999994

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=94.27  E-value=0.024  Score=59.73  Aligned_cols=44  Identities=34%  Similarity=0.653  Sum_probs=39.7

Q ss_pred             cceeEeeccccCCcccccceeEeeccC--------------CCCchhhhhhhccccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDM--------------PEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~--------------p~~~~~yQ~~~~~~~~~~  143 (448)
                      .+|+|||+++++|+|. +++.|+++..              |.....|.|.+|||||..
T Consensus       373 ~~VLVATdi~e~GlDi-~v~~VI~~~~~k~~~~~~G~~~~~p~s~~~~~QR~GRAGR~g  430 (677)
T 3rc3_A          373 CKILVATDAIGMGLNL-SIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGRFS  430 (677)
T ss_dssp             CCEEEECGGGGSSCCC-CBSEEEESCSBC-----------CBCCHHHHHHHHTTBTCTT
T ss_pred             eEEEEeCcHHHCCcCc-CccEEEECCccccccccCCccccccCCHHHHHHHhcCCCCCC
Confidence            4899999999999999 9999999887              667889999999999954

>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19

Probab=94.23  E-value=0.05  Score=57.41  Aligned_cols=65  Identities=14%  Similarity=0.038  Sum_probs=49.6

Q ss_pred             hhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhc-cCCCeEEEEeeccHHHHHHHHHHHHHhhc
Q psy1548         133 LHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRELAFQISKEYERFSK  205 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  205 (448)
                      |++      ++..  .+.+++|.|+.|||||.+..--+...+.. .....++|+|+.|+..+.++.+.+....+
T Consensus         7 Q~~------av~~--~~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~Aa~em~~Rl~~~l~   72 (673)
T 1uaa_A            7 QQQ------AVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLG   72 (673)
T ss_dssp             HHH------HHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             HHH------HHhC--CCCCEEEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHcC
Confidence            888      5543  26789999999999998765555555543 22345899999999999999999887654

>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=94.22  E-value=0.013  Score=62.83  Aligned_cols=44  Identities=23%  Similarity=0.418  Sum_probs=40.4

Q ss_pred             cceeEeeccccCCcccccceeEeeccC------------------CCCchhhhhhhcccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDM------------------PEDSDTYLHRVARAGRF  142 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~------------------p~~~~~yQ~~~~~~~~~  142 (448)
                      .+|.|||+++++|+|.++++.|+++..                  |.+...|.|.+|||||.
T Consensus       370 ~kVlVAT~iae~GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~  431 (773)
T 2xau_A          370 RKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT  431 (773)
T ss_dssp             EEEEEECTHHHHTCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSS
T ss_pred             eEEEEeCcHHHhCcCcCCeEEEEeCCCccceeeccccCccccccccCCHHHHHhhccccCCC
Confidence            379999999999999999999999776                  78889999999999995

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=94.14  E-value=0.08  Score=47.10  Aligned_cols=40  Identities=15%  Similarity=0.048  Sum_probs=26.0

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE  191 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~  191 (448)
                      |.=.++.+|.|+|||... +..+......  +.+++++.|...
T Consensus        28 G~I~vitG~M~sGKTT~L-lr~~~r~~~~--g~kvli~kp~~D   67 (219)
T 3e2i_A           28 GWIECITGSMFSGKSEEL-IRRLRRGIYA--KQKVVVFKPAID   67 (219)
T ss_dssp             CEEEEEEECTTSCHHHHH-HHHHHHHHHT--TCCEEEEEEC--
T ss_pred             ceEEEEECCCCCCHHHHH-HHHHHHHHHc--CCceEEEEeccC
Confidence            555688999999999654 4444444332  347899988764

>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=94.12  E-value=0.032  Score=59.34  Aligned_cols=46  Identities=30%  Similarity=0.329  Sum_probs=41.7

Q ss_pred             ccceeEeeccccCCccccc--------------------------------c-----eeEeeccCCCCchhhhhhhcccc
Q psy1548          98 CWRILVATNLFGRGMDIER--------------------------------V-----NIVFNYDMPEDSDTYLHRVARAG  140 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~--------------------------------~-----~~v~~~~~p~~~~~yQ~~~~~~~  140 (448)
                      .|.|.||||++|||+|...                                |     ..|+++..|...+.|-+..||+|
T Consensus       489 ~G~VtIATnmAgRGtDI~l~gn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGl~VI~te~pes~riy~qr~GRTG  568 (853)
T 2fsf_A          489 PAAVTIATNMAGRGTDIVLGGSWQAEVAALENPTAEQIEKIKADWQVRHDAVLEAGGLHIIGTERHESRRIDNQLRGRSG  568 (853)
T ss_dssp             TTCEEEEESCCSSCSCCCTTCCHHHHHHHCSSCCSSHHHHHHHHHHHHHHHHHHTTSEEEEESSCCSSHHHHHHHHTTSS
T ss_pred             CCeEEEecccccCCcCccCCCchHhhhhhcccchhHHHHHHHHHhhhhhhHHHhcCCcEEEEccCCCCHHHHHhhccccc
Confidence            4689999999999999986                                4     58999999999999999999999


Q ss_pred             ccc
Q psy1548         141 RFG  143 (448)
Q Consensus       141 ~~~  143 (448)
                      |..
T Consensus       569 RqG  571 (853)
T 2fsf_A          569 RQG  571 (853)
T ss_dssp             GGG
T ss_pred             cCC
Confidence            954

>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A*

Probab=94.05  E-value=0.052  Score=61.39  Aligned_cols=62  Identities=26%  Similarity=0.319  Sum_probs=49.3

Q ss_pred             hhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccC---CCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         133 LHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTD---SNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~---~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      |++      ++..-  +++++|.|+.|||||.+.+--++..+....   ...+++++++|++.+..+.+.+..
T Consensus        15 Q~~------~i~~~--~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~aa~e~~~ri~~   79 (1232)
T 3u4q_A           15 QWN------AIVST--GQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAE   79 (1232)
T ss_dssp             HHH------HHHCC--SSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHHHHHHHHHHHH
T ss_pred             HHH------HHhCC--CCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHHHHHHHHHHHH
Confidence            888      66543  889999999999999887666666665432   345899999999999998887766

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=93.93  E-value=0.24  Score=49.09  Aligned_cols=134  Identities=13%  Similarity=0.157  Sum_probs=72.3

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee--ccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE  226 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~  226 (448)
                      +.-+++.||+|+|||.....-+ ..+...  +.+++++.  +.+.-+.+   .+..+.... ++.+.....+.       
T Consensus        97 ~~vI~lvG~~GsGKTTt~~kLA-~~l~~~--G~kVllv~~D~~r~~a~e---qL~~~~~~~-gv~~~~~~~~~-------  162 (433)
T 3kl4_A           97 PFIIMLVGVQGSGKTTTAGKLA-YFYKKR--GYKVGLVAADVYRPAAYD---QLLQLGNQI-GVQVYGEPNNQ-------  162 (433)
T ss_dssp             SEEEEECCCTTSCHHHHHHHHH-HHHHHT--TCCEEEEEECCSCHHHHH---HHHHHHHTT-TCCEECCTTCS-------
T ss_pred             CeEEEEECCCCCCHHHHHHHHH-HHHHHc--CCeEEEEecCccchhHHH---HHHHHHHhc-CCceeeccccC-------
Confidence            5678889999999997643322 222222  33565555  34443322   344444333 43332111110       


Q ss_pred             HHhcCCCcEEEEcHHHHH-HHHHCCCCcCCCeeEEEecchhHHH--hhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHH
Q psy1548         227 YLKTHNPQIVVGTPGRIL-ALVRNKKLNLSLLKHFILDECDKML--EQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIR  303 (448)
Q Consensus       227 ~l~~~~~~IlV~Tp~~l~-~~l~~~~~~~~~i~~lViDEah~l~--~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~  303 (448)
                                  .|..+. ..+..  ......+++++|++-++.  ....+...+..+.+...+..-++.++|+...+..
T Consensus       163 ------------dp~~i~~~al~~--a~~~~~DvvIIDTaGr~~~~~d~~lm~el~~i~~~~~pd~vlLVlDa~~gq~a~  228 (433)
T 3kl4_A          163 ------------NPIEIAKKGVDI--FVKNKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQKAY  228 (433)
T ss_dssp             ------------CHHHHHHHHHHH--TTTTTCSEEEEEECCCSSSCCTTHHHHHHHHHHHHHCCSEEEEEEEGGGGGGGH
T ss_pred             ------------CHHHHHHHHHHH--HHhcCCCEEEEECCCCccccCCHHHHHHHHHHHHhhCCcceEEEEeCccchHHH
Confidence                        122221 12221  112456789999997643  2225666777777766666667788888766666


Q ss_pred             HHHHHhc
Q psy1548         304 PVCKKFM  310 (448)
Q Consensus       304 ~~~~~~l  310 (448)
                      ..+..|.
T Consensus       229 ~~a~~f~  235 (433)
T 3kl4_A          229 DLASRFH  235 (433)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            6666554

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=93.81  E-value=0.21  Score=46.97  Aligned_cols=40  Identities=13%  Similarity=0.275  Sum_probs=26.4

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEec
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSA  296 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SA  296 (448)
                      ..-.++|+||+|.+..  .....+...+...+....+|+.+.
T Consensus       109 ~~~~vliiDe~~~l~~--~~~~~L~~~le~~~~~~~~i~~~~  148 (327)
T 1iqp_A          109 ASFKIIFLDEADALTQ--DAQQALRRTMEMFSSNVRFILSCN  148 (327)
T ss_dssp             CSCEEEEEETGGGSCH--HHHHHHHHHHHHTTTTEEEEEEES
T ss_pred             CCCeEEEEeCCCcCCH--HHHHHHHHHHHhcCCCCeEEEEeC
Confidence            4567899999998755  334455566666666666666543

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=93.77  E-value=0.14  Score=46.08  Aligned_cols=40  Identities=13%  Similarity=0.135  Sum_probs=26.7

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE  191 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~  191 (448)
                      |+=.++.|+.|+|||...+-. +.+..  ..+.+++++-|...
T Consensus        19 g~l~v~~G~MgsGKTT~lL~~-~~r~~--~~g~kvli~kp~~D   58 (234)
T 2orv_A           19 GQIQVILGPMFSGKSTELMRR-VRRFQ--IAQYKCLVIKYAKD   58 (234)
T ss_dssp             CEEEEEECCTTSCHHHHHHHH-HHHHH--TTTCCEEEEEETTC
T ss_pred             eEEEEEECCCCCcHHHHHHHH-HHHHH--HCCCeEEEEeecCC
Confidence            565678899999999664433 33332  23457888888764

>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*

Probab=93.76  E-value=0.08  Score=56.35  Aligned_cols=70  Identities=14%  Similarity=0.095  Sum_probs=51.7

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhc-cCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      ..++-   |++      ++..  .+.+++|.|+.|||||.+..--+...+.. .-...++|+|+.|+..|.++.+.+..+
T Consensus        11 ~Ln~~---Q~~------av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vTFTnkAA~Em~~Rl~~~   79 (724)
T 1pjr_A           11 HLNKE---QQE------AVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSL   79 (724)
T ss_dssp             TSCHH---HHH------HHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHH
T ss_pred             hCCHH---HHH------HHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHH
Confidence            34455   888      6544  35789999999999998865555555543 223457999999999999999888876


Q ss_pred             hc
Q psy1548         204 SK  205 (448)
Q Consensus       204 ~~  205 (448)
                      .+
T Consensus        80 l~   81 (724)
T 1pjr_A           80 LG   81 (724)
T ss_dssp             HG
T ss_pred             hc
Confidence            43

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=93.59  E-value=0.52  Score=43.42  Aligned_cols=20  Identities=30%  Similarity=0.245  Sum_probs=16.6

Q ss_pred             eeCcceeeeccCCChhHHHH
Q psy1548         147 VLGMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       147 ~~g~~vli~apTGsGKT~~~  166 (448)
                      ..++.+++.||+|+|||...
T Consensus        49 ~~~~~~ll~G~~GtGKT~la   68 (285)
T 3h4m_A           49 EPPKGILLYGPPGTGKTLLA   68 (285)
T ss_dssp             CCCSEEEEESSSSSSHHHHH
T ss_pred             CCCCeEEEECCCCCcHHHHH
Confidence            34678999999999999664

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=93.56  E-value=0.074  Score=46.55  Aligned_cols=38  Identities=13%  Similarity=0.118  Sum_probs=25.3

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeecc
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT  189 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt  189 (448)
                      |+=.++.||.|+|||.-.+-. +......  +.+++++.|.
T Consensus        20 g~l~fiyG~MgsGKTt~Ll~~-i~n~~~~--~~kvl~~kp~   57 (195)
T 1w4r_A           20 GQIQVILGPMFSGKSTELMRR-VRRFQIA--QYKCLVIKYA   57 (195)
T ss_dssp             CEEEEEEECTTSCHHHHHHHH-HHHHHHT--TCCEEEEEET
T ss_pred             eEEEEEECCCCCcHHHHHHHH-HHHHHHc--CCeEEEEccc
Confidence            566789999999999553333 3333222  3578888887

>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=93.52  E-value=0.029  Score=58.52  Aligned_cols=44  Identities=23%  Similarity=0.385  Sum_probs=38.6

Q ss_pred             ccceeEeeccccCCcccccceeE--------------------eeccCCCCchhhhhhhcccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIV--------------------FNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v--------------------~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ..+|+|||+++++|+|.+ ++.|                    ++|..|.....|.|.+|||||.
T Consensus       401 ~~~VLVaTdv~~rGiDi~-v~~VId~g~~~~P~~~~~~~~~~~i~~d~P~s~~~yiQR~GRaGR~  464 (618)
T 2whx_A          401 DWDFVVTTDISEMGANFR-AGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRN  464 (618)
T ss_dssp             CCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCC
T ss_pred             CcEEEEECcHHHcCcccC-ceEEEECcceecceecccCCCceEEcccccCCHHHHHHhccccCCC
Confidence            348999999999999996 8777                    6777789999999999999994

>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=93.40  E-value=0.13  Score=56.99  Aligned_cols=37  Identities=16%  Similarity=0.179  Sum_probs=25.7

Q ss_pred             HHHHHHh-hccceeEe----eccccCCcccccc-eeEeeccCC
Q psy1548          90 EILRAIV-DCWRILVA----TNLFGRGMDIERV-NIVFNYDMP  126 (448)
Q Consensus        90 ~~~~~~~-~~~~~~~~----~~~~~~~~d~~~~-~~v~~~~~p  126 (448)
                      ..++.+. ...+|+||    |+++++|+|.++| +.|+++..|
T Consensus       310 ~~l~~F~~G~~~VLVaTas~Tdv~~rGIDip~VI~~VI~~~~P  352 (1054)
T 1gku_B          310 GDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCP  352 (1054)
T ss_dssp             HHHHHHHHTSCSEEEEECC------CCSCCTTTCCEEEEESCC
T ss_pred             HHHHHHHcCCCcEEEEecCCCCeeEeccccCCcccEEEEeCCC
Confidence            4444443 34589999    9999999999996 999999999

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=93.39  E-value=0.033  Score=58.65  Aligned_cols=43  Identities=21%  Similarity=0.373  Sum_probs=38.4

Q ss_pred             cceeEeeccccCCcccccceeEee--------------------ccCCCCchhhhhhhcccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFN--------------------YDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~--------------------~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      .+|+|||+++++|+|.+ ++.|++                    |+.|.....|.|.+||+||.
T Consensus       457 ~~VLVaTdv~e~GIDip-v~~VI~~g~~~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR~  519 (673)
T 2wv9_A          457 WDFVITTDISEMGANFG-ASRVIDCRKSVKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRN  519 (673)
T ss_dssp             CSEEEECGGGGTTCCCC-CSEEEECCEECCEEEECSTTCEEEECCSEECCHHHHHHHHTTSSCC
T ss_pred             ceEEEECchhhcceeeC-CcEEEECCCcccceeeecccccceecccCCCCHHHHHHHhhccCCC
Confidence            37999999999999999 999987                    55788888999999999994

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=93.36  E-value=0.19  Score=48.02  Aligned_cols=39  Identities=18%  Similarity=0.331  Sum_probs=27.0

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      ...+++|+||+|.+..  .....+...+...+....+++.+
T Consensus       109 ~~~~viiiDe~~~l~~--~~~~~L~~~le~~~~~~~~il~~  147 (340)
T 1sxj_C          109 KGFKLIILDEADAMTN--AAQNALRRVIERYTKNTRFCVLA  147 (340)
T ss_dssp             CSCEEEEETTGGGSCH--HHHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CCceEEEEeCCCCCCH--HHHHHHHHHHhcCCCCeEEEEEe
Confidence            4578999999998865  34455666677766666666554

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=93.31  E-value=0.17  Score=48.25  Aligned_cols=39  Identities=18%  Similarity=0.304  Sum_probs=26.0

Q ss_pred             CeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEec
Q psy1548         256 LLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSA  296 (448)
Q Consensus       256 ~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SA  296 (448)
                      ..+++++||+|.+..  .....+..++...+....+++.+.
T Consensus       133 ~~~vliiDE~~~l~~--~~~~~Ll~~le~~~~~~~~il~~~  171 (353)
T 1sxj_D          133 PYKIIILDEADSMTA--DAQSALRRTMETYSGVTRFCLICN  171 (353)
T ss_dssp             SCEEEEETTGGGSCH--HHHHHHHHHHHHTTTTEEEEEEES
T ss_pred             CceEEEEECCCccCH--HHHHHHHHHHHhcCCCceEEEEeC
Confidence            457899999998765  334555566666666666666543

>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=93.23  E-value=0.039  Score=55.38  Aligned_cols=46  Identities=20%  Similarity=0.388  Sum_probs=42.1

Q ss_pred             ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      ...|+|+|+++++|+|.+++..|+++..|.....|.|.+|||||..
T Consensus       394 ~~~vLv~T~~~~~Gldlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g  439 (472)
T 2fwr_A          394 RFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPS  439 (472)
T ss_dssp             SCSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCC
T ss_pred             CCCEEEEcCchhcCcccccCcEEEEECCCCCHHHHHHHHhhccCCC
Confidence            3489999999999999999999999999999989999999999943

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=93.21  E-value=0.042  Score=58.39  Aligned_cols=57  Identities=19%  Similarity=0.282  Sum_probs=42.1

Q ss_pred             CCCHHHHHHHhh-----ccceeEeeccccCCcccccceeEee----cc-------CCCCchhhhhhhcccccc
Q psy1548          86 LLKPEILRAIVD-----CWRILVATNLFGRGMDIERVNIVFN----YD-------MPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        86 ~~~~~~~~~~~~-----~~~~~~~~~~~~~~~d~~~~~~v~~----~~-------~p~~~~~yQ~~~~~~~~~  142 (448)
                      +++++..+.+.+     ..+|.|||+.+++|+|.++++.|++    |+       .|.+...|.|.+|||||.
T Consensus       321 ~l~~~~r~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~~~~Qr~GRaGR~  393 (715)
T 2va8_A          321 GLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRP  393 (715)
T ss_dssp             TSCHHHHHHHHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHHHHHHHHTTBCCT
T ss_pred             CCCHHHHHHHHHHHHcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHHHHHHHhhhcCCC
Confidence            344444444433     3489999999999999999999998    87       788889999999999994

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=93.16  E-value=0.13  Score=49.51  Aligned_cols=18  Identities=39%  Similarity=0.477  Sum_probs=15.6

Q ss_pred             CcceeeeccCCChhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~  166 (448)
                      +..+++.||+|+|||...
T Consensus        45 ~~~vli~G~~G~GKTtl~   62 (386)
T 2qby_A           45 PNNIFIYGLTGTGKTAVV   62 (386)
T ss_dssp             CCCEEEEECTTSSHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            568999999999999664

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=93.15  E-value=0.35  Score=45.56  Aligned_cols=39  Identities=15%  Similarity=0.340  Sum_probs=25.6

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      ...+++||||+|.|...  -...+.+.+..-|+...+|+.+
T Consensus        81 ~~~kvviIdead~lt~~--a~naLLk~LEep~~~t~fIl~t  119 (305)
T 2gno_A           81 YTRKYVIVHDCERMTQQ--AANAFLKALEEPPEYAVIVLNT  119 (305)
T ss_dssp             SSSEEEEETTGGGBCHH--HHHHTHHHHHSCCTTEEEEEEE
T ss_pred             CCceEEEeccHHHhCHH--HHHHHHHHHhCCCCCeEEEEEE
Confidence            45789999999988653  3344555566555555555554

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=93.10  E-value=0.15  Score=47.95  Aligned_cols=39  Identities=18%  Similarity=0.233  Sum_probs=25.4

Q ss_pred             CeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEec
Q psy1548         256 LLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSA  296 (448)
Q Consensus       256 ~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SA  296 (448)
                      .-+++||||+|.+...  ....+...+...+....+++.|.
T Consensus       107 ~~~viiiDe~~~l~~~--~~~~L~~~le~~~~~~~~il~~~  145 (323)
T 1sxj_B          107 KHKIVILDEADSMTAG--AQQALRRTMELYSNSTRFAFACN  145 (323)
T ss_dssp             CCEEEEEESGGGSCHH--HHHTTHHHHHHTTTTEEEEEEES
T ss_pred             CceEEEEECcccCCHH--HHHHHHHHHhccCCCceEEEEeC
Confidence            3678999999987553  23344555566566666666553

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=93.04  E-value=0.33  Score=46.30  Aligned_cols=40  Identities=5%  Similarity=0.091  Sum_probs=24.1

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEec
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSA  296 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SA  296 (448)
                      ...+++||||+|.|...  ....+.+.+..-+.+..+|+.|.
T Consensus       107 ~~~kvviIdead~l~~~--a~naLLk~lEep~~~~~~Il~t~  146 (334)
T 1a5t_A          107 GGAKVVWVTDAALLTDA--AANALLKTLEEPPAETWFFLATR  146 (334)
T ss_dssp             SSCEEEEESCGGGBCHH--HHHHHHHHHTSCCTTEEEEEEES
T ss_pred             CCcEEEEECchhhcCHH--HHHHHHHHhcCCCCCeEEEEEeC
Confidence            56789999999988653  23334444444444455555443

>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=93.01  E-value=0.026  Score=59.09  Aligned_cols=42  Identities=26%  Similarity=0.438  Sum_probs=37.2

Q ss_pred             cceeEeeccccCCcccccceeEe----------ecc-----------CCCCchhhhhhhccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVF----------NYD-----------MPEDSDTYLHRVARAGR  141 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~----------~~~-----------~p~~~~~yQ~~~~~~~~  141 (448)
                      .+|+|||+++++|||.+ ++.|+          ||+           .|.....|-|.+||+||
T Consensus       440 ~~VLVATdVaerGIDId-V~~VI~~Gl~~~~ViNyDydP~~gl~~~~~P~s~~syiQRiGRtGR  502 (666)
T 3o8b_A          440 DVVVVATDALMTGYTGD-FDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGR  502 (666)
T ss_dssp             CEEEEECTTHHHHCCCC-BSEEEECCEEEEEEEECCCSSSCEEEEEEEECBHHHHHHHHTTBCS
T ss_pred             CcEEEECChHHccCCCC-CcEEEecCcccccccccccccccccccccCcCCHHHHHHHhccCCC
Confidence            38999999999999985 88877          566           78888999999999999

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=92.99  E-value=0.77  Score=40.43  Aligned_cols=39  Identities=10%  Similarity=0.281  Sum_probs=23.7

Q ss_pred             CeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEec
Q psy1548         256 LLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSA  296 (448)
Q Consensus       256 ~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SA  296 (448)
                      .-.++||||+|.+..  .....+...+...+....+|+.|.
T Consensus       126 ~~~vlviDe~~~l~~--~~~~~l~~~l~~~~~~~~~i~~t~  164 (250)
T 1njg_A          126 RFKVYLIDEVHMLSR--HSFNALLKTLEEPPEHVKFLLATT  164 (250)
T ss_dssp             SSEEEEEETGGGSCH--HHHHHHHHHHHSCCTTEEEEEEES
T ss_pred             CceEEEEECcccccH--HHHHHHHHHHhcCCCceEEEEEeC
Confidence            346899999998644  334445555555555555555543

>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=92.95  E-value=0.062  Score=57.46  Aligned_cols=46  Identities=33%  Similarity=0.304  Sum_probs=41.6

Q ss_pred             ccceeEeeccccCCcccccc----------------------------------------------------eeEeeccC
Q psy1548          98 CWRILVATNLFGRGMDIERV----------------------------------------------------NIVFNYDM  125 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~----------------------------------------------------~~v~~~~~  125 (448)
                      .|.|.||||++|||+|...+                                                    ..|+++..
T Consensus       508 ~G~VtIATnmAgRGtDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGlhVI~te~  587 (922)
T 1nkt_A          508 RGGVTVATNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTER  587 (922)
T ss_dssp             TTCEEEEETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECSC
T ss_pred             CCeEEEecchhhcCccccCCCCHHHHHHHHHhhccccccccchhhHHHHHHHHHHHHHHHHHhhhHHHhcCCcEEEeccC
Confidence            46999999999999999964                                                    58999999


Q ss_pred             CCCchhhhhhhccccccc
Q psy1548         126 PEDSDTYLHRVARAGRFG  143 (448)
Q Consensus       126 p~~~~~yQ~~~~~~~~~~  143 (448)
                      |...+.|-|..||+||..
T Consensus       588 pes~riy~qr~GRTGRqG  605 (922)
T 1nkt_A          588 HESRRIDNQLRGRSGRQG  605 (922)
T ss_dssp             CSSHHHHHHHHHTSSGGG
T ss_pred             CCCHHHHHHHhcccccCC
Confidence            999999999999999944

>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=92.89  E-value=0.068  Score=57.21  Aligned_cols=54  Identities=20%  Similarity=0.325  Sum_probs=43.8

Q ss_pred             HHHHHHHhh-ccceeEeeccccCCcccccceeEeeccCCC-Cchhhhhhhcccccc
Q psy1548          89 PEILRAIVD-CWRILVATNLFGRGMDIERVNIVFNYDMPE-DSDTYLHRVARAGRF  142 (448)
Q Consensus        89 ~~~~~~~~~-~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~-~~~~yQ~~~~~~~~~  142 (448)
                      ..+++.+.+ ..+|+|||+++++|+|.++++.|++++.|. ....+.|.+||+||.
T Consensus       629 ~~v~~~F~~G~~~ILVaT~vie~GIDiP~v~~VIi~d~~r~~l~~l~Qr~GRaGR~  684 (780)
T 1gm5_A          629 DRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRG  684 (780)
T ss_dssp             HHHHHHHTTTSSSBCCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCS
T ss_pred             HHHHHHHHCCCCeEEEECCCCCccccCCCCCEEEEeCCCCCCHHHHHHHhcccCcC
Confidence            455555543 358999999999999999999999999885 566667888999983

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=92.53  E-value=0.051  Score=54.07  Aligned_cols=53  Identities=13%  Similarity=0.214  Sum_probs=41.6

Q ss_pred             HHHHHHhh-ccceeEeeccccCCccccccee-----------------EeeccCCCCchhhhhhhccccccc
Q psy1548          90 EILRAIVD-CWRILVATNLFGRGMDIERVNI-----------------VFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        90 ~~~~~~~~-~~~~~~~~~~~~~~~d~~~~~~-----------------v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      .+++.+.+ ...|+|||+++++|+|.+ +..                 ++++..|.....|.|.+||+||.-
T Consensus       208 ~~~~~f~~g~~~vLVaT~v~e~GiDip-~~~VI~~g~~~~~v~d~~~~vi~~~~p~~~~~~~Qr~GR~GR~g  278 (431)
T 2v6i_A          208 SEYPKCKSEKWDFVITTDISEMGANFK-ADRVIDPRKTIKPILLDGRVSMQGPIAITPASAAQRRGRIGRNP  278 (431)
T ss_dssp             HHTTHHHHSCCSEEEECGGGGTSCCCC-CSEEEECCEEEEEEEETTEEEEEEEEECCHHHHHHHHTTSSCCT
T ss_pred             HHHHhhcCCCCeEEEECchHHcCcccC-CcEEEecCccccceecccceeecccccCCHHHHHHhhhccCCCC
Confidence            34444433 348999999999999998 544                 567788999999999999999943

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=92.52  E-value=1  Score=39.34  Aligned_cols=51  Identities=20%  Similarity=0.319  Sum_probs=36.2

Q ss_pred             CCeeEEEecchhHHHhhhh--hHHHHHHHHHhCCCCCeEEEEeccCCccHHHHH
Q psy1548         255 SLLKHFILDECDKMLEQLE--MRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVC  306 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~--~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~  306 (448)
                      ..+++||+||+-..+.. +  -.+.+..++...|...-+|+.+--.|+++.+.+
T Consensus       119 ~~yDlvILDEi~~al~~-g~l~~~ev~~~l~~Rp~~~~vIlTGr~ap~~l~e~A  171 (196)
T 1g5t_A          119 PLLDMVVLDELTYMVAY-DYLPLEEVISALNARPGHQTVIITGRGCHRDILDLA  171 (196)
T ss_dssp             TTCSEEEEETHHHHHHT-TSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHHHC
T ss_pred             CCCCEEEEeCCCccccC-CCCCHHHHHHHHHhCcCCCEEEEECCCCcHHHHHhC
Confidence            56789999999876554 3  245566777777777777777777777766654

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=92.41  E-value=0.094  Score=57.88  Aligned_cols=58  Identities=29%  Similarity=0.440  Sum_probs=45.9

Q ss_pred             CCCHHHHHHHhh-----ccceeEeeccccCCcccccceeEee----ccC----CCCchhhhhhhccccccc
Q psy1548          86 LLKPEILRAIVD-----CWRILVATNLFGRGMDIERVNIVFN----YDM----PEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        86 ~~~~~~~~~~~~-----~~~~~~~~~~~~~~~d~~~~~~v~~----~~~----p~~~~~yQ~~~~~~~~~~  143 (448)
                      ++.+...+.+.+     ..+|+|||+.+++|+|.+.++.|++    |+.    |.....|.|.+|||||..
T Consensus       415 gl~~~eR~~ve~~F~~G~ikVLVAT~~la~GIDiP~~~vVI~~~~kfd~~~~rp~s~~~y~Qr~GRAGR~G  485 (1010)
T 2xgj_A          415 GLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRG  485 (1010)
T ss_dssp             TSCHHHHHHHHHHHHTTCCSEEEEEGGGGGSTTCCBSEEEESCSEEECSSCEEECCHHHHHHHHTTBCCTT
T ss_pred             CCCHHHHHHHHHHHhcCCCcEEEEehHhhccCCCCCceEEEeCCcccCCcCCccCCHHHHhHhhhhcccCC
Confidence            445544444332     2379999999999999999999999    887    778889999999999953

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=92.29  E-value=0.044  Score=55.58  Aligned_cols=45  Identities=20%  Similarity=0.230  Sum_probs=41.8

Q ss_pred             cceeEee-ccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548          99 WRILVAT-NLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        99 ~~~~~~~-~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      ..|+||| +++++|+|.+.++.|+.+..|.....|.|.+||+||..
T Consensus       398 ~~vLv~T~~~~~~GiDip~v~~vi~~~~~~s~~~~~Q~~GR~gR~g  443 (510)
T 2oca_A          398 GIIIVASYGVFSTGISVKNLHHVVLAHGVKSKIIVLQTIGRVLRKH  443 (510)
T ss_dssp             SCEEEEEHHHHHHSCCCCSEEEEEESSCCCSCCHHHHHHHHHHTTT
T ss_pred             CCEEEEEcChhhcccccccCcEEEEeCCCCCHHHHHHHHhcccccC
Confidence            3799999 99999999999999999999999888999999999954

>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=92.24  E-value=0.056  Score=57.54  Aligned_cols=58  Identities=19%  Similarity=0.271  Sum_probs=44.7

Q ss_pred             cceeEeeccccCCcccccceeEee----cc----CCCCchhhhhhhccccccceeeeeCcceeeecc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFN----YD----MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAK  157 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~----~~----~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~ap  157 (448)
                      -+|.|||+.+++|+|.+.++.|++    |+    .|.+...|.|.+|||||.-.. ..|.-+++..+
T Consensus       321 ~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~g~~-~~G~~~~l~~~  386 (720)
T 2zj8_A          321 IKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYD-EVGEGIIVSTS  386 (720)
T ss_dssp             SCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCTTTC-SEEEEEEECSS
T ss_pred             CeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCCCCC-CCceEEEEecC
Confidence            389999999999999999999998    55    477888999999999994311 12444555443

>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=91.98  E-value=0.067  Score=56.70  Aligned_cols=58  Identities=24%  Similarity=0.364  Sum_probs=45.6

Q ss_pred             CCCHHHHHHHhh-----ccceeEeeccccCCcccccceeEee----cc---CCCCchhhhhhhccccccc
Q psy1548          86 LLKPEILRAIVD-----CWRILVATNLFGRGMDIERVNIVFN----YD---MPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        86 ~~~~~~~~~~~~-----~~~~~~~~~~~~~~~d~~~~~~v~~----~~---~p~~~~~yQ~~~~~~~~~~  143 (448)
                      +++++..+.+.+     ..+|.|||+.+++|+|.++++.|++    |+   .|.+..+|.|.+|||||.-
T Consensus       305 ~l~~~~R~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaGR~g  374 (702)
T 2p6r_A          305 GLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPG  374 (702)
T ss_dssp             TSCHHHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTT
T ss_pred             CCCHHHHHHHHHHHHCCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcCCCC
Confidence            455554444433     2389999999999999999999998    54   6778889999999999943

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=91.80  E-value=0.58  Score=45.53  Aligned_cols=18  Identities=22%  Similarity=0.565  Sum_probs=14.9

Q ss_pred             Ccceee--eccCCChhHHHH
Q psy1548         149 GMDILC--QAKSGMGKTAVF  166 (448)
Q Consensus       149 g~~vli--~apTGsGKT~~~  166 (448)
                      +..+++  .||.|+|||...
T Consensus        50 ~~~~li~i~G~~G~GKT~L~   69 (412)
T 1w5s_A           50 DVNMIYGSIGRVGIGKTTLA   69 (412)
T ss_dssp             CEEEEEECTTCCSSSHHHHH
T ss_pred             CCEEEEeCcCcCCCCHHHHH
Confidence            457888  999999999764

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=91.65  E-value=0.11  Score=53.80  Aligned_cols=44  Identities=20%  Similarity=0.293  Sum_probs=41.0

Q ss_pred             eeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccce
Q psy1548         101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGT  144 (448)
Q Consensus       101 ~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~  144 (448)
                      |.|+|+++++|+|.+.+..|+++..|.....|.|.+||++|..+
T Consensus       502 ilvtt~~l~~GiDip~v~~Vi~~~~~~s~~~~~Q~iGR~~R~~~  545 (590)
T 3h1t_A          502 ILTTSQLLTTGVDAPTCKNVVLARVVNSMSEFKQIVGRGTRLRE  545 (590)
T ss_dssp             EEEESSTTTTTCCCTTEEEEEEESCCCCHHHHHHHHTTSCCCBG
T ss_pred             EEEECChhhcCccchheeEEEEEecCCChHHHHHHHhhhcccCc
Confidence            78899999999999999999999999999999999999999654

>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=91.61  E-value=0.06  Score=60.05  Aligned_cols=45  Identities=29%  Similarity=0.485  Sum_probs=35.4

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCC--------Cchhhhhhhccccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPE--------DSDTYLHRVARAGRFG  143 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~--------~~~~yQ~~~~~~~~~~  143 (448)
                      .+|+|||+.+++|+|.++++.|+++..|.        ....|.|.+|||||..
T Consensus       531 ikVLVAT~vla~GIDiP~v~~VI~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G  583 (1108)
T 3l9o_A          531 LKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRG  583 (1108)
T ss_dssp             CCEEEEESCCCSCCCC--CEEEESCSEEESSSCEEECCHHHHHHHHHHSCCSS
T ss_pred             CeEEEECcHHhcCCCCCCceEEEecCcccCccccccCCHHHHHHhhcccCCCC
Confidence            38999999999999999999999776543        3345889999999943

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=91.50  E-value=0.54  Score=45.09  Aligned_cols=39  Identities=10%  Similarity=0.279  Sum_probs=24.5

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEe
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFS  295 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~S  295 (448)
                      ..-+++||||+|.+..  .....+...+...+....+|+.+
T Consensus       118 ~~~~vliiDe~~~l~~--~~~~~Ll~~le~~~~~~~~Il~~  156 (373)
T 1jr3_A          118 GRFKVYLIDEVHMLSR--HSFNALLKTLEEPPEHVKFLLAT  156 (373)
T ss_dssp             SSSEEEEEECGGGSCH--HHHHHHHHHHHSCCSSEEEEEEE
T ss_pred             CCeEEEEEECcchhcH--HHHHHHHHHHhcCCCceEEEEEe
Confidence            4457899999998755  33444555555555555555544

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=91.20  E-value=0.11  Score=48.02  Aligned_cols=51  Identities=18%  Similarity=0.223  Sum_probs=34.6

Q ss_pred             HHHHHhhc--cc-eeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccc
Q psy1548          91 ILRAIVDC--WR-ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR  141 (448)
Q Consensus        91 ~~~~~~~~--~~-~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~  141 (448)
                      +++.....  .. ++++|.+.++|+|.+....|++|+.|+....|.|.+||++|
T Consensus       155 ~i~~F~~~~~~~v~L~st~~~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R  208 (271)
T 1z5z_A          155 IISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYR  208 (271)
T ss_dssp             HHHHHHHCTTCCEEEEECCTTCCCCCCTTCSEEEECSCCSCTTTC---------
T ss_pred             HHHHhcCCCCCCEEEEehhhhcCCcCcccCCEEEEECCCCChhHHHHHHHhccc
Confidence            44444443  23 68999999999999999999999999998888999899887

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=91.13  E-value=0.26  Score=49.25  Aligned_cols=42  Identities=21%  Similarity=0.177  Sum_probs=26.1

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeec
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH  188 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~P  188 (448)
                      .+..|.-+++.|++|+|||...+--+.+ +... .+..++|+..
T Consensus       199 Gl~~G~liiI~G~pG~GKTtl~l~ia~~-~~~~-~g~~Vl~~s~  240 (454)
T 2r6a_A          199 GFQRSDLIIVAARPSVGKTAFALNIAQN-VATK-TNENVAIFSL  240 (454)
T ss_dssp             SBCTTCEEEEECCTTSCHHHHHHHHHHH-HHHH-SSCCEEEEES
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHHH-HHHh-CCCcEEEEEC
Confidence            3445778999999999999654433333 3221 1335777763

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.08  E-value=1.4  Score=43.05  Aligned_cols=57  Identities=14%  Similarity=0.076  Sum_probs=35.3

Q ss_pred             ccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeecc
Q psy1548          78 HSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAK  157 (448)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~ap  157 (448)
                      +.-+|++.+=-.+..+.+.+.-                    ..++.+|.   .|+..      .++   -.+.+|+.||
T Consensus       143 p~v~~~dIgGl~~~k~~l~e~v--------------------~~Pl~~pe---~f~~~------gi~---~prGvLL~GP  190 (405)
T 4b4t_J          143 PDSTYDMVGGLTKQIKEIKEVI--------------------ELPVKHPE---LFESL------GIA---QPKGVILYGP  190 (405)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHT--------------------HHHHHCHH---HHHHH------TCC---CCCCEEEESC
T ss_pred             CCCCHHHhCCHHHHHHHHHHHH--------------------HHHHhCHH---HHHhC------CCC---CCCceEEeCC
Confidence            4457888776677777776653                    00123332   23444      222   2478999999


Q ss_pred             CCChhHHHH
Q psy1548         158 SGMGKTAVF  166 (448)
Q Consensus       158 TGsGKT~~~  166 (448)
                      .|+|||+.+
T Consensus       191 PGTGKTllA  199 (405)
T 4b4t_J          191 PGTGKTLLA  199 (405)
T ss_dssp             SSSSHHHHH
T ss_pred             CCCCHHHHH
Confidence            999999764

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=90.86  E-value=0.093  Score=58.48  Aligned_cols=30  Identities=23%  Similarity=0.454  Sum_probs=28.3

Q ss_pred             ccceeEe----eccccCCccccc-ceeEeeccCCC
Q psy1548          98 CWRILVA----TNLFGRGMDIER-VNIVFNYDMPE  127 (448)
Q Consensus        98 ~~~~~~~----~~~~~~~~d~~~-~~~v~~~~~p~  127 (448)
                      ..+|+||    |+++++|+|+++ ++.|++|+.|.
T Consensus       354 ~~~VLVatas~TdvlarGIDip~~V~~VI~~d~P~  388 (1104)
T 4ddu_A          354 KINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPS  388 (1104)
T ss_dssp             SCSEEEEETTTHHHHCCSCCCTTTCCEEEEESCCE
T ss_pred             CCCEEEEecCCCCeeEecCcCCCCCCEEEEECCCC
Confidence            3589999    999999999999 99999999998

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=90.78  E-value=0.7  Score=45.77  Aligned_cols=57  Identities=21%  Similarity=0.266  Sum_probs=32.6

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee--ccHHHHHHHHHHHHHhhccCCCceE
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKV  212 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~v  212 (448)
                      +.-+++.+++|+|||....--+ ..+..  .+.+++++.  |.+.-+.+   +++.+.... ++.+
T Consensus       100 p~vIlivG~~G~GKTTt~~kLA-~~l~~--~G~kVllv~~D~~R~aa~e---qL~~~~~~~-gvpv  158 (443)
T 3dm5_A          100 PTILLMVGIQGSGKTTTVAKLA-RYFQK--RGYKVGVVCSDTWRPGAYH---QLRQLLDRY-HIEV  158 (443)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHH-HHHHT--TTCCEEEEECCCSSTHHHH---HHHHHHGGG-TCEE
T ss_pred             CeEEEEECcCCCCHHHHHHHHH-HHHHH--CCCeEEEEeCCCcchhHHH---HHHHHHHhc-CCcE
Confidence            4568899999999997653222 22322  234566665  55554433   455555444 5544

>3hjh_A Transcription-repair-coupling factor; MFD, mutation frequency decline, ATP-binding, DNA DAMA repair, DNA-binding, helicase, hydrolase; 1.95A {Escherichia coli} PDB: 2b2n_A* 4dfc_A

Probab=90.63  E-value=0.92  Score=45.56  Aligned_cols=87  Identities=11%  Similarity=0.113  Sum_probs=55.1

Q ss_pred             eCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcC-------cc
Q psy1548         148 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGG-------LP  220 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~-------~~  220 (448)
                      .|....+.+-||||||++..- +...    . +..+|||+|+...|.|+++.++.|..   + .+..+-.-       ..
T Consensus        13 ~~~~~~l~g~~gs~ka~~~a~-l~~~----~-~~p~lvv~~~~~~A~~l~~~l~~~~~---~-~v~~fp~~e~lpyd~~~   82 (483)
T 3hjh_A           13 AGEQRLLGELTGAACATLVAE-IAER----H-AGPVVLIAPDMQNALRLHDEISQFTD---Q-MVMNLADWETLPYDSFS   82 (483)
T ss_dssp             TTCEEEEECCCTTHHHHHHHH-HHHH----S-SSCEEEEESSHHHHHHHHHHHHHTCS---S-CEEECCCCCSCTTCSSC
T ss_pred             CCCeEEEeCCCchHHHHHHHH-HHHH----h-CCCEEEEeCCHHHHHHHHHHHHhhCC---C-cEEEEeCcccccccccC
Confidence            466788999999999976332 2222    1 22589999999999999999998863   2 23333221       00


Q ss_pred             cH-----Hh---HHHHhcCCCcEEEEcHHHHH
Q psy1548         221 IQ-----KD---EEYLKTHNPQIVVGTPGRIL  244 (448)
Q Consensus       221 ~~-----~~---~~~l~~~~~~IlV~Tp~~l~  244 (448)
                      ..     ..   ...+..+...|+|+|+..++
T Consensus        83 p~~~~~~~Rl~~l~~L~~~~~~ivv~sv~al~  114 (483)
T 3hjh_A           83 PHQDIISSRLSTLYQLPTMQRGVLIVPVNTLM  114 (483)
T ss_dssp             CCHHHHHHHHHHHHHGGGCCSSEEEEEHHHHH
T ss_pred             CChHHHHHHHHHHHHHHhCCCCEEEEEHHHHh
Confidence            00     11   12333445679999987765

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=90.15  E-value=0.36  Score=48.04  Aligned_cols=42  Identities=21%  Similarity=0.093  Sum_probs=25.9

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeec
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH  188 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~P  188 (448)
                      .+..|.-+++.|++|+|||...+--+.+....  .+..++++..
T Consensus       196 Gl~~G~l~ii~G~pg~GKT~lal~ia~~~a~~--~g~~vl~~sl  237 (444)
T 2q6t_A          196 TLGPGSLNIIAARPAMGKTAFALTIAQNAALK--EGVGVGIYSL  237 (444)
T ss_dssp             CCCTTCEEEEEECTTSCHHHHHHHHHHHHHHT--TCCCEEEEES
T ss_pred             CcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHh--CCCeEEEEEC
Confidence            34456788999999999996543333333221  1335777664

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=90.01  E-value=3.3  Score=40.73  Aligned_cols=18  Identities=28%  Similarity=0.381  Sum_probs=15.6

Q ss_pred             CcceeeeccCCChhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~  166 (448)
                      .+-+|+.||+|+|||+.+
T Consensus       206 prGiLL~GPPGtGKT~la  223 (428)
T 4b4t_K          206 PRGVLLYGPPGTGKTMLV  223 (428)
T ss_dssp             CCEEEEESCTTTTHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            467999999999999764

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=89.90  E-value=0.46  Score=45.39  Aligned_cols=41  Identities=24%  Similarity=0.272  Sum_probs=26.4

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeec
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH  188 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~P  188 (448)
                      .+..|.-+++.|++|+|||...+--+.+...   .+..++|++.
T Consensus        42 Gl~~G~LiiIaG~pG~GKTt~al~ia~~~a~---~g~~Vl~fSl   82 (338)
T 4a1f_A           42 GFNKGSLVIIGARPSMGKTSLMMNMVLSALN---DDRGVAVFSL   82 (338)
T ss_dssp             SBCTTCEEEEEECTTSCHHHHHHHHHHHHHH---TTCEEEEEES
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHH---cCCeEEEEeC
Confidence            3445677899999999999654433333322   3446777763

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=89.90  E-value=0.099  Score=57.65  Aligned_cols=43  Identities=23%  Similarity=0.389  Sum_probs=34.4

Q ss_pred             cceeEeeccccCCcccccceeEeeccCC---------CCchhhhhhhcccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMP---------EDSDTYLHRVARAGRF  142 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p---------~~~~~yQ~~~~~~~~~  142 (448)
                      .+|+|||+++++|+|.++ +.|+....|         .....|.|.+|||||.
T Consensus       426 ~kVLvAT~~~a~GIDiP~-~~VVi~~~~k~dg~~~~~~s~~~y~Qr~GRAGR~  477 (997)
T 4a4z_A          426 IKVLFATETFAMGLNLPT-RTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRR  477 (997)
T ss_dssp             CSEEEECTHHHHSCCCCC-SEEEESCSEEEETTEEEECCHHHHHHHHGGGCCT
T ss_pred             CcEEEEchHhhCCCCCCC-ceEEEeccccccCccCCCCCHHHHhHHhcccccC
Confidence            489999999999999999 444443333         3778899999999994

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=89.57  E-value=0.91  Score=40.00  Aligned_cols=22  Identities=27%  Similarity=0.253  Sum_probs=18.2

Q ss_pred             eeeeCcceeeeccCCChhHHHH
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~  166 (448)
                      .+..|.-+++.||+|+|||...
T Consensus        19 gi~~G~~~~i~G~~GsGKTtl~   40 (235)
T 2w0m_A           19 GIPQGFFIALTGEPGTGKTIFS   40 (235)
T ss_dssp             SEETTCEEEEECSTTSSHHHHH
T ss_pred             CCcCCCEEEEEcCCCCCHHHHH
Confidence            4556888999999999999554

>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=89.53  E-value=0.17  Score=55.57  Aligned_cols=55  Identities=16%  Similarity=0.318  Sum_probs=47.3

Q ss_pred             HHHHHHHhhc---cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548          89 PEILRAIVDC---WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        89 ~~~~~~~~~~---~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      ..+++...+.   ..|+|||++.++|+|.+.+..|++|+.|.....|.|.+||++|..
T Consensus       544 ~~~l~~F~~g~~~~~vLvaT~v~~~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~G  601 (968)
T 3dmq_A          544 DRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIG  601 (968)
T ss_dssp             HHHHHHHHSTTSSCEEEECSCCTTCSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCSS
T ss_pred             HHHHHHHhCCCCcccEEEecchhhcCCCcccCcEEEEecCCCCHHHHHHHhhccccCC
Confidence            4455555543   579999999999999999999999999999999999999999854

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=89.31  E-value=0.12  Score=48.36  Aligned_cols=16  Identities=38%  Similarity=0.528  Sum_probs=13.9

Q ss_pred             ceeeeccCCChhHHHH
Q psy1548         151 DILCQAKSGMGKTAVF  166 (448)
Q Consensus       151 ~vli~apTGsGKT~~~  166 (448)
                      ++++.||+|+|||...
T Consensus        40 ~~ll~G~~G~GKt~la   55 (319)
T 2chq_A           40 HLLFSGPPGTGKTATA   55 (319)
T ss_dssp             CEEEESSSSSSHHHHH
T ss_pred             eEEEECcCCcCHHHHH
Confidence            5899999999999654

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=89.21  E-value=1.4  Score=45.86  Aligned_cols=116  Identities=11%  Similarity=0.083  Sum_probs=65.6

Q ss_pred             CCCeEEEEeccCCccHHHHHHHhcCCCeEEEEcCcccccccceeEEEEE-cC-----cch-----HHHHHHHHHhhCCCC
Q psy1548         287 HTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVK-LK-----ENE-----KNKKLFELLDVLEFN  355 (448)
Q Consensus       287 ~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~-~~-----~~~-----k~~~L~~ll~~~~~~  355 (448)
                      ....+|++|||+.+ ...+...+.-.+..+.....  ....+..-.+.. ++     .+.     -...+..++... ++
T Consensus       374 ~~~~~il~SaTL~p-~~~~~~~lGl~~~~~~~~sp--f~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~i~~l~~~~-~g  449 (620)
T 4a15_A          374 KESKTIHMSGTLDP-FDFYSDITGFEIPFKKIGEI--FPPENRYIAYYDGVSSKYDTLDEKELDRMATVIEDIILKV-KK  449 (620)
T ss_dssp             GGSEEEEEESSCCS-HHHHHHHHCCCCCEEECCCC--SCGGGEEEEEECCC-------CHHHHHHHHHHHHHHHHHH-CS
T ss_pred             hCCeEEEEccCCCc-HHHHHHHhCCCceeeecCCC--CCHHHeEEEEeCCCCCcCCCCCHHHHHHHHHHHHHHHHhC-CC
Confidence            45679999999986 44444443322333333222  112222111110 11     011     112233444433 46


Q ss_pred             eEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEE
Q psy1548         356 QVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAIT  410 (448)
Q Consensus       356 ~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~  410 (448)
                      .++||++|....+.+++.|+.  +... ...+++..+|..++++|+ ++.++.+.
T Consensus       450 ~~lvlF~Sy~~l~~v~~~l~~--~~~~-~~q~~~~~~~~~ll~~f~-~~~~vL~~  500 (620)
T 4a15_A          450 NTIVYFPSYSLMDRVENRVSF--EHMK-EYRGIDQKELYSMLKKFR-RDHGTIFA  500 (620)
T ss_dssp             CEEEEESCHHHHHHHTSSCCS--CCEE-CCTTCCSHHHHHHHHHHT-TSCCEEEE
T ss_pred             CEEEEeCCHHHHHHHHHHHHh--cchh-ccCCCChhHHHHHHHHhc-cCCcEEEE
Confidence            799999999999999998873  3322 566677778999999999 55444333

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=88.93  E-value=2.4  Score=42.57  Aligned_cols=18  Identities=33%  Similarity=0.368  Sum_probs=15.7

Q ss_pred             CcceeeeccCCChhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~  166 (448)
                      .+.+++.||+|+|||..+
T Consensus       238 ~~~vLL~GppGtGKT~lA  255 (489)
T 3hu3_A          238 PRGILLYGPPGTGKTLIA  255 (489)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CCcEEEECcCCCCHHHHH
Confidence            467999999999999764

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=88.72  E-value=1.8  Score=38.39  Aligned_cols=44  Identities=9%  Similarity=-0.084  Sum_probs=27.0

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhcc---CCCeEEEEeec
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETT---DSNVYVLVMCH  188 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~---~~~~~~lil~P  188 (448)
                      .+..|.-+++.+|+|+|||.....-+...+...   ..+..++++..
T Consensus        20 gi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~   66 (243)
T 1n0w_A           20 GIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDT   66 (243)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEES
T ss_pred             CCcCCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEEC
Confidence            456688899999999999976544333322211   01235666653

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=87.29  E-value=0.68  Score=43.71  Aligned_cols=52  Identities=8%  Similarity=-0.075  Sum_probs=31.4

Q ss_pred             eCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         148 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .| -+++.+|.|+|||...+-.+.+ ......+.+++++..-..+...   .++++.
T Consensus        28 ~G-iteI~G~pGsGKTtL~Lq~~~~-~~~~g~g~~vlyId~E~s~~~~---ra~~lG   79 (333)
T 3io5_A           28 SG-LLILAGPSKSFKSNFGLTMVSS-YMRQYPDAVCLFYDSEFGITPA---YLRSMG   79 (333)
T ss_dssp             SE-EEEEEESSSSSHHHHHHHHHHH-HHHHCTTCEEEEEESSCCCCHH---HHHHTT
T ss_pred             CC-eEEEECCCCCCHHHHHHHHHHH-HHhcCCCceEEEEeccchhhHH---HHHHhC
Confidence            35 5899999999999664433333 3222224478888865554322   355554

>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=87.23  E-value=0.36  Score=54.09  Aligned_cols=45  Identities=22%  Similarity=0.284  Sum_probs=38.5

Q ss_pred             ccceeEeeccccCCcccccceeEeeccC-CCCchhhhhhhcccccc
Q psy1548          98 CWRILVATNLFGRGMDIERVNIVFNYDM-PEDSDTYLHRVARAGRF  142 (448)
Q Consensus        98 ~~~~~~~~~~~~~~~d~~~~~~v~~~~~-p~~~~~yQ~~~~~~~~~  142 (448)
                      ...|+|||+++++|+|.++++.|+.+.. +..+..|.|.+||+||.
T Consensus       864 ~~~VLVaT~v~e~GiDip~v~~VIi~~~~~~~l~~l~Qr~GRvgR~  909 (1151)
T 2eyq_A          864 RFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRS  909 (1151)
T ss_dssp             SCCEEEESSTTGGGSCCTTEEEEEETTTTSSCHHHHHHHHTTCCBT
T ss_pred             CCcEEEECCcceeeecccCCcEEEEeCCCCCCHHHHHHHHhccCcC
Confidence            3489999999999999999999987665 45777788999999994

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=86.96  E-value=1.5  Score=40.94  Aligned_cols=20  Identities=25%  Similarity=0.318  Sum_probs=16.5

Q ss_pred             eCcceeeeccCCChhHHHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVFV  167 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~  167 (448)
                      .|+-+++.+|+|+|||....
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~  123 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLA  123 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            46788999999999997643

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=86.73  E-value=0.47  Score=49.47  Aligned_cols=96  Identities=13%  Similarity=0.136  Sum_probs=55.9

Q ss_pred             ceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhc
Q psy1548         151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKT  230 (448)
Q Consensus       151 ~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~  230 (448)
                      -.++.|+-|.|||.+..+.+-.. .     ..++|.+|+.+=+..+.    .+...                        
T Consensus       194 ~~vlta~RGRGKSa~lG~~~a~~-~-----~~~~vtAP~~~a~~~l~----~~~~~------------------------  239 (671)
T 2zpa_A          194 VAAVTAARGRGKSALAGQLISRI-A-----GRAIVTAPAKASTDVLA----QFAGE------------------------  239 (671)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHS-S-----SCEEEECSSCCSCHHHH----HHHGG------------------------
T ss_pred             eEEEecCCCCCHHHHHHHHHHHH-H-----hCcEEECCCHHHHHHHH----HHhhC------------------------
Confidence            46899999999997655544432 2     13688999987554332    22210                        


Q ss_pred             CCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCC
Q psy1548         231 HNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLS  299 (448)
Q Consensus       231 ~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~  299 (448)
                         .|-+..|+.+.   .    ...+.+++|||||=.+.-     +.+..++...    ..++||.|+.
T Consensus       240 ---~i~~~~Pd~~~---~----~~~~~dlliVDEAAaIp~-----pll~~ll~~~----~~v~~~tTv~  289 (671)
T 2zpa_A          240 ---KFRFIAPDALL---A----SDEQADWLVVDEAAAIPA-----PLLHQLVSRF----PRTLLTTTVQ  289 (671)
T ss_dssp             ---GCCBCCHHHHH---H----SCCCCSEEEEETGGGSCH-----HHHHHHHTTS----SEEEEEEEBS
T ss_pred             ---CeEEeCchhhh---h----CcccCCEEEEEchhcCCH-----HHHHHHHhhC----CeEEEEecCC
Confidence               12233565432   1    134578999999985533     3344444432    2467777753

>2l82_A Designed protein OR32; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, de novo protein; NMR {Artificial gene}

Probab=86.69  E-value=4.2  Score=31.16  Aligned_cols=47  Identities=15%  Similarity=0.227  Sum_probs=38.3

Q ss_pred             EEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcC
Q psy1548         357 VVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDF  403 (448)
Q Consensus       357 ~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g  403 (448)
                      .++|.+..+-...+...+++.|..+..++++.....|.+.+++|...
T Consensus         5 fvvfssdpeilkeivreikrqgvrvvllysdqdekrrrerleefekq   51 (162)
T 2l82_A            5 FVVFSSDPEILKEIVREIKRQGVRVVLLYSDQDEKRRRERLEEFEKQ   51 (162)
T ss_dssp             EEEEESCHHHHHHHHHHHHHTTCEEEEEECCSCHHHHHHHHHHHHTT
T ss_pred             EEEecCCHHHHHHHHHHHHhCCeEEEEEecCchHHHHHHHHHHHHHc
Confidence            45677777777788888888899999999998888888888888763

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=85.78  E-value=0.62  Score=54.53  Aligned_cols=44  Identities=9%  Similarity=0.003  Sum_probs=29.8

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHH
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE  191 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~  191 (448)
                      -+..|+++++.+|+|+|||..+...+....   ..+.+++++..-..
T Consensus      1423 Gi~~g~~vll~GppGtGKT~LA~ala~ea~---~~G~~v~Fi~~e~~ 1466 (2050)
T 3cmu_A         1423 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQ---REGKTCAFIDAEHA 1466 (2050)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHHH---TTTCCEEEECTTSC
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHH---HcCCcEEEEEcccc
Confidence            455689999999999999976544333332   23447887775543

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=85.49  E-value=0.8  Score=44.05  Aligned_cols=43  Identities=12%  Similarity=0.050  Sum_probs=27.9

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccH
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR  190 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~  190 (448)
                      -+..|.-+++.+|+|+|||... +.++..+...  +..++++..-.
T Consensus        57 Gi~~G~i~~I~GppGsGKSTLa-l~la~~~~~~--gg~VlyId~E~   99 (356)
T 3hr8_A           57 GYPRGRIVEIFGQESSGKTTLA-LHAIAEAQKM--GGVAAFIDAEH   99 (356)
T ss_dssp             SEETTEEEEEEESTTSSHHHHH-HHHHHHHHHT--TCCEEEEESSC
T ss_pred             CccCCcEEEEECCCCCCHHHHH-HHHHHHHHhc--CCeEEEEeccc
Confidence            4556788999999999999543 4444333322  33677776543

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=83.88  E-value=0.44  Score=39.14  Aligned_cols=18  Identities=11%  Similarity=0.099  Sum_probs=15.9

Q ss_pred             eCcceeeeccCCChhHHH
Q psy1548         148 LGMDILCQAKSGMGKTAV  165 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~  165 (448)
                      .+.++++.||+|+|||..
T Consensus        26 ~~~~vll~G~~GtGKt~l   43 (143)
T 3co5_A           26 RTSPVFLTGEAGSPFETV   43 (143)
T ss_dssp             CSSCEEEEEETTCCHHHH
T ss_pred             CCCcEEEECCCCccHHHH
Confidence            467899999999999965

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=82.19  E-value=1.2  Score=44.01  Aligned_cols=44  Identities=9%  Similarity=0.078  Sum_probs=31.3

Q ss_pred             eCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAF  194 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~  194 (448)
                      ...++++.|+||+|||... -+++..+...  +..++|+=|..++..
T Consensus        52 ~~~h~~i~G~tGsGKs~~~-~~li~~~~~~--g~~viv~Dpkge~~~   95 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLL-RELAYTGLLR--GDRMVIVDPNGDMLS   95 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHH-HHHHHHHHHT--TCEEEEEEETTHHHH
T ss_pred             CcceEEEECCCCCCHHHHH-HHHHHHHHHC--CCcEEEEeCCCchhH
Confidence            4579999999999999874 3344443332  347888889888754

>3gk5_A Uncharacterized rhodanese-related protein TVG0868615; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.40A {Thermoplasma volcanium GSS1}

Probab=82.18  E-value=1.1  Score=34.85  Aligned_cols=44  Identities=18%  Similarity=0.268  Sum_probs=36.1

Q ss_pred             HHHhhC-CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCH
Q psy1548         347 ELLDVL-EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQ  390 (448)
Q Consensus       347 ~ll~~~-~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~  390 (448)
                      ..+... ...++++||.+-.++...+..|++.|+++..+.||+..
T Consensus        47 ~~~~~l~~~~~ivvyC~~G~rs~~aa~~L~~~G~~v~~l~GG~~~   91 (108)
T 3gk5_A           47 EKWKILERDKKYAVICAHGNRSAAAVEFLSQLGLNIVDVEGGIQS   91 (108)
T ss_dssp             HHGGGSCTTSCEEEECSSSHHHHHHHHHHHTTTCCEEEETTHHHH
T ss_pred             HHHHhCCCCCeEEEEcCCCcHHHHHHHHHHHcCCCEEEEcCcHHH
Confidence            334443 34589999999999999999999999999999999654

>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=81.77  E-value=0.74  Score=46.24  Aligned_cols=52  Identities=17%  Similarity=0.210  Sum_probs=39.3

Q ss_pred             HHHHHhhcc--c-eeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          91 ILRAIVDCW--R-ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        91 ~~~~~~~~~--~-~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      +++...+..  . ++++|.+.+.|+|.+....|++++.|.....|.|.+||++|.
T Consensus       384 ~~~~F~~~~~~~vil~st~~~~~Glnl~~~~~vi~~d~~~~~~~~~Q~~gR~~R~  438 (500)
T 1z63_A          384 IISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRI  438 (500)
T ss_dssp             HHHHHHHCTTCCCCEEECCCC-CCCCCTTCSEEEESSCCSCC---CHHHHTTTTT
T ss_pred             HHHHhcCCCCCCEEEEecccccCCCchhhCCEEEEeCCCCCcchHHHHHHHHHHc
Confidence            444444432  2 688999999999999999999999999888889999998883

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=81.52  E-value=3.2  Score=44.10  Aligned_cols=16  Identities=25%  Similarity=0.486  Sum_probs=14.3

Q ss_pred             ceeeeccCCChhHHHH
Q psy1548         151 DILCQAKSGMGKTAVF  166 (448)
Q Consensus       151 ~vli~apTGsGKT~~~  166 (448)
                      ++++.||||+|||..+
T Consensus       523 ~~Ll~Gp~GtGKT~lA  538 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELA  538 (758)
T ss_dssp             EEEEESCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5999999999999764

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=81.49  E-value=2.2  Score=41.09  Aligned_cols=42  Identities=17%  Similarity=0.020  Sum_probs=27.1

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeecc
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT  189 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt  189 (448)
                      -+..|.-+++.+++|+|||... +.++..+...  +..++|+..-
T Consensus        70 Gl~~G~li~I~G~pGsGKTtla-l~la~~~~~~--g~~vlyi~~E  111 (366)
T 1xp8_A           70 GIPRGRITEIYGPESGGKTTLA-LAIVAQAQKA--GGTCAFIDAE  111 (366)
T ss_dssp             SEETTSEEEEEESTTSSHHHHH-HHHHHHHHHT--TCCEEEEESS
T ss_pred             CccCCcEEEEEcCCCCChHHHH-HHHHHHHHHC--CCeEEEEECC
Confidence            4556788999999999999654 3333333222  2357777644

>3foj_A Uncharacterized protein; protein SSP1007, structural genomics, PSI-2, protein structure initiative; 1.60A {Staphylococcus saprophyticus subsp}

Probab=81.43  E-value=1.1  Score=34.04  Aligned_cols=38  Identities=21%  Similarity=0.316  Sum_probs=33.2

Q ss_pred             CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCH
Q psy1548         353 EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQ  390 (448)
Q Consensus       353 ~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~  390 (448)
                      +..++++||.+-.++...+..|++.|+++..+.||+..
T Consensus        55 ~~~~ivvyC~~g~rs~~a~~~L~~~G~~v~~l~GG~~~   92 (100)
T 3foj_A           55 DNETYYIICKAGGRSAQVVQYLEQNGVNAVNVEGGMDE   92 (100)
T ss_dssp             TTSEEEEECSSSHHHHHHHHHHHTTTCEEEEETTHHHH
T ss_pred             CCCcEEEEcCCCchHHHHHHHHHHCCCCEEEecccHHH
Confidence            34689999999999999999999999999999998643

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=80.92  E-value=1.8  Score=38.58  Aligned_cols=55  Identities=15%  Similarity=0.086  Sum_probs=32.5

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      .+..|.-+++.||+|+|||....--+..... .  +..++++.... -..++.+.+..+
T Consensus        19 Gl~~G~~~~i~G~~GsGKTtl~~~~~~~~~~-~--~~~v~~~~~e~-~~~~~~~~~~~~   73 (247)
T 2dr3_A           19 GIPERNVVLLSGGPGTGKTIFSQQFLWNGLK-M--GEPGIYVALEE-HPVQVRQNMAQF   73 (247)
T ss_dssp             SEETTCEEEEEECTTSSHHHHHHHHHHHHHH-T--TCCEEEEESSS-CHHHHHHHHHTT
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHHHh-c--CCeEEEEEccC-CHHHHHHHHHHc
Confidence            4556888999999999999764333333222 2  23577776432 234555555443

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=80.61  E-value=0.91  Score=44.89  Aligned_cols=57  Identities=14%  Similarity=0.116  Sum_probs=37.1

Q ss_pred             ccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeecc
Q psy1548          78 HSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAK  157 (448)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~ap  157 (448)
                      +..+|.+.+--.++.+.+.+.-                    +..+.+|..   |+..      .++   -.+.+|+.||
T Consensus       176 p~~t~~digGl~~~k~~l~e~v--------------------~~pl~~pe~---f~~~------g~~---~prGvLLyGP  223 (434)
T 4b4t_M          176 PTETYSDVGGLDKQIEELVEAI--------------------VLPMKRADK---FKDM------GIR---APKGALMYGP  223 (434)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHT--------------------HHHHHCSHH---HHHH------CCC---CCCEEEEESC
T ss_pred             CCCChHhcCcHHHHHHHHHHHH--------------------HHHHhCHHH---HHhC------CCC---CCCeeEEECc
Confidence            4457888887788888877653                    001334422   3544      332   2478999999


Q ss_pred             CCChhHHHH
Q psy1548         158 SGMGKTAVF  166 (448)
Q Consensus       158 TGsGKT~~~  166 (448)
                      +|+|||+.+
T Consensus       224 PGTGKTllA  232 (434)
T 4b4t_M          224 PGTGKTLLA  232 (434)
T ss_dssp             TTSSHHHHH
T ss_pred             CCCCHHHHH
Confidence            999999764

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=80.45  E-value=1.3  Score=43.67  Aligned_cols=27  Identities=33%  Similarity=0.395  Sum_probs=19.0

Q ss_pred             eCcceeeeccCCChhHHHHHHHHHHhhh
Q psy1548         148 LGMDILCQAKSGMGKTAVFVLATLQQLE  175 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~~l~~l~~l~  175 (448)
                      .|.-+++.||||||||.. +-.++..+.
T Consensus       166 ~ggii~I~GpnGSGKTTl-L~allg~l~  192 (418)
T 1p9r_A          166 PHGIILVTGPTGSGKSTT-LYAGLQELN  192 (418)
T ss_dssp             SSEEEEEECSTTSCHHHH-HHHHHHHHC
T ss_pred             cCCeEEEECCCCCCHHHH-HHHHHhhcC
Confidence            356789999999999965 334444443

---

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	448
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	9e-39
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	3e-32
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	3e-26
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	8e-26
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	1e-22
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	4e-22
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	3e-21
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	3e-20
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	1e-19
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	2e-18
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	2e-17
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	3e-14
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	4e-12
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	9e-12
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	2e-10
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	7e-05
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	8e-10
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	3e-09
d1s2ma2	171	c.37.1.19 (A:252-422) Putative ATP-dependent RNA h	2e-07
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	5e-07
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	3e-06
d2rb4a1	168	c.37.1.19 (A:307-474) ATP-dependent RNA helicase D	3e-06
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	5e-06
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	7e-06
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	3e-05
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	4e-05
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	6e-04
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	1e-04
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	7e-04
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	0.001
d1oywa3	200	c.37.1.19 (A:207-406) RecQ helicase domain {Escher	0.001
d1yksa1	140	c.37.1.14 (A:185-324) YFV helicase domain {Yellow	0.004

>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 =  137 bits (345), Expect = 9e-39
 Identities = 159/239 (66%), Positives = 173/239 (72%), Gaps = 32/239 (13%)

Query: 80  SGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARA 139
           SGFRDFLLKPE+LRAIVDC                        ++ P +        A  
Sbjct: 1   SGFRDFLLKPELLRAIVDC-----------------------GFEHPSEVQHECIPQAIL 37

Query: 140 GRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKE 199
           G          D+LCQAKSGMGKTAVFVLATLQQLE     V VLVMCHTRELAFQISKE
Sbjct: 38  GM---------DVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKE 88

Query: 200 YERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKH 259
           YERFSKYM N+KV VFFGGL I+KDEE LK + P IVVGTPGRILAL RNK LNL  +KH
Sbjct: 89  YERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKH 148

Query: 260 FILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
           FILDECDKMLEQL+MRRDVQEIFR +PH KQVMMFSATLSKEIRPVC+KFM DPME++V
Sbjct: 149 FILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 207

>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 =  119 bits (300), Expect = 3e-32
 Identities = 61/170 (35%), Positives = 96/170 (56%), Gaps = 5/170 (2%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
             +I+ QA++G GKTA F +  ++ +   +     +++  TRELA Q++ E E       
Sbjct: 42  EYNIVAQARTGSGKTASFAIPLIELVNENNGIEA-IILTPTRELAIQVADEIESLKGNK- 99

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
           N+K+   +GG  I    + LK  N  IVVGTPGRIL  +    LNL  +K+FILDE D+M
Sbjct: 100 NLKIAKIYGGKAIYPQIKALK--NANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEM 157

Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
           L      +DV++I  +    K++++FSAT+ +EI  + KK+M D   +  
Sbjct: 158 LNM-GFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKA 206

>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 =  103 bits (258), Expect = 3e-26
 Identities = 61/170 (35%), Positives = 93/170 (54%), Gaps = 2/170 (1%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D++ QA+SG GKTA F ++ LQQ+E        LV+  TRELA QI K       YM 
Sbjct: 49  GYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYM- 107

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
                   GG  ++ + + L+   P I+VGTPGR+  ++  + L+   +K F+LDE D+M
Sbjct: 108 GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEM 167

Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
                 +  + +IF+      QV++ SAT+  ++  V KKFM DP+ + V
Sbjct: 168 -LSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILV 216

>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 =  102 bits (254), Expect = 8e-26
 Identities = 62/170 (36%), Positives = 94/170 (55%), Gaps = 4/170 (2%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D+L QA+SG GKT  F +A LQ+++T+      L++  TRELA QI K     + +M 
Sbjct: 47  GHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMD 106

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
                   G     +D E L+  + QIVVGTPGR+   ++ ++     +K FILDE D+M
Sbjct: 107 IKVHACIGGT-SFVEDAEGLR--DAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEM 163

Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
           L     +  + +IF   P T QV++ SAT+  ++  V  KFM +P+ + V
Sbjct: 164 LSS-GFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILV 212

>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 = 93.1 bits (230), Expect = 1e-22
 Identities = 61/237 (25%), Positives = 111/237 (46%), Gaps = 34/237 (14%)

Query: 80  SGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARA 139
           + F D+ LK E+L  I +                         ++ P         +A +
Sbjct: 3   NEFEDYCLKRELLMGIFEM-----------------------GWEKPSPIQEESIPIALS 39

Query: 140 GRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKE 199
           GR         DIL +AK+G GK+  +++  L++L+    N+  +V+  TRELA Q+S+ 
Sbjct: 40  GR---------DILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQI 90

Query: 200 YERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKH 259
             + SK+M   KV    GG  ++ D   L      ++  TPGRIL L++     +  ++ 
Sbjct: 91  CIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVI-ATPGRILDLIKKGVAKVDHVQM 149

Query: 260 FILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEV 316
            +LDE DK+L Q +  + +++I  + P  +Q++++SAT    ++      +  P E+
Sbjct: 150 IVLDEADKLLSQ-DFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI 205

>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 = 92.7 bits (229), Expect = 4e-22
 Identities = 52/182 (28%), Positives = 89/182 (48%), Gaps = 14/182 (7%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSN---------VYVLVMCHTRELAFQISKE 199
             DI+  A++G GKTA F++  +  L   D N            L++  TRELA QI  E
Sbjct: 58  HRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSE 117

Query: 200 YERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKH 259
            ++FS     ++  V +GG                ++V TPGR++  +   K++L   K+
Sbjct: 118 SQKFSLNT-PLRSCVVYGGADTHSQIRE-VQMGCHLLVATPGRLVDFIEKNKISLEFCKY 175

Query: 260 FILDE---CDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEV 316
            +LDE      M  + ++R+ ++E    S   +Q +MFSAT  KEI+ +   F+++ + +
Sbjct: 176 IVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFM 235

Query: 317 YV 318
            V
Sbjct: 236 TV 237

>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 = 89.9 bits (222), Expect = 3e-21
 Identities = 59/170 (34%), Positives = 91/170 (53%), Gaps = 3/170 (1%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G D++ Q++SG GKTA F ++ LQ L+        L++  TRELA QI K       YM 
Sbjct: 54  GRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYM- 112

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
           N++     GG  + +D   L  +   +V GTPGR+  ++R + L    +K  +LDE D+M
Sbjct: 113 NVQCHACIGGTNVGEDIRKLD-YGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEM 171

Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
                 +  + +++R  P   QV++ SATL  EI  +  KFM DP+ + V
Sbjct: 172 -LNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILV 220

>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 = 88.8 bits (219), Expect = 3e-20
 Identities = 30/255 (11%), Positives = 66/255 (25%), Gaps = 36/255 (14%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
               +     G GKT  ++ A +++       +  L++  TR +A ++ +          
Sbjct: 9   KRLTIMDLHPGAGKTKRYLPAIVREA--IKRGLRTLILAPTRVVAAEMEEALRGLPIRYQ 66

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
              +                 T    + +         + +  + +      I+DE    
Sbjct: 67  TPAI-------------RAEHTGREIVDLMCHATFTMRLLSP-IRVPNYNLIIMDEAHFT 112

Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHG 328
                +        R        +  +AT      P  +                     
Sbjct: 113 DPA-SIAARGYISTRVEMGEAAGIFMTATPPGSRDPFPQSNAPI---------------- 155

Query: 329 LQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGM 388
                 ++ E   N     + D     + V FV S+     ++  L +     + + R  
Sbjct: 156 -MDEEREIPERSWNSGHEWVTD--FKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKT 212

Query: 389 TQEERLKKYQEFKDF 403
              E +K      DF
Sbjct: 213 FDSEYIKTRTNDWDF 227

>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 = 85.7 bits (211), Expect = 1e-19
 Identities = 25/181 (13%), Positives = 57/181 (31%), Gaps = 23/181 (12%)

Query: 145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS 204
           + +        A +G+GKT+  +  +L             V+  T  L  Q ++   +++
Sbjct: 54  RILRKESFAATAPTGVGKTSFGLAMSLFLALK---GKRCYVIFPTSLLVIQAAETIRKYA 110

Query: 205 KYMSNIKVGV-----FFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKH 259
           +    +                +K+       N +IV+ T   +          L     
Sbjct: 111 EKA-GVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFL----SKHYRELGHFDF 165

Query: 260 FILDECDKMLEQ----------LEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKF 309
             +D+ D +L+           L    D++           +M+ +AT  K  +    + 
Sbjct: 166 IFVDDVDAILKASKNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFRQ 225

Query: 310 M 310
           +
Sbjct: 226 L 226

>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 = 2e-18
 Identities = 53/172 (30%), Positives = 81/172 (47%), Gaps = 3/172 (1%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G DIL +AK+G GKTA FV+    +      N    ++          + +  R      
Sbjct: 38  GRDILARAKNGTGKTAAFVIP-TLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHC 96

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
            I   V  GG  ++ D   L      I+VGTPGR+L L   K  +LS    FI+DE DKM
Sbjct: 97  GISCMVTTGGTNLRDDILRLN-ETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKM 155

Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDD 320
           L + + +  +++I    P T Q ++FSAT    ++    K +H P E+ + +
Sbjct: 156 LSR-DFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLME 206

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 168

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 = 77.4 bits (189), Expect = 2e-17
 Identities = 98/165 (59%), Positives = 112/165 (67%), Gaps = 46/165 (27%)

Query: 328 GLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRG 387
           GLQQ+YVKLK+NEKN+KLF+LLDVLEFNQVVIFVKSV RCIAL+ LL EQNFPA++IHRG
Sbjct: 1   GLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRG 60

Query: 388 MTQEERLKKYQEFKDFH------------------------------------------- 404
           M QEERL +YQ+FKDF                                            
Sbjct: 61  MPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGR 120

Query: 405 ---KGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIE 446
              KGLAITF SDENDAKILN+VQDRF+V+ISELPDEID+S+YIE
Sbjct: 121 FGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIE 165

>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 = 69.3 bits (168), Expect = 3e-14
 Identities = 52/172 (30%), Positives = 96/172 (55%), Gaps = 3/172 (1%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G  ++ Q+++G GKT  ++L  +++++   + V  ++   TRELA QI  E  + +K+  
Sbjct: 38  GESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCP 97

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHN--PQIVVGTPGRILALVRNKKLNLSLLKHFILDECD 266
             ++ V    +     ++ L+  N  P IV+GTPGRI   +R + L++      ++DE D
Sbjct: 98  KDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEAD 157

Query: 267 KMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
            ML+      DV +I    P   Q+++FSAT+ ++++P  KK+M +P  V+V
Sbjct: 158 LMLDM-GFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHV 208

>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 = 63.1 bits (152), Expect = 4e-12
 Identities = 25/178 (14%), Positives = 54/178 (30%), Gaps = 14/178 (7%)

Query: 146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK 205
            + G D L    +G GK+  + +  L     T      +V+     L      + +    
Sbjct: 37  VLSGRDCLVVMPTGGGKSLCYQIPALLLNGLT------VVVSPLISLMKDQVDQLQANGV 90

Query: 206 YMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDEC 265
             + +            +     +T   +++   P R++     + L         +DE 
Sbjct: 91  AAACLNSTQTRE--QQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEA 148

Query: 266 DKMLEQLEMRRD---VQEIFRSSPHTKQVMMFSATLSKEIR-PVCKKF-MHDPMEVYV 318
             + +     R         R    T   M  +AT     R  + +   ++DP  + +
Sbjct: 149 HCISQWGHDFRPEYAALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDP-LIQI 205

>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 = 61.7 bits (148), Expect = 9e-12
 Identities = 26/194 (13%), Positives = 65/194 (33%), Gaps = 15/194 (7%)

Query: 145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS 204
                 + L    +G+GKT + ++    +L      V +L           + +  E F 
Sbjct: 19  AKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTK-----PLVLQHAESFR 73

Query: 205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDE 264
           +  +     +         +E        +++V TP  I   +   +++L  +   + DE
Sbjct: 74  RLFNLPPEKIVALTGEKSPEERSKAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDE 133

Query: 265 CDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLS---KEIRPVCKKFMHDPMEVYVDDE 321
             + +        +   ++       V+  +A+     ++I  V      + +E   ++ 
Sbjct: 134 AHRAVGN-YAYVFIAREYKRQAKNPLVIGLTASPGSTPEKIMEVINNLGIEHIEYRSENS 192

Query: 322 AKLTLHGLQQHYVK 335
             +      + YVK
Sbjct: 193 PDV------RPYVK 200

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 299

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]

 Score = 59.2 bits (143), Expect = 2e-10
 Identities = 7/45 (15%), Positives = 16/45 (35%), Gaps = 3/45 (6%)

Query: 100 RILVATNLFGRGM---DIERVNIVFNYDMPEDSDTYLHRVARAGR 141
             ++  N          ++    +    +P+D+ +   R  R GR
Sbjct: 98  DSVIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGR 142

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 299

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]

 Score = 42.2 bits (99), Expect = 7e-05
 Identities = 19/112 (16%), Positives = 38/112 (33%), Gaps = 13/112 (11%)

Query: 348 LLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEF------- 400
            L+V++  + +IF  S  +C  L+  L      AV+ +RG+                   
Sbjct: 30  PLEVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDAL 89

Query: 401 KDFHKG-LAITFASDENDAKIL-NNVQDRFDVSISELPDEIDLSTYIE--GR 448
                G        +    + +  ++   F +  + LP   D  +  +  GR
Sbjct: 90  MTGFTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLP--QDAVSRTQRRGR 139

>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 = 56.1 bits (134), Expect = 8e-10
 Identities = 25/153 (16%), Positives = 59/153 (38%), Gaps = 11/153 (7%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           G ++L    +  GKT +  +A +++      ++Y   +   R LA +  + ++++ K   
Sbjct: 40  GKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLY---VVPLRALAGEKYESFKKWEKIGL 96

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
            I +           +       +  I+V T  +  +L+RN+   +  +   ++DE   +
Sbjct: 97  RIGISTGDY------ESRDEHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLL 150

Query: 269 LEQ--LEMRRDVQEIFRSSPHTKQVMMFSATLS 299
             +        +    R      +V+  SAT  
Sbjct: 151 DSEKRGATLEILVTKMRRMNKALRVIGLSATAP 183

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 286

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 = 55.7 bits (133), Expect = 3e-09
 Identities = 24/129 (18%), Positives = 47/129 (36%), Gaps = 13/129 (10%)

Query: 32  FPHSKMADNDDLLDYE-DEENTEQIV-------ADGAGDALAKQKEVKGAYVSIHSSGFR 83
             H KM    +++  +   +   +I+                 +  +K       +S   
Sbjct: 140 LDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKEN 199

Query: 84  DFLLKPEILRAIVDCWR-----ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVAR 138
           D  L     + I+D +      +LVAT++   G+D+  V++V  Y+    +   + R  R
Sbjct: 200 DRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGR 259

Query: 139 AGRFGTKAV 147
            GR     V
Sbjct: 260 TGRHMPGRV 268

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 171

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 = 48.9 bits (115), Expect = 2e-07
 Identities = 34/168 (20%), Positives = 58/168 (34%), Gaps = 47/168 (27%)

Query: 324 LTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVS 383
           LTL G+ Q+Y  ++E +K   L  L   L+ NQ +IF  S  R   L+  +++  +    
Sbjct: 2   LTLKGITQYYAFVEERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYY 61

Query: 384 IH--------------------RGMTQEERLKKYQEFKDFH------------------- 404
            H                    R +   + L +  + +  +                   
Sbjct: 62  SHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIG 121

Query: 405 -------KGLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYI 445
                   GLAI   +  ND   L  ++      I+ +P  ID S Y+
Sbjct: 122 RSGRFGHLGLAINLIN-WNDRFNLYKIEQELGTEIAAIPATIDKSLYV 168

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 138

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]

 Score = 46.6 bits (110), Expect = 5e-07
 Identities = 10/47 (21%), Positives = 20/47 (42%), Gaps = 3/47 (6%)

Query: 98  CWRILVATNLFGRGMDIER---VNIVFNYDMPEDSDTYLHRVARAGR 141
              ++VAT+    G   +    ++   +   P+D+ +   R  R GR
Sbjct: 78  GDVVVVATDALMTGFTGDFDSVIDCNTSDGKPQDAVSRTQRRGRTGR 124

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]} Length = 181

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]

 Score = 45.6 bits (107), Expect = 3e-06
 Identities = 25/118 (21%), Positives = 43/118 (36%), Gaps = 11/118 (9%)

Query: 41  DDLLD--YEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIVDC 98
           DDL+    E  E  E+ +       +A+          I  +     +   E +  I D 
Sbjct: 18  DDLIGEIRERVERNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDL 77

Query: 99  ----WRILVATNLFGRGMDIERVNIVFNYDMPEDSD-----TYLHRVARAGRFGTKAV 147
               + +LV  NL   G+DI  V++V   D  ++       + +  + RA R     V
Sbjct: 78  RLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHV 135

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 155

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 = 44.2 bits (103), Expect = 5e-06
 Identities = 21/50 (42%), Positives = 34/50 (68%)

Query: 98  CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV 147
             RIL+AT++  RG+D+  +N V NY +P++ ++Y+HR+ R GR G K  
Sbjct: 78  KIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGK 127

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 162

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 = 43.8 bits (102), Expect = 7e-06
 Identities = 28/86 (32%), Positives = 45/86 (52%)

Query: 62  DALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVF 121
           + L  +       VS   S          +        RIL++T+L  RG+D+++V++V 
Sbjct: 41  EELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVI 100

Query: 122 NYDMPEDSDTYLHRVARAGRFGTKAV 147
           NYD+P + + Y+HR+ R GRFG K V
Sbjct: 101 NYDLPANKENYIHRIGRGGRFGRKGV 126

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 162

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 = 42.2 bits (98), Expect = 3e-05
 Identities = 34/158 (21%), Positives = 57/158 (36%), Gaps = 48/158 (30%)

Query: 330 QQHYVKL-KENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGM 388
           +Q YV + +E  K + L +L D +   Q VIF  +  +   L+T L    F   +I+  +
Sbjct: 2   KQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDL 61

Query: 389 TQEERLKKYQEFKDF--------------------------------------------- 403
            Q+ER    +EF+                                               
Sbjct: 62  PQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRF 121

Query: 404 -HKGLAITFASDENDAKILNNVQDRFDVSISELPDEID 440
             KG+AI F ++E D   +  ++  +   I ELP +I 
Sbjct: 122 GRKGVAINFVTNE-DVGAMRELEKFYSTQIEELPSDIA 158

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 168

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 = 41.8 bits (97), Expect = 4e-05
 Identities = 28/83 (33%), Positives = 43/83 (51%), Gaps = 1/83 (1%)

Query: 323 KLTLHGLQQHYVKL-KENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPA 381
           +LTL G++Q +V + +E  K   L +L D L   Q VIF  +  +   L+  + E NF  
Sbjct: 2   ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTV 61

Query: 382 VSIHRGMTQEERLKKYQEFKDFH 404
            S+H  M Q+ER    +EF+   
Sbjct: 62  SSMHGDMPQKERESIMKEFRSGA 84

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 168

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 = 38.4 bits (88), Expect = 6e-04
 Identities = 20/51 (39%), Positives = 39/51 (76%)

Query: 97  DCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV 147
              R+L++T+++ RG+D+ +V+++ NYD+P + + Y+HR+ R+GR+G K V
Sbjct: 83  GASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGV 133

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]} 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: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 40.7 bits (94), Expect = 1e-04
 Identities = 9/47 (19%), Positives = 20/47 (42%)

Query: 97  DCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG 143
             +R +V++ +   G+D+   N+         +  Y+ R+ R  R  
Sbjct: 137 GRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPS 183

>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 = 39.0 bits (90), Expect = 7e-04
 Identities = 12/104 (11%), Positives = 32/104 (30%), Gaps = 7/104 (6%)

Query: 329 LQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGM 388
           ++        +E    L  +L+ L     +I+ ++      +   L            G+
Sbjct: 1   VRNVEDVAVNDESISTLSSILEKLG-TGGIIYARTGEEAEEIYESLKN------KFRIGI 53

Query: 389 TQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFDVSI 432
               +   Y++F +      I  A          ++ +R   ++
Sbjct: 54  VTATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAV 97

>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 = 38.2 bits (88), Expect = 0.001
 Identities = 9/56 (16%), Positives = 18/56 (32%), Gaps = 9/56 (16%)

Query: 97  DCWRILVATNLF----GRGMDI-ERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV 147
                L+ T  +     RG+D+ ER+        P    ++   +        + V
Sbjct: 68  GEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCP----SFRVTIEDIDSLSPQMV 119

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]} 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: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 38.1 bits (87), Expect = 0.001
 Identities = 31/130 (23%), Positives = 57/130 (43%), Gaps = 7/130 (5%)

Query: 21  FFRAFIRFSSSFPHSKMADNDDLLDYEDEENTEQIV----ADGAGDALAKQKEVKGAYVS 76
           F R  IR+        +   D L+ Y  E+  +  +    +    +  A + + KG   +
Sbjct: 2   FDRPNIRYMLMEKFKPL---DQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAA 58

Query: 77  IHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRV 136
            + +G  + +      +   D  +I+VAT  FG G++   V  V ++D+P + ++Y    
Sbjct: 59  AYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQET 118

Query: 137 ARAGRFGTKA 146
            RAGR G  A
Sbjct: 119 GRAGRDGLPA 128

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 140

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]

 Score = 35.4 bits (80), Expect = 0.004
 Identities = 23/149 (15%), Positives = 44/149 (29%), Gaps = 17/149 (11%)

Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
           GM  +     G GKT  F+   L +       +  LV+  TR +  ++ + +        
Sbjct: 7   GMTTVLDFHPGAGKTRRFLPQILAECARR--RLRTLVLAPTRVVLSEMKEAFHGLDVKFH 64

Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
                    G  +     +              R+L   R     +      I+DE   +
Sbjct: 65  TQAFSAHGSGREVIDAMCHATLTY---------RMLEPTRVVNWEV-----IIMDEAHFL 110

Query: 269 LEQLEMRRDVQEIFRSSPHTKQVMMFSAT 297
                  R        +  +  ++M +AT
Sbjct: 111 DPASIAARGWAAHRARANESATILM-TAT 138

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	448
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	100.0
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	100.0
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	100.0
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	100.0
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	100.0
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.92
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.91
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.91
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.91
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.89
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.71
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.7
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.69
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.69
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.67
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.67
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.64
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.6
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.6
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.58
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.56
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.48
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.23
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.11
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.0
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	98.91
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	98.86
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	98.82
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	98.48
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	98.47
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	98.46
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	98.28
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	98.25
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	98.11
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	98.0
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	97.98
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	97.88
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	97.87
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	97.86
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	97.85
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	97.8
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	97.74
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	97.66
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	97.64
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	97.58
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	97.54
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	97.49
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	97.45
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	97.29
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	96.78
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	96.72
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	96.53
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	96.5
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	96.42
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.2
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	96.17
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	96.08
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	96.05
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	95.91
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	95.9
d2qy9a2	211	GTPase domain of the signal recognition particle r	95.87
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	95.85
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	95.48
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	95.45
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	95.35
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	95.32
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	95.12
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	95.11
d1okkd2	207	GTPase domain of the signal recognition particle r	95.06
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	95.0
d1vmaa2	213	GTPase domain of the signal recognition particle r	94.9
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	94.85
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	94.65
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	94.45
d1j8yf2	211	GTPase domain of the signal sequence recognition p	94.34
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	94.3
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	93.82
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	93.76
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	92.59
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	92.54
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	92.32
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	92.07
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	91.37
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	90.39
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	90.33
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	89.68
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	89.67
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	89.32
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	89.25
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	87.72
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	87.28
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	86.91
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	85.7
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	85.25
d1yt8a4	130	Thiosulfate sulfurtransferase PA2603 {Pseudomonas	84.47
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	84.3
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	83.92
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	83.76
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	83.69
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	83.0
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	82.98
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	82.71
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	82.57
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	82.49
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	81.27
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	81.24
d1tq1a_	119	Thiosulfate sulfurtransferase/Senescence-associate	81.19
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	80.43
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	80.28
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	80.16

>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=100.00  E-value=3e-42  Score=314.68  Aligned_cols=205  Identities=33%  Similarity=0.574  Sum_probs=195.6

Q ss_pred             cCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccC
Q psy1548          79 SSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKS  158 (448)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apT  158 (448)
                      ..+|+++++++++++++.+.|                       |..|+++   |.+      +||.++.|+|++++|||
T Consensus        16 ~~sF~~l~L~~~l~~~L~~~g-----------------------~~~pt~I---Q~~------aIp~il~g~dvi~~a~T   63 (222)
T d2j0sa1          16 TPTFDTMGLREDLLRGIYAYG-----------------------FEKPSAI---QQR------AIKQIIKGRDVIAQSQS   63 (222)
T ss_dssp             CCSGGGGCCCHHHHHHHHHHT-----------------------CCSCCHH---HHH------HHHHHHTTCCEEEECCT
T ss_pred             CCCHHHCCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHHCCCCeEEEcCc
Confidence            357999999999999999999                       9999999   999      99999999999999999


Q ss_pred             CChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEE
Q psy1548         159 GMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVG  238 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~  238 (448)
                      |||||++|++|+++.+......++++|++||++|+.|+++.++.+++.. ++++..++|+.....+...+..+ ++|+|+
T Consensus        64 GSGKTlayllPil~~l~~~~~~~~~lil~PtreLa~Qi~~~~~~l~~~~-~i~~~~~~g~~~~~~~~~~l~~~-~~Ilv~  141 (222)
T d2j0sa1          64 GTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLDYG-QHVVAG  141 (222)
T ss_dssp             TSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTT-TCCEEEECTTSCHHHHHHHHHHC-CSEEEE
T ss_pred             chhhhhhhcccccccccccccCceeEEecchHHHHHHHHHHHHHHhCcc-ceeEEEEeecccchhhHHHhccC-CeEEeC
Confidence            9999999999999999888888999999999999999999999999887 89999999999988888888776 899999


Q ss_pred             cHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEE
Q psy1548         239 TPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV  318 (448)
Q Consensus       239 Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~  318 (448)
                      ||+++.+++..+...+++++++|+||||+|++. +|...+..+++.+|+.+|++++|||+++++.++++.++.+|+.+.+
T Consensus       142 TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~-~f~~~i~~I~~~l~~~~Q~ilfSAT~~~~v~~l~~~~l~~Pv~I~V  220 (222)
T d2j0sa1         142 TPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNK-GFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILV  220 (222)
T ss_dssp             CHHHHHHHHHTTSSCCTTCCEEEEETHHHHTST-TTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECC
T ss_pred             CCCcHHhcccccccccccceeeeecchhHhhhc-CcHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEE
Confidence            999999999999999999999999999999998 9999999999999999999999999999999999999999988765

>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=100.00  E-value=1.1e-41  Score=308.66  Aligned_cols=207  Identities=78%  Similarity=1.222  Sum_probs=194.6

Q ss_pred             CCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCC
Q psy1548          80 SGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSG  159 (448)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTG  159 (448)
                      ++|+++++++++++++.+.|                       |..|+++   |++      +||.+++|+|++++||||
T Consensus         1 s~F~dl~L~~~l~~~l~~~g-----------------------~~~pt~i---Q~~------aip~il~g~dvl~~A~TG   48 (207)
T d1t6na_           1 SGFRDFLLKPELLRAIVDCG-----------------------FEHPSEV---QHE------CIPQAILGMDVLCQAKSG   48 (207)
T ss_dssp             CCSTTSCCCHHHHHHHHHTT-----------------------CCCCCHH---HHH------HHHHHHTTCCEEEECCTT
T ss_pred             CCccccCcCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHHcCCCeEEEeccc
Confidence            47999999999999999999                       9999999   999      999999999999999999


Q ss_pred             ChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEc
Q psy1548         160 MGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGT  239 (448)
Q Consensus       160 sGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~T  239 (448)
                      ||||++|++|+++.+.....+++++|++||++|+.|+.+.++.+....+.+++..++|+.....+...+....++|+|+|
T Consensus        49 sGKTla~~lp~l~~~~~~~~~~~~lil~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~T  128 (207)
T d1t6na_          49 MGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGT  128 (207)
T ss_dssp             SCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEEC
T ss_pred             cccccccccceeeeecccCCCceEEEEeccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeC
Confidence            99999999999999988888899999999999999999999999988767888889999988888777776679999999


Q ss_pred             HHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEE
Q psy1548         240 PGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV  318 (448)
Q Consensus       240 p~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~  318 (448)
                      |+++.++++++.+.+++++++|+||||.|++..++...+..+++.+++.+|++++|||+++++.++++.++++|..|.+
T Consensus       129 P~rl~~~~~~~~~~l~~l~~lVlDEaD~ll~~~~~~~~i~~I~~~~~~~~Q~il~SAT~~~~v~~l~~~~l~~P~~I~V  207 (207)
T d1t6na_         129 PGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV  207 (207)
T ss_dssp             HHHHHHHHHTTSSCCTTCCEEEEESHHHHHSSHHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEEC
T ss_pred             cchhhhhccCCceeccccceeehhhhhhhhhcCCcHHHHHHHHHhCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEeC
Confidence            9999999999999999999999999999998448999999999999999999999999999999999999999988753

>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=100.00  E-value=4.3e-41  Score=304.41  Aligned_cols=203  Identities=30%  Similarity=0.514  Sum_probs=191.4

Q ss_pred             CCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCC
Q psy1548          80 SGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSG  159 (448)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTG  159 (448)
                      .+|+++++++++++++.+.|                       |..|+++   |++      +||.+++|+|++++||||
T Consensus         3 ~~F~~l~L~~~l~~~l~~~g-----------------------~~~pt~i---Q~~------aip~il~g~dvl~~a~TG   50 (206)
T d1veca_           3 NEFEDYCLKRELLMGIFEMG-----------------------WEKPSPI---QEE------SIPIALSGRDILARAKNG   50 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTT-----------------------CCSCCHH---HHH------HHHHHHTTCCEEEECCSS
T ss_pred             CChhccCcCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHHcCCCEEeeccCc
Confidence            57999999999999999999                       9999999   999      999999999999999999


Q ss_pred             ChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEc
Q psy1548         160 MGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGT  239 (448)
Q Consensus       160 sGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~T  239 (448)
                      ||||++|++|+++.+.....+++++|++||++|+.|+++.+..+.+...+..+....|+.....+...+..+ ++|+|+|
T Consensus        51 sGKTlayllP~l~~~~~~~~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~-~~ivv~T  129 (206)
T d1veca_          51 TGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDT-VHVVIAT  129 (206)
T ss_dssp             STTHHHHHHHHHHHCCTTSCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSC-CSEEEEC
T ss_pred             cccccccccchhhcccccccCcceEEEeecchhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHhc-cCeEEeC
Confidence            999999999999999888888999999999999999999999998877678888888888777776666665 9999999


Q ss_pred             HHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEE
Q psy1548         240 PGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEV  316 (448)
Q Consensus       240 p~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i  316 (448)
                      |+++.+++..+...+++++++|+||||.|++. +|..++..+++.+++++|++++|||+++++.++++.++.+|..|
T Consensus       130 Pgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~-~f~~~i~~I~~~~~~~~Q~~l~SAT~~~~v~~l~~~~l~~P~~I  205 (206)
T d1veca_         130 PGRILDLIKKGVAKVDHVQMIVLDEADKLLSQ-DFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             HHHHHHHHHTTCSCCTTCCEEEEETHHHHTST-TTHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             CccccccccchhccccccceEEEecccccccc-chHHHHHHHHHhCCCCCEEEEEEecCCHHHHHHHHHHCCCCEEE
Confidence            99999999999999999999999999999998 99999999999999999999999999999999999999999875

>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=100.00  E-value=2.1e-40  Score=302.09  Aligned_cols=209  Identities=33%  Similarity=0.557  Sum_probs=192.1

Q ss_pred             eccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeec
Q psy1548          77 IHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQA  156 (448)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~a  156 (448)
                      ....+|+++++++.+++++.+.|                       |..|+++   |++      +||.++.|+|++++|
T Consensus         9 e~i~sF~~l~L~~~l~~~L~~~g-----------------------~~~pt~i---Q~~------aip~il~g~dvl~~a   56 (218)
T d2g9na1           9 EIVDSFDDMNLSESLLRGIYAYG-----------------------FEKPSAI---QQR------AILPCIKGYDVIAQA   56 (218)
T ss_dssp             CCCCCGGGSCCCHHHHHHHHHHT-----------------------CCSCCHH---HHH------HHHHHHHTCCEEEEC
T ss_pred             CccCCHHHCCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHHcCCCEEEEc
Confidence            34568999999999999999999                       9999999   999      999999999999999


Q ss_pred             cCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEE
Q psy1548         157 KSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV  236 (448)
Q Consensus       157 pTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~Il  236 (448)
                      |||||||++|++|+++.+.....++++||++||++|+.|+++.++.+.... +..+..+.++.....+......+.++|+
T Consensus        57 ~TGsGKTlayllp~l~~i~~~~~~~~alil~Pt~eL~~Q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~Iv  135 (218)
T d2g9na1          57 QSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEAPHII  135 (218)
T ss_dssp             CTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHHTTT-TCCEEEECC--CCCSTTTSSSSCCCSEE
T ss_pred             ccchhhhhhhhhhhhheecccccCccEEEEcccchhhhhHHHHHhhhcccc-ceeEEeeecccchhHHHHHHhcCCCEEE
Confidence            999999999999999999888888999999999999999999999999988 7888888887766655555555568999


Q ss_pred             EEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEE
Q psy1548         237 VGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEV  316 (448)
Q Consensus       237 V~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i  316 (448)
                      |+||+++.+++.++...+++++++|+||||.|++. +|...+..+++.+++++|++++|||+++++.++++.++.+|..+
T Consensus       136 V~TP~rl~~~l~~~~~~~~~l~~lVlDEaD~ll~~-~f~~~~~~Il~~~~~~~Q~il~SAT~~~~v~~~~~~~l~~pv~i  214 (218)
T d2g9na1         136 VGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSR-GFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRI  214 (218)
T ss_dssp             EECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHHT-TCHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             EeCChhHHHHHhcCCcccccceEEEeeecchhhcC-chHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHCCCCEEE
Confidence            99999999999999999999999999999999998 99999999999999999999999999999999999999999988


Q ss_pred             EEc
Q psy1548         317 YVD  319 (448)
Q Consensus       317 ~~~  319 (448)
                      .+.
T Consensus       215 ~v~  217 (218)
T d2g9na1         215 LVK  217 (218)
T ss_dssp             ECC
T ss_pred             EEe
Confidence            764

>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=100.00  E-value=1.2e-39  Score=295.88  Aligned_cols=206  Identities=35%  Similarity=0.559  Sum_probs=185.1

Q ss_pred             eeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeee
Q psy1548          76 SIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQ  155 (448)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~  155 (448)
                      +....+|+++++++++++++.+.|                       |..|+++   |++      +||.++.|+|++++
T Consensus         6 ~~~~~sF~~l~l~~~l~~~L~~~g-----------------------~~~pt~i---Q~~------aip~il~g~dvl~~   53 (212)
T d1qdea_           6 DKVVYKFDDMELDENLLRGVFGYG-----------------------FEEPSAI---QQR------AIMPIIEGHDVLAQ   53 (212)
T ss_dssp             CCCCCCGGGGTCCHHHHHHHHHHT-----------------------CCSCCHH---HHH------HHHHHHTTCCEEEE
T ss_pred             cccccChhhCCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHHcCCCEEee
Confidence            344568999999999999999999                       9999999   999      99999999999999


Q ss_pred             ccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcE
Q psy1548         156 AKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQI  235 (448)
Q Consensus       156 apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~I  235 (448)
                      +|||||||++|++|+++++.....+++++|++||++|+.|+...+..+.... ...+....++.....+...++  .++|
T Consensus        54 a~TGsGKT~a~~lp~i~~l~~~~~~~~~lil~pt~el~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~--~~~I  130 (212)
T d1qdea_          54 AQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLR--DAQI  130 (212)
T ss_dssp             CCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTS-CCCEEEECC----------CT--TCSE
T ss_pred             cccccchhhhhHhhhHhhhhccCCCcceEEEcccHHHhhhhhhhhccccccc-ccceeeEeeccchhHHHHHhc--CCcE
Confidence            9999999999999999999888889999999999999999999999998877 788888888877666655543  3899


Q ss_pred             EEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeE
Q psy1548         236 VVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPME  315 (448)
Q Consensus       236 lV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~  315 (448)
                      +|+||+++.+++..+.+.+++++++|+||||.|++. +|...+..+++.+++.+|++++|||++++++++++.++++|+.
T Consensus       131 vI~TP~~l~~~~~~~~~~l~~l~~lVlDEad~lld~-~f~~~v~~I~~~~~~~~Q~vl~SAT~~~~v~~l~~~~l~~Pv~  209 (212)
T d1qdea_         131 VVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSS-GFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVR  209 (212)
T ss_dssp             EEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHT-TCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEE
T ss_pred             EEECCCccccccccCceecCcceEEeehhhhhhccc-chHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHHCCCCEE
Confidence            999999999999999999999999999999999998 9999999999999999999999999999999999999999988


Q ss_pred             EE
Q psy1548         316 VY  317 (448)
Q Consensus       316 i~  317 (448)
                      |.
T Consensus       210 i~  211 (212)
T d1qdea_         210 IL  211 (212)
T ss_dssp             EC
T ss_pred             Ee
Confidence            74

>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=100.00  E-value=4.6e-38  Score=284.75  Aligned_cols=203  Identities=36%  Similarity=0.542  Sum_probs=192.9

Q ss_pred             CcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCC
Q psy1548          81 GFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGM  160 (448)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGs  160 (448)
                      +|+++++++.+++++.+.|                       |..|+++   |++      +||.++.|+|++++|||||
T Consensus         2 sF~~l~L~~~l~~~L~~~g-----------------------~~~pt~i---Q~~------aip~il~g~dvi~~a~tGs   49 (206)
T d1s2ma1           2 TFEDFYLKRELLMGIFEAG-----------------------FEKPSPI---QEE------AIPVAITGRDILARAKNGT   49 (206)
T ss_dssp             CGGGGCCCHHHHHHHHHTT-----------------------CCSCCHH---HHH------HHHHHHHTCCEEEECCTTS
T ss_pred             ChHHcCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHHcCCCEEEecCCcc
Confidence            6999999999999999999                       9999999   999      9999999999999999999


Q ss_pred             hhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcH
Q psy1548         161 GKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTP  240 (448)
Q Consensus       161 GKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp  240 (448)
                      |||++|++|+++.+.....+.++++++|+.+++.|....+..+.... ++++...+|+.....+...+..+ ++|+|+||
T Consensus        50 GKTlay~lp~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~l~~~-~~Ili~TP  127 (206)
T d1s2ma1          50 GKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHC-GISCMVTTGGTNLRDDILRLNET-VHILVGTP  127 (206)
T ss_dssp             CHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTT-TCCEEEECSSSCHHHHHHHTTSC-CSEEEECH
T ss_pred             hhhhhhccccccccccccccccceeeccchhhhhhhhhhhhhccccc-CeeEEeecCccchhhHHHHhccc-ceEEEECC
Confidence            99999999999999888888899999999999999999999998887 99999999999888777777665 99999999


Q ss_pred             HHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEE
Q psy1548         241 GRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV  318 (448)
Q Consensus       241 ~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~  318 (448)
                      +++.++++.+.+.+.+++++|+||||.|++. +|...+..+++.+++.+|++++|||+|+++.++++.++.+|..+.+
T Consensus       128 ~~l~~~l~~~~~~l~~l~~lV~DEaD~l~~~-~f~~~v~~I~~~l~~~~Q~il~SATl~~~v~~~~~~~l~~P~~I~~  204 (206)
T d1s2ma1         128 GRVLDLASRKVADLSDCSLFIMDEADKMLSR-DFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINL  204 (206)
T ss_dssp             HHHHHHHHTTCSCCTTCCEEEEESHHHHSSH-HHHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESC
T ss_pred             cccccccccceeecccceEEEeechhhhhhh-hhHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEe
Confidence            9999999999999999999999999999998 9999999999999999999999999999999999999999988754

>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=100.00  E-value=1.1e-37  Score=282.58  Aligned_cols=202  Identities=34%  Similarity=0.533  Sum_probs=187.0

Q ss_pred             CCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCc-ceeeeccC
Q psy1548          80 SGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGM-DILCQAKS  158 (448)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~-~vli~apT  158 (448)
                      ++|+++++++++++++.+.|                       |..|+++   |++      +||.++.|+ |+++++||
T Consensus         4 msf~~l~l~~~l~~~l~~~g-----------------------~~~pt~i---Q~~------~ip~~l~g~~d~iv~a~T   51 (208)
T d1hv8a1           4 MNFNELNLSDNILNAIRNKG-----------------------FEKPTDI---QMK------VIPLFLNDEYNIVAQART   51 (208)
T ss_dssp             CCGGGSSCCHHHHHHHHHHT-----------------------CCSCCHH---HHH------HHHHHHHTCSEEEEECCS
T ss_pred             cCHHHcCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHHcCCCCeeeechh
Confidence            58999999999999999999                       9999999   999      999999985 99999999


Q ss_pred             CChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEE
Q psy1548         159 GMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVG  238 (448)
Q Consensus       159 GsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~  238 (448)
                      |+|||++|++|+++.... ..+++++|++||++|+.|+.+.++.+.... +.++...+|+.+...+...+..  ++|+|+
T Consensus        52 GsGKT~~~~l~~~~~~~~-~~~~~~lil~pt~~l~~q~~~~~~~~~~~~-~~~v~~~~g~~~~~~~~~~l~~--~~IlV~  127 (208)
T d1hv8a1          52 GSGKTASFAIPLIELVNE-NNGIEAIILTPTRELAIQVADEIESLKGNK-NLKIAKIYGGKAIYPQIKALKN--ANIVVG  127 (208)
T ss_dssp             SSSHHHHHHHHHHHHSCS-SSSCCEEEECSCHHHHHHHHHHHHHHHCSS-CCCEEEECTTSCHHHHHHHHHT--CSEEEE
T ss_pred             cccccceeeccccccccc-ccCcceEEEeeccccchhhhhhhhhhcccC-CeEEEEeeCCCChHHHHHhcCC--CCEEEE
Confidence            999999999999987654 456799999999999999999999999887 8899999999887777666543  899999


Q ss_pred             cHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEEE
Q psy1548         239 TPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV  318 (448)
Q Consensus       239 Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~~  318 (448)
                      ||+++.++++++.+.+++++++|+||||+|++. ++...+..+++.+++++|++++|||+|+++.+++++++.+|..+.+
T Consensus       128 TP~~l~~~l~~~~~~~~~l~~lViDEad~l~~~-~~~~~i~~I~~~~~~~~Q~i~~SAT~~~~v~~~~~~~l~~~~~I~~  206 (208)
T d1hv8a1         128 TPGRILDHINRGTLNLKNVKYFILDEADEMLNM-GFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKA  206 (208)
T ss_dssp             CHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTT-TTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEEC
T ss_pred             ChHHHHHHHHcCCCCcccCcEEEEEChHHhhcC-CChHHHHHHHHhCCCCCeEEEEEccCCHHHHHHHHHHCCCCeEEEE
Confidence            999999999999999999999999999999998 9999999999999999999999999999999999999999987764

>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=100.00  E-value=8.1e-38  Score=288.83  Aligned_cols=206  Identities=28%  Similarity=0.453  Sum_probs=188.6

Q ss_pred             ccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeecc
Q psy1548          78 HSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAK  157 (448)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~ap  157 (448)
                      ...+|+++++++++++++.+.|                       |..|+++   |+.      +||.++.|+|++++||
T Consensus        19 ~~~~F~~l~l~~~l~~~L~~~g-----------------------~~~pt~i---Q~~------~ip~il~g~dvvi~a~   66 (238)
T d1wrba1          19 VIENFDELKLDPTIRNNILLAS-----------------------YQRPTPI---QKN------AIPAILEHRDIMACAQ   66 (238)
T ss_dssp             CCCSSGGGSCCCSTTTTTTTTT-----------------------CCSCCHH---HHH------HHHHHHTTCCEEEECC
T ss_pred             ccCCHHHCCCCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HhhhhhCCCCEEEECC
Confidence            4568999999999999999999                       9999999   999      9999999999999999


Q ss_pred             CCChhHHHHHHHHHHhhhcc---------CCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHH
Q psy1548         158 SGMGKTAVFVLATLQQLETT---------DSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYL  228 (448)
Q Consensus       158 TGsGKT~~~~l~~l~~l~~~---------~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l  228 (448)
                      ||||||++|++|+++.+...         ..+++++|++||++|+.|+.+.+..++... ++++..+.|+.....+....
T Consensus        67 TGsGKTlayllp~l~~l~~~~~~~~~~~~~~~~~alil~pt~el~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~  145 (238)
T d1wrba1          67 TGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNT-PLRSCVVYGGADTHSQIREV  145 (238)
T ss_dssp             TTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCSHHHHHHH
T ss_pred             CCCCcceeeHHHHHHHHHhcccccccccCCCCceEEEeccchhhhcchheeeeecccCC-CcEEEEEeccchhhHHHhhc
Confidence            99999999999999988432         245789999999999999999999999888 89999999998887777666


Q ss_pred             hcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCC----CCCeEEEEeccCCccHHH
Q psy1548         229 KTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSP----HTKQVMMFSATLSKEIRP  304 (448)
Q Consensus       229 ~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~----~~~q~i~~SAT~~~~~~~  304 (448)
                      ..+ +||+|+||++|.+++..+...+.+++++|+||||.+++. +|..++..+++.+.    .++|++++|||++.+++.
T Consensus       146 ~~~-~~ivV~TP~~l~~~~~~~~~~l~~v~~lViDEaD~ll~~-~f~~~i~~Il~~~~~~~~~~~Q~il~SAT~~~~v~~  223 (238)
T d1wrba1         146 QMG-CHLLVATPGRLVDFIEKNKISLEFCKYIVLDEADRMLDM-GFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQK  223 (238)
T ss_dssp             SSC-CSEEEECHHHHHHHHHTTSBCCTTCCEEEEETHHHHHHT-TCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHH
T ss_pred             ccC-CceeecCHHHHHhHHccCceeccccceeeeehhhhhhhh-ccHHHHHHHHHHhcCCCCCCCEEEEEeeeCCHHHHH
Confidence            664 999999999999999999999999999999999999998 99999999998764    257999999999999999


Q ss_pred             HHHHhcCCCeEEEE
Q psy1548         305 VCKKFMHDPMEVYV  318 (448)
Q Consensus       305 ~~~~~l~~~~~i~~  318 (448)
                      +++.++.+|+.+.+
T Consensus       224 l~~~~~~~p~~i~v  237 (238)
T d1wrba1         224 LAADFLYNYIFMTV  237 (238)
T ss_dssp             HHHHHCSSCEEEEE
T ss_pred             HHHHHCCCCEEEEe
Confidence            99999999988765

>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=100.00  E-value=7.1e-36  Score=271.04  Aligned_cols=204  Identities=32%  Similarity=0.527  Sum_probs=182.7

Q ss_pred             CcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCC
Q psy1548          81 GFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGM  160 (448)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGs  160 (448)
                      .|+++++++++++++.+.|                       |..|+++   |++      +||.++.|+|++++|||||
T Consensus         2 ~F~~l~L~~~l~~~l~~~g-----------------------~~~pt~i---Q~~------aip~~l~G~dvii~a~TGS   49 (209)
T d1q0ua_           2 QFTRFPFQPFIIEAIKTLR-----------------------FYKPTEI---QER------IIPGALRGESMVGQSQTGT   49 (209)
T ss_dssp             CGGGSCCCHHHHHHHHHTT-----------------------CCSCCHH---HHH------HHHHHHHTCCEEEECCSSH
T ss_pred             ccccCCcCHHHHHHHHHCC-----------------------CCCCCHH---HHH------HHHHHHCCCCeEeeccccc
Confidence            6999999999999999999                       9999999   999      9999999999999999999


Q ss_pred             hhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCC---CceEEEEEcCcccHHhHHHHhcCCCcEEE
Q psy1548         161 GKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS---NIKVGVFFGGLPIQKDEEYLKTHNPQIVV  237 (448)
Q Consensus       161 GKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~---~~~v~~~~g~~~~~~~~~~l~~~~~~IlV  237 (448)
                      |||++|++|+++.+.........++++|+..++.+....+........   ...+....++.+...+...... +++|+|
T Consensus        50 GKTlayllp~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~Ilv  128 (209)
T d1q0ua_          50 GKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNV-QPHIVI  128 (209)
T ss_dssp             HHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSS-CCSEEE
T ss_pred             ccceeeeeeeccccccccccccccccccccchhHHHHHHHHhhhccccccccccccccccchhhHHHHHHhcc-CceEEE
Confidence            999999999999988887888999999999999999888877665442   3556666666655544433434 499999


Q ss_pred             EcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhcCCCeEEE
Q psy1548         238 GTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVY  317 (448)
Q Consensus       238 ~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~~~~~i~  317 (448)
                      +||+++..++.+....+.+++++|+||||.++++ +|...+..+++.+++++|++++|||+|+++.++++.++++|..+.
T Consensus       129 ~TP~~l~~~~~~~~~~~~~l~~lViDEad~ll~~-~f~~~v~~I~~~~~~~~Q~il~SATl~~~v~~l~~~~l~~p~~i~  207 (209)
T d1q0ua_         129 GTPGRINDFIREQALDVHTAHILVVDEADLMLDM-GFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVH  207 (209)
T ss_dssp             ECHHHHHHHHHTTCCCGGGCCEEEECSHHHHHHT-TCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEE
T ss_pred             ecCchhhhhhhhhccccccceEEEEeeccccccc-ccHHHHHHHHHHCCCCCEEEEEEccCCHHHHHHHHHHCCCCEEEE
Confidence            9999999999998889999999999999999998 999999999999999999999999999999999999999998876


Q ss_pred             E
Q psy1548         318 V  318 (448)
Q Consensus       318 ~  318 (448)
                      +
T Consensus       208 V  208 (209)
T d1q0ua_         208 V  208 (209)
T ss_dssp             C
T ss_pred             e
Confidence            4

>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=99.92  E-value=2.5e-25  Score=199.79  Aligned_cols=181  Identities=15%  Similarity=0.218  Sum_probs=141.1

Q ss_pred             CCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHH
Q psy1548          87 LKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVF  166 (448)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~  166 (448)
                      +++.+...+.+.|                       |..|++.   |++      +++.+++|+|+++++|||+|||.++
T Consensus        10 ~~~~~~~~l~~~g-----------------------~~~l~~~---Q~~------ai~~l~~~~~~il~apTGsGKT~~a   57 (202)
T d2p6ra3          10 ISSYAVGILKEEG-----------------------IEELFPP---QAE------AVEKVFSGKNLLLAMPTAAGKTLLA   57 (202)
T ss_dssp             HHHHHHHHHHCC--------------------------CCCCC---CHH------HHHHHTTCSCEEEECSSHHHHHHHH
T ss_pred             hhHHHHHHHHHcC-----------------------CCCCCHH---HHH------HHHHHHcCCCEEEEcCCCCchhHHH
Confidence            4567788888888                       9999998   999      9999999999999999999999999


Q ss_pred             HHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHH
Q psy1548         167 VLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILAL  246 (448)
Q Consensus       167 ~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~  246 (448)
                      .++++..+..   +.++|+++|+++|+.|+.+.++++...  ..++....|+......    ..+.++|+++||..+..+
T Consensus        58 ~l~i~~~~~~---~~~vl~l~P~~~L~~q~~~~~~~~~~~--~~~v~~~~~~~~~~~~----~~~~~~ii~~~~~~~~~~  128 (202)
T d2p6ra3          58 EMAMVREAIK---GGKSLYVVPLRALAGEKYESFKKWEKI--GLRIGISTGDYESRDE----HLGDCDIIVTTSEKADSL  128 (202)
T ss_dssp             HHHHHHHHHT---TCCEEEEESSHHHHHHHHHHHTTTTTT--TCCEEEECSSCBCCSS----CSTTCSEEEEEHHHHHHH
T ss_pred             HHHHHHHhhc---cCcceeecccHHHHHHHHHHHHHHhhc--cccceeeccCcccccc----cccccceeeeccHHHHHH
Confidence            9999887654   347999999999999999999888764  4566666665443221    122478999999999999


Q ss_pred             HHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHH---HHhCCCCCeEEEEeccCCccHHHHHHHhcC
Q psy1548         247 VRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEI---FRSSPHTKQVMMFSATLSKEIRPVCKKFMH  311 (448)
Q Consensus       247 l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i---~~~l~~~~q~i~~SAT~~~~~~~~~~~~l~  311 (448)
                      +......+.+++++|+||+|.+.+. .+...+..+   ++..++++|+++||||+++ ..++. .|+.
T Consensus       129 ~~~~~~~~~~~~~ii~DE~h~~~~~-~r~~~~~~~l~~i~~~~~~~~~l~lSATl~n-~~~~~-~~l~  193 (202)
T d2p6ra3         129 IRNRASWIKAVSCLVVDEIHLLDSE-KRGATLEILVTKMRRMNKALRVIGLSATAPN-VTEIA-EWLD  193 (202)
T ss_dssp             HHTTCSGGGGCCEEEETTGGGGGCT-TTHHHHHHHHHHHHHHCTTCEEEEEECCCTT-HHHHH-HHTT
T ss_pred             HhccchhhhhhhhccccHHHHhccc-ccchHHHHHHHHHHhcCCCCcEEEEcCCCCc-HHHHH-HHcC
Confidence            9888888899999999999998775 444443333   4455678999999999976 45555 4544

>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=99.91  E-value=1e-25  Score=203.00  Aligned_cols=189  Identities=14%  Similarity=0.114  Sum_probs=138.6

Q ss_pred             CcccCCCCHHHHHHHhhc-cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeeccCC
Q psy1548          81 GFRDFLLKPEILRAIVDC-WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSG  159 (448)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTG  159 (448)
                      ..+.++|++...+.+.+. |                       |..+++.   |++      +++.++.|+|+++++|||
T Consensus         3 ~~e~~~l~~~~~~~l~~~fg-----------------------~~~~rp~---Q~~------ai~~~l~g~~vlv~apTG   50 (206)
T d1oywa2           3 QAEVLNLESGAKQVLQETFG-----------------------YQQFRPG---QEE------IIDTVLSGRDCLVVMPTG   50 (206)
T ss_dssp             CCCCSSHHHHHHHHHHHTTC-----------------------CSSCCTT---HHH------HHHHHHTTCCEEEECSCH
T ss_pred             chhhCCCCHHHHHHHHHhcC-----------------------CCCCCHH---HHH------HHHHHHcCCCEEEEcCCC
Confidence            356677888888888776 5                       7666665   999      999999999999999999


Q ss_pred             ChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccH---HhHHHHhcCCCcEE
Q psy1548         160 MGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQ---KDEEYLKTHNPQIV  236 (448)
Q Consensus       160 sGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~---~~~~~l~~~~~~Il  236 (448)
                      +|||++|.+|++..      ..++++++|+++|+.|+.+.++.+..     ......+.....   ........+..+|+
T Consensus        51 sGKT~~~~~~~~~~------~~~~~~v~P~~~L~~q~~~~l~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~i~  119 (206)
T d1oywa2          51 GGKSLCYQIPALLL------NGLTVVVSPLISLMKDQVDQLQANGV-----AAACLNSTQTREQQLEVMTGCRTGQIRLL  119 (206)
T ss_dssp             HHHHHHHHHHHHHS------SSEEEEECSCHHHHHHHHHHHHHTTC-----CEEEECTTSCHHHHHHHHHHHHHTCCSEE
T ss_pred             CCCcchhhhhhhhc------cCceEEeccchhhhhhHHHHHHhhcc-----cccccccccccccchhHHHHHhcCCceEE
Confidence            99999999999864      34899999999999999999988753     223332222211   12223334458999


Q ss_pred             EEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhh--HH---HHHHHHHhCCCCCeEEEEeccCCccHHH-HHHHh-
Q psy1548         237 VGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEM--RR---DVQEIFRSSPHTKQVMMFSATLSKEIRP-VCKKF-  309 (448)
Q Consensus       237 V~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~--~~---~~~~i~~~l~~~~q~i~~SAT~~~~~~~-~~~~~-  309 (448)
                      ++||..+............+++++|+||||++.++ +.  +.   .+..+...+ +++|+++||||+++.+.+ +++++ 
T Consensus       120 ~~t~~~~~~~~~~~~~~~~~v~~lviDEaH~~~~~-~~~~~~~~~~~~~l~~~~-~~~~ii~lSATl~~~v~~di~~~L~  197 (206)
T d1oywa2         120 YIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQW-GHDFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLG  197 (206)
T ss_dssp             EECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTT-SSCCCHHHHGGGGHHHHC-TTSCEEEEESCCCHHHHHHHHHHHT
T ss_pred             EEechhhhchhhcccchhheeeeeeeeeeeeeecc-ccchHHHHHHHHHHHHhC-CCCceEEEEeCCCHHHHHHHHHHcC
Confidence            99999886544444455778999999999998776 32  22   223344445 468999999999998754 55554 


Q ss_pred             cCCCe
Q psy1548         310 MHDPM  314 (448)
Q Consensus       310 l~~~~  314 (448)
                      +.+|.
T Consensus       198 l~~p~  202 (206)
T d1oywa2         198 LNDPL  202 (206)
T ss_dssp             CCSCE
T ss_pred             CCCCc
Confidence            77885

>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=99.91  E-value=6.3e-25  Score=209.46  Aligned_cols=227  Identities=12%  Similarity=0.085  Sum_probs=147.8

Q ss_pred             eeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHh
Q psy1548         145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD  224 (448)
Q Consensus       145 ~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~  224 (448)
                      .+.+|+++++.||||||||++|+.+++......  +.++||++||++|+.|+.+.++.+..........           
T Consensus         5 ~~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~--~~~~lvi~Ptr~La~q~~~~l~~~~~~~~~~~~~-----------   71 (305)
T d2bmfa2           5 IFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKR--GLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIR-----------   71 (305)
T ss_dssp             SSSTTCEEEECCCTTSSTTTTHHHHHHHHHHHH--TCCEEEEESSHHHHHHHHHHTTTSCCBCCC---------------
T ss_pred             HhhcCCcEEEEECCCCCHHHHHHHHHHHHHHhc--CCEEEEEccHHHHHHHHHHHHhcCCcceeeeEEe-----------
Confidence            455789999999999999999988888765443  4589999999999999888776654322111110           


Q ss_pred             HHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhh--hHHHHHHHHHhCCCCCeEEEEeccCCccH
Q psy1548         225 EEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLE--MRRDVQEIFRSSPHTKQVMMFSATLSKEI  302 (448)
Q Consensus       225 ~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~--~~~~~~~i~~~l~~~~q~i~~SAT~~~~~  302 (448)
                        ........++++||+.+..+... ...+.+++++|+||||++..+ +  +...+..+..  ....+++++|||++...
T Consensus        72 --~~~~~~~~i~~~t~~~l~~~~~~-~~~~~~~~~vViDE~H~~~~~-~~~~~~~l~~~~~--~~~~~~v~~SAT~~~~~  145 (305)
T d2bmfa2          72 --AEHTGREIVDLMCHATFTMRLLS-PIRVPNYNLIIMDEAHFTDPA-SIAARGYISTRVE--MGEAAGIFMTATPPGSR  145 (305)
T ss_dssp             ------CCCSEEEEEHHHHHHHHTS-SSCCCCCSEEEEESTTCCSHH-HHHHHHHHHHHHH--HTSCEEEEECSSCTTCC
T ss_pred             --ecccCccccccCCcHHHHHHHhc-CccccceeEEEeeeeeecchh-hHHHHHHHHHhhc--cccceEEEeecCCCcce
Confidence              11112367999999988776654 445788999999999988765 3  2222222221  35678999999997653


Q ss_pred             HHHHHHhcCCCeEEEEcCcccccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEE
Q psy1548         303 RPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAV  382 (448)
Q Consensus       303 ~~~~~~~l~~~~~i~~~~~~~~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~  382 (448)
                      .....  ...|...               .........+...+..+  ....++++|||+++++|+.+++.|++.|+++.
T Consensus       146 ~~~~~--~~~~~~~---------------~~~~~~~~~~~~~~~~~--~~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~  206 (305)
T d2bmfa2         146 DPFPQ--SNAPIMD---------------EEREIPERSWNSGHEWV--TDFKGKTVWFVPSIKAGNDIAACLRKNGKKVI  206 (305)
T ss_dssp             CSSCC--CSSCEEE---------------EECCCCCSCCSSCCHHH--HSSCSCEEEECSCHHHHHHHHHHHHHHTCCCE
T ss_pred             eeecc--cCCcceE---------------EEEeccHHHHHHHHHHH--HhhCCCEEEEeccHHHHHHHHHHHHhCCCCEE
Confidence            21100  0011111               11111111111111111  22357899999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         383 SIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       383 ~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                      .+||++.+..|.    .|++|.  ..+.++|+.
T Consensus       207 ~l~~~~~~~~~~----~~~~~~--~~~lvaT~~  233 (305)
T d2bmfa2         207 QLSRKTFDSEYI----KTRTND--WDFVVTTDI  233 (305)
T ss_dssp             ECCTTCHHHHGG----GGGTSC--CSEEEECGG
T ss_pred             EeCCcChHHHHh----hhhccc--hhhhhhhHH
Confidence            999999776554    566665  456666654

>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=99.91  E-value=3.1e-25  Score=204.26  Aligned_cols=168  Identities=17%  Similarity=0.283  Sum_probs=124.2

Q ss_pred             ccCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         123 YDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       123 ~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      +..|+++   |++      +++.++.|+|++++||||+|||++++++++.....   +.++||++||++|+.|+++.+++
T Consensus        41 ~~~p~~~---Q~~------~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~---~~rvliv~Pt~~La~Q~~~~l~~  108 (237)
T d1gkub1          41 VGEPRAI---QKM------WAKRILRKESFAATAPTGVGKTSFGLAMSLFLALK---GKRCYVIFPTSLLVIQAAETIRK  108 (237)
T ss_dssp             TCSCCHH---HHH------HHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTT---SCCEEEEESCHHHHHHHHHHHHH
T ss_pred             cCCCCHH---HHH------HHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHh---cCeEEEEeccHHHHHHHHHHHHH
Confidence            8899988   999      99999999999999999999999999999876543   45899999999999999999999


Q ss_pred             hhccCCCce----EEEEEcCcccHHhHHHHh-cCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHH
Q psy1548         203 FSKYMSNIK----VGVFFGGLPIQKDEEYLK-THNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRD  277 (448)
Q Consensus       203 ~~~~~~~~~----v~~~~g~~~~~~~~~~l~-~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~  277 (448)
                      +...+ ++.    +....++.........+. ...++|+|+||+++.+.    ...+++++++|+||+|.+++. +.  .
T Consensus       109 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~----~~~~~~~~~vVvDE~d~~l~~-~~--~  180 (237)
T d1gkub1         109 YAEKA-GVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKH----YRELGHFDFIFVDDVDAILKA-SK--N  180 (237)
T ss_dssp             HHTTT-CCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHC----STTSCCCSEEEESCHHHHHTS-TH--H
T ss_pred             HHHHc-CCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHHh----hhhcCCCCEEEEEChhhhhhc-cc--c
Confidence            98766 433    334444444333333332 22478999999987542    334678999999999999875 22  1


Q ss_pred             HHHHHH-------------hCCCCCeEEEEeccCCccHHHH-HHHhc
Q psy1548         278 VQEIFR-------------SSPHTKQVMMFSATLSKEIRPV-CKKFM  310 (448)
Q Consensus       278 ~~~i~~-------------~l~~~~q~i~~SAT~~~~~~~~-~~~~l  310 (448)
                      +..++.             ..+...|++++|||+++..+.. .+.++
T Consensus       181 ~~~~~~~~g~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~l~r~ll  227 (237)
T d1gkub1         181 VDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFRQLL  227 (237)
T ss_dssp             HHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSCCCTTHHHHHHHH
T ss_pred             hhHHHHhcCChHHHHHHHhhCCCCCeEEEEeCCCCcccHHHHHHHHh
Confidence            222222             2245678999999998765443 34444

>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=99.89  E-value=4e-23  Score=184.76  Aligned_cols=163  Identities=15%  Similarity=0.213  Sum_probs=127.4

Q ss_pred             hhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCC
Q psy1548         130 DTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN  209 (448)
Q Consensus       130 ~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  209 (448)
                      ++||.+      ++..+. ++|+|+++|||+|||+++++++...+...  +.+++|++|+++|+.|+.+.+.++.... +
T Consensus        11 r~~Q~~------~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~~--~~~il~i~P~~~L~~q~~~~~~~~~~~~-~   80 (200)
T d1wp9a1          11 RIYQEV------IYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKY--GGKVLMLAPTKPLVLQHAESFRRLFNLP-P   80 (200)
T ss_dssp             CHHHHH------HHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHHS--CSCEEEECSSHHHHHHHHHHHHHHBCSC-G
T ss_pred             CHHHHH------HHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHhc--CCcEEEEcCchHHHHHHHHHHHHhhccc-c
Confidence            455999      776654 67899999999999999998887766543  3479999999999999999999998776 7


Q ss_pred             ceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCC
Q psy1548         210 IKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTK  289 (448)
Q Consensus       210 ~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~  289 (448)
                      .++....++............  ++++++||+.+...+......+.+++++|+||||++... .....+...+.......
T Consensus        81 ~~v~~~~~~~~~~~~~~~~~~--~~i~i~t~~~~~~~~~~~~~~~~~~~~vIiDE~H~~~~~-~~~~~~~~~~~~~~~~~  157 (200)
T d1wp9a1          81 EKIVALTGEKSPEERSKAWAR--AKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGN-YAYVFIAREYKRQAKNP  157 (200)
T ss_dssp             GGEEEECSCSCHHHHHHHHHH--CSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTT-CHHHHHHHHHHHHCSSC
T ss_pred             cceeeeecccchhHHHHhhhc--ccccccccchhHHHHhhhhhhccccceEEEEehhhhhcc-hhHHHHHHHHHhcCCCC
Confidence            888777777665544444433  589999999999999988888999999999999988765 33333444444445667


Q ss_pred             eEEEEeccCCccHHHH
Q psy1548         290 QVMMFSATLSKEIRPV  305 (448)
Q Consensus       290 q~i~~SAT~~~~~~~~  305 (448)
                      +++++|||++.....+
T Consensus       158 ~~l~~SATp~~~~~~~  173 (200)
T d1wp9a1         158 LVIGLTASPGSTPEKI  173 (200)
T ss_dssp             CEEEEESCSCSSHHHH
T ss_pred             cEEEEEecCCCcHHHH
Confidence            8999999986654444

>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=99.71  E-value=6e-17  Score=139.78  Aligned_cols=120  Identities=82%  Similarity=1.234  Sum_probs=106.1

Q ss_pred             ceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC---
Q psy1548         328 GLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH---  404 (448)
Q Consensus       328 ~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~---  404 (448)
                      +++|+|+.+.+++|.+.|.++++....+++||||++++.++.+++.|.+.|+++..+||+|++++|..+++.|++|+   
T Consensus         1 ~l~q~~v~~~~~~K~~~L~~ll~~~~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~i   80 (168)
T d1t5ia_           1 GLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRI   80 (168)
T ss_dssp             CCEEEEEECCGGGHHHHHHHHHHHSCCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSE
T ss_pred             CcEEEEEEeChHHHHHHHHHHHHhCCCCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhcccccee
Confidence            47899999999999999999999998899999999999999999999999999999999999999999999999998   


Q ss_pred             -------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccc
Q psy1548         405 -------------------------------------------KGLAITFASDENDAKILNNVQDRFDVSISELPDEIDL  441 (448)
Q Consensus       405 -------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~  441 (448)
                                                                 .|.+|+|+++..+..+++.+++.++..+.++|++++.
T Consensus        81 Lv~T~~~~~Gid~~~~~~vi~~~~p~~~~~yiqr~GR~gR~g~~g~~i~l~~~~~~~~~~~~i~~~~~~~~~elp~~~~i  160 (168)
T d1t5ia_          81 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDI  160 (168)
T ss_dssp             EEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGGGCCCEEEEEECSHHHHHHHHHHHHHHCCCEEECC-----
T ss_pred             eeccccccchhhcccchhhhhhhcccchhhHhhhhhhcccCCCccEEEEEECchHHHHHHHHHHHHHcCCcccCCchhhH
Confidence                                                       7899999999878999999999999999999999998


Q ss_pred             cccccC
Q psy1548         442 STYIEG  447 (448)
Q Consensus       442 ~~~~~~  447 (448)
                      .+++++
T Consensus       161 ~~~~e~  166 (168)
T d1t5ia_         161 SSYIEQ  166 (168)
T ss_dssp             ----CC
T ss_pred             HHHHhc
Confidence            888764

>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=99.70  E-value=7e-18  Score=158.10  Aligned_cols=156  Identities=13%  Similarity=0.179  Sum_probs=113.7

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .+..+++||++      ++..++..+..++.+|||+|||++....+.. +... ...++||++|+++|+.|+.+.+..+.
T Consensus       110 ~~~~~rdyQ~~------av~~~l~~~~~il~~pTGsGKT~i~~~i~~~-~~~~-~~~k~Liivp~~~Lv~Q~~~~f~~~~  181 (282)
T d1rifa_         110 KRIEPHWYQKD------AVFEGLVNRRRILNLPTSAGRSLIQALLARY-YLEN-YEGKILIIVPTTALTTQMADDFVDYR  181 (282)
T ss_dssp             EECCCCHHHHH------HHHHHHHHSEEEECCCTTSCHHHHHHHHHHH-HHHH-CSSEEEEECSSHHHHHHHHHHHHHHT
T ss_pred             CccccchHHHH------HHHHHHhcCCceeEEEcccCccHHHHHHHHH-hhhc-ccceEEEEEcCchhHHHHHHHHHHhh
Confidence            45667999999      9989998899999999999999886544432 2222 23489999999999999999999987


Q ss_pred             ccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHh
Q psy1548         205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRS  284 (448)
Q Consensus       205 ~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~  284 (448)
                      ... ...+..+.++.......    ....+|+|+|++.+..+   ....+++++++|+||||++..     ..+..++..
T Consensus       182 ~~~-~~~~~~~~~g~~~~~~~----~~~~~i~i~t~qs~~~~---~~~~~~~f~~VIvDEaH~~~a-----~~~~~il~~  248 (282)
T d1rifa_         182 LFS-HAMIKKIGGGASKDDKY----KNDAPVVVGTWQTVVKQ---PKEWFSQFGMMMNDECHLATG-----KSISSIISG  248 (282)
T ss_dssp             SCC-GGGEEECSTTCSSTTCC----CTTCSEEEECHHHHTTS---CGGGGGGEEEEEEETGGGCCH-----HHHHHHTTT
T ss_pred             ccc-cccceeecceecccccc----cccceEEEEeeehhhhh---cccccCCCCEEEEECCCCCCc-----hhHHHHHHh
Confidence            654 45566666665432211    11368999999876533   334567899999999997644     345667766


Q ss_pred             CCCCCeEEEEeccCCcc
Q psy1548         285 SPHTKQVMMFSATLSKE  301 (448)
Q Consensus       285 l~~~~q~i~~SAT~~~~  301 (448)
                      +.+....++||||++..
T Consensus       249 ~~~~~~rlGlTaT~~~~  265 (282)
T d1rifa_         249 LNNCMFKFGLSGSLRDG  265 (282)
T ss_dssp             CTTCCEEEEECSSCCTT
T ss_pred             ccCCCeEEEEEeecCCC
Confidence            65555569999998654

>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=99.69  E-value=2.7e-16  Score=141.54  Aligned_cols=154  Identities=17%  Similarity=0.175  Sum_probs=119.2

Q ss_pred             hhhhccccccceeeee----C--cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhcc
Q psy1548         133 LHRVARAGRFGTKAVL----G--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKY  206 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~----g--~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  206 (448)
                      |..      ++..+..    +  .+.+++|.||||||.+|+.++...+.   .+.++++++||..|+.|.++.++++...
T Consensus        60 Q~~------~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~---~g~qv~~l~Pt~~La~Q~~~~~~~~~~~  130 (233)
T d2eyqa3          60 QAQ------AINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD---NHKQVAVLVPTTLLAQQHYDNFRDRFAN  130 (233)
T ss_dssp             HHH------HHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT---TTCEEEEECSSHHHHHHHHHHHHHHSTT
T ss_pred             HHH------HHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHH---cCCceEEEccHHHhHHHHHHHHHHHHhh
Confidence            777      6555433    3  47899999999999999999988774   3559999999999999999999998888


Q ss_pred             CCCceEEEEEcCcccHHh---HHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHH
Q psy1548         207 MSNIKVGVFFGGLPIQKD---EEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFR  283 (448)
Q Consensus       207 ~~~~~v~~~~g~~~~~~~---~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~  283 (448)
                      + ++++..++|.......   ...+..+.++|+|||-..+.     ..+.++++.++|+||-|+.    ++..  +..++
T Consensus       131 ~-~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~-----~~~~f~~LgLiIiDEeH~f----g~kQ--~~~l~  198 (233)
T d2eyqa3         131 W-PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-----SDVKFKDLGLLIVDEEHRF----GVRH--KERIK  198 (233)
T ss_dssp             T-TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-----SCCCCSSEEEEEEESGGGS----CHHH--HHHHH
T ss_pred             C-CCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhc-----cCCccccccceeeechhhh----hhHH--HHHHH
Confidence            7 8899999998875543   44567788999999975443     4556899999999999964    2222  23344


Q ss_pred             hCCCCCeEEEEeccCCccHHHHHH
Q psy1548         284 SSPHTKQVMMFSATLSKEIRPVCK  307 (448)
Q Consensus       284 ~l~~~~q~i~~SAT~~~~~~~~~~  307 (448)
                      ....+..++++|||..++...++.
T Consensus       199 ~~~~~~~~l~~SATPiprtl~~~~  222 (233)
T d2eyqa3         199 AMRANVDILTLTATPIPRTLNMAM  222 (233)
T ss_dssp             HHHTTSEEEEEESSCCCHHHHHHH
T ss_pred             hhCCCCCEEEEecchhHHHHHHHH
Confidence            445678899999998777554443

>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=99.69  E-value=2.3e-17  Score=137.37  Aligned_cols=135  Identities=15%  Similarity=0.142  Sum_probs=89.7

Q ss_pred             eeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHH
Q psy1548         147 VLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEE  226 (448)
Q Consensus       147 ~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~  226 (448)
                      ..|+++++++|||+|||.+++.+++......  +.++++++|+++++.|..+.+...     ...+....+....     
T Consensus         5 ~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~--~~~vli~~p~~~l~~q~~~~~~~~-----~~~~~~~~~~~~~-----   72 (140)
T d1yksa1           5 KKGMTTVLDFHPGAGKTRRFLPQILAECARR--RLRTLVLAPTRVVLSEMKEAFHGL-----DVKFHTQAFSAHG-----   72 (140)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHHT--TCCEEEEESSHHHHHHHHHHTTTS-----CEEEESSCCCCCC-----
T ss_pred             HcCCcEEEEcCCCCChhHHHHHHHHHHhhhc--CceeeeeecchhHHHHHHHHhhhh-----hhhhccccccccc-----
Confidence            4589999999999999988876666655443  458999999999999977665432     2222211111111     


Q ss_pred             HHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhH-HHHHHHHHhCCCCCeEEEEeccCC
Q psy1548         227 YLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMR-RDVQEIFRSSPHTKQVMMFSATLS  299 (448)
Q Consensus       227 ~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~-~~~~~i~~~l~~~~q~i~~SAT~~  299 (448)
                         .....+.+.|...+..... ....+.+++++|+||||.+... .+. ..+...+.. .++.++++||||+|
T Consensus        73 ---~~~~~~~~~~~~~l~~~~~-~~~~~~~~~lvIiDEaH~~~~~-~~~~~~~~~~~~~-~~~~~~l~lTATPp  140 (140)
T d1yksa1          73 ---SGREVIDAMCHATLTYRML-EPTRVVNWEVIIMDEAHFLDPA-SIAARGWAAHRAR-ANESATILMTATPP  140 (140)
T ss_dssp             ---CSSCCEEEEEHHHHHHHHT-SSSCCCCCSEEEETTTTCCSHH-HHHHHHHHHHHHH-TTSCEEEEECSSCT
T ss_pred             ---ccccchhhhhHHHHHHHHh-ccccccceeEEEEccccccChh-hHHHHHHHHHHhh-CCCCCEEEEEcCCC
Confidence               1124678888887766543 4456789999999999987443 221 122222222 35789999999987

>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=99.67  E-value=5.5e-16  Score=134.19  Aligned_cols=121  Identities=31%  Similarity=0.475  Sum_probs=114.4

Q ss_pred             ccccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcC
Q psy1548         324 LTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDF  403 (448)
Q Consensus       324 ~~~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g  403 (448)
                      .++.++.|+|+.+++.+|...|.++++..+.+++||||++++.|+.++..|...|+.+..+||+|++++|..++++|++|
T Consensus         2 ~tl~~i~q~yi~v~~~~K~~~L~~ll~~~~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~~   81 (171)
T d1s2ma2           2 LTLKGITQYYAFVEERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQG   81 (171)
T ss_dssp             CBCTTEEEEEEECCGGGHHHHHHHHHHHSCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             CCccceEEEEEEcCHHHHHHHHHHHHHhCCCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhcccC
Confidence            46788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             C----------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCCCCCCCc
Q psy1548         404 H----------------------------------------------KGLAITFASDENDAKILNNVQDRFDVSISELPD  437 (448)
Q Consensus       404 ~----------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~  437 (448)
                      +                                              .|.+|+|++.. |...++.|++.++.++.++|.
T Consensus        82 ~~~ilv~Td~~~~Gid~~~v~~VI~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~v~~~-e~~~~~~i~~~l~~~~~~~p~  160 (171)
T d1s2ma2          82 KVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWN-DRFNLYKIEQELGTEIAAIPA  160 (171)
T ss_dssp             SSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCTTCCEEEEEEECGG-GHHHHHHHHHHHTCCCEECCS
T ss_pred             ccccccchhHhhhccccceeEEEEecCCcchHHHHHHHhhhcccCCCccEEEEEeCHH-HHHHHHHHHHHHCCCCCCCCc
Confidence            9                                              89999999887 889999999999999999999


Q ss_pred             cccccccc
Q psy1548         438 EIDLSTYI  445 (448)
Q Consensus       438 ~~~~~~~~  445 (448)
                      .++...|.
T Consensus       161 ~~d~~~~~  168 (171)
T d1s2ma2         161 TIDKSLYV  168 (171)
T ss_dssp             SCCGGGTC
T ss_pred             ccchhhhh
Confidence            99987664

>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=99.67  E-value=7.5e-17  Score=144.16  Aligned_cols=140  Identities=20%  Similarity=0.161  Sum_probs=101.4

Q ss_pred             cCCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         124 DMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       124 ~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      .....+++||++      ++..++.+++.++.+|||+|||++++..+ ..+     +.++||+||+++|+.|+.+.++.+
T Consensus        66 ~~~~~Lr~yQ~e------av~~~~~~~~~ll~~~tG~GKT~~a~~~~-~~~-----~~~~Liv~p~~~L~~q~~~~~~~~  133 (206)
T d2fz4a1          66 DAEISLRDYQEK------ALERWLVDKRGCIVLPTGSGKTHVAMAAI-NEL-----STPTLIVVPTLALAEQWKERLGIF  133 (206)
T ss_dssp             CCCCCCCHHHHH------HHHHHTTTSEEEEEESSSTTHHHHHHHHH-HHS-----CSCEEEEESSHHHHHHHHHHHGGG
T ss_pred             CCCCCcCHHHHH------HHHHHHhCCCcEEEeCCCCCceehHHhHH-HHh-----cCceeEEEcccchHHHHHHHHHhh
Confidence            344568999999      88888888899999999999998865443 332     237999999999999999998877


Q ss_pred             hccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHH
Q psy1548         204 SKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFR  283 (448)
Q Consensus       204 ~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~  283 (448)
                      .    ...+....|+..          ...+|+|+|.+.+......   ...++++||+||||++... .    +..++.
T Consensus       134 ~----~~~~~~~~~~~~----------~~~~i~i~t~~~~~~~~~~---~~~~~~lvIiDEaH~~~a~-~----~~~i~~  191 (206)
T d2fz4a1         134 G----EEYVGEFSGRIK----------ELKPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPAE-S----YVQIAQ  191 (206)
T ss_dssp             C----GGGEEEESSSCB----------CCCSEEEEEHHHHHHTHHH---HTTTCSEEEEECSSCCCTT-T----HHHHHH
T ss_pred             c----ccchhhcccccc----------cccccccceehhhhhhhHh---hCCcCCEEEEECCeeCCcH-H----HHHHHh
Confidence            5    334444444432          1257999999987664432   2356789999999987543 2    344555


Q ss_pred             hCCCCCeEEEEeccC
Q psy1548         284 SSPHTKQVMMFSATL  298 (448)
Q Consensus       284 ~l~~~~q~i~~SAT~  298 (448)
                      .++ ....++||||+
T Consensus       192 ~~~-~~~~lgLTATl  205 (206)
T d2fz4a1         192 MSI-APFRLGLTATF  205 (206)
T ss_dssp             TCC-CSEEEEEEESC
T ss_pred             ccC-CCcEEEEecCC
Confidence            553 44578999997

>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=99.64  E-value=2.4e-16  Score=144.50  Aligned_cols=155  Identities=23%  Similarity=0.222  Sum_probs=117.4

Q ss_pred             hhhhhhccccccceeeee----C--cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         131 TYLHRVARAGRFGTKAVL----G--MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       131 ~yQ~~~~~~~~~~~~~~~----g--~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .-|+.      ++..+..    +  .+.|++|.||||||.+|+.+++..+..+   .++++++||..|+.|.++.++++.
T Consensus        86 ~~Q~~------ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g---~q~~~m~Pt~~La~Qh~~~~~~~f  156 (264)
T d1gm5a3          86 NAQKR------AHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAG---FQTAFMVPTSILAIQHYRRTVESF  156 (264)
T ss_dssp             HHHHH------HHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHT---SCEEEECSCHHHHHHHHHHHHHHH
T ss_pred             chHHH------HHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhcc---cceeEEeehHhhhHHHHHHHHHhh
Confidence            33999      7766643    2  4789999999999999999998887654   489999999999999999999999


Q ss_pred             ccCCCceEEEEEcCcccHHh---HHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHH
Q psy1548         205 KYMSNIKVGVFFGGLPIQKD---EEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEI  281 (448)
Q Consensus       205 ~~~~~~~v~~~~g~~~~~~~---~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i  281 (448)
                      ..+ ++++..++|+....+.   ...+.+|.++|+|||-.-+..     .+.++++.++|+||-|+..-.      -+..
T Consensus       157 ~~~-~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~-----~~~f~~LglviiDEqH~fgv~------Qr~~  224 (264)
T d1gm5a3         157 SKF-NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-----DVHFKNLGLVIIDEQHRFGVK------QREA  224 (264)
T ss_dssp             TCS-SCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-----CCCCSCCCEEEEESCCCC-----------CC
T ss_pred             hhc-cccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcC-----CCCccccceeeeccccccchh------hHHH
Confidence            887 8899999998875543   445567889999999865432     345789999999999965321      1222


Q ss_pred             HHhCCCCCeEEEEeccCCccHHHHH
Q psy1548         282 FRSSPHTKQVMMFSATLSKEIRPVC  306 (448)
Q Consensus       282 ~~~l~~~~q~i~~SAT~~~~~~~~~  306 (448)
                      +.....++.++++|||..++...+.
T Consensus       225 l~~~~~~~~~l~~SATPiprtl~~~  249 (264)
T d1gm5a3         225 LMNKGKMVDTLVMSATPIPRSMALA  249 (264)
T ss_dssp             CCSSSSCCCEEEEESSCCCHHHHHH
T ss_pred             HHHhCcCCCEEEEECCCCHHHHHHH
Confidence            3333456789999999776654443

>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=99.60  E-value=5.3e-15  Score=126.54  Aligned_cols=112  Identities=30%  Similarity=0.504  Sum_probs=103.5

Q ss_pred             eeEEEEEcCc-chHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC---
Q psy1548         329 LQQHYVKLKE-NEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH---  404 (448)
Q Consensus       329 i~~~~~~~~~-~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~---  404 (448)
                      |+|+|+.+.. +.|++.|..+++..+..++||||+++..++.+++.|...|+++..+||+|++.+|.++++.|+.|+   
T Consensus         1 I~q~~~~v~~~e~K~~~L~~ll~~~~~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~i   80 (162)
T d1fuka_           1 IKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRI   80 (162)
T ss_dssp             CEEEEEEEESGGGHHHHHHHHHHHTTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSE
T ss_pred             CEEEEEEeCCcHHHHHHHHHHHHhCCCCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhcccce
Confidence            5788888865 559999999999999999999999999999999999999999999999999999999999999999   


Q ss_pred             -------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccc
Q psy1548         405 -------------------------------------------KGLAITFASDENDAKILNNVQDRFDVSISELPDEIDL  441 (448)
Q Consensus       405 -------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~  441 (448)
                                                                 .|.+++|++.. |...++.++++++..++++|.++..
T Consensus        81 Lv~Tdv~~rGiDi~~v~~VI~~d~P~~~~~yihR~GR~gR~g~~g~~i~~~~~~-d~~~~~~i~~~~~~~~~~ip~~~~~  159 (162)
T d1fuka_          81 LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNE-DVGAMRELEKFYSTQIEELPSDIAT  159 (162)
T ss_dssp             EEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC-----CEEEEEEETT-THHHHHHHHHHSSCCCEECCSCCTT
T ss_pred             eeccccccccccCCCceEEEEeccchhHHHHHhhccccccCCCccEEEEEcCHH-HHHHHHHHHHHHcCcCCCCChHHHH
Confidence                                                       88999999876 8899999999999999999998754

>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=99.60  E-value=1.7e-15  Score=125.98  Aligned_cols=126  Identities=17%  Similarity=0.138  Sum_probs=86.3

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHh
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK  229 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~  229 (448)
                      +..++.+|||+|||..+...++      ..+.+++|++|+++|++|+.+.+.++...    ......++.....      
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~~------~~~~~vli~~P~~~l~~q~~~~~~~~~~~----~~~~~~~~~~~~~------   72 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAYA------AQGYKVLVLNPSVAATLGFGAYMSKAHGV----DPNIRTGVRTITT------   72 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHHH------TTTCCEEEEESCHHHHHHHHHHHHHHHSC----CCEEECSSCEECC------
T ss_pred             CEEEEEeCCCCCHHHHHHHHHH------HcCCcEEEEcChHHHHHHHHHHHHHHhhc----ccccccccccccc------
Confidence            5678999999999976533322      23458999999999999999998887643    3333444432211      


Q ss_pred             cCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCC--CCCeEEEEeccC
Q psy1548         230 THNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSP--HTKQVMMFSATL  298 (448)
Q Consensus       230 ~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~--~~~q~i~~SAT~  298 (448)
                        ...+.++|.+.+...   ....+.+++++|+||+|++..  .....+..+++.+.  ...+++++|||.
T Consensus        73 --~~~~~~~~~~~~~~~---~~~~~~~~~~vIiDE~H~~~~--~~~~~~~~~l~~~~~~~~~~~l~~TATP  136 (136)
T d1a1va1          73 --GSPITYSTYGKFLAD---GGCSGGAYDIIICDECHSTDA--TSILGIGTVLDQAETAGARLVVLATATP  136 (136)
T ss_dssp             --CCSEEEEEHHHHHHT---TGGGGCCCSEEEEETTTCCSH--HHHHHHHHHHHHTTTTTCSEEEEEESSC
T ss_pred             --ccceEEEeeeeeccc---cchhhhcCCEEEEecccccCH--HHHHHHHHHHHHHHHCCCCcEEEEeCCC
Confidence              246888998876433   344578899999999997643  33334555555443  466899999994

>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=99.58  E-value=1e-14  Score=125.43  Aligned_cols=117  Identities=32%  Similarity=0.553  Sum_probs=108.9

Q ss_pred             cccccceeEEEEEcCcc-hHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHh
Q psy1548         323 KLTLHGLQQHYVKLKEN-EKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFK  401 (448)
Q Consensus       323 ~~~~~~i~~~~~~~~~~-~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~  401 (448)
                      +.++.+++|+|+.+++. .|...|.++++.....++||||+++..|+.++..|+..|+++..+||+|++++|.++++.|+
T Consensus         2 ~~tl~~i~q~~v~v~~~~~K~~~L~~ll~~~~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk   81 (168)
T d2j0sa2           2 ELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFR   81 (168)
T ss_dssp             GCSCTTEEEEEEEESSTTHHHHHHHHHHHHHTSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHH
T ss_pred             CCCCCCcEEEEEEecChHHHHHHHHHHHHhCCCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHh
Confidence            46788999999999875 59999999999988899999999999999999999999999999999999999999999999


Q ss_pred             cCC----------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCCCCCC
Q psy1548         402 DFH----------------------------------------------KGLAITFASDENDAKILNNVQDRFDVSISEL  435 (448)
Q Consensus       402 ~g~----------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~  435 (448)
                      +|+                                              .|.+++|++.. |...++.|++.++..+.++
T Consensus        82 ~g~~~iLv~Td~~~rGiDi~~v~~VIn~d~P~~~~~yihR~GR~gR~g~~G~~i~~~~~~-d~~~~~~i~~~~~~~i~e~  160 (168)
T d2j0sa2          82 SGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKND-DIRILRDIEQYYSTQIDEM  160 (168)
T ss_dssp             HTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEEGG-GHHHHHHHHHHTTCCCEEC
T ss_pred             cCCccEEeccchhcccccccCcceEEEecCCcCHHHHHhhhccccccCCCcEEEEEECHH-HHHHHHHHHHHHcCcCCCC
Confidence            998                                              79999999887 8889999999999999999


Q ss_pred             Ccccc
Q psy1548         436 PDEID  440 (448)
Q Consensus       436 p~~~~  440 (448)
                      |.++.
T Consensus       161 p~~~~  165 (168)
T d2j0sa2         161 PMNVA  165 (168)
T ss_dssp             CSCCT
T ss_pred             CcChH
Confidence            98754

>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=99.48  E-value=3.4e-13  Score=114.32  Aligned_cols=107  Identities=28%  Similarity=0.400  Sum_probs=99.3

Q ss_pred             cceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC--
Q psy1548         327 HGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH--  404 (448)
Q Consensus       327 ~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~--  404 (448)
                      .+|+|+|+.++..+|.+.|..+++.. +.++||||++++.|+.++..|++.|+.+..+||++++.+|..++++|++|+  
T Consensus         2 ~nI~~~~i~v~~~~K~~~L~~ll~~~-~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~~~~   80 (155)
T d1hv8a2           2 ANIEQSYVEVNENERFEALCRLLKNK-EFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIR   80 (155)
T ss_dssp             SSSEEEEEECCGGGHHHHHHHHHCST-TCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSS
T ss_pred             CCeEEEEEEeChHHHHHHHHHHHccC-CCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhcccce
Confidence            57999999999999999999999865 458999999999999999999999999999999999999999999999999  


Q ss_pred             --------------------------------------------CceEEEEecChhhHHHHHHHHHHhcCCCCCC
Q psy1548         405 --------------------------------------------KGLAITFASDENDAKILNNVQDRFDVSISEL  435 (448)
Q Consensus       405 --------------------------------------------~g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~  435 (448)
                                                                  .|.+|+|+++. |...+..|++.++.++.++
T Consensus        81 ilv~T~~~~~Gid~~~v~~Vi~~d~p~~~~~y~qr~GR~gR~g~~g~~i~~~~~~-d~~~~~~i~~~~~~~i~~l  154 (155)
T d1hv8a2          81 ILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIINRR-EYKKLRYIERAMKLKIKKL  154 (155)
T ss_dssp             EEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCSSSCCEEEEEECTT-SHHHHHHHHHHHTCCCCCB
T ss_pred             eeeehhHHhhhhhhccCcEEEEecCCCCHHHHHHHHHhcCcCCCCceEEEEEchH-HHHHHHHHHHHHCCCcccc
Confidence                                                        78899999876 8889999999999988775

>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=99.23  E-value=2.7e-12  Score=113.08  Aligned_cols=117  Identities=17%  Similarity=0.213  Sum_probs=98.2

Q ss_pred             ccceeEEEEEcCcchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCC
Q psy1548         326 LHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHK  405 (448)
Q Consensus       326 ~~~i~~~~~~~~~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~  405 (448)
                      .+||.  |..++..+|.+.|..+++...+.++||||+|++.|+.++..|+..|+.+..+||+|++++|.++++.|++|+ 
T Consensus         4 RpNi~--y~v~~~~~k~~~L~~~l~~~~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~-   80 (200)
T d1oywa3           4 RPNIR--YMLMEKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDD-   80 (200)
T ss_dssp             CTTEE--EEEEECSSHHHHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTS-
T ss_pred             CCCcE--EEEEcCCcHHHHHHHHHHhcCCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhccc-
Confidence            35564  344556678999999999988889999999999999999999999999999999999999999999999988 


Q ss_pred             ceEEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         406 GLAITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       406 g~~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                       +.|+++|+...+++  ++.+.-.+-..++|.++..+.++.||
T Consensus        81 -~~ilvaTd~~~~Gi--D~p~v~~VI~~~~P~~~~~y~qr~GR  120 (200)
T d1oywa3          81 -LQIVVATVAFGMGI--NKPNVRFVVHFDIPRNIESYYQETGR  120 (200)
T ss_dssp             -CSEEEECTTSCTTT--CCTTCCEEEESSCCSSHHHHHHHHTT
T ss_pred             -ceEEEecchhhhcc--CCCCCCEEEECCCccchHHHHHHhhh
Confidence             46888888654544  45555556677889999999998888

>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=99.11  E-value=8.2e-12  Score=109.92  Aligned_cols=135  Identities=20%  Similarity=0.241  Sum_probs=89.8

Q ss_pred             eeecCceeEEeecCCCccccccccCCC-ccccccccccccccchhhhhhhhccCceeeeccCCcccCCCCHHHHHHHhhc
Q psy1548          20 LFFRAFIRFSSSFPHSKMADNDDLLDY-EDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIVDC   98 (448)
Q Consensus        20 ~~~r~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   98 (448)
                      ||+|+||+|.+....++....-+++.. .......+..+....+.........+..+...+.+........-+..+....
T Consensus         1 s~~RpNi~y~v~~~~~k~~~L~~~l~~~~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~   80 (200)
T d1oywa3           1 SFDRPNIRYMLMEKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDD   80 (200)
T ss_dssp             CCCCTTEEEEEEECSSHHHHHHHHHHHTTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTS
T ss_pred             CCCCCCcEEEEEcCCcHHHHHHHHHHhcCCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhccc
Confidence            799999999997776664443333322 3334566766665555555555555554555544333222222222223334


Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccceeeeeCcceeeecc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAVLGMDILCQAK  157 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~ap  157 (448)
                      .+|+|||++++||||+++++.|+||..|..+..|-|++|||||...   .|..+++..|
T Consensus        81 ~~ilvaTd~~~~GiD~p~v~~VI~~~~P~~~~~y~qr~GR~gR~g~---~g~ai~~~~~  136 (200)
T d1oywa3          81 LQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGL---PAEAMLFYDP  136 (200)
T ss_dssp             CSEEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTTSS---CEEEEEEECH
T ss_pred             ceEEEecchhhhccCCCCCCEEEECCCccchHHHHHHhhhhhcCCC---CceEEEecCH
Confidence            5899999999999999999999999999999999999999999442   3445555444

>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=99.00  E-value=2.3e-09  Score=100.18  Aligned_cols=157  Identities=13%  Similarity=0.071  Sum_probs=95.4

Q ss_pred             Cchhhhhhhccccccceee---------eeCcceeeeccCCChhHHHHHHHHHHhhhcc----CCCeEEEEeeccHHHHH
Q psy1548         128 DSDTYLHRVARAGRFGTKA---------VLGMDILCQAKSGMGKTAVFVLATLQQLETT----DSNVYVLVMCHTRELAF  194 (448)
Q Consensus       128 ~~~~yQ~~~~~~~~~~~~~---------~~g~~vli~apTGsGKT~~~~l~~l~~l~~~----~~~~~~lil~Pt~~L~~  194 (448)
                      .+++||.+      ++..+         ..+..+|+.-.+|.|||+..+.-+...+...    +...++|||||.. |..
T Consensus        55 ~Lr~hQ~~------gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia~l~~l~~~~~~~~~~~~~~LIV~P~s-l~~  127 (298)
T d1z3ix2          55 VLRPHQRE------GVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPSS-LVR  127 (298)
T ss_dssp             TCCHHHHH------HHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECHH-HHH
T ss_pred             cccHHHHH------HHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHHHHHHHHHHhcccccCCCCcEEEEccch-hhH
Confidence            35777999      44322         2356789999999999986543222222222    1224699999986 788


Q ss_pred             HHHHHHHHhhccCCCceEEEEEcCcccHHhHH--H-Hhc----CCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhH
Q psy1548         195 QISKEYERFSKYMSNIKVGVFFGGLPIQKDEE--Y-LKT----HNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDK  267 (448)
Q Consensus       195 q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~--~-l~~----~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~  267 (448)
                      |+.+++.++...  ...+..++|+........  . ...    ...+++++|.+.+.....  .+...+.+++|+||+|+
T Consensus       128 qW~~Ei~k~~~~--~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~--~l~~~~~~~vI~DEaH~  203 (298)
T d1z3ix2         128 NWYNEVGKWLGG--RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAE--VLHKGKVGLVICDEGHR  203 (298)
T ss_dssp             HHHHHHHHHHGG--GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTT--TTTTSCCCEEEETTGGG
T ss_pred             HHHHHHHhhcCC--ceeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccchh--cccccceeeeecccccc
Confidence            999999998754  345555555543222111  1 111    135799999988765432  22234567899999998


Q ss_pred             HHhhhhhHHHHHHHHHhCCCCCeEEEEeccCC
Q psy1548         268 MLEQLEMRRDVQEIFRSSPHTKQVMMFSATLS  299 (448)
Q Consensus       268 l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~  299 (448)
                      +-.. . ......+ ..+ +....+++|||+-
T Consensus       204 ikn~-~-s~~~~a~-~~l-~~~~rllLTGTPi  231 (298)
T d1z3ix2         204 LKNS-D-NQTYLAL-NSM-NAQRRVLISGTPI  231 (298)
T ss_dssp             CCTT-C-HHHHHHH-HHH-CCSEEEEECSSCS
T ss_pred             cccc-c-chhhhhh-hcc-ccceeeeecchHH
Confidence            8653 2 2222222 223 3446789999973

>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=98.91  E-value=2.2e-09  Score=91.06  Aligned_cols=60  Identities=15%  Similarity=0.172  Sum_probs=53.9

Q ss_pred             CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecC
Q psy1548         353 EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASD  414 (448)
Q Consensus       353 ~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~  414 (448)
                      .+.++||||+|++.|+.++..|++.|+.+..+||+|++.+|.+++++|++|+  +.|+++|+
T Consensus        30 ~g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~--~~vLVaT~   89 (174)
T d1c4oa2          30 RGERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGH--YDCLVGIN   89 (174)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTS--CSEEEESC
T ss_pred             cCCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCC--eEEEEeee
Confidence            5779999999999999999999999999999999999999999999999999  23444443

>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=98.86  E-value=3.6e-10  Score=97.38  Aligned_cols=62  Identities=10%  Similarity=0.121  Sum_probs=56.2

Q ss_pred             CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChh
Q psy1548         353 EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDEN  416 (448)
Q Consensus       353 ~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~  416 (448)
                      .+.++||||+++.+++.++..|++.|+++..+||+|++.+|.+++++|++|+  +.|+++|+-.
T Consensus        30 ~~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~--~~vLVaTdv~   91 (181)
T d1t5la2          30 RNERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGK--YDVLVGINLL   91 (181)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTS--CSEEEESCCC
T ss_pred             cCCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCC--CCEEEehhHH
Confidence            4679999999999999999999999999999999999999999999999999  4666666643

>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=98.82  E-value=2.4e-09  Score=96.18  Aligned_cols=154  Identities=18%  Similarity=0.232  Sum_probs=94.5

Q ss_pred             Cchhhhhhhccccccceeee----eCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHh
Q psy1548         128 DSDTYLHRVARAGRFGTKAV----LGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF  203 (448)
Q Consensus       128 ~~~~yQ~~~~~~~~~~~~~~----~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  203 (448)
                      .+++||.+      ++..+.    .+..+|+..++|.|||+..+ .++..+.......++||+||. .+..|+.+.+.++
T Consensus        12 ~L~~yQ~~------~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i-~~~~~~~~~~~~~~~LIv~p~-~l~~~W~~e~~~~   83 (230)
T d1z63a1          12 NLRPYQIK------GFSWMRFMNKLGFGICLADDMGLGKTLQTI-AVFSDAKKENELTPSLVICPL-SVLKNWEEELSKF   83 (230)
T ss_dssp             CCCHHHHH------HHHHHHHHHHTTCCEEECCCTTSCHHHHHH-HHHHHHHHTTCCSSEEEEECS-TTHHHHHHHHHHH
T ss_pred             chhHHHHH------HHHHHHHhhhcCCCEEEEeCCCCChHHHHH-Hhhhhhhhcccccccceecch-hhhhHHHHHHHhh
Confidence            46889999      554332    35568999999999999864 444444444444579999995 5678888888888


Q ss_pred             hccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHH
Q psy1548         204 SKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFR  283 (448)
Q Consensus       204 ~~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~  283 (448)
                      ...   ..+....+......      ....+|+++|.+.+...-.   +.--..+++|+||+|.+... .. ... ....
T Consensus        84 ~~~---~~~~~~~~~~~~~~------~~~~~vvi~~~~~~~~~~~---l~~~~~~~vI~DEah~~k~~-~s-~~~-~~~~  148 (230)
T d1z63a1          84 APH---LRFAVFHEDRSKIK------LEDYDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKNP-QT-KIF-KAVK  148 (230)
T ss_dssp             CTT---SCEEECSSSTTSCC------GGGSSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSCT-TS-HHH-HHHH
T ss_pred             ccc---ccceeeccccchhh------ccCcCEEEeeHHHHHhHHH---HhcccceEEEEEhhhccccc-ch-hhh-hhhh
Confidence            643   33333322211111      1126899999988754222   11234578999999988654 21 122 2233


Q ss_pred             hCCCCCeEEEEeccCC-ccHHHH
Q psy1548         284 SSPHTKQVMMFSATLS-KEIRPV  305 (448)
Q Consensus       284 ~l~~~~q~i~~SAT~~-~~~~~~  305 (448)
                      .+. ....+++|||.- +...++
T Consensus       149 ~l~-a~~r~~LTgTPi~n~~~dl  170 (230)
T d1z63a1         149 ELK-SKYRIALTGTPIENKVDDL  170 (230)
T ss_dssp             TSC-EEEEEEECSSCSTTCHHHH
T ss_pred             hhc-cceEEEEecchHHhHHHHH
Confidence            343 345689999963 444444

>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=98.48  E-value=3.3e-10  Score=93.12  Aligned_cols=90  Identities=20%  Similarity=0.252  Sum_probs=64.6

Q ss_pred             hhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChhhHHHHHHHHHHhc
Q psy1548         350 DVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDENDAKILNNVQDRFD  429 (448)
Q Consensus       350 ~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~d~~~l~~i~~~~~  429 (448)
                      +...++++||||+|++.|+.|++.|++.|+++..+|++|+.++       |++|+  ..++++|+...+++=-++....+
T Consensus        31 ~~~~~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~~~-------~~~~~--~~vlvaTd~~~~GiD~~v~~Vi~  101 (138)
T d1jr6a_          31 EVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSV-------IPTNG--DVVVVATDALMTGFTGDFDSVID  101 (138)
T ss_dssp             HHHTTSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCSCC-------CTTSS--CEEEEESSSSCSSSCCCBSEEEE
T ss_pred             hhcCCCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchhhh-------hhhhh--cceeehhHHHHhccccccceEEE
Confidence            3445789999999999999999999999999999999999654       56666  57788887543332001111112


Q ss_pred             CCC-CCCCccccccccccCC
Q psy1548         430 VSI-SELPDEIDLSTYIEGR  448 (448)
Q Consensus       430 ~~~-~~~p~~~~~~~~~~~~  448 (448)
                      ..+ .++|.+++.+.++.||
T Consensus       102 ~~~~~~~P~~~~~y~qr~GR  121 (138)
T d1jr6a_         102 CNTSDGKPQDAVSRTQRRGR  121 (138)
T ss_dssp             CSEETTEECCHHHHHHHHTT
T ss_pred             EEecCCCCCCHHHHHhHhcc
Confidence            111 4568888888888887

>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=98.47  E-value=4.4e-07  Score=80.96  Aligned_cols=165  Identities=18%  Similarity=0.209  Sum_probs=115.1

Q ss_pred             CCCCchhhhhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhh
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS  204 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  204 (448)
                      .|..+   |...|.      .+..|  -|....||-|||++..+|+.-....++   .+-|++..--||..=.+++..+.
T Consensus        80 RhyDV---QLiGgi------~L~~G--~iaem~TGEGKTL~a~l~a~l~al~g~---~vhvvTvNdyLA~RDae~m~~iy  145 (273)
T d1tf5a3          80 FPFKV---QLMGGV------ALHDG--NIAEMKTGEGKTLTSTLPVYLNALTGK---GVHVVTVNEYLASRDAEQMGKIF  145 (273)
T ss_dssp             CCCHH---HHHHHH------HHHTT--SEEECCTTSCHHHHHHHHHHHHHTTSS---CEEEEESSHHHHHHHHHHHHHHH
T ss_pred             EEehh---HHHHHH------HHHhh--hheeecCCCcchhHHHHHHHHHHhcCC---CceEEecCccccchhhhHHhHHH
Confidence            56677   777333      33444  588999999999999998876554433   47778888889988788888888


Q ss_pred             ccCCCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHH-HHHHHCC------CCcCCCeeEEEecchhHHHhh------
Q psy1548         205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRI-LALVRNK------KLNLSLLKHFILDECDKMLEQ------  271 (448)
Q Consensus       205 ~~~~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l-~~~l~~~------~~~~~~i~~lViDEah~l~~~------  271 (448)
                      ..+ +++|++...+.+.........   +||+++|...+ .++|+.+      ......+.+.|+||+|.++=+      
T Consensus       146 ~~l-Glsvg~~~~~~~~~~r~~~Y~---~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDsiliDeartpl  221 (273)
T d1tf5a3         146 EFL-GLTVGLNLNSMSKDEKREAYA---ADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPL  221 (273)
T ss_dssp             HHT-TCCEEECCTTSCHHHHHHHHH---SSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEE
T ss_pred             HHc-CCCccccccccCHHHHHHHhh---CCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchhhhhhccCCce
Confidence            888 999999988877655554443   69999999887 4555432      222466889999999988643      


Q ss_pred             --hh-----hHHHHHHHHHhCCCCCeEEEEeccCCccHHHHHHHhc
Q psy1548         272 --LE-----MRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFM  310 (448)
Q Consensus       272 --~~-----~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~~~~l  310 (448)
                        .+     ..-.++..++..   .++.+||.|...+..++.+-|.
T Consensus       222 iisg~~~~~a~it~q~~f~~y---~~l~gmtgta~~~~~e~~~iy~  264 (273)
T d1tf5a3         222 IISGQSMTLATITFQNYFRMY---EKLAGMTGTAKTEEEEFRNIYN  264 (273)
T ss_dssp             EEEEEEEEEEEEEHHHHHTTS---SEEEEEESCCGGGHHHHHHHHC
T ss_pred             EeccCccchhhhhHHHHHHHH---HHHhCCccccHHHHHHHHhccC
Confidence              00     001134445444   3678888888766666665554

>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=98.28  E-value=4.3e-08  Score=85.73  Aligned_cols=71  Identities=15%  Similarity=0.112  Sum_probs=55.9

Q ss_pred             HHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCC------------------------------CcEEEEeCCCCH
Q psy1548         341 KNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQN------------------------------FPAVSIHRGMTQ  390 (448)
Q Consensus       341 k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g------------------------------~~~~~lh~~~~~  390 (448)
                      ..+.+.+.+..  ++++||||+|++.|+.+|..|.+..                              ..+.++||+|++
T Consensus        29 ~~~l~~~~i~~--~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~  106 (201)
T d2p6ra4          29 FEELVEECVAE--NGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLN  106 (201)
T ss_dssp             HHHHHHHHHHT--TCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCH
T ss_pred             HHHHHHHHHHc--CCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhh
Confidence            34455565654  5789999999999999998886420                              127889999999


Q ss_pred             HHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         391 EERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       391 ~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                      ++|..+++.|++|.  +.|+++|+.
T Consensus       107 ~~r~~ie~~f~~g~--i~vlvaT~~  129 (201)
T d2p6ra4         107 GQRRVVEDAFRRGN--IKVVVATPT  129 (201)
T ss_dssp             HHHHHHHHHHHTTS--CCEEEECST
T ss_pred             hhHHHHHHHHhCCC--ceEEEechH
Confidence            99999999999988  677777764

>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=98.25  E-value=1.6e-07  Score=86.71  Aligned_cols=105  Identities=18%  Similarity=0.183  Sum_probs=78.2

Q ss_pred             hHHHHHHHHH----hhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeC--------CCCHHHHHHHHHHHhcCCCce
Q psy1548         340 EKNKKLFELL----DVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHR--------GMTQEERLKKYQEFKDFHKGL  407 (448)
Q Consensus       340 ~k~~~L~~ll----~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~--------~~~~~eR~~~l~~F~~g~~g~  407 (448)
                      .|...|.+++    ....+.++||||+++..|+.+++.|.+.|+++..+||        +|++.+|..+++.|++|+  .
T Consensus       143 pK~~~l~~~l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~--~  220 (286)
T d1wp9a2         143 PKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGE--F  220 (286)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTS--C
T ss_pred             cHHHHHHHHHHHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHcCC--C
Confidence            4555555554    4456789999999999999999999999999988876        577778999999999998  4


Q ss_pred             EEEEecChhhHHHHHHHHHHhcCCCCCCCccccccccccCC
Q psy1548         408 AITFASDENDAKILNNVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       408 ~I~~~t~~~d~~~l~~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      .|+++|+....++  ++.+.-.+-..++|.+...+.++.||
T Consensus       221 ~vLv~T~~~~~Gl--d~~~~~~Vi~~d~~~~~~~~~Qr~GR  259 (286)
T d1wp9a2         221 NVLVATSVGEEGL--DVPEVDLVVFYEPVPSAIRSIQRRGR  259 (286)
T ss_dssp             SEEEECGGGGGGG--GSTTCCEEEESSCCHHHHHHHHHHTT
T ss_pred             cEEEEccceeccc--cCCCCCEEEEeCCCCCHHHHHHHHHh
Confidence            6677777655554  55555555566667776677777776

>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=98.11  E-value=1e-08  Score=93.18  Aligned_cols=93  Identities=17%  Similarity=0.173  Sum_probs=62.3

Q ss_pred             CCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHH----------HHHHHHHhcCCCceEEEEecChhhHHHH-H
Q psy1548         354 FNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEER----------LKKYQEFKDFHKGLAITFASDENDAKIL-N  422 (448)
Q Consensus       354 ~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR----------~~~l~~F~~g~~g~~I~~~t~~~d~~~l-~  422 (448)
                      ++++||||+|++.|+.++..|++.|+++..+|++|+++.|          ..+++.|+.|+.  .+.++|+....... -
T Consensus        36 ggk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~--dvVVaT~~~a~g~~gi  113 (299)
T d1a1va2          36 GGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDF--DSVIDCNTCVTQTVDF  113 (299)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCB--SEEEECCEEEEEEEEC
T ss_pred             CCCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCC--cEEEEEeehhccCCCC
Confidence            6799999999999999999999999999999999999887          568899998873  44444432111000 0


Q ss_pred             HHHHHhcCCCCCCCccccccccccCC
Q psy1548         423 NVQDRFDVSISELPDEIDLSTYIEGR  448 (448)
Q Consensus       423 ~i~~~~~~~~~~~p~~~~~~~~~~~~  448 (448)
                      ++...+.+...++|.+...+.++.||
T Consensus       114 Did~V~~VI~~d~P~SvesyIQRiGR  139 (299)
T d1a1va2         114 SLDPTFTIETTTLPQDAVSRTQRRGR  139 (299)
T ss_dssp             CCSSSCEEEEEEEECBHHHHHHHHTT
T ss_pred             CCCcceEEEeCCCCCCHHHHHhhccc
Confidence            11111223333567777777777776

>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=98.00  E-value=5.7e-08  Score=84.95  Aligned_cols=62  Identities=21%  Similarity=0.314  Sum_probs=55.4

Q ss_pred             cchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCC
Q psy1548         338 ENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       338 ~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~  404 (448)
                      ...|.+.|.++++...+.++||||++...++.+++.|.     +..+||+++.++|..++++|++|+
T Consensus        77 ~~~K~~~l~~ll~~~~~~k~lvf~~~~~~~~~l~~~l~-----~~~i~g~~~~~~R~~~l~~F~~~~  138 (200)
T d2fwra1          77 SKNKIRKLREILERHRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREEREEILEGFRTGR  138 (200)
T ss_dssp             CSHHHHHHHHHHHHTSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHHHHTHHHHHHHSS
T ss_pred             cHHHHHHHHHHHHhCCCCcEEEEeCcHHHHHHHHhhcC-----cceeeCCCCHHHHHHHHHHhhcCC
Confidence            34688999999999888899999999999999998874     345899999999999999999998

>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=97.98  E-value=1.8e-06  Score=72.80  Aligned_cols=46  Identities=37%  Similarity=0.985  Sum_probs=43.0

Q ss_pred             hccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          97 DCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        97 ~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ....++|||++++||+|+++++.|++|+.|.....|.+++||+||.
T Consensus        83 g~~~iLv~Td~~~rGiDi~~v~~VIn~d~P~~~~~yihR~GR~gR~  128 (168)
T d2j0sa2          83 GASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRY  128 (168)
T ss_dssp             TSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGG
T ss_pred             CCccEEeccchhcccccccCcceEEEecCCcCHHHHHhhhcccccc
Confidence            3458999999999999999999999999999999999999999983

>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=97.88  E-value=3.2e-06  Score=70.77  Aligned_cols=90  Identities=29%  Similarity=0.520  Sum_probs=57.5

Q ss_pred             cccccccccchhhhhhhhccCceeeeccCCcccCCCCHHHHHHH-hhccceeEeeccccCCcccccceeEeeccCCCCch
Q psy1548          52 TEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAI-VDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSD  130 (448)
Q Consensus        52 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~  130 (448)
                      ..........+.........+..+...+.+..... ....++.. ....+++|||++++||+|.+++..|++|+.|....
T Consensus        31 iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~-r~~~l~~f~~~~~~iLv~Tdv~~rGiDi~~v~~VI~~d~P~~~~  109 (162)
T d1fuka_          31 VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQE-RDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKE  109 (162)
T ss_dssp             EEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHH-HHHHHHHHHTTSCSEEEEEGGGTTTCCCCSCSEEEESSCCSSGG
T ss_pred             EEEEEEEchHHHHHHHHhhcCceEEEeccCCchhh-HHHHHHHHhhcccceeeccccccccccCCCceEEEEeccchhHH
Confidence            33443333334444444444544444443322211 12223333 23348999999999999999999999999999999


Q ss_pred             hhhhhhcccccc
Q psy1548         131 TYLHRVARAGRF  142 (448)
Q Consensus       131 ~yQ~~~~~~~~~  142 (448)
                      .|-+.+||+||.
T Consensus       110 ~yihR~GR~gR~  121 (162)
T d1fuka_         110 NYIHRIGRGGRF  121 (162)
T ss_dssp             GGGGSSCSCC--
T ss_pred             HHHhhccccccC
Confidence            999999999883

>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=97.87  E-value=1.2e-06  Score=78.88  Aligned_cols=68  Identities=13%  Similarity=0.238  Sum_probs=58.6

Q ss_pred             cchHHHHHHHHHhhCCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecC
Q psy1548         338 ENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASD  414 (448)
Q Consensus       338 ~~~k~~~L~~ll~~~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~  414 (448)
                      +++|...|..+++... .++||||+|++.|+.++..|++.      +||+|++.+|.+++++|++|+.  .|+++|.
T Consensus        10 ~~~~~~~l~~~l~~~~-~~~iif~~~~~~~~~l~~~l~~~------~hg~~~~~~R~~~~~~f~~g~~--~vLVaT~   77 (248)
T d1gkub2          10 NDESISTLSSILEKLG-TGGIIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDYEKFVEGEI--DHLIGTA   77 (248)
T ss_dssp             SCCCTTTTHHHHTTSC-SCEEEEESSHHHHHHHHHTTTTS------SCEEECTTSSSHHHHHHHHTSC--SEEEEEC
T ss_pred             CchHHHHHHHHHHHhC-CCEEEEECCHHHHHHHHHHHHHh------ccCCCCHHHHHHHHHHHHhCCC--eEEEEec
Confidence            4668888999998764 57999999999999999999864      7999999999999999999984  5666664

>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=97.86  E-value=1.8e-06  Score=71.77  Aligned_cols=100  Identities=25%  Similarity=0.429  Sum_probs=64.2

Q ss_pred             ccCCCccccccccccccccchhhhhhhhccCceeeeccCCcccCCCCHHHHHHH-hhccceeEeeccccCCcccccceeE
Q psy1548          42 DLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAI-VDCWRILVATNLFGRGMDIERVNIV  120 (448)
Q Consensus        42 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~d~~~~~~v  120 (448)
                      ++++..+.......................+..+...+.+..... ....++.. .....++|||+++++|+|.++++.|
T Consensus        22 ~ll~~~~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~-r~~~~~~f~~~~~~ilv~T~~~~~Gid~~~v~~V  100 (155)
T d1hv8a2          22 RLLKNKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQ-REKVIRLFKQKKIRILIATDVMSRGIDVNDLNCV  100 (155)
T ss_dssp             HHHCSTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHH-HHHHHHHHHTTSSSEEEECTTHHHHCCCSCCSEE
T ss_pred             HHHccCCCCEEEEECchHHHHHHHhhhcccccccccccccchhhh-hhhhhhhhhcccceeeeehhHHhhhhhhccCcEE
Confidence            455444444455554444334444444444444433333322111 12223333 3335899999999999999999999


Q ss_pred             eeccCCCCchhhhhhhcccccc
Q psy1548         121 FNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus       121 ~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ++|+.|.....|.|.+||+||.
T Consensus       101 i~~d~p~~~~~y~qr~GR~gR~  122 (155)
T d1hv8a2         101 INYHLPQNPESYMHRIGRTGRA  122 (155)
T ss_dssp             EESSCCSCHHHHHHHSTTTCCS
T ss_pred             EEecCCCCHHHHHHHHHhcCcC
Confidence            9999999999999999999984

>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=97.85  E-value=3.6e-05  Score=66.20  Aligned_cols=61  Identities=15%  Similarity=0.109  Sum_probs=55.4

Q ss_pred             CCCeEEEEECccHHHHHHHHHHHhC--CCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         353 EFNQVVIFVKSVTRCIALSTLLSEQ--NFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       353 ~~~~~IIF~~s~~~a~~l~~~L~~~--g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                      .++++.+.||..+..+.++..+++.  ++++..+||.|+++++.+++++|++|+  +.|+++|+-
T Consensus        30 rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g~--~~ILv~Ttv   92 (211)
T d2eyqa5          30 RGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQR--FNVLVCTTI   92 (211)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTS--CCEEEESST
T ss_pred             cCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcCC--cceEEEehh
Confidence            5789999999999999999999884  789999999999999999999999999  578888874

>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=97.80  E-value=6.1e-06  Score=73.91  Aligned_cols=75  Identities=15%  Similarity=0.202  Sum_probs=61.7

Q ss_pred             cchHHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhC-CCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEec
Q psy1548         338 ENEKNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQ-NFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFAS  413 (448)
Q Consensus       338 ~~~k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~-g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t  413 (448)
                      ...|...+.+++...  .+.++||||+.....+.+...|.+. |.++..+||+++.++|.++++.|+++... .+.+++
T Consensus        67 ~S~K~~~l~~~l~~~~~~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~-~vll~~  144 (244)
T d1z5za1          67 RSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSV-KFIVLS  144 (244)
T ss_dssp             TCHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTC-CEEEEE
T ss_pred             hhhHHHHHHHHHHhhcccccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccc-hhcccc
Confidence            346888888888653  5679999999999999999988765 88999999999999999999999987633 344444

>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=97.74  E-value=1.6e-05  Score=64.43  Aligned_cols=85  Identities=19%  Similarity=0.198  Sum_probs=60.6

Q ss_pred             ccccccccccccchhhhhhhhccCceeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeec----c
Q psy1548          49 EENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNY----D  124 (448)
Q Consensus        49 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~----~  124 (448)
                      .....+..+....+.........+......+.+.....+.       .....|+|||++++||+| ++++.|+|+    .
T Consensus        36 ~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~~~~~-------~~~~~vlvaTd~~~~GiD-~~v~~Vi~~~~~~~  107 (138)
T d1jr6a_          36 GRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIP-------TNGDVVVVATDALMTGFT-GDFDSVIDCNTSDG  107 (138)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCSCCCT-------TSSCEEEEESSSSCSSSC-CCBSEEEECSEETT
T ss_pred             CCEEEEeCcHHHHHHHHHHHhccccchhhhhccchhhhhh-------hhhcceeehhHHHHhccc-cccceEEEEEecCC
Confidence            3445666555555555555555566555555554433322       234589999999999999 999999885    4


Q ss_pred             CCCCchhhhhhhccccc
Q psy1548         125 MPEDSDTYLHRVARAGR  141 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~  141 (448)
                      .|..++.|.|++|||||
T Consensus       108 ~P~~~~~y~qr~GR~gR  124 (138)
T d1jr6a_         108 KPQDAVSRTQRRGRTGR  124 (138)
T ss_dssp             EECCHHHHHHHHTTBCS
T ss_pred             CCCCHHHHHhHhccccC
Confidence            69999999999999998

>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=97.66  E-value=3.4e-05  Score=65.43  Aligned_cols=77  Identities=22%  Similarity=0.297  Sum_probs=50.8

Q ss_pred             hhhhhccCceeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCC-----Cchhhhhhhccc
Q psy1548          65 AKQKEVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPE-----DSDTYLHRVARA  139 (448)
Q Consensus        65 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~-----~~~~yQ~~~~~~  139 (448)
                      .......|..+...+.+.+.-....-+.+.-....+|+|||++++||+|.|+++.|++|+.|.     ..+.|-+..|||
T Consensus        48 ~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv~~rGiDip~v~~VI~~d~p~~~~~~s~~~yi~R~GRa  127 (181)
T d1t5la2          48 TDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRA  127 (181)
T ss_dssp             HHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCCCSSSCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGG
T ss_pred             HHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhHHHccCCCCCCCEEEEecCCcccccccHHHHHHHHHhh
Confidence            334444455555555443333222222333334569999999999999999999999999996     355566677777


Q ss_pred             cc
Q psy1548         140 GR  141 (448)
Q Consensus       140 ~~  141 (448)
                      ||
T Consensus       128 gR  129 (181)
T d1t5la2         128 AR  129 (181)
T ss_dssp             TT
T ss_pred             cc
Confidence            77

>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=97.64  E-value=1.5e-05  Score=67.01  Aligned_cols=91  Identities=19%  Similarity=0.248  Sum_probs=62.6

Q ss_pred             cccccccccchhhhhhhhccCceeeeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCCC---
Q psy1548          52 TEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPED---  128 (448)
Q Consensus        52 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~---  128 (448)
                      ..++......+.........|......+.+.+......-+.++.....+|+|+|++++||+|.|+++.|++|..|..   
T Consensus        35 lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v~~~GiDip~V~~Vi~~~~~~~~~~  114 (174)
T d1c4oa2          35 LVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFL  114 (174)
T ss_dssp             EEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTTSCSGG
T ss_pred             EEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEEEEeeeeeeeeccCCCCcEEEEecccccccc
Confidence            33444444344445555566666666666555444434444444555699999999999999999999999996654   


Q ss_pred             --chhhhhhhcccccc
Q psy1548         129 --SDTYLHRVARAGRF  142 (448)
Q Consensus       129 --~~~yQ~~~~~~~~~  142 (448)
                        .+.|-+.+|||||.
T Consensus       115 ~~~~~~iq~~GR~gR~  130 (174)
T d1c4oa2         115 RSERSLIQTIGRAARN  130 (174)
T ss_dssp             GSHHHHHHHHGGGTTS
T ss_pred             chhHHHHHHhhhhhhc
Confidence              36688888999984

>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=97.58  E-value=9.9e-06  Score=68.34  Aligned_cols=46  Identities=50%  Similarity=0.971  Sum_probs=42.8

Q ss_pred             hccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          97 DCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        97 ~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ....++|||+++++|+|.+.+..|++|+.|.....|.+.+||+||.
T Consensus        81 ~~~~ilv~Td~~~~Gid~~~v~~VI~~d~p~~~~~y~qr~GR~gR~  126 (171)
T d1s2ma2          81 GKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRF  126 (171)
T ss_dssp             TSSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCT
T ss_pred             CccccccchhHhhhccccceeEEEEecCCcchHHHHHHHhhhcccC
Confidence            3348999999999999999999999999999999999999999883

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {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: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=97.54  E-value=6.2e-05  Score=71.00  Aligned_cols=146  Identities=15%  Similarity=0.211  Sum_probs=80.5

Q ss_pred             hhhhhhhccccccceeeeeCcceeeeccCCChhHHHHH--HHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccC
Q psy1548         130 DTYLHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFV--LATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYM  207 (448)
Q Consensus       130 ~~yQ~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~--l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  207 (448)
                      .+.|.+      ++..++.++-++|+||.|+|||.+..  +..+.... ...+.++++.+||..-+..+.+.........
T Consensus       150 ~~~Q~~------A~~~al~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~-~~~~~~I~l~ApTgkAA~~L~e~~~~~~~~~  222 (359)
T d1w36d1         150 INWQKV------AAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMA-DGERCRIRLAAPTGKAAARLTESLGKALRQL  222 (359)
T ss_dssp             CCHHHH------HHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTC-SSCCCCEEEEBSSHHHHHHHHHHHTHHHHHS
T ss_pred             ccHHHH------HHHHHHcCCeEEEEcCCCCCceehHHHHHHHHHHHH-hccCCeEEEecCcHHHHHHHHHHHHHHHhhc
Confidence            345999      88888888899999999999997642  22233222 2345689999999988877666554433222


Q ss_pred             CCceEEEEEcCcccHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCC
Q psy1548         208 SNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPH  287 (448)
Q Consensus       208 ~~~~v~~~~g~~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~  287 (448)
                      + ...... ...  ......+    ...+-.+++.  ..+.........++++||||+-++ +    ...+..++..++.
T Consensus       223 ~-~~~~~~-~~~--~~~~~t~----~~ll~~~~~~--~~~~~~~~~~l~~d~lIIDEaSmv-~----~~l~~~ll~~~~~  287 (359)
T d1w36d1         223 P-LTDEQK-KRI--PEDASTL----HRLLGAQPGS--QRLRHHAGNPLHLDVLVVDEASMI-D----LPMMSRLIDALPD  287 (359)
T ss_dssp             S-CCSCCC-CSC--SCCCBTT----TSCC-------------CTTSCCSCSEEEECSGGGC-B----HHHHHHHHHTCCT
T ss_pred             C-chhhhh-hhh--hhhhhHH----HHHHhhhhcc--hHHHHhhhcccccceeeehhhhcc-C----HHHHHHHHHHhcC
Confidence            1 000000 000  0000000    0011111110  112223334556789999999854 2    2345677788888


Q ss_pred             CCeEEEEecc
Q psy1548         288 TKQVMMFSAT  297 (448)
Q Consensus       288 ~~q~i~~SAT  297 (448)
                      ..++|++.=.
T Consensus       288 ~~~lILvGD~  297 (359)
T d1w36d1         288 HARVIFLGDR  297 (359)
T ss_dssp             TCEEEEEECT
T ss_pred             CCEEEEECCh
Confidence            8888887543

>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=97.45  E-value=0.00018  Score=67.33  Aligned_cols=76  Identities=17%  Similarity=0.138  Sum_probs=63.6

Q ss_pred             chHHHHHHHHHhh---CCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecC
Q psy1548         339 NEKNKKLFELLDV---LEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASD  414 (448)
Q Consensus       339 ~~k~~~L~~ll~~---~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~  414 (448)
                      ..|...|..++..   ..+.++|||++.....+.+...|...|+++..+||+++..+|..+++.|+++..+..|.++++
T Consensus       100 S~Kl~~L~~ll~~~~~~~g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~vlLls~  178 (346)
T d1z3ix1         100 SGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSS  178 (346)
T ss_dssp             SHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCCEEEEEG
T ss_pred             CHHHHHHHHHHHHHHHhcCCceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHHHHHHHhhhcccccceeeeecc
Confidence            4588887777754   356799999999999999999999999999999999999999999999999875444444443

>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=97.29  E-value=5.6e-05  Score=63.31  Aligned_cols=44  Identities=95%  Similarity=1.447  Sum_probs=41.7

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhcccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      ..|+|||+++++|+|.+.+..|++|..|.....|.+.+||+||.
T Consensus        78 ~~iLv~T~~~~~Gid~~~~~~vi~~~~p~~~~~yiqr~GR~gR~  121 (168)
T d1t5ia_          78 RRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRF  121 (168)
T ss_dssp             CSEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGG
T ss_pred             ceeeeccccccchhhcccchhhhhhhcccchhhHhhhhhhcccC
Confidence            47999999999999999999999999999999999999999983

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [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: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=96.78  E-value=0.00074  Score=61.41  Aligned_cols=65  Identities=14%  Similarity=0.038  Sum_probs=47.1

Q ss_pred             hhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhc-cCCCeEEEEeeccHHHHHHHHHHHHHhhc
Q psy1548         133 LHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLET-TDSNVYVLVMCHTRELAFQISKEYERFSK  205 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  205 (448)
                      |++      ++..  ...+++|.|+.|||||.+.+--+...+.. .....+++++++|++++..+...+.++..
T Consensus         6 Q~~------av~~--~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~a~~~i~~~~~~~~~   71 (306)
T d1uaaa1           6 QQQ------AVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLG   71 (306)
T ss_dssp             HHH------HHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             HHH------HHhC--CCCCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHHHHHHHHHHHHHhcC
Confidence            888      5543  24568999999999998765444443332 22334799999999999999888877654

>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=96.72  E-value=7.6e-05  Score=64.44  Aligned_cols=74  Identities=18%  Similarity=0.266  Sum_probs=49.8

Q ss_pred             hHHHHHHHHHhh-C-CCCeEEEEECccHHHH--------HHHHHHHhC---CCcEEEEeCCCCHHHHHHHHHHHhcCCCc
Q psy1548         340 EKNKKLFELLDV-L-EFNQVVIFVKSVTRCI--------ALSTLLSEQ---NFPAVSIHRGMTQEERLKKYQEFKDFHKG  406 (448)
Q Consensus       340 ~k~~~L~~ll~~-~-~~~~~IIF~~s~~~a~--------~l~~~L~~~---g~~~~~lh~~~~~~eR~~~l~~F~~g~~g  406 (448)
                      ++.+.+.+.++. . .++++.+.||..+..+        ..++.|.+.   ++++..+||+|++++|.+++++|++|+  
T Consensus        13 ~~~~~v~~~I~~el~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~--   90 (206)
T d1gm5a4          13 DRVNEVYEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGR--   90 (206)
T ss_dssp             STHHHHHHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTS--
T ss_pred             ccHHHHHHHHHHHHHcCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCC--
Confidence            344455555543 2 5668888898765443        344455443   677889999999999999999999999  


Q ss_pred             eEEEEecCh
Q psy1548         407 LAITFASDE  415 (448)
Q Consensus       407 ~~I~~~t~~  415 (448)
                      +.|+++|+-
T Consensus        91 ~~iLVaTtV   99 (206)
T d1gm5a4          91 YDILVSTTV   99 (206)
T ss_dssp             SSBCCCSSC
T ss_pred             EEEEEEehh
Confidence            567777774

>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=96.53  E-value=0.0011  Score=58.87  Aligned_cols=100  Identities=8%  Similarity=0.070  Sum_probs=57.4

Q ss_pred             CCCccccccccCCCccccccccccccccchhhhhhhhccCceeeeccCCcccCCCCHHHHHHH-hhccceeEee----cc
Q psy1548          33 PHSKMADNDDLLDYEDEENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAI-VDCWRILVAT----NL  107 (448)
Q Consensus        33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~----~~  107 (448)
                      .+++.....+++....+....++...............      ..|.+...-.. ..+++.+ .....|+|||    +.
T Consensus        10 ~~~~~~~l~~~l~~~~~~~iif~~~~~~~~~l~~~l~~------~~hg~~~~~~R-~~~~~~f~~g~~~vLVaT~a~~~v   82 (248)
T d1gkub2          10 NDESISTLSSILEKLGTGGIIYARTGEEAEEIYESLKN------KFRIGIVTATK-KGDYEKFVEGEIDHLIGTAHYYGT   82 (248)
T ss_dssp             SCCCTTTTHHHHTTSCSCEEEEESSHHHHHHHHHTTTT------SSCEEECTTSS-SHHHHHHHHTSCSEEEEECC----
T ss_pred             CchHHHHHHHHHHHhCCCEEEEECCHHHHHHHHHHHHH------hccCCCCHHHH-HHHHHHHHhCCCeEEEEeccccch
Confidence            34444444455554445566666555444443333221      12333333333 4445555 4455899999    67


Q ss_pred             ccCCccccc-ceeEeeccCCCCchhhhhhhccccccc
Q psy1548         108 FGRGMDIER-VNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus       108 ~~~~~d~~~-~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      ++||||+|+ ++.|+||+.|+-.   | .+||+||+.
T Consensus        83 ~~rGlDip~~v~~VI~~d~P~~~---~-r~gR~~R~g  115 (248)
T d1gkub2          83 LVRGLDLPERIRFAVFVGCPSFR---V-TIEDIDSLS  115 (248)
T ss_dssp             --CCSCCTTTCCEEEEESCCEEE---E-ECSCGGGSC
T ss_pred             hhhccCccccccEEEEeCCCcch---h-hhhhhhccC
Confidence            899999996 9999999999644   4 578887743

>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=96.50  E-value=0.0011  Score=60.41  Aligned_cols=57  Identities=16%  Similarity=0.159  Sum_probs=43.2

Q ss_pred             CCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecChh
Q psy1548         354 FNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDEN  416 (448)
Q Consensus       354 ~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~~  416 (448)
                      .++++|||++..+++.+++.|++.|.++..+||.+..+++.    .|++++  ..|.++|+..
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~----~~~~~~--~~~~~~t~~~   92 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYP----TIKQKK--PDFILATDIA   92 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC------------CC--CSEEEESSST
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHh----hhhcCC--cCEEEEechh
Confidence            67899999999999999999999999999999999988765    466776  3567777653

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [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: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=96.42  E-value=0.0021  Score=58.77  Aligned_cols=65  Identities=15%  Similarity=0.131  Sum_probs=47.6

Q ss_pred             hhhhccccccceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccC-CCeEEEEeeccHHHHHHHHHHHHHhhc
Q psy1548         133 LHRVARAGRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTD-SNVYVLVMCHTRELAFQISKEYERFSK  205 (448)
Q Consensus       133 Q~~~~~~~~~~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~-~~~~~lil~Pt~~L~~q~~~~~~~~~~  205 (448)
                      |++      ++..  .+..++|.|+.|||||.+.+--+.+.+.... ..-+++++++|+..+..+...+.....
T Consensus        16 Q~~------~v~~--~~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~aa~~~~~~~~~~~~   81 (318)
T d1pjra1          16 QQE------AVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLG   81 (318)
T ss_dssp             HHH------HHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHHG
T ss_pred             HHH------HHhC--CCCCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHHHHHHHHHHHHhhcc
Confidence            888      6653  2467999999999999886655544443322 234799999999999998888776543

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=96.20  E-value=0.012  Score=50.29  Aligned_cols=141  Identities=11%  Similarity=0.069  Sum_probs=70.1

Q ss_pred             ceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEee--ccHHHHHHHHHHHHHhhccCCCceEEEEEcCcc
Q psy1548         143 GTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMC--HTRELAFQISKEYERFSKYMSNIKVGVFFGGLP  220 (448)
Q Consensus       143 ~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~  220 (448)
                      +|.....+=+++.+|||+|||.+..--+.. +...  +.++.+++  ..|.=+.+   +++.++..+ ++.+.......+
T Consensus         4 lp~~~~~~vi~lvGp~GvGKTTTiaKLA~~-~~~~--g~kV~lit~Dt~R~gA~e---QL~~~a~~l-~v~~~~~~~~~~   76 (207)
T d1ls1a2           4 LPVLKDRNLWFLVGLQGSGKTTTAAKLALY-YKGK--GRRPLLVAADTQRPAARE---QLRLLGEKV-GVPVLEVMDGES   76 (207)
T ss_dssp             CCCCCSSEEEEEECCTTTTHHHHHHHHHHH-HHHT--TCCEEEEECCSSCHHHHH---HHHHHHHHH-TCCEEECCTTCC
T ss_pred             CCCCCCCcEEEEECCCCCCHHHHHHHHHHH-HHHC--CCcEEEEecccccchHHH---HHHHHHHhc-CCccccccccch
Confidence            344444434567999999999775443333 2222  22455555  35555544   455555544 565555443332


Q ss_pred             cHHhHHHHhcCCCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCc
Q psy1548         221 IQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSK  300 (448)
Q Consensus       221 ~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~  300 (448)
                      ...-....               ..+.     ...+.+++++|=+=+..........+..+.+..++..-++.++|+...
T Consensus        77 ~~~~~~~~---------------~~~~-----~~~~~d~vlIDTaGr~~~d~~~~~el~~~~~~~~~~~~llv~~a~~~~  136 (207)
T d1ls1a2          77 PESIRRRV---------------EEKA-----RLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQ  136 (207)
T ss_dssp             HHHHHHHH---------------HHHH-----HHHTCCEEEEECCCCSSCCHHHHHHHHHHHHHHCCSEEEEEEEGGGTH
T ss_pred             hhHHHHHH---------------HHHH-----hhccCcceeecccccchhhhhhHHHHHHHHhhcCCceEEEEeccccch
Confidence            22110000               0000     012223344444433222113344555666666666667888888887


Q ss_pred             cHHHHHHHhc
Q psy1548         301 EIRPVCKKFM  310 (448)
Q Consensus       301 ~~~~~~~~~l  310 (448)
                      +..+.+..|.
T Consensus       137 ~~~~~~~~f~  146 (207)
T d1ls1a2         137 EALSVARAFD  146 (207)
T ss_dssp             HHHHHHHHHH
T ss_pred             hHHHHHHHHH
Confidence            7666666543

>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=96.17  E-value=0.00087  Score=60.76  Aligned_cols=43  Identities=30%  Similarity=0.525  Sum_probs=40.2

Q ss_pred             cceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccc
Q psy1548          99 WRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR  141 (448)
Q Consensus        99 ~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~  141 (448)
                      ..|+|||+++++|+|.++++.|++|+.|.....|-|.+||+||
T Consensus       220 ~~vLv~T~~~~~Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR  262 (286)
T d1wp9a2         220 FNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGR  262 (286)
T ss_dssp             CSEEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCS
T ss_pred             CcEEEEccceeccccCCCCCEEEEeCCCCCHHHHHHHHHhCCC
Confidence            4799999999999999999999999999998888888999888

>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=96.08  E-value=0.012  Score=49.77  Aligned_cols=42  Identities=12%  Similarity=0.296  Sum_probs=30.9

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccC
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATL  298 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~  298 (448)
                      ...+++|+||||.|..  .....+.+.+..-|++..+++.|...
T Consensus        78 ~~~KviIId~ad~l~~--~aqNaLLK~LEEPp~~t~fiLit~~~  119 (198)
T d2gnoa2          78 YTRKYVIVHDCERMTQ--QAANAFLKALEEPPEYAVIVLNTRRW  119 (198)
T ss_dssp             SSSEEEEETTGGGBCH--HHHHHTHHHHHSCCTTEEEEEEESCG
T ss_pred             CCCEEEEEeCccccch--hhhhHHHHHHhCCCCCceeeeccCCh
Confidence            4568899999999866  35556666777777777777776554

>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=96.05  E-value=0.036  Score=48.09  Aligned_cols=41  Identities=10%  Similarity=0.277  Sum_probs=27.4

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEecc
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSAT  297 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT  297 (448)
                      ...+++||||+|.|...  ....+...+...+.+..+++.+-.
T Consensus       114 ~~~kviiIde~d~l~~~--~q~~Llk~lE~~~~~~~~il~tn~  154 (239)
T d1njfa_         114 GRFKVYLIDEVHMLSRH--SFNALLKTLEEPPEHVKFLLATTD  154 (239)
T ss_dssp             SSSEEEEEETGGGSCHH--HHHHHHHHHHSCCTTEEEEEEESC
T ss_pred             CCCEEEEEECcccCCHH--HHHHHHHHHhcCCCCeEEEEEcCC
Confidence            45679999999988653  334556666666666666665543

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {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: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.91  E-value=0.0021  Score=56.57  Aligned_cols=41  Identities=10%  Similarity=0.282  Sum_probs=28.4

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEecc
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSAT  297 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT  297 (448)
                      ...+++|+||+|.+..  .....+..++...+.++.+++.+..
T Consensus       130 ~~~~iiiide~d~l~~--~~~~~l~~~~e~~~~~~~~Il~tn~  170 (252)
T d1sxje2         130 HRYKCVIINEANSLTK--DAQAALRRTMEKYSKNIRLIMVCDS  170 (252)
T ss_dssp             -CCEEEEEECTTSSCH--HHHHHHHHHHHHSTTTEEEEEEESC
T ss_pred             CCceEEEecccccccc--ccchhhhcccccccccccceeeecc
Confidence            4467899999998865  3455567777777777766665443

>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=95.90  E-value=0.0022  Score=54.84  Aligned_cols=66  Identities=18%  Similarity=0.230  Sum_probs=48.0

Q ss_pred             eeccCCcccCCCCHHHHHHHhhccceeEeeccccCCcccccceeEeeccCCC-Cchhhhhhhccccc
Q psy1548          76 SIHSSGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPE-DSDTYLHRVARAGR  141 (448)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~-~~~~yQ~~~~~~~~  141 (448)
                      ...|...+.-....-+.+.......|+|||.++++|||.|++..++.++.|. .+..+.|..||+||
T Consensus        68 ~~lHG~m~~~eke~~m~~F~~g~~~iLVaTtViE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR  134 (206)
T d1gm5a4          68 GLMHGRLSQEEKDRVMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGR  134 (206)
T ss_dssp             CCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCC
T ss_pred             EEEeecccHHHHHHHHHHHHCCCEEEEEEehhhhccccccCCcEEEEEccCCccHHHHHhhhhheee
Confidence            3344444444444444444555679999999999999999999998888775 56665666789888

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {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: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=95.87  E-value=0.017  Score=49.30  Aligned_cols=60  Identities=25%  Similarity=0.254  Sum_probs=33.3

Q ss_pred             eeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeecc-HHHHHHHHHHHHHhhccCCCceEEEEEc
Q psy1548         152 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHT-RELAFQISKEYERFSKYMSNIKVGVFFG  217 (448)
Q Consensus       152 vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt-~~L~~q~~~~~~~~~~~~~~~~v~~~~g  217 (448)
                      +++.||||+|||.+..--+. ++... +....|+-+-| |.=+.+   +++.++..+ ++.+.....
T Consensus        12 i~lvGptGvGKTTTiAKLA~-~~~~~-g~kV~lit~Dt~R~gA~e---QL~~~a~~l-~v~~~~~~~   72 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLAR-QFEQQ-GKSVMLAAGDTFRAAAVE---QLQVWGQRN-NIPVIAQHT   72 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHHH-HHHTT-TCCEEEECCCTTCHHHHH---HHHHHHHHT-TCCEECCST
T ss_pred             EEEECCCCCCHHHHHHHHHH-HHHHC-CCcEEEEecccccccchh---hhhhhhhhc-CCccccccc
Confidence            56799999999987654332 33322 22234444444 443433   566666655 666544333

>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=95.85  E-value=0.01  Score=50.90  Aligned_cols=46  Identities=15%  Similarity=0.222  Sum_probs=26.8

Q ss_pred             CCeeEEEecchhHHHhhhhhHHHHHHHHHhC-CCCCeEEEEeccCCc
Q psy1548         255 SLLKHFILDECDKMLEQLEMRRDVQEIFRSS-PHTKQVMMFSATLSK  300 (448)
Q Consensus       255 ~~i~~lViDEah~l~~~~~~~~~~~~i~~~l-~~~~q~i~~SAT~~~  300 (448)
                      ...++++||++|.+.........+-.++..+ ..+.++++.|...|.
T Consensus        96 ~~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~  142 (213)
T d1l8qa2          96 KSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQ  142 (213)
T ss_dssp             HTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGG
T ss_pred             hhccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcch
Confidence            3567899999998865423333344444443 345666665554443

>d1a5ta2 c.37.1.20 (A:1-207) 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=95.48  E-value=0.014  Score=49.78  Aligned_cols=42  Identities=7%  Similarity=0.119  Sum_probs=29.7

Q ss_pred             CCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEecc
Q psy1548         254 LSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSAT  297 (448)
Q Consensus       254 ~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT  297 (448)
                      ....+++|+||+|.|..  .....+.+++...+++..+++.+..
T Consensus       106 ~~~~kviIide~d~l~~--~a~n~Llk~lEep~~~~~fIl~t~~  147 (207)
T d1a5ta2         106 LGGAKVVWVTDAALLTD--AAANALLKTLEEPPAETWFFLATRE  147 (207)
T ss_dssp             TSSCEEEEESCGGGBCH--HHHHHHHHHHTSCCTTEEEEEEESC
T ss_pred             cCccceEEechhhhhhh--hhhHHHHHHHHhhcccceeeeeecC
Confidence            35678999999998876  3455666677776777766665543

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {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: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.45  E-value=0.011  Score=51.00  Aligned_cols=45  Identities=18%  Similarity=0.203  Sum_probs=30.8

Q ss_pred             CCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCc
Q psy1548         254 LSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSK  300 (448)
Q Consensus       254 ~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~  300 (448)
                      ...-+++|+||+|.+...  ....+...+...+....+++.+.....
T Consensus        99 ~~~~kviiiDe~d~~~~~--~~~~ll~~~e~~~~~~~~i~~~~~~~~  143 (224)
T d1sxjb2          99 PGKHKIVILDEADSMTAG--AQQALRRTMELYSNSTRFAFACNQSNK  143 (224)
T ss_dssp             TTCCEEEEEESGGGSCHH--HHHTTHHHHHHTTTTEEEEEEESCGGG
T ss_pred             CcceEEEEEecccccchh--HHHHHhhhccccccceeeeeccCchhh
Confidence            345678999999988774  344455566666777777777666543

>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=95.35  E-value=0.011  Score=50.25  Aligned_cols=94  Identities=7%  Similarity=0.163  Sum_probs=69.5

Q ss_pred             CCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHh---HHHHhcCCCcEEEEcHHHHHHHHHCCCCcCC
Q psy1548         179 SNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKD---EEYLKTHNPQIVVGTPGRILALVRNKKLNLS  255 (448)
Q Consensus       179 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~---~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~  255 (448)
                      .+.++.||||..+-...+.+.++++   +|+.++.+++|..+..+.   ...+.++..+|+|+|.      +-+..++..
T Consensus        30 rGgQvy~V~p~I~~~e~~~~~l~~~---~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Tt------vIEvGiDvp  100 (211)
T d2eyqa5          30 RGGQVYYLYNDVENIQKAAERLAEL---VPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT------IIETGIDIP  100 (211)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHH---CTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS------TTGGGSCCT
T ss_pred             cCCeEEEEEcCccchhhHHHHHHHh---CCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEeh------hhhhccCCC
Confidence            4569999999988777766666665   468899999998876544   3445677899999997      345678899


Q ss_pred             CeeEEEecchhHHHhhhhhHHHHHHHHHhCC
Q psy1548         256 LLKHFILDECDKMLEQLEMRRDVQEIFRSSP  286 (448)
Q Consensus       256 ~i~~lViDEah~l~~~~~~~~~~~~i~~~l~  286 (448)
                      +..++|+..|+++    +. .++.++.....
T Consensus       101 nA~~iiI~~a~rf----GL-aQLhQLRGRVG  126 (211)
T d2eyqa5         101 TANTIIIERADHF----GL-AQLHQLRGRVG  126 (211)
T ss_dssp             TEEEEEETTTTSS----CH-HHHHHHHTTCC
T ss_pred             CCcEEEEecchhc----cc-cccccccceee
Confidence            9999999999965    22 33555554443

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {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: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.32  E-value=0.066  Score=45.86  Aligned_cols=48  Identities=19%  Similarity=0.335  Sum_probs=29.2

Q ss_pred             CeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEeccCCccHHHH
Q psy1548         256 LLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPV  305 (448)
Q Consensus       256 ~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~  305 (448)
                      ..+.+|+||+|.+...  ....+..++...+....++..+.........+
T Consensus       108 ~~~viiiDe~d~l~~~--~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l  155 (237)
T d1sxjd2         108 PYKIIILDEADSMTAD--AQSALRRTMETYSGVTRFCLICNYVTRIIDPL  155 (237)
T ss_dssp             SCEEEEETTGGGSCHH--HHHHHHHHHHHTTTTEEEEEEESCGGGSCHHH
T ss_pred             CceEEEEecccccCHH--HHHHHhhccccccccccccccccccccccccc
Confidence            4568999999988663  34445555666566666665554444333333

>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=95.12  E-value=0.0077  Score=51.26  Aligned_cols=58  Identities=22%  Similarity=0.289  Sum_probs=44.9

Q ss_pred             CCCCHHHHHHHhh---cc--ceeEeeccccCCcccccceeEee-------ccCCCCchhhhhhhcccccc
Q psy1548          85 FLLKPEILRAIVD---CW--RILVATNLFGRGMDIERVNIVFN-------YDMPEDSDTYLHRVARAGRF  142 (448)
Q Consensus        85 ~~~~~~~~~~~~~---~~--~~~~~~~~~~~~~d~~~~~~v~~-------~~~p~~~~~yQ~~~~~~~~~  142 (448)
                      -+++++..+.+.+   .|  +|+|||..+++|+|.+...-|+.       +..|....+|.|.+|||||.
T Consensus       102 ~~l~~~~r~~ie~~f~~g~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~GRAGR~  171 (201)
T d2p6ra4         102 AGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRP  171 (201)
T ss_dssp             TTSCHHHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCT
T ss_pred             HHhhhhhHHHHHHHHhCCCceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHhcccCCC
Confidence            3555554444332   33  89999999999999999888885       66777888999999999993

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon 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: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.11  E-value=0.094  Score=44.82  Aligned_cols=42  Identities=12%  Similarity=0.198  Sum_probs=25.9

Q ss_pred             CCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEecc
Q psy1548         254 LSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSAT  297 (448)
Q Consensus       254 ~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SAT  297 (448)
                      .....++++||+|.+...  ....+..++...+....+++.+..
T Consensus       107 ~~~~~iilide~d~~~~~--~~~~ll~~l~~~~~~~~~i~~~n~  148 (231)
T d1iqpa2         107 GASFKIIFLDEADALTQD--AQQALRRTMEMFSSNVRFILSCNY  148 (231)
T ss_dssp             GCSCEEEEEETGGGSCHH--HHHHHHHHHHHTTTTEEEEEEESC
T ss_pred             CCCceEEeehhhhhcchh--HHHHHhhhcccCCcceEEEeccCC
Confidence            445678999999988663  334455555555555555554433

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=95.06  E-value=0.024  Score=48.24  Aligned_cols=63  Identities=16%  Similarity=0.112  Sum_probs=33.6

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeec-cHHHHHHHHHHHHHhhccCCCceEEEEEc
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH-TRELAFQISKEYERFSKYMSNIKVGVFFG  217 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~P-t~~L~~q~~~~~~~~~~~~~~~~v~~~~g  217 (448)
                      ++-+++.||||+|||.+..--+. ++... +...++|-+- .|.=+.+   +++.++..+ ++.+.....
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~-~~~~~-g~kV~lit~Dt~R~gA~e---QL~~~a~~l-~i~~~~~~~   69 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGR-YYQNL-GKKVMFCAGDTFRAAGGT---QLSEWGKRL-SIPVIQGPE   69 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHH-HHHTT-TCCEEEECCCCSSTTHHH---HHHHHHHHH-TCCEECCCT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH-HHHHC-CCcEEEEEeccccccchh---hHhhccccc-CceEEeccC
Confidence            45567899999999987553332 23322 2223344333 4555555   344444444 555444333

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {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: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.00  E-value=0.048  Score=46.59  Aligned_cols=45  Identities=16%  Similarity=0.297  Sum_probs=28.7

Q ss_pred             CCCcCCCeeEEEecchhHHHhhhhhHHHHHHHHHhCCCCCeEEEEec
Q psy1548         250 KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSA  296 (448)
Q Consensus       250 ~~~~~~~i~~lViDEah~l~~~~~~~~~~~~i~~~l~~~~q~i~~SA  296 (448)
                      ........+.+|+||+|.+...  ....+..++...++...+++.+.
T Consensus        93 ~~~~~~~~kiiiiDe~d~~~~~--~~~~Ll~~le~~~~~~~~~~~~~  137 (227)
T d1sxjc2          93 RQIFSKGFKLIILDEADAMTNA--AQNALRRVIERYTKNTRFCVLAN  137 (227)
T ss_dssp             CCSSSCSCEEEEETTGGGSCHH--HHHHHHHHHHHTTTTEEEEEEES
T ss_pred             ccccCCCeEEEEEeccccchhh--HHHHHHHHhhhcccceeeccccC
Confidence            3344455678999999988664  34455566666666665555443

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {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: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=94.90  E-value=0.036  Score=47.25  Aligned_cols=60  Identities=17%  Similarity=0.131  Sum_probs=32.8

Q ss_pred             ceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeec-cHHHHHHHHHHHHHhhccCCCceEEEEE
Q psy1548         151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH-TRELAFQISKEYERFSKYMSNIKVGVFF  216 (448)
Q Consensus       151 ~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~P-t~~L~~q~~~~~~~~~~~~~~~~v~~~~  216 (448)
                      -++++||||+|||.+..--+. ++.... ....||-+- .|.=+.+   +++.++..+ ++.+....
T Consensus        13 vi~lvGptGvGKTTTiAKLAa-~~~~~~-~kV~lit~Dt~R~gA~e---QL~~~a~~l-~i~~~~~~   73 (213)
T d1vmaa2          13 VIMVVGVNGTGKTTSCGKLAK-MFVDEG-KSVVLAAADTFRAAAIE---QLKIWGERV-GATVISHS   73 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH-HHHHTT-CCEEEEEECTTCHHHHH---HHHHHHHHH-TCEEECCS
T ss_pred             EEEEECCCCCCHHHHHHHHHH-HHHHCC-CceEEEeecccccchhH---HHHHHhhhc-CccccccC
Confidence            356789999999977543332 333222 224455454 4444444   455555554 56554433

>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=94.85  E-value=0.037  Score=45.36  Aligned_cols=77  Identities=19%  Similarity=0.146  Sum_probs=56.2

Q ss_pred             EEcCcchHHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEE
Q psy1548         334 VKLKENEKNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITF  411 (448)
Q Consensus       334 ~~~~~~~k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~  411 (448)
                      ++....+|+.++.+.+...  .+.++||+|.|.+.++.+++.|++.|++...+++....++-.-+-   +.|..| .|++
T Consensus        12 vf~T~~eK~~AIi~eV~~~~~~grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~II~---~Ag~~g-~VtI   87 (175)
T d1tf5a4          12 IYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIE---EAGQKG-AVTI   87 (175)
T ss_dssp             EESSHHHHHHHHHHHHHHHHHHTCCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHHHHT---TTTSTT-CEEE
T ss_pred             EEcCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHHHHH---hccCCC-ceee
Confidence            4456778988888777543  467999999999999999999999999999999886554443333   334433 4444


Q ss_pred             ecC
Q psy1548         412 ASD  414 (448)
Q Consensus       412 ~t~  414 (448)
                      +|.
T Consensus        88 ATN   90 (175)
T d1tf5a4          88 ATN   90 (175)
T ss_dssp             EET
T ss_pred             hhh
Confidence            443

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {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: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=94.45  E-value=0.16  Score=44.09  Aligned_cols=17  Identities=29%  Similarity=0.438  Sum_probs=14.9

Q ss_pred             cceeeeccCCChhHHHH
Q psy1548         150 MDILCQAKSGMGKTAVF  166 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~  166 (448)
                      +.+|+.||.|+|||...
T Consensus        43 ~giLl~GppGtGKT~la   59 (247)
T d1ixza_          43 KGVLLVGPPGVGKTHLA   59 (247)
T ss_dssp             SEEEEECCTTSSHHHHH
T ss_pred             ceEEEecCCCCChhHHH
Confidence            56999999999999764

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=94.34  E-value=0.11  Score=43.99  Aligned_cols=57  Identities=16%  Similarity=0.130  Sum_probs=27.0

Q ss_pred             eeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeec-cHHHHHHHHHHHHHhhccCCCceEEE
Q psy1548         152 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCH-TRELAFQISKEYERFSKYMSNIKVGV  214 (448)
Q Consensus       152 vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~P-t~~L~~q~~~~~~~~~~~~~~~~v~~  214 (448)
                      +++.||||+|||.+..--+. ++.... ...++|-+- .|.=+.+   +++.++..+ ++.+..
T Consensus        15 i~lvGptGvGKTTTiAKLA~-~~~~~g-~kV~lit~Dt~R~ga~e---QL~~~a~~l-~v~~~~   72 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLAY-FYKKKG-FKVGLVGADVYRPAALE---QLQQLGQQI-GVPVYG   72 (211)
T ss_dssp             EEEECSCCC----HHHHHHH-HHHHTT-CCEEEEECCCSSHHHHH---HHHHHHHHH-TCCEEC
T ss_pred             EEEECCCCCCHHHHHHHHHH-HHHHCC-CceEEEEeeccccchhH---HHHHhcccc-Ccceee
Confidence            56789999999977543332 333322 223444443 3444433   455555554 555543

>d1t5la1 c.37.1.19 (A:2-414) 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=94.30  E-value=0.018  Score=54.45  Aligned_cols=66  Identities=27%  Similarity=0.293  Sum_probs=48.7

Q ss_pred             CCCCchhhhhhhccccccceeeee----C-cceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHH
Q psy1548         125 MPEDSDTYLHRVARAGRFGTKAVL----G-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKE  199 (448)
Q Consensus       125 ~p~~~~~yQ~~~~~~~~~~~~~~~----g-~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~  199 (448)
                      .|+.-   |=+      +|..+..    | ++.++.|-||||||++.. .++...     +..+|||+|+..+|.|+++.
T Consensus        11 ~p~gD---QP~------aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA-~l~~~~-----~rp~LVVt~n~~~A~qL~~d   75 (413)
T d1t5la1          11 EPQGD---QPQ------AIAKLVDGLRRGVKHQTLLGATGTGKTFTIS-NVIAQV-----NKPTLVIAHNKTLAGQLYSE   75 (413)
T ss_dssp             CCCTT---HHH------HHHHHHHHHHHTCSEEEEEECTTSCHHHHHH-HHHHHH-----TCCEEEECSSHHHHHHHHHH
T ss_pred             CCCCC---CHH------HHHHHHHHHhcCCCcEEEeCCCCcHHHHHHH-HHHHHh-----CCCEEEEeCCHHHHHHHHHH
Confidence            46666   766      5555554    4 578999999999997643 233332     22589999999999999999


Q ss_pred             HHHhhc
Q psy1548         200 YERFSK  205 (448)
Q Consensus       200 ~~~~~~  205 (448)
                      ++.|..
T Consensus        76 L~~~l~   81 (413)
T d1t5la1          76 LKEFFP   81 (413)
T ss_dssp             HHHHCT
T ss_pred             HHHHcC
Confidence            999874

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

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: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=93.82  E-value=0.028  Score=51.33  Aligned_cols=43  Identities=16%  Similarity=0.373  Sum_probs=30.7

Q ss_pred             eeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHH
Q psy1548         146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTREL  192 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L  192 (448)
                      +..+++++|+||||||||.. +-+++..+.   ...+++.+--+.||
T Consensus       163 v~~~~nili~G~tgSGKTT~-l~al~~~i~---~~~rivtiEd~~El  205 (323)
T d1g6oa_         163 IAIGKNVIVCGGTGSGKTTY-IKSIMEFIP---KEERIISIEDTEEI  205 (323)
T ss_dssp             HHHTCCEEEEESTTSSHHHH-HHHHGGGSC---TTCCEEEEESSCCC
T ss_pred             HHhCCCEEEEeeccccchHH-HHHHhhhcc---cccceeeccchhhh
Confidence            34578999999999999954 445554442   34478888777776

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=93.76  E-value=0.061  Score=42.47  Aligned_cols=87  Identities=24%  Similarity=0.221  Sum_probs=51.1

Q ss_pred             eeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhccCCCceEEEEEcCcccHHhHHHHhcC
Q psy1548         152 ILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTH  231 (448)
Q Consensus       152 vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~  231 (448)
                      -++.||..||||.- ++-.+.+....  +.+++++-|...-         +...   .+  ....|..            
T Consensus         5 ~~i~GpMfsGKTte-Li~~~~~~~~~--~~kv~~ikp~~D~---------R~~~---~i--~s~~g~~------------   55 (139)
T d2b8ta1           5 EFITGPMFAGKTAE-LIRRLHRLEYA--DVKYLVFKPKIDT---------RSIR---NI--QSRTGTS------------   55 (139)
T ss_dssp             EEEECSTTSCHHHH-HHHHHHHHHHT--TCCEEEEEECCCG---------GGCS---SC--CCCCCCS------------
T ss_pred             EEEEccccCHHHHH-HHHHHHHHHHC--CCcEEEEEEcccc---------cccc---eE--EcccCce------------
Confidence            36789999999954 45555544433  3368888888641         1110   11  1111111            


Q ss_pred             CCcEEEEcHHHHHHHHHCCCCcCCCeeEEEecchhHH
Q psy1548         232 NPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM  268 (448)
Q Consensus       232 ~~~IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah~l  268 (448)
                      .+.+.+.+...+...+..... ..+.+++.+||++-+
T Consensus        56 ~~~~~~~~~~~~~~~~~~~~~-~~~~dvI~IDE~QFf   91 (139)
T d2b8ta1          56 LPSVEVESAPEILNYIMSNSF-NDETKVIGIDEVQFF   91 (139)
T ss_dssp             SCCEEESSTHHHHHHHHSTTS-CTTCCEEEECSGGGS
T ss_pred             eeeEEeccchhhHHHHHhhcc-ccCcCEEEechhhhc
Confidence            134666666666666654433 357889999999954

>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=92.59  E-value=0.017  Score=51.54  Aligned_cols=92  Identities=13%  Similarity=0.158  Sum_probs=56.8

Q ss_pred             cccccccccccchhhhhhhhccCceeeeccCCcccCCC----------CHHHHHHHhhccceeEeeccccCC---ccccc
Q psy1548          50 ENTEQIVADGAGDALAKQKEVKGAYVSIHSSGFRDFLL----------KPEILRAIVDCWRILVATNLFGRG---MDIER  116 (448)
Q Consensus        50 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~---~d~~~  116 (448)
                      ........+...+.........|......+.+.+.-..          ...+.........++|+|+...+|   +|.+.
T Consensus        38 k~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~~giDid~  117 (299)
T d1a1va2          38 RHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSLDP  117 (299)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEEEECCCSS
T ss_pred             CEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccCCCCCCCc
Confidence            33455555554555555555555544444433322111          111222233344889999999885   56666


Q ss_pred             ceeEeeccCCCCchhhhhhhccccc
Q psy1548         117 VNIVFNYDMPEDSDTYLHRVARAGR  141 (448)
Q Consensus       117 ~~~v~~~~~p~~~~~yQ~~~~~~~~  141 (448)
                      +..|+++..|..+..|-|.+||+||
T Consensus       118 V~~VI~~d~P~SvesyIQRiGRTGR  142 (299)
T d1a1va2         118 TFTIETTTLPQDAVSRTQRRGRTGR  142 (299)
T ss_dssp             SCEEEEEEEECBHHHHHHHHTTBCS
T ss_pred             ceEEEeCCCCCCHHHHHhhccccCC
Confidence            6789999999999999999999999

>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=92.54  E-value=0.21  Score=41.74  Aligned_cols=77  Identities=18%  Similarity=0.186  Sum_probs=58.6

Q ss_pred             EEcCcchHHHHHHHHHhhC--CCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEE
Q psy1548         334 VKLKENEKNKKLFELLDVL--EFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITF  411 (448)
Q Consensus       334 ~~~~~~~k~~~L~~ll~~~--~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~  411 (448)
                      ++.....|+.++.+-+...  .+.++||-+.|++..+.++..|++.|++..++++.-...|- .++.  +.|..| .|++
T Consensus        12 Vy~T~~~K~~Avv~ei~~~h~~GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~herEA-eIIA--qAG~~G-aVTI   87 (219)
T d1nkta4          12 IYKTEEAKYIAVVDDVAERYAKGQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEA-TIIA--VAGRRG-GVTV   87 (219)
T ss_dssp             EESCHHHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHH-HHHH--TTTSTT-CEEE
T ss_pred             EEcCHHHHHHHHHHHHHHHHhcCCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhHHHHH-HHHH--hcccCC-cEEe
Confidence            4566778988888877654  56799999999999999999999999999999997443332 3343  356655 6666


Q ss_pred             ecC
Q psy1548         412 ASD  414 (448)
Q Consensus       412 ~t~  414 (448)
                      +|.
T Consensus        88 ATN   90 (219)
T d1nkta4          88 ATN   90 (219)
T ss_dssp             EET
T ss_pred             ecc
Confidence            665

>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=92.32  E-value=0.033  Score=46.94  Aligned_cols=53  Identities=21%  Similarity=0.387  Sum_probs=44.6

Q ss_pred             HHHHHhh-ccceeEeeccccCCcccccceeEeeccCCCCchhhhhhhccccccc
Q psy1548          91 ILRAIVD-CWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG  143 (448)
Q Consensus        91 ~~~~~~~-~~~~~~~~~~~~~~~d~~~~~~v~~~~~p~~~~~yQ~~~~~~~~~~  143 (448)
                      +++...+ ...|+|+|++.+.|+|.+.++.|+.+..|.....|-|.+||++|..
T Consensus       130 ~l~~F~~~~~~vLv~~~~~~~Gidl~~~~~vi~~~~~~s~~~~~Q~iGR~~R~~  183 (200)
T d2fwra1         130 ILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPS  183 (200)
T ss_dssp             HHHHHHHSSCSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCC
T ss_pred             HHHHhhcCCeeeeeecchhhcccCCCCCCEEEEeCCCCCHHHHHHHHHhcCCCC
Confidence            4555543 3479999999999999999999999999999888888999988843

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {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: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.07  E-value=0.06  Score=43.70  Aligned_cols=28  Identities=18%  Similarity=0.398  Sum_probs=20.3

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhccC
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETTD  178 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~~  178 (448)
                      |++++.||.|+|||.. +-.++..+....
T Consensus         2 k~v~ItG~~GtGKTtl-~~~i~~~l~~~~   29 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTL-IHKASEVLKSSG   29 (189)
T ss_dssp             CCEEEESCCSSCHHHH-HHHHHHHHHHTT
T ss_pred             cEEEEECCCCCcHHHH-HHHHHHHHHHCC
Confidence            7899999999999974 344555554443

>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=91.37  E-value=0.36  Score=38.55  Aligned_cols=52  Identities=19%  Similarity=0.301  Sum_probs=40.7

Q ss_pred             CCCeeEEEecchhHHHhhhhh--HHHHHHHHHhCCCCCeEEEEeccCCccHHHHH
Q psy1548         254 LSLLKHFILDECDKMLEQLEM--RRDVQEIFRSSPHTKQVMMFSATLSKEIRPVC  306 (448)
Q Consensus       254 ~~~i~~lViDEah~l~~~~~~--~~~~~~i~~~l~~~~q~i~~SAT~~~~~~~~~  306 (448)
                      -...+++|+||+-..+.. ++  ...+..+++..|...-+|+..-.+|+++.+.+
T Consensus        92 ~~~~dllILDEi~~Ai~~-gli~~~~v~~ll~~rp~~~evVlTGr~~p~~L~e~A  145 (157)
T d1g5ta_          92 DPLLDMVVLDELTYMVAY-DYLPLEEVISALNARPGHQTVIITGRGCHRDILDLA  145 (157)
T ss_dssp             CTTCSEEEEETHHHHHHT-TSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHHHC
T ss_pred             cCccCEEeHHHHHHHHHc-CCCCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhc
Confidence            355789999999988776 53  56777888888888888888888888766654

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

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: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.39  E-value=0.94  Score=39.11  Aligned_cols=18  Identities=33%  Similarity=0.368  Sum_probs=15.2

Q ss_pred             CcceeeeccCCChhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~  166 (448)
                      .+.+|+.||.|+|||...
T Consensus        38 ~~giLL~GppGtGKT~l~   55 (258)
T d1e32a2          38 PRGILLYGPPGTGKTLIA   55 (258)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CceeEEecCCCCCchHHH
Confidence            357999999999999753

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=90.33  E-value=0.15  Score=40.25  Aligned_cols=40  Identities=10%  Similarity=0.096  Sum_probs=26.4

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE  191 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~  191 (448)
                      |.=-++.||..||||.- ++-.+.+....  +.+++++-|...
T Consensus         7 G~l~lI~GpMfSGKTte-Li~~~~~~~~~--g~~vl~i~~~~D   46 (141)
T d1xx6a1           7 GWVEVIVGPMYSGKSEE-LIRRIRRAKIA--KQKIQVFKPEID   46 (141)
T ss_dssp             CEEEEEECSTTSSHHHH-HHHHHHHHHHT--TCCEEEEEEC--
T ss_pred             eeEEEEEeccccHHHHH-HHHHHHHhhhc--CCcEEEEEeccc
Confidence            33357789999999954 55555554433  346899999865

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {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: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.68  E-value=0.6  Score=36.07  Aligned_cols=38  Identities=11%  Similarity=0.142  Sum_probs=26.2

Q ss_pred             ceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHH
Q psy1548         151 DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE  191 (448)
Q Consensus       151 ~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~  191 (448)
                      =-++.||..||||.- ++-.+......  +.+++++-|...
T Consensus         4 L~li~GpMfsGKTt~-Li~~~~~~~~~--g~~v~~ikp~~D   41 (133)
T d1xbta1           4 IQVILGPMFSGKSTE-LMRRVRRFQIA--QYKCLVIKYAKD   41 (133)
T ss_dssp             EEEEECCTTSCHHHH-HHHHHHHHHTT--TCCEEEEEETTC
T ss_pred             EEEEEecccCHHHHH-HHHHHHHHHHc--CCcEEEEecccc
Confidence            347889999999954 55555554433  346888888764

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {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: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=89.67  E-value=0.15  Score=48.02  Aligned_cols=49  Identities=8%  Similarity=0.064  Sum_probs=32.6

Q ss_pred             ceeeeeCcceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHH
Q psy1548         143 GTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAF  194 (448)
Q Consensus       143 ~~~~~~g~~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~  194 (448)
                      +|.-...++++|.|+||+|||.+. ..++..+...  +..++|+=|..++..
T Consensus        44 ~~~~~~~~H~~I~G~tGsGKT~~l-~~li~~~~~~--g~~~iiiD~kge~~~   92 (433)
T d1e9ra_          44 MPRDAEPRHLLVNGATGTGKSVLL-RELAYTGLLR--GDRMVIVDPNGDMLS   92 (433)
T ss_dssp             CCGGGGGGCEEEEECTTSSHHHHH-HHHHHHHHHT--TCEEEEEEETTHHHH
T ss_pred             cCCCcccceEEEEeCCCCcHHHHH-HHHHHHHHhC--CCCEEEEeCChhHHH
Confidence            333344579999999999999764 3344433332  346888889887643

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

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: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=89.32  E-value=0.064  Score=51.05  Aligned_cols=18  Identities=33%  Similarity=0.503  Sum_probs=16.2

Q ss_pred             CcceeeeccCCChhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~  166 (448)
                      .+|+|+.||||+|||+.+
T Consensus        49 ksNILliGPTGvGKTlLA   66 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIA   66 (443)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             cccEEEECCCCCCHHHHH
Confidence            579999999999999875

>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=89.25  E-value=0.57  Score=40.80  Aligned_cols=61  Identities=13%  Similarity=0.068  Sum_probs=50.3

Q ss_pred             CCCeEEEEECccHHHHHHHHHHHh----CCCcEEEEeCCCCHHHHHHHHHHHhcCCCceEEEEecCh
Q psy1548         353 EFNQVVIFVKSVTRCIALSTLLSE----QNFPAVSIHRGMTQEERLKKYQEFKDFHKGLAITFASDE  415 (448)
Q Consensus       353 ~~~~~IIF~~s~~~a~~l~~~L~~----~g~~~~~lh~~~~~~eR~~~l~~F~~g~~g~~I~~~t~~  415 (448)
                      .+.++++-++|.--|.+.++.+++    .|+.+..+||+++..+|.+++...++|+  +.|.+.|-.
T Consensus       131 ~g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~--~~iiIGThs  195 (264)
T d1gm5a3         131 AGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQ--IDVVIGTHA  195 (264)
T ss_dssp             HTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSC--CCEEEECTT
T ss_pred             cccceeEEeehHhhhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCC--CCEEEeehH
Confidence            367999999998888877766655    4889999999999999999999999998  355555543

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

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: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=87.72  E-value=0.18  Score=47.12  Aligned_cols=25  Identities=36%  Similarity=0.476  Sum_probs=18.8

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhh
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLE  175 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~  175 (448)
                      .=+|+.||||||||.+ +..++..+.
T Consensus       159 GliLvtGpTGSGKSTT-l~~~l~~~~  183 (401)
T d1p9ra_         159 GIILVTGPTGSGKSTT-LYAGLQELN  183 (401)
T ss_dssp             EEEEEECSTTSCHHHH-HHHHHHHHC
T ss_pred             ceEEEEcCCCCCccHH-HHHHhhhhc
Confidence            3488999999999966 455666654

>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=87.28  E-value=1.5  Score=37.24  Aligned_cols=52  Identities=13%  Similarity=0.065  Sum_probs=47.7

Q ss_pred             CCCeEEEEECccHHHHHHHHHHHh----CCCcEEEEeCCCCHHHHHHHHHHHhcCC
Q psy1548         353 EFNQVVIFVKSVTRCIALSTLLSE----QNFPAVSIHRGMTQEERLKKYQEFKDFH  404 (448)
Q Consensus       353 ~~~~~IIF~~s~~~a~~l~~~L~~----~g~~~~~lh~~~~~~eR~~~l~~F~~g~  404 (448)
                      .+.++++.+++..-+...++.+++    .+.++..+||.++..+|..+.+.+.+|+
T Consensus       103 ~g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~  158 (233)
T d2eyqa3         103 NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGK  158 (233)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTC
T ss_pred             cCCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCC
Confidence            467999999999999999998886    4788999999999999999999999998

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

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: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=86.91  E-value=0.12  Score=46.63  Aligned_cols=18  Identities=33%  Similarity=0.503  Sum_probs=16.0

Q ss_pred             CcceeeeccCCChhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~  166 (448)
                      ++++|+.||||+|||..+
T Consensus        49 ~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            478999999999999765

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {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: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=85.70  E-value=0.19  Score=39.48  Aligned_cols=19  Identities=21%  Similarity=0.258  Sum_probs=16.0

Q ss_pred             CcceeeeccCCChhHHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVFV  167 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~  167 (448)
                      .|++++.||+|+|||..+-
T Consensus         2 ~k~I~l~G~~GsGKSTvak   20 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGR   20 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            3689999999999997653

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

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: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=85.25  E-value=0.49  Score=40.58  Aligned_cols=24  Identities=17%  Similarity=0.163  Sum_probs=17.9

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhh
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQL  174 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l  174 (448)
                      .++++.||+|+|||.+. -.+...+
T Consensus        44 ~~lll~GppGtGKT~l~-~~l~~~l   67 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTL-RKLWELY   67 (276)
T ss_dssp             CEEEEECCTTSSHHHHH-HHHHHHH
T ss_pred             CceEEECCCCCCHHHHH-HHHHHHH
Confidence            57999999999999764 3344444

>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=84.47  E-value=0.61  Score=35.72  Aligned_cols=39  Identities=8%  Similarity=0.066  Sum_probs=34.6

Q ss_pred             CCCCeEEEEECccHHHHHHHHHHHhCCCcEEEEeCCCCH
Q psy1548         352 LEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQ  390 (448)
Q Consensus       352 ~~~~~~IIF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~~  390 (448)
                      ...+++++||.+-.++...+..|++.|+++..+.||+..
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            456789999999999999999999999999999999753

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {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: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=84.30  E-value=6  Score=32.22  Aligned_cols=115  Identities=11%  Similarity=0.055  Sum_probs=61.3

Q ss_pred             cceeeeccCCChhHHHHHHHHHHhhhcc-----CCCeEEEEeeccHHHH------HHHHHHHHHhhccC--CCceEEEEE
Q psy1548         150 MDILCQAKSGMGKTAVFVLATLQQLETT-----DSNVYVLVMCHTRELA------FQISKEYERFSKYM--SNIKVGVFF  216 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~~l~~l~~l~~~-----~~~~~~lil~Pt~~L~------~q~~~~~~~~~~~~--~~~~v~~~~  216 (448)
                      .|+++.||.|.|||...-- +.+.+..+     -.+.+ ++-.-...|+      -++.+.++.+....  ..-.+.++.
T Consensus        44 ~n~lLvG~pGVGKTalv~~-LA~ri~~~~vp~~L~~~~-i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfI  121 (195)
T d1jbka_          44 NNPVLIGEPGVGKTAIVEG-LAQRIINGEVPEGLKGRR-VLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFI  121 (195)
T ss_dssp             CEEEEECCTTSCHHHHHHH-HHHHHHHTCSCGGGTTCE-EEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEE
T ss_pred             CCeEEEecCCcccHHHHHH-HHHHHHhCCCCHHHcCce-EEEeeHHHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEEc
Confidence            5899999999999976432 23333221     12334 4444444443      24444444433221  012334443


Q ss_pred             cCc-------------ccHHh-HHHHhcCCCc-EEEEcHHHHHHHHHCCCCcCCCeeEEEecchh
Q psy1548         217 GGL-------------PIQKD-EEYLKTHNPQ-IVVGTPGRILALVRNKKLNLSLLKHFILDECD  266 (448)
Q Consensus       217 g~~-------------~~~~~-~~~l~~~~~~-IlV~Tp~~l~~~l~~~~~~~~~i~~lViDEah  266 (448)
                      ...             +...- .-.+..+... |.-+||+.+..++..+.--...+..+-++|.+
T Consensus       122 Deih~l~~~g~~~g~~d~~~~Lkp~L~rg~l~~IgatT~eey~~~~e~d~aL~rrF~~I~V~Ep~  186 (195)
T d1jbka_         122 DELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPS  186 (195)
T ss_dssp             ETGGGGTT------CCCCHHHHHHHHHTTSCCEEEEECHHHHHHHTTTCHHHHTTEEEEECCCCC
T ss_pred             chHHHHhcCCCCCCcccHHHHHHHHHhCCCceEEecCCHHHHHHHHHcCHHHHhcCCEeecCCCC
Confidence            321             11111 1123344444 45578888888877766556778889998875

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=83.92  E-value=0.21  Score=40.04  Aligned_cols=18  Identities=39%  Similarity=0.702  Sum_probs=15.8

Q ss_pred             CcceeeeccCCChhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~  166 (448)
                      +.++++.||+|+|||...
T Consensus         5 ~~~I~i~G~~GsGKTT~~   22 (174)
T d1y63a_           5 GINILITGTPGTGKTSMA   22 (174)
T ss_dssp             SCEEEEECSTTSSHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHH
Confidence            568999999999999764

>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), N-terminal 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: Exodeoxyribonuclease V beta chain (RecB), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=83.76  E-value=0.85  Score=42.74  Aligned_cols=54  Identities=20%  Similarity=0.172  Sum_probs=37.8

Q ss_pred             CcceeeeccCCChhHHHHHHHHHHhhhccC---------CCeEEEEeeccHHHHHHHHHHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVFVLATLQQLETTD---------SNVYVLVMCHTRELAFQISKEYER  202 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~~l~~l~~l~~~~---------~~~~~lil~Pt~~L~~q~~~~~~~  202 (448)
                      ...+||.|+.|||||.+..--++..+....         ..-.+|+|+=|+.=|.++.+.+..
T Consensus        16 ~g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~   78 (485)
T d1w36b1          16 QGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRS   78 (485)
T ss_dssp             SSCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHH
T ss_pred             CCCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHH
Confidence            356899999999999886665665553221         113589999998877777666544

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {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: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=83.69  E-value=0.26  Score=42.05  Aligned_cols=17  Identities=29%  Similarity=0.489  Sum_probs=14.7

Q ss_pred             cceeeeccCCChhHHHH
Q psy1548         150 MDILCQAKSGMGKTAVF  166 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~  166 (448)
                      .++|+.||+|+|||.++
T Consensus        36 ~~~L~~GPpGtGKT~lA   52 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLA   52 (238)
T ss_dssp             CCEEEESSTTSSHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            36899999999999765

>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=83.00  E-value=0.45  Score=38.59  Aligned_cols=46  Identities=30%  Similarity=0.346  Sum_probs=35.7

Q ss_pred             hhccceeEeeccccCCcccc---cce-----eEeeccCCCCchhhhhhhccccc
Q psy1548          96 VDCWRILVATNLFGRGMDIE---RVN-----IVFNYDMPEDSDTYLHRVARAGR  141 (448)
Q Consensus        96 ~~~~~~~~~~~~~~~~~d~~---~~~-----~v~~~~~p~~~~~yQ~~~~~~~~  141 (448)
                      ...|.|.||||++|||.|..   .|.     .|+.-..|...+-.+|..||+||
T Consensus        80 g~~g~VtIATNmAGRGtDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gR  133 (175)
T d1tf5a4          80 GQKGAVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGR  133 (175)
T ss_dssp             TSTTCEEEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSG
T ss_pred             cCCCceeehhhHHHcCCCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhh
Confidence            34468999999999998875   222     56766677777777888899998

>d1c4oa1 c.37.1.19 (A:2-409) 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=82.98  E-value=0.58  Score=43.59  Aligned_cols=54  Identities=22%  Similarity=0.280  Sum_probs=39.6

Q ss_pred             eeeCc-ceeeeccCCChhHHHHHHHHHHhhhccCCCeEEEEeeccHHHHHHHHHHHHHhhc
Q psy1548         146 AVLGM-DILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK  205 (448)
Q Consensus       146 ~~~g~-~vli~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  205 (448)
                      +..|. .+.+.|.+||||+++.. .+....     +..+|||+|+...|.++++.+..+..
T Consensus        24 L~~g~~~~~L~GlsgS~ka~~~A-~l~~~~-----~rp~LvVt~~~~~A~~l~~dL~~~l~   78 (408)
T d1c4oa1          24 LRDGERFVTLLGATGTGKTVTMA-KVIEAL-----GRPALVLAPNKILAAQLAAEFRELFP   78 (408)
T ss_dssp             HHTTCSEEEEEECTTSCHHHHHH-HHHHHH-----TCCEEEEESSHHHHHHHHHHHHHHCT
T ss_pred             HhcCCCcEEEecCCCCHHHHHHH-HHHHHh-----CCCEEEEeCCHHHHHHHHHHHHHhcC
Confidence            33454 47889999999996532 222222     12589999999999999999998874

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=82.71  E-value=0.21  Score=40.04  Aligned_cols=19  Identities=26%  Similarity=0.372  Sum_probs=15.9

Q ss_pred             eCcceeeeccCCChhHHHH
Q psy1548         148 LGMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       148 ~g~~vli~apTGsGKT~~~  166 (448)
                      .|+-+++.||+|||||...
T Consensus         3 ~g~iI~l~G~~GsGKSTia   21 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIA   21 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4667889999999999753

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=82.57  E-value=0.23  Score=40.00  Aligned_cols=18  Identities=11%  Similarity=0.191  Sum_probs=15.3

Q ss_pred             CcceeeeccCCChhHHHH
Q psy1548         149 GMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       149 g~~vli~apTGsGKT~~~  166 (448)
                      -|.+++.||+|+|||...
T Consensus         7 ~K~I~i~G~~GsGKTTla   24 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLV   24 (192)
T ss_dssp             CEEEEEECCTTSHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHH
Confidence            367999999999999654

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {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: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=82.49  E-value=0.3  Score=41.61  Aligned_cols=17  Identities=29%  Similarity=0.456  Sum_probs=14.8

Q ss_pred             cceeeeccCCChhHHHH
Q psy1548         150 MDILCQAKSGMGKTAVF  166 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~  166 (448)
                      .++|+.||+|+|||..+
T Consensus        36 ~~~Ll~GPpG~GKTtla   52 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLA   52 (239)
T ss_dssp             CCEEEECCTTSCHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            47899999999999764

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

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: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=81.27  E-value=0.28  Score=45.18  Aligned_cols=17  Identities=35%  Similarity=0.440  Sum_probs=15.3

Q ss_pred             cceeeeccCCChhHHHH
Q psy1548         150 MDILCQAKSGMGKTAVF  166 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~  166 (448)
                      .++|..||||.|||..+
T Consensus        69 ~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             cceeeeCCCCccHHHHH
Confidence            67999999999999765

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {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: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=81.24  E-value=0.28  Score=38.27  Aligned_cols=15  Identities=33%  Similarity=0.355  Sum_probs=12.8

Q ss_pred             eeeeccCCChhHHHH
Q psy1548         152 ILCQAKSGMGKTAVF  166 (448)
Q Consensus       152 vli~apTGsGKT~~~  166 (448)
                      +++.|++|||||..+
T Consensus         5 Iii~G~pGsGKTTla   19 (152)
T d1ly1a_           5 ILTIGCPGSGKSTWA   19 (152)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            678999999999753

>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=81.19  E-value=0.49  Score=35.62  Aligned_cols=38  Identities=21%  Similarity=0.246  Sum_probs=33.2

Q ss_pred             CCCeEEEEECccHHHHHHHHHHHhCCC-cEEEEeCCCCH
Q psy1548         353 EFNQVVIFVKSVTRCIALSTLLSEQNF-PAVSIHRGMTQ  390 (448)
Q Consensus       353 ~~~~~IIF~~s~~~a~~l~~~L~~~g~-~~~~lh~~~~~  390 (448)
                      +..++|+||++-.++...+..|.+.|+ ++..+.||+..
T Consensus        71 ~~~~iv~~C~~G~rs~~a~~~L~~~G~~nv~~l~GG~~~  109 (119)
T d1tq1a_          71 QSDNIIVGCQSGGRSIKATTDLLHAGFTGVKDIVGGYSA  109 (119)
T ss_dssp             TTSSEEEEESSCSHHHHHHHHHHHHHCCSEEEEECCHHH
T ss_pred             CCcEEEEEcCCcCcHHHHHHHHHhcccCCeEEecChHHH
Confidence            356899999999999999999999998 69999999854

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=80.43  E-value=0.31  Score=38.65  Aligned_cols=16  Identities=19%  Similarity=0.362  Sum_probs=13.7

Q ss_pred             ceeeeccCCChhHHHH
Q psy1548         151 DILCQAKSGMGKTAVF  166 (448)
Q Consensus       151 ~vli~apTGsGKT~~~  166 (448)
                      -+++.||+|||||..+
T Consensus         4 lI~i~G~~GsGKTTva   19 (176)
T d2bdta1           4 LYIITGPAGVGKSTTC   19 (176)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999764

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=80.28  E-value=0.41  Score=37.95  Aligned_cols=17  Identities=35%  Similarity=0.491  Sum_probs=14.5

Q ss_pred             cceeeeccCCChhHHHH
Q psy1548         150 MDILCQAKSGMGKTAVF  166 (448)
Q Consensus       150 ~~vli~apTGsGKT~~~  166 (448)
                      .++++.||.|||||...
T Consensus         5 ~~I~i~G~pGsGKTTia   21 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLG   21 (173)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            46889999999999754

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=80.16  E-value=0.25  Score=39.61  Aligned_cols=21  Identities=29%  Similarity=0.359  Sum_probs=17.4

Q ss_pred             eeeCcceeeeccCCChhHHHH
Q psy1548         146 AVLGMDILCQAKSGMGKTAVF  166 (448)
Q Consensus       146 ~~~g~~vli~apTGsGKT~~~  166 (448)
                      ...|.-|++.|++|||||..+
T Consensus         3 ~~~g~~I~l~G~~GsGKTTia   23 (183)
T d1m8pa3           3 ATQGFTIFLTGYMNSGKDAIA   23 (183)
T ss_dssp             TTCCEEEEEECSTTSSHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHH
Confidence            345778899999999999764