Psyllid ID: psy2760

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330---
Protein Sequence
MELHKVTESSIKIYVDHRALIIPRGGLFWDTLYEYDVITILDPGPRIDDLPPVFPDVEKLLEDLNIGGLDELSIHDFNKHLKFWKPKVQLVAGIINLIQLGGENASKFEQGLWESHEVISGDAKEEQEKATVFPSNEEENNVIPQEVDIPILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLLEDLNIGGLDELSIHDFNKHLKFWKPKVQLDDLFDWTMASDATTLEIFTYNKT
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccEEEEEccccccccccccccccccccccccccHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHHHHHccccEEEccccHHHHHHHHHHHHHHccccccccccccccccccHHHHHHHcccccccEEEEccccccccccEEEEEEcccHHHHHccccccEEEEccc
Secondary Structure Prediction (SSPRO)
ccccEEcccEEEEEEcccEEEEcccccccccccHEEEEEEEcccccccccccccccHHHHHHHcccccccccccccccccccEEcccccccccccccEEccccccHHccccHcccccccccccccccccccccccccHHHHHccccccccccccccccccccccEEEEEEccccccccccHcccccccccccccccHHHHHHHHHHHccccEEEEEEccccHHHHHHHHHHHHHHcccEEEEccHHHHHHHHHHHHHHHHHcccEEEEccEEEcccccEEEHHHHHHHHHHHccccHHHHHHcccccccHHHHHHHHHHccccEEEEEEEccc
Coil and Loop (DISEMBL)
MELHKVTESSIKIYVDhraliiprgglfwdtlyeydvitildpgpriddlppvfpDVEKLLEDlniggldelsIHDFNKHLKFWKPKVQLVAGIINLIQLGGENASKFEQGLWESHevisgdakeeqekatvfpsneeennvipqevdipilkisntlpkhvtQTEWAEmldvskpvldfdakvpimahtwpFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSqnhktrtiytspikalsnqkYRDFRETfqdvgliddlppvfpDVEKLLEDlniggldelsIHDFNKHLkfwkpkvqlddlfdwtmasdattleIFTYNKT
Flexible Loop (DISEMBL)
MELHKVTESSIKIYVDHRALIIPRGGLFWDTLYEYDVITILDPGPRIDDLPPVFPDVEKLLEDLNIGGLDELSIHDFNKHLKFWKPKVQLVAGIINLIQLGGENASKFEQGLWESHEVISGDAKEEQEKAtvfpsneeennvipqevdipilKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALsqnhktrtiytspikalsnqkyRDFRETFQDVGLIDDLPPVFPDVEKLLEDLNIGGLDELSIHDFNKHLKFWKPKVQLDDLFDWTmasdattleiftynkt
Low Complexity Region (SEG)
MELHKVTESSIKIYVDHRALIIPRGGLFWDTLYEYDVITILDPGPRIDDLPPVFPDVEKLLEDLNIGGLDELSIHDFNKHLKFWKPKVQLVAGIINLIQLGGENASKFEQGLWESHEVISGDAKEEQEKATVFPSNEEENNVIPQEVDIPILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLLEDLNIGGLDELSIHDFNKHLKFWKPKVQLDDLFDWTMASDATTLEIFTYNKT
Disordered region (IsUnstruct)
*********SIKIYVDHRALIIPRGGLFWDTLYEYDVITILDPGPRIDDLPPVFPDVEKLLEDLNIGGLDELSIHDFNKHLKFWKPKVQLVAGIINLIQLGGENASKFEQGLWE****************************IPQEVDIPILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLLEDLNIGGLDELSIHDFNKHLKFWKPKVQLDDLFDWTMASDATTLEIFTY***
Disordered Region (DISOPRED)
********SSIKIYVDHRALIIPRGGLFWDTLYEYDVITIL********************EDLNIGGLDEL***********************************************************************************************AEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLLEDLNIGGLDELSIHDFNKHLKFWKPKVQLDDLFDWTMASDATTLEIFTYN**
Disordered Region (DISEMBL)
********SSIKIYVDHRALIIPRGGLFWDTLYEYDVITILDPGPRIDDLPPVFPDVEKLLEDLNIGGLDELSIHDFNKHLKFWKPKVQLVAGIINLIQLGGENASKFEQGLWESHEVISGDAKEEQEKATVFPSNEEENNVIPQEVDIPILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLLEDLNIGGLDELSIHDFNKHLKFWKPKVQLDDLFDWTMASDATTLEIFTYNKT
Disordered Region (DISPRO)
**LHKVTESSIKIYVDHRALIIPRGGLFWDTLYEYDVITILDPGPRIDDLPPVFPDVEKLLEDLNIGGLDELSIHDFNKHLKFWKPKVQLVAGIINLIQLGGE****************************************PQEVDIPILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLLEDLNIGGLDELSIHDFNKHLKFWKPKVQLDDLFDWTMASDATTLEIFTYNKT
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MELHKVTESSIKIYVDHRALIIPRGGLFWDTLYEYDVITILDPGPRIDDLPPVFPDVEKLLEDLNIGGLDELSIHDFNKHLKFWKPKVQLVAGIINLIQLGGENASKFEQGLWESHEVISGDAKEEQEKATVFPSNEEENNVIPQEVDIPILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLLEDLNIGGLDELSIHDFNKHLKFWKPKVQLDDLFDWTMASDATTLEIFTYNKT
Positional Conservation
no confident homologs detected

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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	333	2.2.26 [Sep-21-2011]
Q15477	1246	Helicase SKI2W OS=Homo sa	yes	N/A	0.645	0.172	0.385	1e-35
P35207	1287	Antiviral helicase SKI2 O	yes	N/A	0.423	0.109	0.496	2e-32
O59801	1213	Putative ATP-dependent RN	yes	N/A	0.354	0.097	0.576	5e-31
Q23223	1026	mRNA transport homolog 4	no	N/A	0.282	0.091	0.563	2e-23
P42285	1042	Superkiller viralicidic a	no	N/A	0.270	0.086	0.577	3e-22
Q9CZU3	1040	Superkiller viralicidic a	no	N/A	0.255	0.081	0.6	3e-22
O14232	1117	ATP-dependent RNA helicas	no	N/A	0.282	0.084	0.553	2e-21
P47047	1073	ATP-dependent RNA helicas	no	N/A	0.282	0.087	0.563	3e-21
O13799	1030	Uncharacterized helicase	no	N/A	0.282	0.091	0.553	3e-21
B9DFG3	1171	DEAD-box ATP-dependent RN	no	N/A	0.276	0.078	0.438	4e-12

>sp|Q15477|SKIV2_HUMAN Helicase SKI2W OS=Homo sapiens GN=SKIV2L PE=1 SV=3

 Score =  150 bits (380), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 93/241 (38%), Positives = 125/241 (51%), Gaps = 26/241 (10%)

Query: 67  GGLDELSIHDFNKH------LKFWKPKVQLVAGIINLIQLGGENASKFEQGLWESHEVIS 120
           GG+DE +I D N        + F K  + +  G    +    ++      GL     ++ 
Sbjct: 157 GGMDEPTITDLNTREEAEEEIDFEKDLLTIPPGFKKGMDFAPKDCPTPAPGLLSLSCMLE 216

Query: 121 ----GDAKEEQEKATVFPSNEEENNVIPQEVDIPILKISN----------------TLPK 160
               G   E++ +A   P     + V       P+ + S+                  P+
Sbjct: 217 PLDLGGGDEDENEAVGQPGGPRGDTVSASPCSAPLARASSLEDLVLKEASTAVSTPEAPE 276

Query: 161 HVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSA 220
             +Q +WA  +D + PV DF   +P  A  W FE DVFQKQAI+ LE H+ VFV AHTSA
Sbjct: 277 PPSQEQWAIPVDATSPVGDFYRLIPQPAFQWAFEPDVFQKQAILHLERHDSVFVAAHTSA 336

Query: 221 GKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKL 280
           GKTV+AEYAIAL+Q H TRTIYTSPIKALSNQK+RDFR TF DVGL+     + P+   L
Sbjct: 337 GKTVVAEYAIALAQKHMTRTIYTSPIKALSNQKFRDFRNTFGDVGLLTGDVQLHPEASCL 396

Query: 281 L 281
           +
Sbjct: 397 I 397

Helicase; has ATPase activity. Component of the SKI complex which is thought to be involved in exosome-mediated RNA decay and associates with transcriptionally active genes in a manner dependent on PAF1 complex (PAF1C).
Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: -

>sp|P35207|SKI2_YEAST Antiviral helicase SKI2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SKI2 PE=1 SV=2

 Score =  139 bits (351), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 73/147 (49%), Positives = 102/147 (69%), Gaps = 6/147 (4%)

Query: 138 EENNVIPQEVDIPILK-ISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELD 196
           E + ++P  +D    K +S ++P    + EWA ++D++  + +FD  +P  A +WPFELD
Sbjct: 275 EIDELLPIGIDFGRTKPVSKSVP---VKKEWAHVVDLNHKIENFDELIPNPARSWPFELD 331

Query: 197 VFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRD 256
            FQK+A+  LE+ + VFV AHTSAGKTV+AEYAIA++  + T+TIYTSPIKALSNQK+RD
Sbjct: 332 TFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRNMTKTIYTSPIKALSNQKFRD 391

Query: 257 FRETFQDV--GLIDDLPPVFPDVEKLL 281
           F+ETF DV  GLI     + PD   L+
Sbjct: 392 FKETFDDVNIGLITGDVQINPDANCLI 418

RNA helicase component of the SKI complex involved in 3'-mRNA degradation pathway. Represses dsRNA virus propagation by specifically blocking translation of viral mRNAs, perhaps recognizing the absence of CAP or poly(A). Essential for cell growth only in the presence of M1 replicon.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|O59801|SKI2_SCHPO Putative ATP-dependent RNA helicase C550.03c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPCC550.03c PE=3 SV=1

 Score =  135 bits (340), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 68/118 (57%), Positives = 86/118 (72%)

Query: 164 QTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKT 223
           Q ++A ++D S P+ +F   VP MA  +PFELD FQK+AI  LE  + VFV AHTSAGKT
Sbjct: 250 QPDYAHVVDSSAPIENFQQLVPEMALDFPFELDNFQKEAIYHLEMGDSVFVAAHTSAGKT 309

Query: 224 VIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLL 281
           V+AEYAIAL+Q H T+ IYTSPIKALSNQK+RDF+  F+DVG++     V P+   LL
Sbjct: 310 VVAEYAIALAQKHMTKAIYTSPIKALSNQKFRDFKHKFEDVGILTGDVQVNPEGSCLL 367

RNA helicase component of the SKI complex involved in 3'-mRNA degradation pathway.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|Q23223|MTR4_CAEEL mRNA transport homolog 4 OS=Caenorhabditis elegans GN=mtr-4 PE=3 SV=1

 Score =  110 bits (274), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 53/94 (56%), Positives = 66/94 (70%)

Query: 188 AHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIK 247
           A  +PF+LD FQKQAI+ ++ +  V V+AHTSAGKTV+A YAIA     K R IYTSPIK
Sbjct: 119 AKYYPFQLDAFQKQAILCIDNNQSVLVSAHTSAGKTVVATYAIAKCLREKQRVIYTSPIK 178

Query: 248 ALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLL 281
           ALSNQKYR+  E F+DVGL+     + PD   L+
Sbjct: 179 ALSNQKYRELEEEFKDVGLMTGDVTLNPDASCLV 212

Caenorhabditis elegans (taxid: 6239)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|P42285|SK2L2_HUMAN Superkiller viralicidic activity 2-like 2 OS=Homo sapiens GN=SKIV2L2 PE=1 SV=3

 Score =  106 bits (264), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 52/90 (57%), Positives = 64/90 (71%)

Query: 178 LDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHK 237
           L    +V   A  +PF LD FQ++AI  ++ +  V V+AHTSAGKTV AEYAIAL+   K
Sbjct: 123 LPLKPRVGKAAKEYPFILDAFQREAIQCVDNNQSVLVSAHTSAGKTVCAEYAIALALREK 182

Query: 238 TRTIYTSPIKALSNQKYRDFRETFQDVGLI 267
            R I+TSPIKALSNQKYR+  E FQDVGL+
Sbjct: 183 QRVIFTSPIKALSNQKYREMYEEFQDVGLM 212

May be involved in pre-mRNA splicing. Associated with the RNA exosome complex and involved in the 3'processing of the 7S pre-RNA to the mature 5.8S rRNA.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9CZU3|SK2L2_MOUSE Superkiller viralicidic activity 2-like 2 OS=Mus musculus GN=Skiv2l2 PE=2 SV=1

 Score =  106 bits (264), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 51/85 (60%), Positives = 63/85 (74%)

Query: 183 KVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIY 242
           +V   A  +PF LD FQ++AI  ++ +  V V+AHTSAGKTV AEYAIAL+   K R I+
Sbjct: 126 RVGKAAKEYPFILDAFQREAIQCVDNNQSVLVSAHTSAGKTVCAEYAIALALREKQRVIF 185

Query: 243 TSPIKALSNQKYRDFRETFQDVGLI 267
           TSPIKALSNQKYR+  E FQDVGL+
Sbjct: 186 TSPIKALSNQKYREMYEEFQDVGLM 210

May be involved in pre-mRNA splicing. Associated with the RNA exosome complex and involved in the 3'processing of the 7S pre-RNA to the mature 5.8S rRNA.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|O14232|MTR4_SCHPO ATP-dependent RNA helicase mtr4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=mtr4 PE=1 SV=1

 Score =  103 bits (257), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 52/94 (55%), Positives = 62/94 (65%)

Query: 188 AHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIK 247
           A T+PF LD FQ  +I  +E    V V+AHTSAGKTV+AEYA+A S   K R IYTSPIK
Sbjct: 192 ARTYPFTLDPFQAVSIACIERQESVLVSAHTSAGKTVVAEYAVAQSLRDKQRVIYTSPIK 251

Query: 248 ALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLL 281
           ALSNQKYR+    F DVGL+     + PD   L+
Sbjct: 252 ALSNQKYRELLAEFGDVGLMTGDVTINPDATCLV 285

Component of the TRAMP complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. Polyadenylation is required for the degradative activity of the exosome on several of its nuclear RNA substrates (By similarity). Required for heterochromatic gene silencing at centromeric repeats by either exosome- or RNAi-mediated degradation of heterochromatic transcripts.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|P47047|MTR4_YEAST ATP-dependent RNA helicase DOB1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=MTR4 PE=1 SV=1

 Score =  102 bits (255), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 53/94 (56%), Positives = 63/94 (67%)

Query: 188 AHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIK 247
           A T+PF LD FQ  AI  ++    V V+AHTSAGKTV+AEYAIA S  +K R IYTSPIK
Sbjct: 143 ARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIK 202

Query: 248 ALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLL 281
           ALSNQKYR+    F DVGL+     + PD   L+
Sbjct: 203 ALSNQKYRELLAEFGDVGLMTGDITINPDAGCLV 236

ATP-dependent RNA helicase required for the 3'-end formation of 5.8S RNA. Cofactor for the exosome complex that unwinds secondary structure in pre-rRNA. Required for nucleocytoplasmic transport of mRNA. May serve as a chaperone which translocates or normalizes the structure of mRNAs in preparation for export. Component of the TRAMP complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. Polyadenylation is required for the degradative activity of the exosome on several of its nuclear RNA substrates.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|O13799|YE02_SCHPO Uncharacterized helicase C17H9.02 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC17H9.02 PE=1 SV=1

 Score =  102 bits (255), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 52/94 (55%), Positives = 63/94 (67%)

Query: 188 AHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIK 247
           A T+PFELD FQ  AI  +E    V V+AHTSAGKTVIAEYAIA +  ++ R IYTSPIK
Sbjct: 119 AKTYPFELDPFQSTAIKCVERMESVLVSAHTSAGKTVIAEYAIAQALKNRQRVIYTSPIK 178

Query: 248 ALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLL 281
           +LSNQKYR+    F DVGL+     + P    L+
Sbjct: 179 SLSNQKYRELLSEFGDVGLMTGDVSINPSASCLI 212

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|B9DFG3|ISE2_ARATH DEAD-box ATP-dependent RNA helicase ISE2, chloroplastic OS=Arabidopsis thaliana GN=ISE2 PE=1 SV=2

 Score = 72.4 bits (176), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 43/98 (43%), Positives = 59/98 (60%), Gaps = 6/98 (6%)

Query: 172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIA 231
           D    ++D D  + I    + F +D FQ+ AI      + V V+A TS+GKT+IAE A  
Sbjct: 136 DFGVEMIDIDELISI----YDFRIDKFQRLAIEAFLRGSSVVVSAPTSSGKTLIAEAAAV 191

Query: 232 LSQNHKTRTIYTSPIKALSNQKYRDFRETFQD--VGLI 267
            +     R  YT+P+KALSNQK+R+FRETF D  VGL+
Sbjct: 192 STVAKGRRLFYTTPLKALSNQKFREFRETFGDDNVGLL 229

Essential protein required during embryogenesis. Involved in post-transcriptional gene silencing. Modulates the determination of cell fate. Necessary for normal plasmodesmata (PD) development and aperture regulation.

Arabidopsis thaliana (taxid: 3702)

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	333
170034314	1216	antiviral helicase SKI2 [Culex quinquefa	0.351	0.096	0.769	6e-46
270010333	1500	hypothetical protein TcasGA2_TC009717, p	0.528	0.117	0.554	7e-45
312385895	1749	hypothetical protein AND_00228 [Anophele	0.369	0.070	0.691	2e-44
347969420	1223	AGAP003182-PA [Anopheles gambiae str. PE	0.351	0.095	0.743	2e-44
242017221	1184	Helicase, putative [Pediculus humanus co	0.519	0.146	0.573	5e-43
91086489	1177	PREDICTED: similar to antiviral helicase	0.465	0.131	0.590	2e-42
357617976	1252	hypothetical protein KGM_14675 [Danaus p	0.471	0.125	0.569	5e-40
345491941	1153	PREDICTED: helicase SKI2W-like [Nasonia	0.645	0.186	0.403	8e-40
307177450	1136	Helicase SKI2W [Camponotus floridanus]	0.378	0.110	0.629	2e-39
427793717	1160	Putative nuclear exosomal rna helicase m	0.351	0.100	0.683	3e-39

>gi|170034314|ref|XP_001845019.1| antiviral helicase SKI2 [Culex quinquefasciatus] gi|167875652|gb|EDS39035.1| antiviral helicase SKI2 [Culex quinquefasciatus]

 Score =  190 bits (483), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 90/117 (76%), Positives = 101/117 (86%)

Query: 151 ILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHN 210
           +LKI+NT    V   EWAE+LDVSKPV DF  K+P MAH +PFELD+FQKQAIIKLEEHN
Sbjct: 224 VLKIANTGTNGVKTAEWAEILDVSKPVTDFHTKIPEMAHRYPFELDIFQKQAIIKLEEHN 283

Query: 211 HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLI 267
           HVFV AHTSAGKTV+AEYAIALS+ H T+TIYTSPIKALSNQKYRDF+ TF+DVGLI
Sbjct: 284 HVFVAAHTSAGKTVVAEYAIALSKKHMTKTIYTSPIKALSNQKYRDFKSTFEDVGLI 340

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270010333|gb|EFA06781.1| hypothetical protein TcasGA2_TC009717, partial [Tribolium castaneum]

 Score =  187 bits (474), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 102/184 (55%), Positives = 127/184 (69%), Gaps = 8/184 (4%)

Query: 85  KPKVQLVAGIINLIQLGGENASKFEQGLWESHEVISGDAKEEQEKATVFPSNEEENNVIP 144
           K  V++ A ++NL ++  E+ + F  G  E+  +   D   E ++    P  EE   V+P
Sbjct: 157 KESVEVPANVVNLFEIIQEDPNFF--GTLENANIKKPDDISEHKQRETLPEEEE---VLP 211

Query: 145 QEVDIPILKISNTLP-KHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAI 203
              D PILKIS   P      TEWA +LD SKPV DF  ++P MA+ +PFELD FQK AI
Sbjct: 212 N--DPPILKISTVPPPTEFKSTEWAILLDTSKPVKDFKERIPEMAYEFPFELDTFQKLAI 269

Query: 204 IKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD 263
           ++LE+HNHVFV AHTSAGKTV+AEYAIALSQ H TRTIYTSPIKALSNQKYRDF++ F+D
Sbjct: 270 LQLEQHNHVFVAAHTSAGKTVVAEYAIALSQKHMTRTIYTSPIKALSNQKYRDFKKEFKD 329

Query: 264 VGLI 267
           VGLI
Sbjct: 330 VGLI 333

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312385895|gb|EFR30287.1| hypothetical protein AND_00228 [Anopheles darlingi]

 Score =  185 bits (470), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 85/123 (69%), Positives = 102/123 (82%)

Query: 145 QEVDIPILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAII 204
           Q    P+L IS     ++   EWAE+LD+SKPV DF  K+P+MAH +PFELD+FQKQAI+
Sbjct: 701 QHRTAPVLNISANSGNNLQSAEWAEILDISKPVDDFYVKIPVMAHRFPFELDIFQKQAIL 760

Query: 205 KLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDV 264
           KLEEH+HVFV AHTSAGKTV+AEYAIALS+ H T++IYTSPIKALSNQKYRDF+ TFQDV
Sbjct: 761 KLEEHSHVFVAAHTSAGKTVVAEYAIALSKKHLTKSIYTSPIKALSNQKYRDFKTTFQDV 820

Query: 265 GLI 267
           GL+
Sbjct: 821 GLM 823

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347969420|ref|XP_312880.4| AGAP003182-PA [Anopheles gambiae str. PEST] gi|333468516|gb|EAA08476.4| AGAP003182-PA [Anopheles gambiae str. PEST]

 Score =  185 bits (470), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 87/117 (74%), Positives = 99/117 (84%)

Query: 151 ILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHN 210
           +LKIS      +   EWAEMLD+SKPV DF  K+P MAH +PFELD+FQKQAI+KLEEH+
Sbjct: 236 VLKISTVTNNALQSAEWAEMLDISKPVDDFYVKIPTMAHRFPFELDIFQKQAILKLEEHS 295

Query: 211 HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLI 267
           HVFV AHTSAGKTV+AEYAIALS+ H T+TIYTSPIKALSNQKYRDF+ TFQDVGLI
Sbjct: 296 HVFVAAHTSAGKTVVAEYAIALSKKHMTKTIYTSPIKALSNQKYRDFKTTFQDVGLI 352

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242017221|ref|XP_002429090.1| Helicase, putative [Pediculus humanus corporis] gi|212513954|gb|EEB16352.1| Helicase, putative [Pediculus humanus corporis]

 Score =  181 bits (458), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 105/183 (57%), Positives = 127/183 (69%), Gaps = 10/183 (5%)

Query: 92  AGIINLIQL--GGENASKFEQGLWESHEVISGDAKEEQEKATVFPSNEEENNV--IPQEV 147
           +  INL+ L  GG++  +       S E+ + + K E +  T   S EE + +  IP EV
Sbjct: 132 SNFINLVDLLKGGQHLLEVTNS---SFELENEEDKHENKNDTEEISVEESDVISSIPNEV 188

Query: 148 --DIPILKISNTLP-KHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAII 204
               P++++S+  P K VT TEWAE++DVS PV DF  K+P MA  + FELD FQKQAI+
Sbjct: 189 AFKAPVIRLSDVTPLKGVTSTEWAEVIDVSLPVTDFYEKIPDMAFKYNFELDTFQKQAIL 248

Query: 205 KLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDV 264
           KLEEH  V V AHTSAGKTVIAEYAIALSQ H TRTIYTSPIKALSNQKYRDFR TF+DV
Sbjct: 249 KLEEHCSVLVAAHTSAGKTVIAEYAIALSQRHMTRTIYTSPIKALSNQKYRDFRNTFKDV 308

Query: 265 GLI 267
           GLI
Sbjct: 309 GLI 311

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91086489|ref|XP_970674.1| PREDICTED: similar to antiviral helicase SKI2 [Tribolium castaneum]

 Score =  179 bits (454), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 95/161 (59%), Positives = 113/161 (70%), Gaps = 6/161 (3%)

Query: 108 FEQGLWESHEVISGDAKEEQEKATVFPSNEEENNVIPQEVDIPILKISNTLP-KHVTQTE 166
            + G  E+  +   D   E ++    P  EE   V+P   D PILKIS   P      TE
Sbjct: 156 LDTGTLENANIKKPDDISEHKQRETLPEEEE---VLPN--DPPILKISTVPPPTEFKSTE 210

Query: 167 WAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIA 226
           WA +LD SKPV DF  ++P MA+ +PFELD FQK AI++LE+HNHVFV AHTSAGKTV+A
Sbjct: 211 WAILLDTSKPVKDFKERIPEMAYEFPFELDTFQKLAILQLEQHNHVFVAAHTSAGKTVVA 270

Query: 227 EYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLI 267
           EYAIALSQ H TRTIYTSPIKALSNQKYRDF++ F+DVGLI
Sbjct: 271 EYAIALSQKHMTRTIYTSPIKALSNQKYRDFKKEFKDVGLI 311

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357617976|gb|EHJ71092.1| hypothetical protein KGM_14675 [Danaus plexippus]

 Score =  171 bits (433), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 94/165 (56%), Positives = 118/165 (71%), Gaps = 8/165 (4%)

Query: 111 GLWESHEVISGDAKEEQEKATVFPSNEEEN----NVI--PQEV-DIPILKISNTLPK-HV 162
           GLW+  E    +  +  +K  +    EE+N     +I  P E+ +IPIL I+N+  K  V
Sbjct: 215 GLWKDDENEKNEVSKPIKKIQIEKDKEEDNFLESTIIRPPVELPEIPILNITNSAVKLGV 274

Query: 163 TQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGK 222
           T TEWAEM+DVS PV DF  K+  MAH++PFELD FQKQAI+KLEE +HVFV AHTSAGK
Sbjct: 275 TSTEWAEMIDVSLPVPDFKEKIKDMAHSYPFELDSFQKQAILKLEEGHHVFVAAHTSAGK 334

Query: 223 TVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLI 267
           TV+AEYAIA+S+ + TR IYTSPIKALSNQKY DF + F +VGL+
Sbjct: 335 TVVAEYAIAMSRRNCTRAIYTSPIKALSNQKYNDFNKMFGEVGLL 379

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345491941|ref|XP_001599855.2| PREDICTED: helicase SKI2W-like [Nasonia vitripennis]

 Score =  170 bits (431), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 109/270 (40%), Positives = 154/270 (57%), Gaps = 55/270 (20%)

Query: 51  PPVFPDVEKLLEDLNIGGLDELSIHDFNKHLKFWKPKVQLVAGI-INLIQLG-------- 101
           PP+ PD+   L++  I   ++L+IH  +K  ++W+ K ++++ +  NL  LG        
Sbjct: 20  PPILPDIRTELKEY-IVNPEKLAIHQVDKVQQYWERKPKILSLLEANLTPLGTTLKYERD 78

Query: 102 ------GENASKFEQGLWES--------------HEVISGDAK---------EEQEKATV 132
                 GE      Q + E+               E + G+A          +E +K + 
Sbjct: 79  PITGHIGEIQEVLMQNIGETVRNSMSMARAPGPISEGVKGNASNFLFWPGGFDEPQKTSK 138

Query: 133 FPSNEE--ENNV-------------IPQEVDIPILKISNTLPKHVTQTEWAEMLDVSKPV 177
             + +   ENN+             +P+E  +P+ KIS   PK+  +T+WAE +D+  PV
Sbjct: 139 RETIQVDFENNLKTLAKGFSAGIEFMPEESKVPVFKISEA-PKYNMKTKWAEQIDIMIPV 197

Query: 178 LDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHK 237
            DFD K+P  A T+P+ELD FQKQAI+KLEE   VFV AHTSAGKT IAEYAIA+SQ H 
Sbjct: 198 NDFDKKIPDPAMTFPYELDTFQKQAILKLEEQCDVFVAAHTSAGKTTIAEYAIAMSQKHM 257

Query: 238 TRTIYTSPIKALSNQKYRDFRETFQDVGLI 267
           TRTIYTSPIKALSNQK+R+F+E F++VGLI
Sbjct: 258 TRTIYTSPIKALSNQKFREFKEKFENVGLI 287

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307177450|gb|EFN66577.1| Helicase SKI2W [Camponotus floridanus]

 Score =  169 bits (427), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 80/127 (62%), Positives = 103/127 (81%), Gaps = 1/127 (0%)

Query: 141 NVIPQEVDIPILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQK 200
           +++P+E +IP+LKIS   P+ V +TEWAE LDVS P+ DFD ++P  A  + +ELD FQK
Sbjct: 154 SILPEETNIPVLKISEKQPEFV-KTEWAEQLDVSAPITDFDKRIPDPAIKFEYELDTFQK 212

Query: 201 QAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRET 260
           QAI+KLE++++VFV AHTSAGKT +AEYAIALSQ H TR IYTSPIKALSNQKYR+F+  
Sbjct: 213 QAILKLEQNSNVFVAAHTSAGKTTVAEYAIALSQKHMTRVIYTSPIKALSNQKYREFKRK 272

Query: 261 FQDVGLI 267
           F+ VGL+
Sbjct: 273 FESVGLL 279

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|427793717|gb|JAA62310.1| Putative nuclear exosomal rna helicase mtr4 dead-box superfamily, partial [Rhipicephalus pulchellus]

 Score =  168 bits (425), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 80/117 (68%), Positives = 92/117 (78%)

Query: 151 ILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHN 210
           +LKISN         EWAE +D+SKP+LDF  KVP  A +WPFELD FQK+AI  LE  +
Sbjct: 228 VLKISNVTNDRSVCLEWAEQVDISKPMLDFHEKVPDPAFSWPFELDTFQKKAIAHLENRD 287

Query: 211 HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLI 267
            VFV AHTSAGKTV+AEYAIALS+ H TRTIYTSPIKALSN+KYRDF+ETF D+GLI
Sbjct: 288 SVFVAAHTSAGKTVVAEYAIALSRRHMTRTIYTSPIKALSNEKYRDFKETFTDIGLI 344

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

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	333
FB|FBgn0039117	1197	tst "twister" [Drosophila mela	0.459	0.127	0.543	3.1e-37
UNIPROTKB|E2RSD6	1246	SKIV2L "Uncharacterized protei	0.369	0.098	0.626	1.8e-36
RGD|1303059	1241	Skiv2l "superkiller viralicidi	0.603	0.161	0.446	4.6e-36
UNIPROTKB|F1RQW4	1246	SKIV2L "Uncharacterized protei	0.369	0.098	0.626	6.1e-36
UNIPROTKB|E1BMS0	1246	LOC100139548 "Uncharacterized	0.369	0.098	0.617	2.1e-35
UNIPROTKB|F1LP39	1206	Skiv2l "Protein Skiv2l" [Rattu	0.567	0.156	0.453	2.3e-35
ZFIN|ZDB-GENE-010430-5	1249	skiv2l "superkiller viralicidi	0.306	0.081	0.696	5.5e-35
UNIPROTKB|Q15477	1246	SKIV2L "Helicase SKI2W" [Homo	0.369	0.098	0.601	7.1e-35
UNIPROTKB|F8VNU1	1088	SKIV2L "Helicase SKI2W" [Homo	0.369	0.113	0.601	2.4e-34
UNIPROTKB|B4DM01	1088	SKIV2L "cDNA FLJ57529, highly	0.369	0.113	0.601	3e-34

FB|FBgn0039117 tst "twister" [Drosophila melanogaster (taxid:7227)]

 Score = 412 (150.1 bits), Expect = 3.1e-37, P = 3.1e-37
 Identities = 87/160 (54%), Positives = 115/160 (71%)

Query:   112 LWESHEVIS-GDAKEEQEKATVFPSNE---EENNVIPQEVDIPILKISNTLPKHVTQTEW 167
             L  S E  S G  K  ++     PS E    +++++  ++  P+L IS T      +++W
Sbjct:   179 LTRSEETSSTGTPKSPKQSNVQLPSEEFRDVDDHIMKADLK-PVLNISTTTKNF--KSDW 235

Query:   168 AEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAE 227
             AEM+D+S+P+ +F  ++P  A  +PFELDVFQKQAI+KLE+  +VFV AHTSAGKTV+AE
Sbjct:   236 AEMVDISQPINNFKEQIPCPAMDFPFELDVFQKQAILKLEQRQYVFVAAHTSAGKTVVAE 295

Query:   228 YAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLI 267
             YAIALS+   TRTIYTSPIKALSNQKYRDFR+TF+DVGLI
Sbjct:   296 YAIALSKRDLTRTIYTSPIKALSNQKYRDFRKTFKDVGLI 335

GO:0004386 "helicase activity" evidence=ISS

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|E2RSD6 SKIV2L "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 381 (139.2 bits), Expect = 1.8e-36, Sum P(2) = 1.8e-36
 Identities = 77/123 (62%), Positives = 90/123 (73%)

Query:   159 PKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHT 218
             PK V Q +WA  +DV+ PV DF   +P  A  W FE DVFQKQAI+ LE H+ VFV AHT
Sbjct:   275 PKPVPQEQWAIPVDVTSPVGDFYRLIPQPAFQWSFEPDVFQKQAILHLERHDSVFVAAHT 334

Query:   219 SAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVE 278
             SAGKTV+AEYAIAL+Q H TRTIYTSPIKALSNQK+RDFR TF DVGL+     + P+  
Sbjct:   335 SAGKTVVAEYAIALAQKHMTRTIYTSPIKALSNQKFRDFRNTFGDVGLLTGDVQLHPEAS 394

Query:   279 KLL 281
              L+
Sbjct:   395 CLI 397

GO:0055087 "Ski complex" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

RGD|1303059 Skiv2l "superkiller viralicidic activity 2-like (S. cerevisiae )" [Rattus norvegicus (taxid:10116)]

 Score = 386 (140.9 bits), Expect = 4.6e-36, Sum P(2) = 4.6e-36
 Identities = 92/206 (44%), Positives = 122/206 (59%)

Query:    77 FNKHLKFWKPKVQLVAGIINLIQLGGE-NASKFEQGLWESHEVISGDAKEEQEKATVFPS 135
             F K + F  PK   V G+++L +L    + S  ++G  E+     GDA      +T    
Sbjct:   190 FKKGVDF-APKAP-VPGLLSLSRLLEPLDLSGGDEGEGEAAGGPRGDAASASPSSTPLIR 247

Query:   136 NEEENNVIPQEVDIPILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFEL 195
                  +++ +E    +  +    P    Q +WA  +DV+ PV DF   +P  A  W FE 
Sbjct:   248 ASSLEDLVLKEASTVVSTLEPLKPP--PQEQWAVPVDVTSPVGDFYRLIPQPAFQWAFEP 305

Query:   196 DVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYR 255
             DVFQKQAI+ LE+H+ VFV AHTSAGKTV+AEYAIAL+Q H TRTIYTSPIKALSNQK+R
Sbjct:   306 DVFQKQAILHLEQHDSVFVAAHTSAGKTVVAEYAIALAQKHMTRTIYTSPIKALSNQKFR 365

Query:   256 DFRETFQDVGLIDDLPPVFPDVEKLL 281
             DFR TF DVGL+     + P+   L+
Sbjct:   366 DFRNTFGDVGLLTGDVQLHPEASCLI 391

GO:0055087 "Ski complex" evidence=ISO

UNIPROTKB|F1RQW4 SKIV2L "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 378 (138.1 bits), Expect = 6.1e-36, Sum P(2) = 6.1e-36
 Identities = 77/123 (62%), Positives = 89/123 (72%)

Query:   159 PKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHT 218
             PK   Q EWA  +DV+ PV DF   +P  A  W FE DVFQKQAI+ LE H+ VFV AHT
Sbjct:   275 PKPPPQEEWAIPVDVTSPVGDFYRLIPQPAFQWAFEPDVFQKQAILHLERHDSVFVAAHT 334

Query:   219 SAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVE 278
             SAGKTV+AEYAIAL+Q H TRTIYTSPIKALSNQK+RDFR TF DVGL+     + P+  
Sbjct:   335 SAGKTVVAEYAIALAQKHMTRTIYTSPIKALSNQKFRDFRNTFGDVGLLTGDVQLHPEAS 394

Query:   279 KLL 281
              L+
Sbjct:   395 CLI 397

GO:0055087 "Ski complex" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|E1BMS0 LOC100139548 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 375 (137.1 bits), Expect = 2.1e-35, Sum P(2) = 2.1e-35
 Identities = 76/123 (61%), Positives = 89/123 (72%)

Query:   159 PKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHT 218
             PK   Q +WA  +DV+ PV DF   +P  A  W FE DVFQKQAI+ LE H+ VFV AHT
Sbjct:   275 PKPPPQEQWAIPVDVTSPVGDFYRLIPQPAFQWAFEPDVFQKQAILHLERHDSVFVAAHT 334

Query:   219 SAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVE 278
             SAGKTV+AEYAIAL+Q H TRTIYTSPIKALSNQK+RDFR TF DVGL+     + P+  
Sbjct:   335 SAGKTVVAEYAIALAQKHMTRTIYTSPIKALSNQKFRDFRNTFGDVGLLTGDVQLHPEAS 394

Query:   279 KLL 281
              L+
Sbjct:   395 CLI 397

GO:0055087 "Ski complex" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1LP39 Skiv2l "Protein Skiv2l" [Rattus norvegicus (taxid:10116)]

 Score = 379 (138.5 bits), Expect = 2.3e-35, Sum P(2) = 2.3e-35
 Identities = 87/192 (45%), Positives = 116/192 (60%)

Query:    91 VAGIINLIQLGGE-NASKFEQGLWESHEVISGDAKEEQEKATVFPSNEEENNVIPQEVDI 149
             V G+++L +L    + S  ++G  E+     GDA      +T         +++ +E   
Sbjct:   167 VPGLLSLSRLLEPLDLSGGDEGEGEAAGGPRGDAASASPSSTPLIRASSLEDLVLKEAST 226

Query:   150 PILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEH 209
              +  +    P    Q +WA  +DV+ PV DF   +P  A  W FE DVFQKQAI+ LE+H
Sbjct:   227 VVSTLEPLKPP--PQEQWAVPVDVTSPVGDFYRLIPQPAFQWAFEPDVFQKQAILHLEQH 284

Query:   210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDD 269
             + VFV AHTSAGKTV+AEYAIAL+Q H TRTIYTSPIKALSNQK+RDFR TF DVGL+  
Sbjct:   285 DSVFVAAHTSAGKTVVAEYAIALAQKHMTRTIYTSPIKALSNQKFRDFRNTFGDVGLLTG 344

Query:   270 LPPVFPDVEKLL 281
                + P+   L+
Sbjct:   345 DVQLHPEASCLI 356

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

ZFIN|ZDB-GENE-010430-5 skiv2l "superkiller viralicidic activity 2 (S. cerevisiae homolog)-like" [Danio rerio (taxid:7955)]

 Score = 372 (136.0 bits), Expect = 5.5e-35, Sum P(2) = 5.5e-35
 Identities = 71/102 (69%), Positives = 84/102 (82%)

Query:   166 EWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVI 225
             +WA  +D+S P  DF  ++P  A  +PFELDVFQKQAI++LE H+ VFV AHTSAGKTV+
Sbjct:   290 KWAIPVDISSPCADFYKRIPDPAFKYPFELDVFQKQAILRLEAHDSVFVAAHTSAGKTVV 349

Query:   226 AEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLI 267
             AEYAIALSQ H TRTIYTSPIKALSNQK+RDF+ TF DVGL+
Sbjct:   350 AEYAIALSQKHMTRTIYTSPIKALSNQKFRDFKNTFGDVGLL 391

GO:0016817 "hydrolase activity, acting on acid anhydrides" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0016818 "hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

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

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|Q15477 SKIV2L "Helicase SKI2W" [Homo sapiens (taxid:9606)]

 Score = 369 (135.0 bits), Expect = 7.1e-35, Sum P(2) = 7.1e-35
 Identities = 74/123 (60%), Positives = 89/123 (72%)

Query:   159 PKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHT 218
             P+  +Q +WA  +D + PV DF   +P  A  W FE DVFQKQAI+ LE H+ VFV AHT
Sbjct:   275 PEPPSQEQWAIPVDATSPVGDFYRLIPQPAFQWAFEPDVFQKQAILHLERHDSVFVAAHT 334

Query:   219 SAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVE 278
             SAGKTV+AEYAIAL+Q H TRTIYTSPIKALSNQK+RDFR TF DVGL+     + P+  
Sbjct:   335 SAGKTVVAEYAIALAQKHMTRTIYTSPIKALSNQKFRDFRNTFGDVGLLTGDVQLHPEAS 394

Query:   279 KLL 281
              L+
Sbjct:   395 CLI 397

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0055087 "Ski complex" evidence=IDA

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

UNIPROTKB|F8VNU1 SKIV2L "Helicase SKI2W" [Homo sapiens (taxid:9606)]

 Score = 369 (135.0 bits), Expect = 2.4e-34, Sum P(2) = 2.4e-34
 Identities = 74/123 (60%), Positives = 89/123 (72%)

Query:   159 PKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHT 218
             P+  +Q +WA  +D + PV DF   +P  A  W FE DVFQKQAI+ LE H+ VFV AHT
Sbjct:   117 PEPPSQEQWAIPVDATSPVGDFYRLIPQPAFQWAFEPDVFQKQAILHLERHDSVFVAAHT 176

Query:   219 SAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVE 278
             SAGKTV+AEYAIAL+Q H TRTIYTSPIKALSNQK+RDFR TF DVGL+     + P+  
Sbjct:   177 SAGKTVVAEYAIALAQKHMTRTIYTSPIKALSNQKFRDFRNTFGDVGLLTGDVQLHPEAS 236

Query:   279 KLL 281
              L+
Sbjct:   237 CLI 239

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|B4DM01 SKIV2L "cDNA FLJ57529, highly similar to Helicase SKI2W (EC 3.6.1.-)" [Homo sapiens (taxid:9606)]

 Score = 369 (135.0 bits), Expect = 3.0e-34, Sum P(2) = 3.0e-34
 Identities = 74/123 (60%), Positives = 89/123 (72%)

Query:   159 PKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHT 218
             P+  +Q +WA  +D + PV DF   +P  A  W FE DVFQKQAI+ LE H+ VFV AHT
Sbjct:   117 PEPPSQEQWAIPVDATSPVGDFYRLIPQPAFQWAFEPDVFQKQAILHLERHDSVFVAAHT 176

Query:   219 SAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVE 278
             SAGKTV+AEYAIAL+Q H TRTIYTSPIKALSNQK+RDFR TF DVGL+     + P+  
Sbjct:   177 SAGKTVVAEYAIALAQKHMTRTIYTSPIKALSNQKFRDFRNTFGDVGLLTGDVQLHPEAS 236

Query:   279 KLL 281
              L+
Sbjct:   237 CLI 239

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

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	333
COG4581	1041	COG4581, COG4581, Superfamily II RNA helicase [DNA	6e-32
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	7e-10
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	1e-07
COG1202	830	COG1202, COG1202, Superfamily II helicase, archaea	4e-07
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	1e-06
PRK01172	674	PRK01172, PRK01172, ski2-like helicase; Provisiona	1e-05
COG1205	851	COG1205, COG1205, Distinct helicase family with a	3e-05
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	3e-04
pfam04851	100	pfam04851, ResIII, Type III restriction enzyme, re	7e-04
TIGR04121	803	TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA	0.002
PRK00254	720	PRK00254, PRK00254, ski2-like helicase; Provisiona	0.003

>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication, recombination, and repair]

 Score =  125 bits (317), Expect = 6e-32
 Identities = 51/89 (57%), Positives = 58/89 (65%), Gaps = 4/89 (4%)

Query: 180 FDAKVPI----MAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN 235
            DA+ P      A  +PFELD FQ++AI  LE    V V A TS+GKTV+AEYAIAL+  
Sbjct: 101 PDAESPFDLAPPAREYPFELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALR 160

Query: 236 HKTRTIYTSPIKALSNQKYRDFRETFQDV 264
              R IYTSPIKALSNQKYRD    F DV
Sbjct: 161 DGQRVIYTSPIKALSNQKYRDLLAKFGDV 189

Length = 1041

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

 Score = 56.9 bits (138), Expect = 7e-10
 Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 3/71 (4%)

Query: 199 QKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIA---LSQNHKTRTIYTSPIKALSNQKYR 255
           Q QAI  +     V V A T +GKT+     I    L +    + +  +P + L+ Q Y 
Sbjct: 4   QAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQIYE 63

Query: 256 DFRETFQDVGL 266
           + ++ F+ +GL
Sbjct: 64  ELKKLFKILGL 74

Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Length = 169

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

 Score = 51.0 bits (122), Expect = 1e-07
 Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 3/79 (3%)

Query: 192 PFELDVFQKQAI-IKLEEHNHVFVTAHTSAGKTVIAEYAI--ALSQNHKTRTIYTSPIKA 248
              L  +QK+AI   L     V + A T +GKT+ A      AL +    R +   P + 
Sbjct: 6   FEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRE 65

Query: 249 LSNQKYRDFRETFQDVGLI 267
           L+ Q   + ++    +GL 
Sbjct: 66  LAEQWAEELKKLGPSLGLK 84

Length = 201

>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific [General function prediction only]

 Score = 51.3 bits (123), Expect = 4e-07
 Identities = 25/62 (40%), Positives = 39/62 (62%), Gaps = 2/62 (3%)

Query: 206 LEEHNHVFVTAHTSAGKTVIAEYA-IALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDV 264
           LE  N + V+A T++GKT+I E A I    +   + ++  P+ AL+NQKY DF+E +  +
Sbjct: 230 LEGENLLVVSA-TASGKTLIGELAGIPRLLSGGKKMLFLVPLVALANQKYEDFKERYSKL 288

Query: 265 GL 266
           GL
Sbjct: 289 GL 290

Length = 830

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

 Score = 49.7 bits (119), Expect = 1e-06
 Identities = 21/55 (38%), Positives = 32/55 (58%), Gaps = 3/55 (5%)

Query: 206 LEEHNHVFVTAHTSAGKTVIAEYAIALS--QNHKTRTIYTSPIKALSNQKYRDFR 258
           L    +V ++A T +GKT+IA  AI LS       + +Y  P+KAL+ +KY +F 
Sbjct: 44  LLSDENVLISAPTGSGKTLIALLAI-LSTLLEGGGKVVYIVPLKALAEEKYEEFS 97

Length = 766

>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional

 Score = 46.4 bits (110), Expect = 1e-05
 Identities = 24/65 (36%), Positives = 40/65 (61%)

Query: 193 FELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQ 252
           FEL   Q+ AI +L +  +V V+  T+AGKT+IA  AI  +     ++IY  P+++L+ +
Sbjct: 21  FELYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLAGLKSIYIVPLRSLAME 80

Query: 253 KYRDF 257
           KY + 
Sbjct: 81  KYEEL 85

Length = 674

>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 = 45.5 bits (108), Expect = 3e-05
 Identities = 20/70 (28%), Positives = 30/70 (42%), Gaps = 2/70 (2%)

Query: 198 FQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAI--ALSQNHKTRTIYTSPIKALSNQKYR 255
            Q  A+  + E  +V VT  T +GKT      I   L ++   R +   P  AL+N +  
Sbjct: 74  HQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNALANDQAE 133

Query: 256 DFRETFQDVG 265
             RE   D+ 
Sbjct: 134 RLRELISDLP 143

Length = 851

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

 Score = 40.0 bits (94), Expect = 3e-04
 Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 5/82 (6%)

Query: 210 NHVFVTAHTSAGKTVIAEYAI--ALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ---DV 264
             V + A T +GKT+ A   I   L      + +  +P + L+NQ     +E F     V
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKV 60

Query: 265 GLIDDLPPVFPDVEKLLEDLNI 286
           G +     +    + L    +I
Sbjct: 61  GYLIGGTSIKQQEKLLSGKTDI 82

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

>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit

 Score = 38.0 bits (89), Expect = 7e-04
 Identities = 17/54 (31%), Positives = 26/54 (48%)

Query: 199 QKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQ 252
           Q++AI +L E     +   T +GKT+ A   IA     K + ++  P K L  Q
Sbjct: 8   QEEAIERLLEKKRGLIVMATGSGKTLTAAALIARLAKGKKKVLFVVPRKDLLEQ 61

Length = 100

>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA ligase-associated

 Score = 39.5 bits (93), Expect = 0.002
 Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 6/75 (8%)

Query: 198 FQKQAIIKLEEHNHVFVTAHTSAGKT------VIAEYAIALSQNHKTRTIYTSPIKALSN 251
           FQ +      E     + A T +GKT       + + A          T+Y +P++AL+ 
Sbjct: 17  FQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEKPKKGLHTLYITPLRALAV 76

Query: 252 QKYRDFRETFQDVGL 266
              R+ +   +++GL
Sbjct: 77  DIARNLQAPIEELGL 91

Members of this protein family are DEAD/DEAH box helicases found associated with a bacterial ATP-dependent DNA ligase, part of a four-gene system that occurs in about 12 % of prokaryotic reference genomes. The actual motif in this family is DE[VILW]H. Length = 803

>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional

 Score = 39.0 bits (91), Expect = 0.003
 Identities = 19/52 (36%), Positives = 35/52 (67%), Gaps = 6/52 (11%)

Query: 218 TSAGKTVIAEYAIA---LSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGL 266
           T++GKT++AE  +    L +  K   +Y  P+KAL+ +KYR+F++ ++ +GL
Sbjct: 48  TASGKTLVAEIVMVNKLLREGGKA--VYLVPLKALAEEKYREFKD-WEKLGL 96

Length = 720

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	333
KOG0947|consensus	1248		99.93
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.87
KOG0948|consensus	1041		99.85
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.81
PRK10689	1147	transcription-repair coupling factor; Provisional	99.79
PRK02362	737	ski2-like helicase; Provisional	99.79
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.76
COG1204	766	Superfamily II helicase [General function predicti	99.72
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.72
PRK00254	720	ski2-like helicase; Provisional	99.71
PRK01172	674	ski2-like helicase; Provisional	99.71
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.71
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.71
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.69
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.69
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.69
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.69
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.69
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.69
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.68
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.67
PTZ00110	545	helicase; Provisional	99.67
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.67
KOG0952|consensus	1230		99.66
PTZ00424	401	helicase 45; Provisional	99.66
PRK13767	876	ATP-dependent helicase; Provisional	99.65
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.62
KOG0338|consensus	691		99.62
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.61
PRK05580	679	primosome assembly protein PriA; Validated	99.6
KOG0331|consensus	519		99.58
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.58
KOG0330|consensus	476		99.57
KOG0345|consensus	567		99.56
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.55
KOG0348|consensus	708		99.55
COG1202	830	Superfamily II helicase, archaea-specific [General	99.54
KOG0347|consensus	731		99.54
COG1205	851	Distinct helicase family with a unique C-terminal	99.54
KOG0343|consensus	758		99.51
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.5
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.49
PRK09401	1176	reverse gyrase; Reviewed	99.48
KOG0342|consensus	543		99.47
KOG0340|consensus	442		99.46
PHA02558	501	uvsW UvsW helicase; Provisional	99.45
KOG0350|consensus	620		99.44
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.44
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.43
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.42
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.41
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.4
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.4
PRK14701	1638	reverse gyrase; Provisional	99.4
KOG0335|consensus	482		99.37
KOG0346|consensus	569		99.36
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.36
KOG0333|consensus	673		99.33
KOG0334|consensus	997		99.31
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.27
PRK13766	773	Hef nuclease; Provisional	99.26
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.25
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.24
KOG0354|consensus	746		99.23
KOG0336|consensus	629		99.14
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.13
KOG0337|consensus	529		99.12
KOG0344|consensus	593		99.12
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.11
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.1
KOG0953|consensus	700		99.09
KOG0339|consensus	731		99.08
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.06
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.06
PHA02653	675	RNA helicase NPH-II; Provisional	99.05
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.03
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.0
KOG0951|consensus	1674		98.98
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	98.97
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	98.97
KOG0341|consensus	610		98.96
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	98.96
PRK09694	878	helicase Cas3; Provisional	98.95
KOG0326|consensus	459		98.94
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	98.92
KOG4284|consensus	980		98.9
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	98.86
PRK14873	665	primosome assembly protein PriA; Provisional	98.86
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	98.85
KOG0328|consensus	400		98.77
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.76
KOG0949|consensus	1330		98.76
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	98.75
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	98.75
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	98.7
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.68
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	98.66
KOG0352|consensus	641		98.65
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.63
KOG0951|consensus	1674		98.62
KOG0332|consensus	477		98.61
KOG0327|consensus	397		98.56
KOG0950|consensus	1008		98.52
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	98.41
KOG0329|consensus	387		98.41
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	98.4
KOG0351|consensus	941		98.39
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	98.38
PRK12904	830	preprotein translocase subunit SecA; Reviewed	98.36
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	98.33
COG4096	875	HsdR Type I site-specific restriction-modification	98.33
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	98.28
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.2
PRK04914	956	ATP-dependent helicase HepA; Validated	98.18
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	98.18
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	98.06
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.05
KOG0353|consensus	695		98.05
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.05
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.03
PRK13107	908	preprotein translocase subunit SecA; Reviewed	98.03
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.02
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.0
KOG0952|consensus	1230		97.97
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	97.94
PF13245	76	AAA_19: Part of AAA domain	97.94
PRK12326	764	preprotein translocase subunit SecA; Reviewed	97.8
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.68
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	97.57
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	97.57
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	97.53
COG4889	1518	Predicted helicase [General function prediction on	97.42
TIGR00376	637	DNA helicase, putative. The gene product may repre	97.36
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.25
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.15
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	97.1
KOG1123|consensus	776		97.09
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	97.06
KOG1803|consensus	649		97.03
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	96.84
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	96.72
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	96.62
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	96.56
KOG0920|consensus	924		96.49
CHL00122	870	secA preprotein translocase subunit SecA; Validate	96.44
PRK11054	684	helD DNA helicase IV; Provisional	96.39
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	96.37
KOG0387|consensus	923		96.34
PRK10875	615	recD exonuclease V subunit alpha; Provisional	96.28
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	96.26
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	96.17
PRK06526	254	transposase; Provisional	96.17
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	96.15
KOG1802|consensus	935		96.15
PRK15483	986	type III restriction-modification system StyLTI en	96.11
PRK05298	652	excinuclease ABC subunit B; Provisional	96.06
PHA02533	534	17 large terminase protein; Provisional	95.97
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	95.76
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	95.72
KOG0926|consensus	1172		95.59
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	95.55
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	95.5
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	95.48
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	95.47
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	95.47
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	95.45
smart00382	148	AAA ATPases associated with a variety of cellular	95.43
PRK13833	323	conjugal transfer protein TrbB; Provisional	95.42
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	95.36
PRK10536	262	hypothetical protein; Provisional	95.35
KOG0349|consensus	725		95.25
PRK08727	233	hypothetical protein; Validated	95.25
PRK08181	269	transposase; Validated	95.24
KOG0922|consensus	674		95.23
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	95.23
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	95.14
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	95.06
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	95.02
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	94.86
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	94.85
PRK13851	344	type IV secretion system protein VirB11; Provision	94.75
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	94.62
KOG0390|consensus	776		94.61
PRK09183	259	transposase/IS protein; Provisional	94.57
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	94.45
PRK04328	249	hypothetical protein; Provisional	94.44
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	94.43
KOG1000|consensus	689		94.4
PF12846	304	AAA_10: AAA-like domain	94.34
COG0610	962	Type I site-specific restriction-modification syst	94.31
PRK05973	237	replicative DNA helicase; Provisional	94.25
KOG1132|consensus	945		94.21
COG1484	254	DnaC DNA replication protein [DNA replication, rec	94.11
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	94.03
KOG1133|consensus	821		94.02
KOG4439|consensus	901		93.96
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	93.93
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	93.89
PRK08533	230	flagellar accessory protein FlaH; Reviewed	93.85
TIGR02237	209	recomb_radB DNA repair and recombination protein R	93.7
PRK13889	988	conjugal transfer relaxase TraA; Provisional	93.64
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	93.58
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	93.55
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	93.53
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	93.53
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	93.47
PRK06835	329	DNA replication protein DnaC; Validated	93.42
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	93.34
COG4626	546	Phage terminase-like protein, large subunit [Gener	93.3
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	93.26
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	93.25
PRK07952	244	DNA replication protein DnaC; Validated	93.25
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	93.19
KOG4150|consensus	1034		93.17
TIGR00064	272	ftsY signal recognition particle-docking protein F	93.13
KOG0389|consensus	941		93.1
PRK04296	190	thymidine kinase; Provisional	93.09
KOG0924|consensus	1042		92.96
cd00983	325	recA RecA is a bacterial enzyme which has roles in	92.95
PRK10436	462	hypothetical protein; Provisional	92.94
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	92.85
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	92.67
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	92.64
PRK09354	349	recA recombinase A; Provisional	92.6
PRK08116	268	hypothetical protein; Validated	92.56
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	92.56
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	92.5
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	92.47
cd01394	218	radB RadB. The archaeal protein radB shares simila	92.41
PRK06067	234	flagellar accessory protein FlaH; Validated	92.39
PRK12377	248	putative replication protein; Provisional	92.38
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	92.13
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	92.07
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	92.04
TIGR02533	486	type_II_gspE general secretory pathway protein E.	92.01
PRK06921	266	hypothetical protein; Provisional	91.88
KOG1131|consensus	755		91.84
KOG0923|consensus	902		91.82
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	91.81
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	91.79
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	91.76
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	91.69
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	91.69
cd03115	173	SRP The signal recognition particle (SRP) mediates	91.67
PRK08084	235	DNA replication initiation factor; Provisional	91.65
COG3973	747	Superfamily I DNA and RNA helicases [General funct	91.65
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	91.63
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	91.59
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	91.59
KOG1002|consensus	791		91.55
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	91.54
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	91.52
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	91.48
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	91.44
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	91.41
PRK13826	1102	Dtr system oriT relaxase; Provisional	91.33
PRK10416	318	signal recognition particle-docking protein FtsY;	91.31
PRK10867	433	signal recognition particle protein; Provisional	91.28
PRK00771	437	signal recognition particle protein Srp54; Provisi	91.27
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	91.11
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	91.1
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	91.08
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	91.04
PRK08903	227	DnaA regulatory inactivator Hda; Validated	90.98
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	90.83
KOG0385|consensus	971		90.71
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	90.59
PRK05642	234	DNA replication initiation factor; Validated	90.46
TIGR00959	428	ffh signal recognition particle protein. This mode	90.35
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	90.3
PRK08939	306	primosomal protein DnaI; Reviewed	90.21
KOG0925|consensus	699		90.18
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	90.16
PRK06893	229	DNA replication initiation factor; Validated	89.96
COG1221	403	PspF Transcriptional regulators containing an AAA-	89.94
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	89.93
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	89.93
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	89.77
PRK09302	509	circadian clock protein KaiC; Reviewed	89.32
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	89.32
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	89.28
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	89.2
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	89.14
PRK14974	336	cell division protein FtsY; Provisional	89.06
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	89.06
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	88.94
COG0593	408	DnaA ATPase involved in DNA replication initiation	88.79
TIGR02746	797	TraC-F-type type-IV secretion system protein TraC.	88.71
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	88.4
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	88.35
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	88.33
PRK13764	602	ATPase; Provisional	88.24
PRK09302	509	circadian clock protein KaiC; Reviewed	88.18
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	88.11
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	88.03
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	88.02
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	87.82
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	87.81
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	87.74
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	87.72
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	87.71
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	87.55
PRK13897	606	type IV secretion system component VirD4; Provisio	87.55
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	87.42
PRK00149	450	dnaA chromosomal replication initiation protein; R	87.41
PRK11823	446	DNA repair protein RadA; Provisional	87.38
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	87.16
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	87.08
PRK12422	445	chromosomal replication initiation protein; Provis	87.07
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	86.96
PRK04195	482	replication factor C large subunit; Provisional	86.8
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	86.64
PRK10865	857	protein disaggregation chaperone; Provisional	86.47
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	86.39
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	86.21
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	86.17
TIGR03744	893	traC_PFL_4706 conjugative transfer ATPase, PFL_470	86.07
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	86.05
KOG2028|consensus	554		85.98
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	85.97
PRK11608	326	pspF phage shock protein operon transcriptional ac	85.95
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	85.74
PRK05541	176	adenylylsulfate kinase; Provisional	85.56
PF13555	62	AAA_29: P-loop containing region of AAA domain	85.48
PRK13880	636	conjugal transfer coupling protein TraG; Provision	85.45
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	85.32
COG2256	436	MGS1 ATPase related to the helicase subunit of the	85.31
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	85.31
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	85.3
TIGR03783	829	Bac_Flav_CT_G Bacteroides conjugation system ATPas	85.25
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	85.24
COG3451	796	VirB4 Type IV secretory pathway, VirB4 components	85.22
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	85.22
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	85.16
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	85.11
PF05729	166	NACHT: NACHT domain	85.0
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	84.98
PRK13700	732	conjugal transfer protein TraD; Provisional	84.93
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	84.8
PLN02165	334	adenylate isopentenyltransferase	84.78
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	84.67
PF00004	132	AAA: ATPase family associated with various cellula	84.5
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	84.44
PRK13876	663	conjugal transfer coupling protein TraG; Provision	84.26
PRK14729	300	miaA tRNA delta(2)-isopentenylpyrophosphate transf	84.25
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	84.22
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	84.17
TIGR02236	310	recomb_radA DNA repair and recombination protein R	83.98
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	83.98
PRK13850	670	type IV secretion system protein VirD4; Provisiona	83.87
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	83.83
PRK09519	790	recA DNA recombination protein RecA; Reviewed	83.82
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	83.8
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	83.76
PF00154	322	RecA: recA bacterial DNA recombination protein; In	83.75
PRK00131	175	aroK shikimate kinase; Reviewed	83.52
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	83.44
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	83.33
TIGR00929	785	VirB4_CagE type IV secretion/conjugal transfer ATP	83.29
PRK12402	337	replication factor C small subunit 2; Reviewed	83.25
PRK05022	509	anaerobic nitric oxide reductase transcription reg	83.24
PRK13721	844	conjugal transfer ATP-binding protein TraC; Provis	83.21
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	83.07
PRK13873	811	conjugal transfer ATPase TrbE; Provisional	83.06
KOG1805|consensus	1100		83.02
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	82.83
COG3587	985	Restriction endonuclease [Defense mechanisms]	82.74
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	82.58
PRK00889	175	adenylylsulfate kinase; Provisional	82.58
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	82.53
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	82.5
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	82.26
KOG1806|consensus	1320		82.1
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	81.96
PRK00300	205	gmk guanylate kinase; Provisional	81.96
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	81.83
PRK13891	852	conjugal transfer protein TrbE; Provisional	81.81
TIGR00767	415	rho transcription termination factor Rho. Members	81.79
PHA02244	383	ATPase-like protein	81.76
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	81.74
COG0606	490	Predicted ATPase with chaperone activity [Posttran	81.66
PRK13822	641	conjugal transfer coupling protein TraG; Provision	81.65
PRK13768	253	GTPase; Provisional	81.62
PRK04301	317	radA DNA repair and recombination protein RadA; Va	81.59
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	81.57
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	81.49
PRK08506	472	replicative DNA helicase; Provisional	81.41
PHA00350	399	putative assembly protein	81.4
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	81.36
PRK14087	450	dnaA chromosomal replication initiation protein; P	81.32
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	81.31
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	81.23
COG3972	660	Superfamily I DNA and RNA helicases [General funct	81.11
PHA00729	226	NTP-binding motif containing protein	81.07
CHL00095	821	clpC Clp protease ATP binding subunit	81.02
KOG0060|consensus	659		81.0
PF09439	181	SRPRB: Signal recognition particle receptor beta s	80.97
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	80.95
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	80.86
KOG0745|consensus	564		80.56
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	80.54
cd03114	148	ArgK-like The function of this protein family is u	80.5
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	80.4
PRK00091	307	miaA tRNA delta(2)-isopentenylpyrophosphate transf	80.39
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	80.37
PRK07261	171	topology modulation protein; Provisional	80.36
PRK08118	167	topology modulation protein; Reviewed	80.35
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	80.34
CHL00181	287	cbbX CbbX; Provisional	80.21

>KOG0947|consensus

Probab=99.93  E-value=7.4e-26  Score=236.33  Aligned_cols=164  Identities=46%  Similarity=0.615  Sum_probs=150.8

Q ss_pred             CCCCCcccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCC
Q psy2760         159 PKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKT  238 (333)
Q Consensus       159 ~~~~~~~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~  238 (333)
                      .......+|+...+++..+.+|.+-.+..+..|||+++++|++||-++.+|.+|+|.|+|++|||+++.+||..+..+++
T Consensus       262 ~t~~~k~~wa~~vd~~~~~~df~~lVpe~a~~~pFelD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq~h~T  341 (1248)
T KOG0947|consen  262 STRPVKFEWAHVVDLSSLVEDFYQLVPEMALIYPFELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQKHMT  341 (1248)
T ss_pred             cCCCccccceeeeecccchHHHHHhchhHHhhCCCCccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHHhhcc
Confidence            33335679999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEEEcccHHHHHHHHHHHHHhcCCcEEEeCCCCCCCCcceEEecc---------------CcceEeccccccccccCcC
Q psy2760         239 RTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLLEDL---------------NIGGLDELSIHDFNKHLKF  303 (333)
Q Consensus       239 ral~l~PtraLa~Q~~~~l~~~f~~vglltGd~~~~~~a~ili~t~---------------~i~liViDe~H~~~~~~R~  303 (333)
                      |++|.+|.+||.+|.+++|++.|+++|++|||.++++.+.|+|+|+               ++..+|.||.||+++..||
T Consensus       342 R~iYTSPIKALSNQKfRDFk~tF~DvgLlTGDvqinPeAsCLIMTTEILRsMLYrgadliRDvE~VIFDEVHYiND~eRG  421 (1248)
T KOG0947|consen  342 RTIYTSPIKALSNQKFRDFKETFGDVGLLTGDVQINPEASCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYINDVERG  421 (1248)
T ss_pred             ceEecchhhhhccchHHHHHHhccccceeecceeeCCCcceEeehHHHHHHHHhcccchhhccceEEEeeeeeccccccc
Confidence            9999999999999999999999999999999999999999999987               6788999999999999999


Q ss_pred             cccccchhh---hhhheeccCc
Q psy2760         304 WKPKVQLDD---LFDWTMASDA  322 (333)
Q Consensus       304 ~~~~~~l~~---l~~l~~~~d~  322 (333)
                      ..|+.-++=   -++++|.|++
T Consensus       422 vVWEEViIMlP~HV~~IlLSAT  443 (1248)
T KOG0947|consen  422 VVWEEVIIMLPRHVNFILLSAT  443 (1248)
T ss_pred             ccceeeeeeccccceEEEEecc
Confidence            999854443   3778887764

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

Probab=99.87  E-value=1.4e-22  Score=217.35  Aligned_cols=137  Identities=42%  Similarity=0.501  Sum_probs=126.7

Q ss_pred             cccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCc-
Q psy2760         186 IMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDV-  264 (333)
Q Consensus       186 ~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~v-  264 (333)
                      .....+||.++++|++|+..+.+|.+|+||||||||||+++.+||..++..|.|++|.+|.+||.+|++++|..+|+++ 
T Consensus       111 ~~~~~~~F~LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~~qrviYTsPIKALsNQKyrdl~~~fgdv~  190 (1041)
T COG4581         111 PPAREYPFELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRDGQRVIYTSPIKALSNQKYRDLLAKFGDVA  190 (1041)
T ss_pred             cHHHhCCCCcCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHcCCceEeccchhhhhhhHHHHHHHHhhhhh
Confidence            3566789999999999999999999999999999999999999999999999999999999999999999999999976 


Q ss_pred             ---EEEeCCCCCCCCcceEEecc---------------CcceEeccccccccccCcCcccccchhhh---hhheeccCc
Q psy2760         265 ---GLIDDLPPVFPDVEKLLEDL---------------NIGGLDELSIHDFNKHLKFWKPKVQLDDL---FDWTMASDA  322 (333)
Q Consensus       265 ---glltGd~~~~~~a~ili~t~---------------~i~liViDe~H~~~~~~R~~~~~~~l~~l---~~l~~~~d~  322 (333)
                         |++|||.++++.+.|+++|+               ++..+|.||+|++++..|||.|+..++-+   +++++.|++
T Consensus       191 ~~vGL~TGDv~IN~~A~clvMTTEILRnMlyrg~~~~~~i~~ViFDEvHyi~D~eRG~VWEE~Ii~lP~~v~~v~LSAT  269 (1041)
T COG4581         191 DMVGLMTGDVSINPDAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIGDRERGVVWEEVIILLPDHVRFVFLSAT  269 (1041)
T ss_pred             hhccceecceeeCCCCceEEeeHHHHHHHhccCcccccccceEEEEeeeeccccccchhHHHHHHhcCCCCcEEEEeCC
Confidence               99999999999999999987               68889999999999999999999755544   567777765

>KOG0948|consensus

Probab=99.85  E-value=8.3e-22  Score=202.38  Aligned_cols=136  Identities=42%  Similarity=0.515  Sum_probs=125.1

Q ss_pred             cccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcE
Q psy2760         186 IMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVG  265 (333)
Q Consensus       186 ~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vg  265 (333)
                      ..++.+||.++|+|.+||.++..+.+|+|+|+|++|||+++.+||..+++.+.|+||.+|.+||.+|.|++|..-|++||
T Consensus       121 ~pAk~YPF~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~kQRVIYTSPIKALSNQKYREl~~EF~DVG  200 (1041)
T KOG0948|consen  121 PPAKTYPFTLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLREKQRVIYTSPIKALSNQKYRELLEEFKDVG  200 (1041)
T ss_pred             CcccCCCcccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHhcCeEEeeChhhhhcchhHHHHHHHhcccc
Confidence            45778999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeCCCCCCCCcceEEecc---------------CcceEeccccccccccCcCcccccchhh---hhhheeccC
Q psy2760         266 LIDDLPPVFPDVEKLLEDL---------------NIGGLDELSIHDFNKHLKFWKPKVQLDD---LFDWTMASD  321 (333)
Q Consensus       266 lltGd~~~~~~a~ili~t~---------------~i~liViDe~H~~~~~~R~~~~~~~l~~---l~~l~~~~d  321 (333)
                      +.|||..+++.+.|+|+|+               .++.+|.||+||..+..||..|+.+++-   .++.+..|+
T Consensus       201 LMTGDVTInP~ASCLVMTTEILRsMLYRGSEvmrEVaWVIFDEIHYMRDkERGVVWEETIIllP~~vr~VFLSA  274 (1041)
T KOG0948|consen  201 LMTGDVTINPDASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDKERGVVWEETIILLPDNVRFVFLSA  274 (1041)
T ss_pred             eeecceeeCCCCceeeeHHHHHHHHHhccchHhheeeeEEeeeehhccccccceeeeeeEEeccccceEEEEec
Confidence            9999999999999999987               6788999999999999999999865443   355665554

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.81  E-value=4.5e-21  Score=207.11  Aligned_cols=221  Identities=18%  Similarity=0.186  Sum_probs=153.9

Q ss_pred             chhhhhhhhhcccccccccccchhHHHhh-cc-----CcccccccccccccccCCchhhhhhhcCCCCCCcccCCCCC-C
Q psy2760          73 SIHDFNKHLKFWKPKVQLVAGIINLIQLG-GE-----NASKFEQGLWESHEVISGDAKEEQEKATVFPSNEEENNVIP-Q  145 (333)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~i-~~-----~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~-~  145 (333)
                      ...++....|+...++++|+++++++..| +.     .++++|+..|++...   +.++             ...+++ +
T Consensus       355 ~~~dy~~l~y~~~~~l~vPv~~~~~~~~y~~~~~~~~~l~~lg~~~w~~~k~---~~~~-------------~~~~~a~~  418 (926)
T TIGR00580       355 IERDYLVLEYAGEDKLYVPVEQLHLISRYVGGSGKNPALDKLGGKSWEKTKA---KVKK-------------SVREIAAK  418 (926)
T ss_pred             cceeEEEEEECCCCEEEEEHHHcCceeeecCCCCCCCcccccCcHHHHHHHH---HHHH-------------HHHHHHHH
Confidence            35678888899999999999999999998 32     588999999998821   1110             001111 1


Q ss_pred             ccCCcccccCCCCCCCCCcccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcC------CcEEEEcCCC
Q psy2760         146 EVDIPILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEH------NHVFVTAHTS  219 (333)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g------~~vlv~apTG  219 (333)
                      ++.....+.............|...                ....|||.+++.|.+|++.+..+      ++++++||||
T Consensus       419 l~~l~a~r~~~~~~~~~~~~~~~~~----------------~~~~~~f~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTG  482 (926)
T TIGR00580       419 LIELYAKRKAIKGHAFPPDLEWQQE----------------FEDSFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVG  482 (926)
T ss_pred             HHHHHHHHHhcCCCCCCCCHHHHHH----------------HHHhCCCCCCHHHHHHHHHHHhhhcccCcCCEEEECCCC
Confidence            1111111211110110011122221                24557889999999999998654      7999999999


Q ss_pred             CcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC----cEEEeCCCCCC-----------CCcceEEecc
Q psy2760         220 AGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD----VGLIDDLPPVF-----------PDVEKLLEDL  284 (333)
Q Consensus       220 SGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~~~-----------~~a~ili~t~  284 (333)
                      ||||++|+.|++.++..+.+++|++||++||.|+++.|+++|++    +++++|..+..           ....++|.|+
T Consensus       483 sGKT~val~a~l~al~~g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp  562 (926)
T TIGR00580       483 FGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTH  562 (926)
T ss_pred             ccHHHHHHHHHHHHHHhCCeEEEEeCcHHHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchH
Confidence            99999999999988888899999999999999999999998874    56788765521           2346788876


Q ss_pred             ----------CcceEeccccccccccCcCcccccchhhhhhheeccCcchhhh
Q psy2760         285 ----------NIGGLDELSIHDFNKHLKFWKPKVQLDDLFDWTMASDATTLEI  327 (333)
Q Consensus       285 ----------~i~liViDe~H~~~~~~R~~~~~~~l~~l~~l~~~~d~~~~e~  327 (333)
                                ++.++|+||.|.|+...|.  ....+-..++.+++|++++-.+
T Consensus       563 ~ll~~~v~f~~L~llVIDEahrfgv~~~~--~L~~~~~~~~vL~~SATpiprt  613 (926)
T TIGR00580       563 KLLQKDVKFKDLGLLIIDEEQRFGVKQKE--KLKELRTSVDVLTLSATPIPRT  613 (926)
T ss_pred             HHhhCCCCcccCCEEEeecccccchhHHH--HHHhcCCCCCEEEEecCCCHHH
Confidence                      6899999999998654322  1111223467888888875443

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=99.79  E-value=2.8e-20  Score=204.77  Aligned_cols=222  Identities=18%  Similarity=0.198  Sum_probs=155.4

Q ss_pred             chhhhhhhhhcccccccccccchhHHHhh-cc-----CcccccccccccccccCCchhhhhhhcCCCCCCcccCCCCC-C
Q psy2760          73 SIHDFNKHLKFWKPKVQLVAGIINLIQLG-GE-----NASKFEQGLWESHEVISGDAKEEQEKATVFPSNEEENNVIP-Q  145 (333)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~i-~~-----~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~-~  145 (333)
                      ...++....|++.+++++|+++++++..| +.     .++++|+..|++..   ++.++             ...+++ +
T Consensus       504 ~~~~~~~l~y~~~~~l~vPv~~~~~~~~y~~~~~~~~~l~~lg~~~w~~~k---~~~~~-------------~~~~~a~~  567 (1147)
T PRK10689        504 IKGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRAR---QKAAE-------------KVRDVAAE  567 (1147)
T ss_pred             cceeEEEEEECCCCeEEeeHHHhCcEeeecCCCCCCCccccCCcHHHHHHH---HHHHH-------------HHHHHHHH
Confidence            34788889999999999999999999998 32     58899999999871   11110             001111 1


Q ss_pred             ccCCcccccCCCCCCCCCcccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcC------CcEEEEcCCC
Q psy2760         146 EVDIPILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEH------NHVFVTAHTS  219 (333)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g------~~vlv~apTG  219 (333)
                      ++..-..+.........+...|...                +...|||.+++.|.+|++.+..+      +++++||+||
T Consensus       568 l~~~~a~r~~~~~~~~~~~~~~~~~----------------~~~~~~~~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TG  631 (1147)
T PRK10689        568 LLDIYAQRAAKEGFAFKHDREQYQL----------------FCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVG  631 (1147)
T ss_pred             HHHHHHHHhhccCCCCCCCHHHHHH----------------HHHhCCCCCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCC
Confidence            2211112211111111111233322                35678999999999999998665      8999999999


Q ss_pred             CcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC----cEEEeCCCCCC-----------CCcceEEecc
Q psy2760         220 AGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD----VGLIDDLPPVF-----------PDVEKLLEDL  284 (333)
Q Consensus       220 SGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~~~-----------~~a~ili~t~  284 (333)
                      +|||++|+.+++.....+.++++++||++||.|+++.|+++|+.    +..++|..+..           ....++|+|+
T Consensus       632 sGKT~val~aa~~~~~~g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp  711 (1147)
T PRK10689        632 FGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTH  711 (1147)
T ss_pred             cCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECH
Confidence            99999999988877788999999999999999999999988864    56677765432           2346888886


Q ss_pred             ----------CcceEeccccccccccCcCcccccchhhhhhheeccCcchhhhh
Q psy2760         285 ----------NIGGLDELSIHDFNKHLKFWKPKVQLDDLFDWTMASDATTLEIF  328 (333)
Q Consensus       285 ----------~i~liViDe~H~~~~~~R~~~~~~~l~~l~~l~~~~d~~~~e~~  328 (333)
                                ++.++|+||.|.|+...+  ....++-..++.+++|++++-.+.
T Consensus       712 ~lL~~~v~~~~L~lLVIDEahrfG~~~~--e~lk~l~~~~qvLl~SATpiprtl  763 (1147)
T PRK10689        712 KLLQSDVKWKDLGLLIVDEEHRFGVRHK--ERIKAMRADVDILTLTATPIPRTL  763 (1147)
T ss_pred             HHHhCCCCHhhCCEEEEechhhcchhHH--HHHHhcCCCCcEEEEcCCCCHHHH
Confidence                      678999999999964321  111122334678899988765543

>PRK02362 ski2-like helicase; Provisional

Probab=99.79  E-value=7e-19  Score=187.08  Aligned_cols=145  Identities=21%  Similarity=0.252  Sum_probs=118.3

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHH-HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIK-LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALS  250 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~-l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa  250 (333)
                      +|++.+.+.++..|+.      .|+|+|.+|++. +.+|+|++++||||||||++|++|++..+.++.+++|++||++||
T Consensus         7 ~lp~~~~~~l~~~g~~------~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~~~kal~i~P~raLa   80 (737)
T PRK02362          7 PLPEGVIEFYEAEGIE------ELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIARGGKALYIVPLRALA   80 (737)
T ss_pred             CCCHHHHHHHHhCCCC------cCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhcCCcEEEEeChHHHH
Confidence            4777888877776665      799999999998 689999999999999999999999998888889999999999999


Q ss_pred             HHHHHHHHHhc--C-CcEEEeCCCCCCC----CcceEEecc---------------CcceEeccccccccccCcCccccc
Q psy2760         251 NQKYRDFRETF--Q-DVGLIDDLPPVFP----DVEKLLEDL---------------NIGGLDELSIHDFNKHLKFWKPKV  308 (333)
Q Consensus       251 ~Q~~~~l~~~f--~-~vglltGd~~~~~----~a~ili~t~---------------~i~liViDe~H~~~~~~R~~~~~~  308 (333)
                      .|++++|++..  + .++.++|+.....    ...++|+|+               ++.++|+||+|++++..||..++.
T Consensus        81 ~q~~~~~~~~~~~g~~v~~~tGd~~~~~~~l~~~~IiV~Tpek~~~llr~~~~~l~~v~lvViDE~H~l~d~~rg~~le~  160 (737)
T PRK02362         81 SEKFEEFERFEELGVRVGISTGDYDSRDEWLGDNDIIVATSEKVDSLLRNGAPWLDDITCVVVDEVHLIDSANRGPTLEV  160 (737)
T ss_pred             HHHHHHHHHhhcCCCEEEEEeCCcCccccccCCCCEEEECHHHHHHHHhcChhhhhhcCEEEEECccccCCCcchHHHHH
Confidence            99999998631  2 2788999876543    357888885               479999999999999999877765


Q ss_pred             chhhh------hhheeccCc
Q psy2760         309 QLDDL------FDWTMASDA  322 (333)
Q Consensus       309 ~l~~l------~~l~~~~d~  322 (333)
                      .+.++      ++.+.+|++
T Consensus       161 il~rl~~~~~~~qii~lSAT  180 (737)
T PRK02362        161 TLAKLRRLNPDLQVVALSAT  180 (737)
T ss_pred             HHHHHHhcCCCCcEEEEccc
Confidence            22222      345666554

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

Probab=99.76  E-value=3.9e-19  Score=191.33  Aligned_cols=226  Identities=19%  Similarity=0.198  Sum_probs=164.4

Q ss_pred             HHHhhcCCccccchhhhhhhhhcccccccccccchhHHHhhcc------CcccccccccccccccCCchhhhhhhcCCCC
Q psy2760          61 LEDLNIGGLDELSIHDFNKHLKFWKPKVQLVAGIINLIQLGGE------NASKFEQGLWESHEVISGDAKEEQEKATVFP  134 (333)
Q Consensus        61 l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~------~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~  134 (333)
                      |+++.++|    ..+|+++..|++.+++++|+++++|+++|..      .+|++|+..|++.   +.+.+          
T Consensus       490 l~tl~~~g----~~~dyL~l~Ya~~dkLyVPVeql~lisrY~g~~~~~p~L~kLG~~~W~k~---K~K~~----------  552 (1139)
T COG1197         490 LETLEVGG----IERDYLELEYAGEDKLYVPVEQLHLISRYVGASDEAPKLHKLGGGAWKKA---KAKAR----------  552 (1139)
T ss_pred             eEEEecCC----CccceEEEEEcCCCeEEEEHHHhhHHhhccCCCCCCccccccCcHHHHHH---HHHHH----------
Confidence            55666777    7899999999999999999999999999933      5899999999988   21111          


Q ss_pred             CCcccCCCCC-CccCCcccccCCCCCCCCCcccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHH----HcC
Q psy2760         135 SNEEENNVIP-QEVDIPILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKL----EEH  209 (333)
Q Consensus       135 ~~~~~~~e~~-~~~~~~~~~~~~~~~~~~~~~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l----~~g  209 (333)
                         +...+++ +++.....+....+....+-..|...                ++..|||.-|+.|..||..+    .++
T Consensus       553 ---~~v~diA~eLi~lyA~R~~~~G~af~~d~~~q~~----------------F~~~FPyeET~DQl~AI~eVk~DM~~~  613 (1139)
T COG1197         553 ---KKVRDIAAELIKLYAKRQAKKGFAFPPDTEWQEE----------------FEASFPYEETPDQLKAIEEVKRDMESG  613 (1139)
T ss_pred             ---HHHHHHHHHHHHHHHHHhhccCCCCCCChHHHHH----------------HHhcCCCcCCHHHHHHHHHHHHHhccC
Confidence               0111122 22222222222211222233345443                47789999999999999996    344


Q ss_pred             --CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEeCCCCC--------------
Q psy2760         210 --NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPV--------------  273 (333)
Q Consensus       210 --~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vglltGd~~~--------------  273 (333)
                        .+.|+||..|-|||.+++-|++.+...|++|.++|||.-||+|+++.|+++|.+..+-.+.++.              
T Consensus       614 kpMDRLiCGDVGFGKTEVAmRAAFkAV~~GKQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~l  693 (1139)
T COG1197         614 KPMDRLICGDVGFGKTEVAMRAAFKAVMDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGL  693 (1139)
T ss_pred             CcchheeecCcCCcHHHHHHHHHHHHhcCCCeEEEEcccHHhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHH
Confidence              4889999999999999999999999999999999999999999999999999974333222221              


Q ss_pred             -CCCcceEEecc----------CcceEeccccccccccCcCcccccchhhhhhheeccCcch
Q psy2760         274 -FPDVEKLLEDL----------NIGGLDELSIHDFNKHLKFWKPKVQLDDLFDWTMASDATT  324 (333)
Q Consensus       274 -~~~a~ili~t~----------~i~liViDe~H~~~~~~R~~~~~~~l~~l~~l~~~~d~~~  324 (333)
                       ....+++|.|+          +++++|+||-|.|+...+-.  ..++-..++.+.+|++|+
T Consensus       694 a~G~vDIvIGTHrLL~kdv~FkdLGLlIIDEEqRFGVk~KEk--LK~Lr~~VDvLTLSATPI  753 (1139)
T COG1197         694 AEGKVDIVIGTHRLLSKDVKFKDLGLLIIDEEQRFGVKHKEK--LKELRANVDVLTLSATPI  753 (1139)
T ss_pred             hcCCccEEEechHhhCCCcEEecCCeEEEechhhcCccHHHH--HHHHhccCcEEEeeCCCC
Confidence             23346888887          79999999999999765321  122344567777777764

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.72  E-value=2e-17  Score=175.87  Aligned_cols=130  Identities=25%  Similarity=0.248  Sum_probs=107.7

Q ss_pred             CChhhhhhhhccccccccCCCCCCHHHHHHHHH-HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC-CCeEEEEcccHHHH
Q psy2760         173 VSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIK-LEEHNHVFVTAHTSAGKTVIAEYAIALSQNH-KTRTIYTSPIKALS  250 (333)
Q Consensus       173 L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~-l~~g~~vlv~apTGSGKTl~~~l~il~~l~~-g~ral~l~PtraLa  250 (333)
                      +...+..+++..++.      ++++.|+.++.. +..++|+++|+|||||||++++++|+..+.+ +.+++|++|+||||
T Consensus        16 ~~~~v~~i~~~~~~~------el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~~~k~vYivPlkALa   89 (766)
T COG1204          16 LDDRVLEILKGDGID------ELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGGGKVVYIVPLKALA   89 (766)
T ss_pred             ccHHHHHHhccCChH------HhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhcCCcEEEEeChHHHH
Confidence            444556666554544      678888888877 4668999999999999999999999988766 58999999999999


Q ss_pred             HHHHHHHH--HhcCC-cEEEeCCCCCCC----CcceEEecc---------------CcceEeccccccccccCcCccccc
Q psy2760         251 NQKYRDFR--ETFQD-VGLIDDLPPVFP----DVEKLLEDL---------------NIGGLDELSIHDFNKHLKFWKPKV  308 (333)
Q Consensus       251 ~Q~~~~l~--~~f~~-vglltGd~~~~~----~a~ili~t~---------------~i~liViDe~H~~~~~~R~~~~~~  308 (333)
                      +|++++|+  +.|+- |++.|||.....    +..++|.|+               .+.++|+||+|++++..||+.-+.
T Consensus        90 ~Ek~~~~~~~~~~GirV~~~TgD~~~~~~~l~~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~~RG~~lE~  169 (766)
T COG1204          90 EEKYEEFSRLEELGIRVGISTGDYDLDDERLARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRTRGPVLES  169 (766)
T ss_pred             HHHHHHhhhHHhcCCEEEEecCCcccchhhhccCCEEEEchHHhhHhhhcCcchhhcccEEEEeeeeecCCcccCceehh
Confidence            99999998  44553 999999998654    356888876               588999999999999999998775

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.72  E-value=5.8e-17  Score=161.60  Aligned_cols=124  Identities=18%  Similarity=0.031  Sum_probs=99.1

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc----------CCCeEE
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN----------HKTRTI  241 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~----------~g~ral  241 (333)
                      +|++.+.+.+...|+.      .|+++|++|++.++.|+|++++||||||||++|++|++..+.          .+.++|
T Consensus        14 ~l~~~l~~~l~~~g~~------~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~l   87 (423)
T PRK04837         14 ALHPQVVEALEKKGFH------NCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRAL   87 (423)
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEE
Confidence            5677777776665655      799999999999999999999999999999999999985441          246899


Q ss_pred             EEcccHHHHHHHHHHHHHhcCC----cEEEeCCCCCC-------CCcceEEecc---------------CcceEeccccc
Q psy2760         242 YTSPIKALSNQKYRDFRETFQD----VGLIDDLPPVF-------PDVEKLLEDL---------------NIGGLDELSIH  295 (333)
Q Consensus       242 ~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~~~-------~~a~ili~t~---------------~i~liViDe~H  295 (333)
                      |++|||+||.|+++.+......    ++.+.|+....       ....++|+|+               ++.++|+||+|
T Consensus        88 il~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~~~~~l~~v~~lViDEad  167 (423)
T PRK04837         88 IMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEAD  167 (423)
T ss_pred             EECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccccEEEEecHH
Confidence            9999999999999888765432    67777775432       2246888886               57889999999


Q ss_pred             cccccC
Q psy2760         296 DFNKHL  301 (333)
Q Consensus       296 ~~~~~~  301 (333)
                      .+.+.+
T Consensus       168 ~l~~~~  173 (423)
T PRK04837        168 RMFDLG  173 (423)
T ss_pred             HHhhcc
Confidence            876543

>PRK00254 ski2-like helicase; Provisional

Probab=99.71  E-value=4.7e-17  Score=172.75  Aligned_cols=145  Identities=19%  Similarity=0.191  Sum_probs=114.8

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHH-HHcCCcEEEEcCCCCcHHHHHHHHHHHHh-cCCCeEEEEcccHHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIK-LEEHNHVFVTAHTSAGKTVIAEYAIALSQ-NHKTRTIYTSPIKAL  249 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~-l~~g~~vlv~apTGSGKTl~~~l~il~~l-~~g~ral~l~PtraL  249 (333)
                      ++++.+.+.++..|+.      .|+++|.+|++. +..|+|++++||||||||++|.+|++..+ ..+.++||++|+++|
T Consensus         7 ~l~~~~~~~l~~~g~~------~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~~~~~l~l~P~~aL   80 (720)
T PRK00254          7 RVDERIKRVLKERGIE------ELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLREGGKAVYLVPLKAL   80 (720)
T ss_pred             CCCHHHHHHHHhCCCC------CCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhcCCeEEEEeChHHH
Confidence            4677888887777766      899999999987 79999999999999999999999998664 467899999999999


Q ss_pred             HHHHHHHHHHh--cC-CcEEEeCCCCCCC----CcceEEecc---------------CcceEeccccccccccCcCcccc
Q psy2760         250 SNQKYRDFRET--FQ-DVGLIDDLPPVFP----DVEKLLEDL---------------NIGGLDELSIHDFNKHLKFWKPK  307 (333)
Q Consensus       250 a~Q~~~~l~~~--f~-~vglltGd~~~~~----~a~ili~t~---------------~i~liViDe~H~~~~~~R~~~~~  307 (333)
                      ++|++++|++.  ++ .++.++|+.....    +..++|+|+               ++.++|+||+|.+++..||....
T Consensus        81 a~q~~~~~~~~~~~g~~v~~~~Gd~~~~~~~~~~~~IiV~Tpe~~~~ll~~~~~~l~~l~lvViDE~H~l~~~~rg~~le  160 (720)
T PRK00254         81 AEEKYREFKDWEKLGLRVAMTTGDYDSTDEWLGKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIHLIGSYDRGATLE  160 (720)
T ss_pred             HHHHHHHHHHHhhcCCEEEEEeCCCCCchhhhccCCEEEEcHHHHHHHHhCCchhhhcCCEEEEcCcCccCCccchHHHH
Confidence            99999999752  12 2788999876432    346888874               57899999999999888887655


Q ss_pred             cchh---hhhhheeccCc
Q psy2760         308 VQLD---DLFDWTMASDA  322 (333)
Q Consensus       308 ~~l~---~l~~l~~~~d~  322 (333)
                      ..+.   ...+.+.+|++
T Consensus       161 ~il~~l~~~~qiI~lSAT  178 (720)
T PRK00254        161 MILTHMLGRAQILGLSAT  178 (720)
T ss_pred             HHHHhcCcCCcEEEEEcc
Confidence            4221   12445556555

>PRK01172 ski2-like helicase; Provisional

Probab=99.71  E-value=5.1e-17  Score=171.15  Aligned_cols=130  Identities=23%  Similarity=0.214  Sum_probs=106.8

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSN  251 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~  251 (333)
                      +|++.+.+.++.       .+|.++++|.++++.+.+|++++++||||||||+++.++++..+..+.+++|++|+++||.
T Consensus         7 ~l~~~~~~~~~~-------~~~~l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~~~k~v~i~P~raLa~   79 (674)
T PRK01172          7 GYDDEFLNLFTG-------NDFELYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLAGLKSIYIVPLRSLAM   79 (674)
T ss_pred             CCCHHHHHHHhh-------CCCCCCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHhCCcEEEEechHHHHH
Confidence            356666665533       2457999999999999999999999999999999999999988877889999999999999


Q ss_pred             HHHHHHHHhc--C-CcEEEeCCCCCCC----CcceEEecc---------------CcceEeccccccccccCcCccccc
Q psy2760         252 QKYRDFRETF--Q-DVGLIDDLPPVFP----DVEKLLEDL---------------NIGGLDELSIHDFNKHLKFWKPKV  308 (333)
Q Consensus       252 Q~~~~l~~~f--~-~vglltGd~~~~~----~a~ili~t~---------------~i~liViDe~H~~~~~~R~~~~~~  308 (333)
                      |++++|++..  + .++..+|+.....    ...++++|+               ++.++|+||+|.+++..||.....
T Consensus        80 q~~~~~~~l~~~g~~v~~~~G~~~~~~~~~~~~dIiv~Tpek~~~l~~~~~~~l~~v~lvViDEaH~l~d~~rg~~le~  158 (674)
T PRK01172         80 EKYEELSRLRSLGMRVKISIGDYDDPPDFIKRYDVVILTSEKADSLIHHDPYIINDVGLIVADEIHIIGDEDRGPTLET  158 (674)
T ss_pred             HHHHHHHHHhhcCCeEEEEeCCCCCChhhhccCCEEEECHHHHHHHHhCChhHHhhcCEEEEecchhccCCCccHHHHH
Confidence            9999997632  2 2778888866442    357888876               478999999999998888876654

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

Probab=99.71  E-value=8e-17  Score=171.47  Aligned_cols=129  Identities=18%  Similarity=0.194  Sum_probs=104.2

Q ss_pred             CcccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh--cCCCeE
Q psy2760         163 TQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ--NHKTRT  240 (333)
Q Consensus       163 ~~~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l--~~g~ra  240 (333)
                      .+..|..  .+++.+.+.++..|+.      .|+++|.+|++.+.+|+|+++++|||||||++|.+|++..+  .++.++
T Consensus        13 ~~~~~~~--~l~~~l~~~L~~~g~~------~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~~~~~a   84 (742)
T TIGR03817        13 RTAPWPA--WAHPDVVAALEAAGIH------RPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADDPRATA   84 (742)
T ss_pred             ccCCCCC--cCCHHHHHHHHHcCCC------cCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhCCCcEE
Confidence            4444443  4677888888777776      79999999999999999999999999999999999999765  346799


Q ss_pred             EEEcccHHHHHHHHHHHHHhcC-C--cEEEeCCCCCC------CCcceEEecc-------------------CcceEecc
Q psy2760         241 IYTSPIKALSNQKYRDFRETFQ-D--VGLIDDLPPVF------PDVEKLLEDL-------------------NIGGLDEL  292 (333)
Q Consensus       241 l~l~PtraLa~Q~~~~l~~~f~-~--vglltGd~~~~------~~a~ili~t~-------------------~i~liViD  292 (333)
                      ||++|||||++|+++.+++... +  ++.++|+.+..      .+..+++.|+                   ++.++|+|
T Consensus        85 L~l~PtraLa~q~~~~l~~l~~~~i~v~~~~Gdt~~~~r~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViD  164 (742)
T TIGR03817        85 LYLAPTKALAADQLRAVRELTLRGVRPATYDGDTPTEERRWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVID  164 (742)
T ss_pred             EEEcChHHHHHHHHHHHHHhccCCeEEEEEeCCCCHHHHHHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEe
Confidence            9999999999999999987532 2  67788987642      2346777775                   35689999


Q ss_pred             ccccccc
Q psy2760         293 SIHDFNK  299 (333)
Q Consensus       293 e~H~~~~  299 (333)
                      |+|.+.+
T Consensus       165 Eah~~~g  171 (742)
T TIGR03817       165 ECHSYRG  171 (742)
T ss_pred             ChhhccC
Confidence            9998854

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.

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.71  E-value=5.8e-17  Score=163.47  Aligned_cols=125  Identities=19%  Similarity=0.122  Sum_probs=101.3

Q ss_pred             ccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC---------CCeEE
Q psy2760         171 LDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH---------KTRTI  241 (333)
Q Consensus       171 ~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~---------g~ral  241 (333)
                      .+|++++...+...++.      .|+++|.+|++.++.|+|++++||||||||++|++|++..+..         ..++|
T Consensus         6 l~l~~~l~~~l~~~g~~------~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aL   79 (456)
T PRK10590          6 LGLSPDILRAVAEQGYR------EPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRAL   79 (456)
T ss_pred             cCCCHHHHHHHHHCCCC------CCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEE
Confidence            35777888877766666      8999999999999999999999999999999999999865422         24799


Q ss_pred             EEcccHHHHHHHHHHHHHhcCC----cEEEeCCCCCCC-------CcceEEecc---------------CcceEeccccc
Q psy2760         242 YTSPIKALSNQKYRDFRETFQD----VGLIDDLPPVFP-------DVEKLLEDL---------------NIGGLDELSIH  295 (333)
Q Consensus       242 ~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~~~~-------~a~ili~t~---------------~i~liViDe~H  295 (333)
                      |++|||+||.|+.+.++..+..    +..++|+.+.+.       ...++|+|+               ++.++|+||+|
T Consensus        80 il~PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~~~~~l~~v~~lViDEah  159 (456)
T PRK10590         80 ILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEAD  159 (456)
T ss_pred             EEeCcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHcCCcccccceEEEeecHH
Confidence            9999999999999999875543    455778776432       346888886               46789999999


Q ss_pred             cccccC
Q psy2760         296 DFNKHL  301 (333)
Q Consensus       296 ~~~~~~  301 (333)
                      .+.+.+
T Consensus       160 ~ll~~~  165 (456)
T PRK10590        160 RMLDMG  165 (456)
T ss_pred             HHhccc
Confidence            876543

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.69  E-value=5.7e-17  Score=171.20  Aligned_cols=135  Identities=16%  Similarity=0.215  Sum_probs=110.0

Q ss_pred             ccCCCCCCHHHHHHHHHHHcC------CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         189 HTWPFELDVFQKQAIIKLEEH------NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       189 ~~~~f~l~~~Q~~ai~~l~~g------~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      ..+||.|++.|++|++.+..+      ++++++||||||||++|.+|++.....|.+++|++||++||.|+++.+++.+.
T Consensus       256 ~~l~f~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~g~q~lilaPT~~LA~Q~~~~l~~l~~  335 (681)
T PRK10917        256 ASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQAALMAPTEILAEQHYENLKKLLE  335 (681)
T ss_pred             HhCCCCCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEeccHHHHHHHHHHHHHHHh
Confidence            357999999999999998655      48999999999999999999998888899999999999999999999998775


Q ss_pred             C----cEEEeCCCCC-----------CCCcceEEecc----------CcceEeccccccccccCcCcccccchhhhhhhe
Q psy2760         263 D----VGLIDDLPPV-----------FPDVEKLLEDL----------NIGGLDELSIHDFNKHLKFWKPKVQLDDLFDWT  317 (333)
Q Consensus       263 ~----vglltGd~~~-----------~~~a~ili~t~----------~i~liViDe~H~~~~~~R~~~~~~~l~~l~~l~  317 (333)
                      .    +++++|+.+.           .....++|+|+          ++.++|+||.|.|+...|..-...  -.....+
T Consensus       336 ~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~v~~~~l~lvVIDE~Hrfg~~qr~~l~~~--~~~~~iL  413 (681)
T PRK10917        336 PLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIIDEQHRFGVEQRLALREK--GENPHVL  413 (681)
T ss_pred             hcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcccchhcccceEEEechhhhhHHHHHHHHhc--CCCCCEE
Confidence            3    7889999873           22456788775          688999999999987766543221  1135678


Q ss_pred             eccCcchh
Q psy2760         318 MASDATTL  325 (333)
Q Consensus       318 ~~~d~~~~  325 (333)
                      ++|++++-
T Consensus       414 ~~SATp~p  421 (681)
T PRK10917        414 VMTATPIP  421 (681)
T ss_pred             EEeCCCCH
Confidence            88887653

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.69  E-value=2.2e-16  Score=157.79  Aligned_cols=124  Identities=15%  Similarity=0.074  Sum_probs=101.0

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc-------CCCeEEEEc
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN-------HKTRTIYTS  244 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~-------~g~ral~l~  244 (333)
                      ++++.+.+.+...|+.      .|+++|.++++.++.|++++++||||+|||++|++|++..+.       .+.+++|++
T Consensus         7 ~l~~~l~~~l~~~g~~------~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~   80 (434)
T PRK11192          7 ELDESLLEALQDKGYT------RPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILT   80 (434)
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEEC
Confidence            5677777777666666      799999999999999999999999999999999999986542       246899999


Q ss_pred             ccHHHHHHHHHHHHHhcCC----cEEEeCCCCCC-------CCcceEEecc---------------CcceEecccccccc
Q psy2760         245 PIKALSNQKYRDFRETFQD----VGLIDDLPPVF-------PDVEKLLEDL---------------NIGGLDELSIHDFN  298 (333)
Q Consensus       245 PtraLa~Q~~~~l~~~f~~----vglltGd~~~~-------~~a~ili~t~---------------~i~liViDe~H~~~  298 (333)
                      ||++||.|+++.++.....    ++.++|+....       ....++|+|+               ++.++|+||+|.+.
T Consensus        81 Pt~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~~~~~~~~v~~lViDEah~~l  160 (434)
T PRK11192         81 PTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRML  160 (434)
T ss_pred             CcHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCcCcccCCEEEEECHHHHh
Confidence            9999999999988775432    78889987643       2346888886               46789999999876


Q ss_pred             ccC
Q psy2760         299 KHL  301 (333)
Q Consensus       299 ~~~  301 (333)
                      +.+
T Consensus       161 ~~~  163 (434)
T PRK11192        161 DMG  163 (434)
T ss_pred             CCC
Confidence            543

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.69  E-value=6.2e-17  Score=169.55  Aligned_cols=138  Identities=14%  Similarity=0.148  Sum_probs=109.6

Q ss_pred             ccCCCCCCHHHHHHHHHHHcC------CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         189 HTWPFELDVFQKQAIIKLEEH------NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       189 ~~~~f~l~~~Q~~ai~~l~~g------~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      ..+||.|++.|++|++.+..+      .+++++||||||||++|+++++.....|.+++|++||++||.|+++.+++.++
T Consensus       230 ~~lpf~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~g~qvlilaPT~~LA~Q~~~~~~~l~~  309 (630)
T TIGR00643       230 ASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLA  309 (630)
T ss_pred             HhCCCCCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEECCHHHHHHHHHHHHHHHhc
Confidence            357899999999999998554      36899999999999999999998888899999999999999999999998876


Q ss_pred             C----cEEEeCCCCCC-----------CCcceEEecc----------CcceEeccccccccccCcCcccccchh-hhhhh
Q psy2760         263 D----VGLIDDLPPVF-----------PDVEKLLEDL----------NIGGLDELSIHDFNKHLKFWKPKVQLD-DLFDW  316 (333)
Q Consensus       263 ~----vglltGd~~~~-----------~~a~ili~t~----------~i~liViDe~H~~~~~~R~~~~~~~l~-~l~~l  316 (333)
                      .    +++++|+....           .+..+++.|+          ++.++|+||.|.|+...|..-...... .....
T Consensus       310 ~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~~~~~~~l~lvVIDEaH~fg~~qr~~l~~~~~~~~~~~~  389 (630)
T TIGR00643       310 PLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKGQGGFTPHV  389 (630)
T ss_pred             ccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhccccccccceEEEechhhccHHHHHHHHHhcccCCCCCE
Confidence            3    78899987642           2346788775          689999999999987766543322100 13457


Q ss_pred             eeccCcchhh
Q psy2760         317 TMASDATTLE  326 (333)
Q Consensus       317 ~~~~d~~~~e  326 (333)
                      +++|++++-+
T Consensus       390 l~~SATp~pr  399 (630)
T TIGR00643       390 LVMSATPIPR  399 (630)
T ss_pred             EEEeCCCCcH
Confidence            8888876433

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.69  E-value=2e-16  Score=159.30  Aligned_cols=124  Identities=14%  Similarity=0.125  Sum_probs=100.3

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC---CCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH---KTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~---g~ral~l~Ptra  248 (333)
                      +|++.+...+...++.      .|+|+|++|++.+..|+|++++||||||||++|.+|++..+..   +.+++|++|||+
T Consensus        10 ~l~~~l~~~l~~~g~~------~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~Ptre   83 (460)
T PRK11776         10 PLPPALLANLNELGYT------EMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRE   83 (460)
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCHH
Confidence            4677777766665655      7999999999999999999999999999999999999976643   457999999999


Q ss_pred             HHHHHHHHHHHhcC---C--cEEEeCCCCCC-------CCcceEEecc---------------CcceEeccccccccccC
Q psy2760         249 LSNQKYRDFRETFQ---D--VGLIDDLPPVF-------PDVEKLLEDL---------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       249 La~Q~~~~l~~~f~---~--vglltGd~~~~-------~~a~ili~t~---------------~i~liViDe~H~~~~~~  301 (333)
                      ||.|+.+.++....   +  +..++|+.+..       ....++|+|+               ++.++|+||+|.+.+.+
T Consensus        84 La~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~~~~~l~~l~~lViDEad~~l~~g  163 (460)
T PRK11776         84 LADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMG  163 (460)
T ss_pred             HHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHcCCccHHHCCEEEEECHHHHhCcC
Confidence            99999998876532   2  66788887653       2346888885               47889999999876543

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.69  E-value=2.1e-16  Score=160.07  Aligned_cols=125  Identities=12%  Similarity=-0.028  Sum_probs=101.1

Q ss_pred             ccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC----------CCeE
Q psy2760         171 LDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH----------KTRT  240 (333)
Q Consensus       171 ~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~----------g~ra  240 (333)
                      .+|++.+.+.+...|+.      .++++|.++++.+..|+|++++||||||||++|++|++..+..          +.++
T Consensus        92 ~~l~~~l~~~l~~~g~~------~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~a  165 (475)
T PRK01297         92 FNLAPELMHAIHDLGFP------YCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRA  165 (475)
T ss_pred             CCCCHHHHHHHHHCCCC------CCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceE
Confidence            35788888887766666      7999999999999999999999999999999999999865421          4689


Q ss_pred             EEEcccHHHHHHHHHHHHHhcCC----cEEEeCCCCCC--------CCcceEEecc---------------CcceEeccc
Q psy2760         241 IYTSPIKALSNQKYRDFRETFQD----VGLIDDLPPVF--------PDVEKLLEDL---------------NIGGLDELS  293 (333)
Q Consensus       241 l~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~~~--------~~a~ili~t~---------------~i~liViDe  293 (333)
                      ||++||++||.|+++.++.....    +..++|+....        ....+++.|+               ++.++|+||
T Consensus       166 Lil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~~lViDE  245 (475)
T PRK01297        166 LIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDE  245 (475)
T ss_pred             EEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcCCcccccCceEEech
Confidence            99999999999999999775432    56677875432        2346888886               467899999


Q ss_pred             cccccccC
Q psy2760         294 IHDFNKHL  301 (333)
Q Consensus       294 ~H~~~~~~  301 (333)
                      +|.+...+
T Consensus       246 ah~l~~~~  253 (475)
T PRK01297        246 ADRMLDMG  253 (475)
T ss_pred             HHHHHhcc
Confidence            99886543

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

Probab=99.69  E-value=1.7e-16  Score=162.75  Aligned_cols=129  Identities=16%  Similarity=0.051  Sum_probs=99.4

Q ss_pred             ccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh----------
Q psy2760         165 TEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ----------  234 (333)
Q Consensus       165 ~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l----------  234 (333)
                      ..|.. .++++.+.+.++..|+.      .|+++|.+|++.++.|+|++++||||||||++|++|++..+          
T Consensus       121 ~~f~~-~~l~~~l~~~L~~~g~~------~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~  193 (518)
T PLN00206        121 LSFSS-CGLPPKLLLNLETAGYE------FPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSE  193 (518)
T ss_pred             cCHHh-CCCCHHHHHHHHHcCCC------CCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccccc
Confidence            34443 35788888877666655      79999999999999999999999999999999999998543          


Q ss_pred             cCCCeEEEEcccHHHHHHHHHHHHHhcCC----cEEEeCCCCC-------CCCcceEEecc---------------Ccce
Q psy2760         235 NHKTRTIYTSPIKALSNQKYRDFRETFQD----VGLIDDLPPV-------FPDVEKLLEDL---------------NIGG  288 (333)
Q Consensus       235 ~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~~-------~~~a~ili~t~---------------~i~l  288 (333)
                      ..+.++||++|||+||.|+.+.++.....    +..+.|+...       .....++|+|+               ++.+
T Consensus       194 ~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~~~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~~~l~~v~~  273 (518)
T PLN00206        194 QRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSV  273 (518)
T ss_pred             cCCceEEEEeCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHHHhcCCCCEEEECHHHHHHHHHcCCccchheeE
Confidence            14678999999999999999888764433    3344554432       22346888876               4678


Q ss_pred             Eecccccccccc
Q psy2760         289 LDELSIHDFNKH  300 (333)
Q Consensus       289 iViDe~H~~~~~  300 (333)
                      +|+||+|.+.+.
T Consensus       274 lViDEad~ml~~  285 (518)
T PLN00206        274 LVLDEVDCMLER  285 (518)
T ss_pred             EEeecHHHHhhc
Confidence            999999987654

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

Probab=99.68  E-value=1.1e-16  Score=169.80  Aligned_cols=138  Identities=20%  Similarity=0.237  Sum_probs=112.8

Q ss_pred             CChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh--------cCCCeEEEEc
Q psy2760         173 VSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ--------NHKTRTIYTS  244 (333)
Q Consensus       173 L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l--------~~g~ral~l~  244 (333)
                      |++.+..+++.. ..      .|++.|.+|++.+.+|+|+|+.||||||||+++++|++..+        ..+..+|||+
T Consensus         8 l~~~v~~~~~~~-~~------~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIs   80 (814)
T COG1201           8 LDPRVREWFKRK-FT------SLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYIS   80 (814)
T ss_pred             cCHHHHHHHHHh-cC------CCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeC
Confidence            566777776654 33      79999999999999999999999999999999999998543        2346899999


Q ss_pred             ccHHHHHHHHHHHHHhcC----CcEEEeCCCCCCCCc-------ceEEecc-----------------CcceEecccccc
Q psy2760         245 PIKALSNQKYRDFRETFQ----DVGLIDDLPPVFPDV-------EKLLEDL-----------------NIGGLDELSIHD  296 (333)
Q Consensus       245 PtraLa~Q~~~~l~~~f~----~vglltGd~~~~~~a-------~ili~t~-----------------~i~liViDe~H~  296 (333)
                      |.|||.+++.+++.....    .+.+.|||++...+.       .+++.|+                 ++-.+|+||+|.
T Consensus        81 PLkALn~Di~~rL~~~~~~~G~~v~vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEiHe  160 (814)
T COG1201          81 PLKALNNDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEIHA  160 (814)
T ss_pred             cHHHHHHHHHHHHHHHHHHcCCccceecCCCChHHhhhccCCCCcEEEeChhHHHHHhcCHHHHHHhcCCcEEEeehhhh
Confidence            999999999999866432    288999998764332       4788776                 788999999999


Q ss_pred             ccccCcCcccccchhhhhhhe
Q psy2760         297 FNKHLKFWKPKVQLDDLFDWT  317 (333)
Q Consensus       297 ~~~~~R~~~~~~~l~~l~~l~  317 (333)
                      +....||..-.+++.++..+.
T Consensus       161 l~~sKRG~~Lsl~LeRL~~l~  181 (814)
T COG1201         161 LAESKRGVQLALSLERLRELA  181 (814)
T ss_pred             hhccccchhhhhhHHHHHhhC
Confidence            999999999888666665443

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.67  E-value=2e-16  Score=164.05  Aligned_cols=124  Identities=15%  Similarity=-0.005  Sum_probs=100.4

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc----------CCCeEE
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN----------HKTRTI  241 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~----------~g~ral  241 (333)
                      +|++.+...+...++.      .|+++|.++|+.++.|+|++++||||||||++|++|++..+.          .+.++|
T Consensus        15 ~l~~~l~~~L~~~g~~------~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raL   88 (572)
T PRK04537         15 DLHPALLAGLESAGFT------RCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRAL   88 (572)
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEE
Confidence            4778888877776666      899999999999999999999999999999999999986542          146899


Q ss_pred             EEcccHHHHHHHHHHHHHhcCC----cEEEeCCCCCCC-------CcceEEecc----------------CcceEecccc
Q psy2760         242 YTSPIKALSNQKYRDFRETFQD----VGLIDDLPPVFP-------DVEKLLEDL----------------NIGGLDELSI  294 (333)
Q Consensus       242 ~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~~~~-------~a~ili~t~----------------~i~liViDe~  294 (333)
                      |++||++|+.|+++.+.+....    ++.++|+.....       ...++|.|+                .+.++|+||+
T Consensus        89 Il~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l~~v~~lViDEA  168 (572)
T PRK04537         89 ILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEA  168 (572)
T ss_pred             EEeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhccccchhheeeeEecCH
Confidence            9999999999999998775443    677888876432       246888885                3456899999


Q ss_pred             ccccccC
Q psy2760         295 HDFNKHL  301 (333)
Q Consensus       295 H~~~~~~  301 (333)
                      |.+.+.+
T Consensus       169 h~lld~g  175 (572)
T PRK04537        169 DRMFDLG  175 (572)
T ss_pred             HHHhhcc
Confidence            9876543

>PTZ00110 helicase; Provisional

Probab=99.67  E-value=3.3e-16  Score=161.57  Aligned_cols=128  Identities=13%  Similarity=0.000  Sum_probs=100.1

Q ss_pred             cchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh--------cCC
Q psy2760         166 EWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ--------NHK  237 (333)
Q Consensus       166 ~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l--------~~g  237 (333)
                      .|.. .++++.+.+.++..++.      .|+++|.++++.++.|++++++||||||||++|++|++..+        ..+
T Consensus       131 ~f~~-~~l~~~l~~~l~~~g~~------~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~g  203 (545)
T PTZ00110        131 SFEY-TSFPDYILKSLKNAGFT------EPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDG  203 (545)
T ss_pred             CHhh-cCCCHHHHHHHHHCCCC------CCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCC
Confidence            4443 35777787777666665      89999999999999999999999999999999999987543        136


Q ss_pred             CeEEEEcccHHHHHHHHHHHHHhcCC----cEEEeCCCCCC-------CCcceEEecc---------------CcceEec
Q psy2760         238 TRTIYTSPIKALSNQKYRDFRETFQD----VGLIDDLPPVF-------PDVEKLLEDL---------------NIGGLDE  291 (333)
Q Consensus       238 ~ral~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~~~-------~~a~ili~t~---------------~i~liVi  291 (333)
                      .++||++|||+||.|+.+.+++....    +..+.|+....       ....++|+|+               .+.++|+
T Consensus       204 p~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~~~~~l~~v~~lVi  283 (545)
T PTZ00110        204 PIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVL  283 (545)
T ss_pred             cEEEEECChHHHHHHHHHHHHHHhcccCccEEEEeCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHcCCCChhhCcEEEe
Confidence            78999999999999999998774332    45566765532       2346888886               4678999


Q ss_pred             ccccccccc
Q psy2760         292 LSIHDFNKH  300 (333)
Q Consensus       292 De~H~~~~~  300 (333)
                      ||+|.+.+.
T Consensus       284 DEAd~mld~  292 (545)
T PTZ00110        284 DEADRMLDM  292 (545)
T ss_pred             ehHHhhhhc
Confidence            999987654

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

Probab=99.67  E-value=2.9e-16  Score=135.32  Aligned_cols=128  Identities=17%  Similarity=0.185  Sum_probs=100.2

Q ss_pred             CHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCC--CeEEEEcccHHHHHHHHHHHHHhcCC----cEEEeC
Q psy2760         196 DVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHK--TRTIYTSPIKALSNQKYRDFRETFQD----VGLIDD  269 (333)
Q Consensus       196 ~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g--~ral~l~PtraLa~Q~~~~l~~~f~~----vglltG  269 (333)
                      +++|.++++.+.+|+++++.||||+|||+++..+++..+..+  .+++|++|+++|++|+++.+++.+..    +..++|
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~   80 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEGKDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLHG   80 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTTSSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEEST
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccCCCceEEEEeecccccccccccccccccccccccccccc
Confidence            689999999999999999999999999999999998766543  49999999999999999999998774    677888


Q ss_pred             CCCCC--------CCcceEEecc---------------CcceEeccccccccccCcCcccccchhh------hhhheecc
Q psy2760         270 LPPVF--------PDVEKLLEDL---------------NIGGLDELSIHDFNKHLKFWKPKVQLDD------LFDWTMAS  320 (333)
Q Consensus       270 d~~~~--------~~a~ili~t~---------------~i~liViDe~H~~~~~~R~~~~~~~l~~------l~~l~~~~  320 (333)
                      +....        .+..+++.|+               .+.++|+||+|.+....++..... +.+      ..+.+++|
T Consensus        81 ~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~iViDE~h~l~~~~~~~~~~~-i~~~~~~~~~~~~i~~S  159 (169)
T PF00270_consen   81 GQSISEDQREVLSNQADILVTTPEQLLDLISNGKINISRLSLIVIDEAHHLSDETFRAMLKS-ILRRLKRFKNIQIILLS  159 (169)
T ss_dssp             TSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSSTGTTESEEEEETHHHHHHTTHHHHHHH-HHHHSHTTTTSEEEEEE
T ss_pred             cccccccccccccccccccccCcchhhccccccccccccceeeccCcccccccccHHHHHHH-HHHHhcCCCCCcEEEEe
Confidence            77633        3467888876               378999999999987542222211 111      25677888


Q ss_pred             Ccch
Q psy2760         321 DATT  324 (333)
Q Consensus       321 d~~~  324 (333)
                      ++..
T Consensus       160 AT~~  163 (169)
T PF00270_consen  160 ATLP  163 (169)
T ss_dssp             SSST
T ss_pred             eCCC
Confidence            7766

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 ....

>KOG0952|consensus

Probab=99.66  E-value=7.6e-17  Score=170.87  Aligned_cols=128  Identities=17%  Similarity=0.255  Sum_probs=103.6

Q ss_pred             CCC-CCCHHHHHHHHHH-HcCCcEEEEcCCCCcHHHHHHHHHHHHhc----------CCCeEEEEcccHHHHHHHHHHHH
Q psy2760         191 WPF-ELDVFQKQAIIKL-EEHNHVFVTAHTSAGKTVIAEYAIALSQN----------HKTRTIYTSPIKALSNQKYRDFR  258 (333)
Q Consensus       191 ~~f-~l~~~Q~~ai~~l-~~g~~vlv~apTGSGKTl~~~l~il~~l~----------~g~ral~l~PtraLa~Q~~~~l~  258 (333)
                      |+| .|+.+|..+|+.+ .++.|.+||||||||||.+|+++|++.+.          .+.+++||+|++|||.++++.|.
T Consensus       106 f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~~~~  185 (1230)
T KOG0952|consen  106 FSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDKFS  185 (1230)
T ss_pred             ccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHHHHh
Confidence            456 8999999999997 88899999999999999999999997664          56899999999999999999999


Q ss_pred             HhcCC----cEEEeCCCCCCCCcceEEeccCcceEeccccccccccCcCcccccchhhhhhheeccCcch
Q psy2760         259 ETFQD----VGLIDDLPPVFPDVEKLLEDLNIGGLDELSIHDFNKHLKFWKPKVQLDDLFDWTMASDATT  324 (333)
Q Consensus       259 ~~f~~----vglltGd~~~~~~a~ili~t~~i~liViDe~H~~~~~~R~~~~~~~l~~l~~l~~~~d~~~  324 (333)
                      ++|..    |.-+|||.+.....   ++.   ..|++.+|++|+..+|.|....++..+++|+++|-++-
T Consensus       186 kkl~~~gi~v~ELTGD~ql~~te---i~~---tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHl  249 (1230)
T KOG0952|consen  186 KKLAPLGISVRELTGDTQLTKTE---IAD---TQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHL  249 (1230)
T ss_pred             hhcccccceEEEecCcchhhHHH---HHh---cCEEEecccceeeeeeeeccchhhhhheeeEEeeeehh
Confidence            99984    67799998865422   121   22346777777777777777777777777777766553

>PTZ00424 helicase 45; Provisional

Probab=99.66  E-value=7.6e-16  Score=151.46  Aligned_cols=123  Identities=11%  Similarity=0.008  Sum_probs=96.4

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~Ptra  248 (333)
                      ++++.+...+...++.      .|+++|.+|++.+..|++++++||||||||++|.++++..+.   .+.++||++||++
T Consensus        34 ~l~~~~~~~l~~~~~~------~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~Pt~~  107 (401)
T PTZ00424         34 KLNEDLLRGIYSYGFE------KPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTRE  107 (401)
T ss_pred             CCCHHHHHHHHHcCCC------CCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECCCHH
Confidence            4666666655444444      799999999999999999999999999999999999987654   4678999999999


Q ss_pred             HHHHHHHHHHHhcCC----cEEEeCCCCCC-------CCcceEEecc---------------CcceEecccccccccc
Q psy2760         249 LSNQKYRDFRETFQD----VGLIDDLPPVF-------PDVEKLLEDL---------------NIGGLDELSIHDFNKH  300 (333)
Q Consensus       249 La~Q~~~~l~~~f~~----vglltGd~~~~-------~~a~ili~t~---------------~i~liViDe~H~~~~~  300 (333)
                      |+.|+.+.+......    ++.+.|+....       ....+++.|+               ++.++|+||+|.+...
T Consensus       108 L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~l~~i~lvViDEah~~~~~  185 (401)
T PTZ00424        108 LAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSR  185 (401)
T ss_pred             HHHHHHHHHHHHhhhcCceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCCcccccccEEEEecHHHHHhc
Confidence            999999988775432    45566665421       2246788876               5688999999987654

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.65  E-value=4.3e-16  Score=168.59  Aligned_cols=129  Identities=20%  Similarity=0.221  Sum_probs=100.7

Q ss_pred             CChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh---------cCCCeEEEE
Q psy2760         173 VSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ---------NHKTRTIYT  243 (333)
Q Consensus       173 L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l---------~~g~ral~l  243 (333)
                      +++.+.++++. ++.      .|+++|++|++.+.+|+|++++||||||||++|.+|++..+         ..+.+++|+
T Consensus        18 l~~~v~~~~~~-~~~------~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyI   90 (876)
T PRK13767         18 LRPYVREWFKE-KFG------TFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYV   90 (876)
T ss_pred             cCHHHHHHHHH-ccC------CCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEE
Confidence            56666666544 222      59999999999999999999999999999999999998543         235679999


Q ss_pred             cccHHHHHHHHHHHHHh-------c---C----C--cEEEeCCCCCCC-------CcceEEecc----------------
Q psy2760         244 SPIKALSNQKYRDFRET-------F---Q----D--VGLIDDLPPVFP-------DVEKLLEDL----------------  284 (333)
Q Consensus       244 ~PtraLa~Q~~~~l~~~-------f---~----~--vglltGd~~~~~-------~a~ili~t~----------------  284 (333)
                      +|||||++|+++++.+.       +   +    +  +++.+||.....       ...++++|+                
T Consensus        91 sPtraLa~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll~~~~~~~~l  170 (876)
T PRK13767         91 SPLRALNNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILLNSPKFREKL  170 (876)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHHhCCCCEEEecHHHHHHHhcChhHHHHH
Confidence            99999999999876531       1   1    2  577899976432       235777775                


Q ss_pred             -CcceEeccccccccccCcCccccc
Q psy2760         285 -NIGGLDELSIHDFNKHLKFWKPKV  308 (333)
Q Consensus       285 -~i~liViDe~H~~~~~~R~~~~~~  308 (333)
                       ++.++|+||+|.+.+..||+....
T Consensus       171 ~~l~~VVIDE~H~l~~~~RG~~l~~  195 (876)
T PRK13767        171 RTVKWVIVDEIHSLAENKRGVHLSL  195 (876)
T ss_pred             hcCCEEEEechhhhccCccHHHHHH
Confidence             467899999999998888876554

>cd00268 DEADc DEAD-box helicases

Probab=99.62  E-value=3.8e-15  Score=132.96  Aligned_cols=131  Identities=15%  Similarity=-0.009  Sum_probs=97.4

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc-----CCCeEEEEcccHHHHHHHHHHHHHhcC--C--c
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN-----HKTRTIYTSPIKALSNQKYRDFRETFQ--D--V  264 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~-----~g~ral~l~PtraLa~Q~~~~l~~~f~--~--v  264 (333)
                      .|+++|+++++.+..|+++++++|||+|||+++.++++..+.     .+.+++|++|+++|+.|+.+.+++...  +  +
T Consensus        21 ~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~L~~q~~~~~~~~~~~~~~~~  100 (203)
T cd00268          21 KPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKV  100 (203)
T ss_pred             CCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHHHHHHHHHHHHHHhccCCceE
Confidence            689999999999999999999999999999999998875442     457899999999999999998877543  2  5


Q ss_pred             EEEeCCCCCCC-------CcceEEecc---------------CcceEeccccccccccCcCccccc---chhhhhhheec
Q psy2760         265 GLIDDLPPVFP-------DVEKLLEDL---------------NIGGLDELSIHDFNKHLKFWKPKV---QLDDLFDWTMA  319 (333)
Q Consensus       265 glltGd~~~~~-------~a~ili~t~---------------~i~liViDe~H~~~~~~R~~~~~~---~l~~l~~l~~~  319 (333)
                      +.++|+.....       +..++++|+               ++.++++||+|.+.....+-....   .+..-..++..
T Consensus       101 ~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~l~~lIvDE~h~~~~~~~~~~~~~~~~~l~~~~~~~~~  180 (203)
T cd00268         101 VVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDRQTLLF  180 (203)
T ss_pred             EEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCCChhhCCEEEEeChHHhhccChHHHHHHHHHhCCcccEEEEE
Confidence            77788766421       446888884               468899999998874432211111   11123446777


Q ss_pred             cCcch
Q psy2760         320 SDATT  324 (333)
Q Consensus       320 ~d~~~  324 (333)
                      |++.+
T Consensus       181 SAT~~  185 (203)
T cd00268         181 SATMP  185 (203)
T ss_pred             eccCC
Confidence            77655

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.

>KOG0338|consensus

Probab=99.62  E-value=5.4e-16  Score=154.77  Aligned_cols=124  Identities=18%  Similarity=0.104  Sum_probs=99.6

Q ss_pred             hccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh------cCCCeEEEE
Q psy2760         170 MLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ------NHKTRTIYT  243 (333)
Q Consensus       170 ~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l------~~g~ral~l  243 (333)
                      ..+||.++...+..+|+.      .|+|+|..+||..+-|++++.||.||||||.+|.+|++..+      ....|+|++
T Consensus       185 ~mNLSRPlLka~~~lGy~------~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL  258 (691)
T KOG0338|consen  185 SMNLSRPLLKACSTLGYK------KPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVL  258 (691)
T ss_pred             hcccchHHHHHHHhcCCC------CCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCcccCcceeEEEE
Confidence            345677777766666655      89999999999999999999999999999999999999543      234789999


Q ss_pred             cccHHHHHHHHHHHHHhc--CC--cEEEeCCCCCCCC-------cceEEecc----------------CcceEecccccc
Q psy2760         244 SPIKALSNQKYRDFRETF--QD--VGLIDDLPPVFPD-------VEKLLEDL----------------NIGGLDELSIHD  296 (333)
Q Consensus       244 ~PtraLa~Q~~~~l~~~f--~~--vglltGd~~~~~~-------a~ili~t~----------------~i~liViDe~H~  296 (333)
                      +|||+|+-|++...++..  .+  +|+..||+....|       -.++|+|+                +|..+|.||+..
T Consensus       259 ~PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDEADR  338 (691)
T KOG0338|consen  259 VPTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEADR  338 (691)
T ss_pred             eccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccceeEEEechHHH
Confidence            999999999998877643  33  8999999987654       25788887                567777888775


Q ss_pred             ccc
Q psy2760         297 FNK  299 (333)
Q Consensus       297 ~~~  299 (333)
                      .-.
T Consensus       339 MLe  341 (691)
T KOG0338|consen  339 MLE  341 (691)
T ss_pred             HHH
Confidence            543

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.61  E-value=4e-15  Score=155.90  Aligned_cols=123  Identities=14%  Similarity=0.125  Sum_probs=98.4

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~Ptra  248 (333)
                      +|++.+...+...|+.      .|+++|.++++.++.|++++++||||||||++|.+|++..+.   .+.++||++|||+
T Consensus        12 ~L~~~ll~al~~~G~~------~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PTre   85 (629)
T PRK11634         12 GLKAPILEALNDLGYE------KPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRE   85 (629)
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCcHH
Confidence            5777887777666665      899999999999999999999999999999999999986553   3568999999999


Q ss_pred             HHHHHHHHHHHhcC---C--cEEEeCCCCCC-------CCcceEEecc---------------CcceEecccccccccc
Q psy2760         249 LSNQKYRDFRETFQ---D--VGLIDDLPPVF-------PDVEKLLEDL---------------NIGGLDELSIHDFNKH  300 (333)
Q Consensus       249 La~Q~~~~l~~~f~---~--vglltGd~~~~-------~~a~ili~t~---------------~i~liViDe~H~~~~~  300 (333)
                      ||.|+++.+.....   +  +..++|+.+..       ....++|.|+               ++.++|+||+|.+...
T Consensus        86 La~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~~l~l~~l~~lVlDEAd~ml~~  164 (629)
T PRK11634         86 LAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRM  164 (629)
T ss_pred             HHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcchhhceEEEeccHHHHhhc
Confidence            99999988766432   2  55567776543       2346888886               4677999999977544

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.60  E-value=4.3e-15  Score=156.91  Aligned_cols=139  Identities=19%  Similarity=0.126  Sum_probs=112.3

Q ss_pred             CCCCCHHHHHHHHHHHc---CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-cEEE
Q psy2760         192 PFELDVFQKQAIIKLEE---HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-VGLI  267 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~---g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-vgll  267 (333)
                      ++.|++.|++|+..+..   ++++++.|+||||||.+|+.++...+..|.++++++||++|+.|++++|++.|+. +.++
T Consensus       142 ~~~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~  221 (679)
T PRK05580        142 PPTLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVL  221 (679)
T ss_pred             CCCCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEE
Confidence            45799999999999865   4789999999999999999988888888999999999999999999999998875 8889


Q ss_pred             eCCCCCC-----------CCcceEEecc--------CcceEeccccccccccC-cCccc-------ccchhhhhhheecc
Q psy2760         268 DDLPPVF-----------PDVEKLLEDL--------NIGGLDELSIHDFNKHL-KFWKP-------KVQLDDLFDWTMAS  320 (333)
Q Consensus       268 tGd~~~~-----------~~a~ili~t~--------~i~liViDe~H~~~~~~-R~~~~-------~~~l~~l~~l~~~~  320 (333)
                      +|+.+..           ....++|.|.        ++.++|+||.|...-.. ++..+       .++......++++|
T Consensus       222 ~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~~p~~~l~liVvDEeh~~s~~~~~~p~y~~r~va~~ra~~~~~~~il~S  301 (679)
T PRK05580        222 HSGLSDGERLDEWRKAKRGEAKVVIGARSALFLPFKNLGLIIVDEEHDSSYKQQEGPRYHARDLAVVRAKLENIPVVLGS  301 (679)
T ss_pred             ECCCCHHHHHHHHHHHHcCCCCEEEeccHHhcccccCCCEEEEECCCccccccCcCCCCcHHHHHHHHhhccCCCEEEEc
Confidence            9887642           2346888875        68999999999775332 22222       12234457899999


Q ss_pred             Ccchhhhhhc
Q psy2760         321 DATTLEIFTY  330 (333)
Q Consensus       321 d~~~~e~~~~  330 (333)
                      +++++|.|..
T Consensus       302 ATps~~s~~~  311 (679)
T PRK05580        302 ATPSLESLAN  311 (679)
T ss_pred             CCCCHHHHHH
Confidence            9999999865

>KOG0331|consensus

Probab=99.58  E-value=4.1e-15  Score=150.77  Aligned_cols=125  Identities=14%  Similarity=0.053  Sum_probs=101.1

Q ss_pred             ccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC---------CCeEE
Q psy2760         171 LDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH---------KTRTI  241 (333)
Q Consensus       171 ~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~---------g~ral  241 (333)
                      .+|+.......+..++.      .|+|+|.++++.++.|++++..|.||||||++|++|++.++..         ++++|
T Consensus        96 ~~ls~~~~~~lk~~g~~------~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vL  169 (519)
T KOG0331|consen   96 LGLSEELMKALKEQGFE------KPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVL  169 (519)
T ss_pred             ccccHHHHHHHHhcCCC------CCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEE
Confidence            34555555555555555      7999999999999999999999999999999999999866543         78999


Q ss_pred             EEcccHHHHHHHHHHHHHhcCC----cEEEeCCCCCCCCc-------ceEEecc---------------CcceEeccccc
Q psy2760         242 YTSPIKALSNQKYRDFRETFQD----VGLIDDLPPVFPDV-------EKLLEDL---------------NIGGLDELSIH  295 (333)
Q Consensus       242 ~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~~~~~a-------~ili~t~---------------~i~liViDe~H  295 (333)
                      +++|||+||.|+.+.+.+....    ...++|+.+..+|.       .++|+|+               .+.++|+||+.
T Consensus       170 VL~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~l~~gvdiviaTPGRl~d~le~g~~~l~~v~ylVLDEAD  249 (519)
T KOG0331|consen  170 VLAPTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEAD  249 (519)
T ss_pred             EEcCcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHHHhcCCcEEEeCChHHHHHHHcCCccccceeEEEeccHH
Confidence            9999999999999999884443    45678888877653       5888887               57889999999


Q ss_pred             cccccC
Q psy2760         296 DFNKHL  301 (333)
Q Consensus       296 ~~~~~~  301 (333)
                      ...+++
T Consensus       250 rMldmG  255 (519)
T KOG0331|consen  250 RMLDMG  255 (519)
T ss_pred             hhhccc
Confidence            776664

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.58  E-value=1.1e-14  Score=147.64  Aligned_cols=114  Identities=13%  Similarity=0.128  Sum_probs=90.3

Q ss_pred             cCCC-CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEe
Q psy2760         190 TWPF-ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLID  268 (333)
Q Consensus       190 ~~~f-~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vgllt  268 (333)
                      .|+| .|+|+|.+|++.++.|+++++++|||||||++|.+|++.   .+..+||++||++|+.|+.+.++...-.+..++
T Consensus         6 ~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~---~~~~~lVi~P~~~L~~dq~~~l~~~gi~~~~l~   82 (470)
T TIGR00614         6 VFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALC---SDGITLVISPLISLMEDQVLQLKASGIPATFLN   82 (470)
T ss_pred             hcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHH---cCCcEEEEecHHHHHHHHHHHHHHcCCcEEEEe
Confidence            3555 899999999999999999999999999999999999864   356799999999999999999976333467777


Q ss_pred             CCCCCC-----------CCcceEEecc-----------------CcceEeccccccccccCcCccc
Q psy2760         269 DLPPVF-----------PDVEKLLEDL-----------------NIGGLDELSIHDFNKHLKFWKP  306 (333)
Q Consensus       269 Gd~~~~-----------~~a~ili~t~-----------------~i~liViDe~H~~~~~~R~~~~  306 (333)
                      |+....           .+..+++.|+                 ++.++|+||+|.+...+..++.
T Consensus        83 ~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~~iViDEaH~i~~~g~~fr~  148 (470)
T TIGR00614        83 SSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRP  148 (470)
T ss_pred             CCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCcCEEEEeCCcccCccccccHH
Confidence            765532           2235665554                 4678999999998766554444

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

>KOG0330|consensus

Probab=99.57  E-value=1.9e-15  Score=146.95  Aligned_cols=115  Identities=17%  Similarity=0.111  Sum_probs=92.2

Q ss_pred             CcccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc---CCCe
Q psy2760         163 TQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN---HKTR  239 (333)
Q Consensus       163 ~~~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~---~g~r  239 (333)
                      .+..|++ .++++.+.+.++..++.      .|+++|+++||.+++|++|++.|.||||||.+|.+||++++-   +..+
T Consensus        59 ~~~sf~d-Lgv~~~L~~ac~~l~~~------~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~  131 (476)
T KOG0330|consen   59 SFKSFAD-LGVHPELLEACQELGWK------KPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPKLFF  131 (476)
T ss_pred             hhcchhh-cCcCHHHHHHHHHhCcC------CCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCCce
Confidence            3444444 46788888888887766      899999999999999999999999999999999999997763   3468


Q ss_pred             EEEEcccHHHHHHHHHHHHHhcCC----cEEEeCCCCCCCCc-------ceEEecc
Q psy2760         240 TIYTSPIKALSNQKYRDFRETFQD----VGLIDDLPPVFPDV-------EKLLEDL  284 (333)
Q Consensus       240 al~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~~~~~a-------~ili~t~  284 (333)
                      +++++|||+||.|+.+.|...-+.    +..+.||.....++       .++|+|+
T Consensus       132 ~lVLtPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~~~L~kkPhilVaTP  187 (476)
T KOG0330|consen  132 ALVLTPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLSKKPHILVATP  187 (476)
T ss_pred             EEEecCcHHHHHHHHHHHHHhccccCeEEEEEecCchHHHHHHHhhcCCCEEEeCc
Confidence            999999999999999999774343    56678887765433       3556655

>KOG0345|consensus

Probab=99.56  E-value=1.9e-14  Score=142.71  Aligned_cols=124  Identities=16%  Similarity=0.049  Sum_probs=100.1

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh--c-----CC-CeEEEE
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ--N-----HK-TRTIYT  243 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l--~-----~g-~ral~l  243 (333)
                      +|++++...+...|+.      .+||.|..+||.++.+++|++-|+||||||++|++|++..+  +     ++ ..+++|
T Consensus        12 ~L~~~l~~~l~~~GF~------~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalII   85 (567)
T KOG0345|consen   12 PLSPWLLEALDESGFE------KMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALII   85 (567)
T ss_pred             CccHHHHHHHHhcCCc------ccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEEEe
Confidence            4788888877766666      69999999999999999999999999999999999998544  1     12 469999


Q ss_pred             cccHHHHHHHHHHHHHh---cCC--cEEEeCCCCCCC--------CcceEEecc-----------------CcceEeccc
Q psy2760         244 SPIKALSNQKYRDFRET---FQD--VGLIDDLPPVFP--------DVEKLLEDL-----------------NIGGLDELS  293 (333)
Q Consensus       244 ~PtraLa~Q~~~~l~~~---f~~--vglltGd~~~~~--------~a~ili~t~-----------------~i~liViDe  293 (333)
                      +|||+|+.|+.......   +.+  +.+++||.+...        ..+++|+|+                 ++.++|+||
T Consensus        86 sPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVLDE  165 (567)
T KOG0345|consen   86 SPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVLDE  165 (567)
T ss_pred             cCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccccceEEecc
Confidence            99999999999776543   333  677888876542        346889887                 467899999


Q ss_pred             cccccccC
Q psy2760         294 IHDFNKHL  301 (333)
Q Consensus       294 ~H~~~~~~  301 (333)
                      +..+.+.+
T Consensus       166 ADrLldmg  173 (567)
T KOG0345|consen  166 ADRLLDMG  173 (567)
T ss_pred             hHhHhccc
Confidence            99888775

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

Probab=99.55  E-value=2.1e-14  Score=147.24  Aligned_cols=123  Identities=15%  Similarity=0.086  Sum_probs=100.9

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc--CC-C-e-EEEEccc
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN--HK-T-R-TIYTSPI  246 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~--~g-~-r-al~l~Pt  246 (333)
                      ++++.+...+...++.      .|+|+|.++||.++.|+++++.|+||||||++|.+|++..+.  .. . . +|+++||
T Consensus        35 ~l~~~ll~~l~~~gf~------~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~PT  108 (513)
T COG0513          35 GLSPELLQALKDLGFE------EPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPT  108 (513)
T ss_pred             CCCHHHHHHHHHcCCC------CCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEECCC
Confidence            3677777777666666      899999999999999999999999999999999999997654  22 1 2 9999999


Q ss_pred             HHHHHHHHHHHHHhcC---C--cEEEeCCCCCCC-------CcceEEecc---------------CcceEeccccccccc
Q psy2760         247 KALSNQKYRDFRETFQ---D--VGLIDDLPPVFP-------DVEKLLEDL---------------NIGGLDELSIHDFNK  299 (333)
Q Consensus       247 raLa~Q~~~~l~~~f~---~--vglltGd~~~~~-------~a~ili~t~---------------~i~liViDe~H~~~~  299 (333)
                      |+||.|+++.+.....   .  +..++|+.+...       ..+++|+|+               .+.++|+||+..+.+
T Consensus       109 RELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~~~l~l~~v~~lVlDEADrmLd  188 (513)
T COG0513         109 RELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLD  188 (513)
T ss_pred             HHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhcCCCEEEECccHHHHHHHcCCcchhhcCEEEeccHhhhhc
Confidence            9999999999877433   2  567889887543       256899987               578899999998877


Q ss_pred             c
Q psy2760         300 H  300 (333)
Q Consensus       300 ~  300 (333)
                      .
T Consensus       189 ~  189 (513)
T COG0513         189 M  189 (513)
T ss_pred             C
Confidence            7

>KOG0348|consensus

Probab=99.55  E-value=1.7e-14  Score=144.81  Aligned_cols=126  Identities=20%  Similarity=0.154  Sum_probs=97.4

Q ss_pred             hccCChhhhhhhh-ccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh---------cCCCe
Q psy2760         170 MLDVSKPVLDFDA-KVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ---------NHKTR  239 (333)
Q Consensus       170 ~~~L~~~l~~~~~-~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l---------~~g~r  239 (333)
                      ..+|++-+.+-++ ..++.      .|+.+|+++||.+++|++++|.++||||||++|++|+.+.+         ..|.-
T Consensus       140 ~LGL~~~lv~~L~~~m~i~------~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~  213 (708)
T KOG0348|consen  140 SLGLHPHLVSHLNTKMKIS------APTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPY  213 (708)
T ss_pred             hcCCCHHHHHHHHHHhccC------ccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccCCce
Confidence            3567777776544 33344      79999999999999999999999999999999999998654         35788


Q ss_pred             EEEEcccHHHHHHHHHHHHHhcCC-----cEEEeCCCCCCC-------CcceEEecc----------------CcceEec
Q psy2760         240 TIYTSPIKALSNQKYRDFRETFQD-----VGLIDDLPPVFP-------DVEKLLEDL----------------NIGGLDE  291 (333)
Q Consensus       240 al~l~PtraLa~Q~~~~l~~~f~~-----vglltGd~~~~~-------~a~ili~t~----------------~i~liVi  291 (333)
                      +++++|||+||.|+|+.++++...     -|.+.||-+...       .-.++|.|+                .+-.+|.
T Consensus       214 ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~LRwlVl  293 (708)
T KOG0348|consen  214 ALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRLRWLVL  293 (708)
T ss_pred             EEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhccchheeeeeeEEEe
Confidence            999999999999999999887765     266777655422       235788877                3455677


Q ss_pred             cccccccccC
Q psy2760         292 LSIHDFNKHL  301 (333)
Q Consensus       292 De~H~~~~~~  301 (333)
                      ||...+.+.+
T Consensus       294 DEaDrlleLG  303 (708)
T KOG0348|consen  294 DEADRLLELG  303 (708)
T ss_pred             cchhHHHhcc
Confidence            7777665543

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

Probab=99.54  E-value=1.5e-14  Score=146.42  Aligned_cols=138  Identities=25%  Similarity=0.328  Sum_probs=114.3

Q ss_pred             ccCChhhhhhhhccccccccCCCCCCHHHHHHHHH-HHcCCcEEEEcCCCCcHHHHHHHHHH-HHhcCCCeEEEEcccHH
Q psy2760         171 LDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIK-LEEHNHVFVTAHTSAGKTVIAEYAIA-LSQNHKTRTIYTSPIKA  248 (333)
Q Consensus       171 ~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~-l~~g~~vlv~apTGSGKTl~~~l~il-~~l~~g~ral~l~Ptra  248 (333)
                      .+++++++..++..|+.      .+.|.|.-|+.. ++.|+|.+|.++|+||||++..+|-+ ..+..|.+-+|++|..|
T Consensus       199 Ldipe~fk~~lk~~G~~------eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~~g~KmlfLvPLVA  272 (830)
T COG1202         199 LDIPEKFKRMLKREGIE------ELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSGGKKMLFLVPLVA  272 (830)
T ss_pred             cCCcHHHHHHHHhcCcc------eecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHhCCCeEEEEehhHH
Confidence            46788899999888888      899999999998 79999999999999999999999766 55667999999999999


Q ss_pred             HHHHHHHHHHHhcCCcE----EEeCCC-----------CCCCCcceEEecc--------------CcceEeccccccccc
Q psy2760         249 LSNQKYRDFRETFQDVG----LIDDLP-----------PVFPDVEKLLEDL--------------NIGGLDELSIHDFNK  299 (333)
Q Consensus       249 La~Q~~~~l~~~f~~vg----lltGd~-----------~~~~~a~ili~t~--------------~i~liViDe~H~~~~  299 (333)
                      ||||.+++|++++++.|    +..|-.           ...+.++++|.|.              +++.+|+||+|++.+
T Consensus       273 LANQKy~dF~~rYs~LglkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg~~lgdiGtVVIDEiHtL~d  352 (830)
T COG1202         273 LANQKYEDFKERYSKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTGKDLGDIGTVVIDEIHTLED  352 (830)
T ss_pred             hhcchHHHHHHHhhcccceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcCCcccccceEEeeeeeeccc
Confidence            99999999999998633    333322           2234578899876              789999999999999


Q ss_pred             cCcCcccccchhhhhh
Q psy2760         300 HLKFWKPKVQLDDLFD  315 (333)
Q Consensus       300 ~~R~~~~~~~l~~l~~  315 (333)
                      ..||-+-.- ++-.++
T Consensus       353 eERG~RLdG-LI~RLr  367 (830)
T COG1202         353 EERGPRLDG-LIGRLR  367 (830)
T ss_pred             hhcccchhh-HHHHHH
Confidence            999988665 444444

>KOG0347|consensus

Probab=99.54  E-value=2.3e-15  Score=151.35  Aligned_cols=119  Identities=13%  Similarity=0.161  Sum_probs=97.7

Q ss_pred             CCCCCcccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcC-CcEEEEcCCCCcHHHHHHHHHHHHh---
Q psy2760         159 PKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEH-NHVFVTAHTSAGKTVIAEYAIALSQ---  234 (333)
Q Consensus       159 ~~~~~~~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g-~~vlv~apTGSGKTl~~~l~il~~l---  234 (333)
                      ......+.|..- .|+..+...+...|+.      .|+++|.-+++++..| .++++.|.||||||++|.+||+..+   
T Consensus       175 ~~~~DvsAW~~l-~lp~~iL~aL~~~gFs------~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~  247 (731)
T KOG0347|consen  175 SSKVDVSAWKNL-FLPMEILRALSNLGFS------RPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLES  247 (731)
T ss_pred             ccccChHHHhcC-CCCHHHHHHHHhcCCC------CCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhc
Confidence            445688899987 8999999888777776      8999999999999888 7999999999999999999998521   


Q ss_pred             -----------cCCCe--EEEEcccHHHHHHHHHHHHHhcCC----cEEEeCCCCCCCCc-------ceEEecc
Q psy2760         235 -----------NHKTR--TIYTSPIKALSNQKYRDFRETFQD----VGLIDDLPPVFPDV-------EKLLEDL  284 (333)
Q Consensus       235 -----------~~g~r--al~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~~~~~a-------~ili~t~  284 (333)
                                 ..+.+  +|+++|||+||.|+.+++......    +..++||+....|.       .++|+|+
T Consensus       248 s~~s~e~~~~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~~p~IVVATP  321 (731)
T KOG0347|consen  248 SDDSQELSNTSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQRPDIVVATP  321 (731)
T ss_pred             cchHhhhhhHHhccCcceeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhcCCCEEEecc
Confidence                       23445  999999999999999999876553    67789998876544       4666665

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

Probab=99.54  E-value=1.8e-14  Score=155.20  Aligned_cols=108  Identities=25%  Similarity=0.228  Sum_probs=89.9

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc--CCCeEEEEcccHHHHHHHHHHHHHhcCC------cE
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN--HKTRTIYTSPIKALSNQKYRDFRETFQD------VG  265 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~--~g~ral~l~PtraLa~Q~~~~l~~~f~~------vg  265 (333)
                      .|++||.+|+..+.+|+|++|++|||||||++|++||+..+.  ...++||++||+|||+.+.++|++....      ++
T Consensus        70 ~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a~AL~lYPtnALa~DQ~~rl~~~~~~~~~~v~~~  149 (851)
T COG1205          70 RLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNALANDQAERLRELISDLPGKVTFG  149 (851)
T ss_pred             cccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcCccEEEEechhhhHhhHHHHHHHHHHhCCCcceee
Confidence            599999999999999999999999999999999999996653  3457899999999999999998775432      57


Q ss_pred             EEeCCCCCCCC-------cceEEecc-------------------CcceEeccccccccccC
Q psy2760         266 LIDDLPPVFPD-------VEKLLEDL-------------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       266 lltGd~~~~~~-------a~ili~t~-------------------~i~liViDe~H~~~~~~  301 (333)
                      .++||+.....       .++++.++                   ++-++|+||+|.+....
T Consensus       150 ~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYrGv~  211 (851)
T COG1205         150 RYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRGVQ  211 (851)
T ss_pred             eecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceeccccc
Confidence            79999886543       25666654                   67889999999886553

>KOG0343|consensus

Probab=99.51  E-value=1.6e-14  Score=145.41  Aligned_cols=123  Identities=17%  Similarity=0.118  Sum_probs=98.3

Q ss_pred             CChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh-------cCCCeEEEEcc
Q psy2760         173 VSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ-------NHKTRTIYTSP  245 (333)
Q Consensus       173 L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l-------~~g~ral~l~P  245 (333)
                      |+.++...++...+.      .++.+|+++|+..++|++|+..|.||||||++|++|++.++       ..|..+|+|+|
T Consensus        76 ls~~t~kgLke~~fv------~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGalIISP  149 (758)
T KOG0343|consen   76 LSQKTLKGLKEAKFV------KMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGALIISP  149 (758)
T ss_pred             CchHHHHhHhhcCCc------cHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCCCCCceeEEecc
Confidence            344444444443333      79999999999999999999999999999999999999554       35788999999


Q ss_pred             cHHHHHHHHHHHHHhcCC----cEEEeCCCCCC------CCcceEEecc----------------CcceEeccccccccc
Q psy2760         246 IKALSNQKYRDFRETFQD----VGLIDDLPPVF------PDVEKLLEDL----------------NIGGLDELSIHDFNK  299 (333)
Q Consensus       246 traLa~Q~~~~l~~~f~~----vglltGd~~~~------~~a~ili~t~----------------~i~liViDe~H~~~~  299 (333)
                      ||+||.|++..+.+.-..    .|++.||....      .+..++|||+                ++-++|.||+..+-+
T Consensus       150 TRELA~QtFevL~kvgk~h~fSaGLiiGG~~~k~E~eRi~~mNILVCTPGRLLQHmde~~~f~t~~lQmLvLDEADR~LD  229 (758)
T KOG0343|consen  150 TRELALQTFEVLNKVGKHHDFSAGLIIGGKDVKFELERISQMNILVCTPGRLLQHMDENPNFSTSNLQMLVLDEADRMLD  229 (758)
T ss_pred             hHHHHHHHHHHHHHHhhccccccceeecCchhHHHHHhhhcCCeEEechHHHHHHhhhcCCCCCCcceEEEeccHHHHHH
Confidence            999999999999774332    79999987653      2357899987                577788899988776


Q ss_pred             cC
Q psy2760         300 HL  301 (333)
Q Consensus       300 ~~  301 (333)
                      ++
T Consensus       230 MG  231 (758)
T KOG0343|consen  230 MG  231 (758)
T ss_pred             Hh
Confidence            64

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.50  E-value=1.3e-13  Score=143.31  Aligned_cols=113  Identities=16%  Similarity=0.166  Sum_probs=89.2

Q ss_pred             cCCC-CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEe
Q psy2760         190 TWPF-ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLID  268 (333)
Q Consensus       190 ~~~f-~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vgllt  268 (333)
                      .|+| .|++.|.++++.++.|+++++++|||+|||++|.+|++.   .+..++|++|+++|+.|+.+.++...-.+..++
T Consensus         8 ~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~---~~g~~lVisPl~sL~~dq~~~l~~~gi~~~~~~   84 (591)
T TIGR01389         8 TFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALL---LKGLTVVISPLISLMKDQVDQLRAAGVAAAYLN   84 (591)
T ss_pred             hcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHH---cCCcEEEEcCCHHHHHHHHHHHHHcCCcEEEEe
Confidence            3666 799999999999999999999999999999999998864   355789999999999999999987433467777


Q ss_pred             CCCCCC-----------CCcceEEecc---------------CcceEeccccccccccCcCcc
Q psy2760         269 DLPPVF-----------PDVEKLLEDL---------------NIGGLDELSIHDFNKHLKFWK  305 (333)
Q Consensus       269 Gd~~~~-----------~~a~ili~t~---------------~i~liViDe~H~~~~~~R~~~  305 (333)
                      |+....           ....+++.|+               ++.++|+||+|.+...+..++
T Consensus        85 s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~~l~~~~l~~iViDEaH~i~~~g~~fr  147 (591)
T TIGR01389        85 STLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLNMLQRIPIALVAVDEAHCVSQWGHDFR  147 (591)
T ss_pred             CCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHHHHhcCCCCEEEEeCCcccccccCccH
Confidence            765432           1234555543               578899999999876544443

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=99.49  E-value=1.9e-13  Score=142.74  Aligned_cols=114  Identities=13%  Similarity=0.115  Sum_probs=88.6

Q ss_pred             CCC-CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEeC
Q psy2760         191 WPF-ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDD  269 (333)
Q Consensus       191 ~~f-~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vglltG  269 (333)
                      |+| .|+++|.++++.+..|+++++++|||+|||++|.+|++..   +..++|++|+++|+.|+.+.++...-.+..+.+
T Consensus        21 fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~---~g~tlVisPl~sL~~dqv~~l~~~gi~~~~~~s   97 (607)
T PRK11057         21 FGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL---DGLTLVVSPLISLMKDQVDQLLANGVAAACLNS   97 (607)
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc---CCCEEEEecHHHHHHHHHHHHHHcCCcEEEEcC
Confidence            566 7999999999999999999999999999999999998743   457999999999999999999874333555655


Q ss_pred             CCCCC-----------CCcceEEecc---------------CcceEeccccccccccCcCcccc
Q psy2760         270 LPPVF-----------PDVEKLLEDL---------------NIGGLDELSIHDFNKHLKFWKPK  307 (333)
Q Consensus       270 d~~~~-----------~~a~ili~t~---------------~i~liViDe~H~~~~~~R~~~~~  307 (333)
                      +....           .+..+++.++               ++.++|+||+|.+...++.++..
T Consensus        98 ~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~~~l~~~~l~~iVIDEaH~i~~~G~~fr~~  161 (607)
T PRK11057         98 TQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLEHLAHWNPALLAVDEAHCISQWGHDFRPE  161 (607)
T ss_pred             CCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHHHHHhhCCCCEEEEeCccccccccCcccHH
Confidence            54321           1224555443               47889999999988776665543

>PRK09401 reverse gyrase; Reviewed

Probab=99.48  E-value=2e-13  Score=151.29  Aligned_cols=115  Identities=13%  Similarity=0.012  Sum_probs=89.8

Q ss_pred             ccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC----c
Q psy2760         189 HTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD----V  264 (333)
Q Consensus       189 ~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----v  264 (333)
                      ..+++.|+++|+++++.++.|++++++||||||||.+++.++.....++.+++|++|||+||.|+++++++....    +
T Consensus        75 ~~~G~~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~f~l~~~~~l~~~g~~alIL~PTreLa~Qi~~~l~~l~~~~~~~~  154 (1176)
T PRK09401         75 KKTGSKPWSLQRTWAKRLLLGESFAIIAPTGVGKTTFGLVMSLYLAKKGKKSYIIFPTRLLVEQVVEKLEKFGEKVGCGV  154 (1176)
T ss_pred             HhcCCCCcHHHHHHHHHHHCCCcEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEEeccHHHHHHHHHHHHHHhhhcCceE
Confidence            345668999999999999999999999999999997555444444456889999999999999999999886543    4


Q ss_pred             EEEeCCCCC-------------CCCcceEEecc-------------CcceEeccccccccccCcC
Q psy2760         265 GLIDDLPPV-------------FPDVEKLLEDL-------------NIGGLDELSIHDFNKHLKF  303 (333)
Q Consensus       265 glltGd~~~-------------~~~a~ili~t~-------------~i~liViDe~H~~~~~~R~  303 (333)
                      ..+.|+...             .....++|+|+             .+.++|+||+|.+...+|.
T Consensus       155 ~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~~l~~~~~~~lVvDEaD~~L~~~k~  219 (1176)
T PRK09401        155 KILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFDELPKKKFDFVFVDDVDAVLKSSKN  219 (1176)
T ss_pred             EEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHHhccccccCEEEEEChHHhhhcccc
Confidence            445554321             12357888886             3788999999998776554

>KOG0342|consensus

Probab=99.47  E-value=6.4e-14  Score=139.52  Aligned_cols=153  Identities=17%  Similarity=0.127  Sum_probs=112.9

Q ss_pred             hhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh-------cCCCeEE
Q psy2760         169 EMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ-------NHKTRTI  241 (333)
Q Consensus       169 ~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l-------~~g~ral  241 (333)
                      +...|++.+...++..|+.      .++++|..+++.++.|+++++.|.||+|||++|++|++..+       +.+..++
T Consensus        85 ~~~~LS~~t~kAi~~~GF~------~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vl  158 (543)
T KOG0342|consen   85 EEGSLSPLTLKAIKEMGFE------TMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVL  158 (543)
T ss_pred             hccccCHHHHHHHHhcCcc------chhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCCCCeeEE
Confidence            3344566665555555555      79999999999999999999999999999999999988443       4678899


Q ss_pred             EEcccHHHHHHHHHHHHHhcC-----CcEEEeCCCCCCCC-------cceEEecc----------------CcceEeccc
Q psy2760         242 YTSPIKALSNQKYRDFRETFQ-----DVGLIDDLPPVFPD-------VEKLLEDL----------------NIGGLDELS  293 (333)
Q Consensus       242 ~l~PtraLa~Q~~~~l~~~f~-----~vglltGd~~~~~~-------a~ili~t~----------------~i~liViDe  293 (333)
                      +++|||+||.|++.+.++...     .++++.||.....+       ..++|+|+                +.-++|+||
T Consensus       159 Ii~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~lvlDE  238 (543)
T KOG0342|consen  159 IICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCLVLDE  238 (543)
T ss_pred             EecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhccccEEEeCCchHHhHhhcCCcchhhccceeEeec
Confidence            999999999999998877653     28999999876433       35788887                344688999


Q ss_pred             cccccccCcCccccc-ch----hhhhhheeccCcchhhhhh
Q psy2760         294 IHDFNKHLKFWKPKV-QL----DDLFDWTMASDATTLEIFT  329 (333)
Q Consensus       294 ~H~~~~~~R~~~~~~-~l----~~l~~l~~~~d~~~~e~~~  329 (333)
                      +..+.+.+  ++... +.    =+..+-++.|+.++-|+.+
T Consensus       239 ADrlLd~G--F~~di~~Ii~~lpk~rqt~LFSAT~~~kV~~  277 (543)
T KOG0342|consen  239 ADRLLDIG--FEEDVEQIIKILPKQRQTLLFSATQPSKVKD  277 (543)
T ss_pred             chhhhhcc--cHHHHHHHHHhccccceeeEeeCCCcHHHHH
Confidence            98876654  33221 11    1234456677776666543

>KOG0340|consensus

Probab=99.46  E-value=1.2e-13  Score=133.14  Aligned_cols=99  Identities=19%  Similarity=0.133  Sum_probs=85.4

Q ss_pred             hccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC---CCeEEEEccc
Q psy2760         170 MLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH---KTRTIYTSPI  246 (333)
Q Consensus       170 ~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~---g~ral~l~Pt  246 (333)
                      ..+|++|+.+-++..++.      .++|+|..+||.++.|++++.||.||||||.+|.+||+..+..   |.=++++.||
T Consensus        11 ~LGl~~Wlve~l~~l~i~------~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTPT   84 (442)
T KOG0340|consen   11 ILGLSPWLVEQLKALGIK------KPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTPT   84 (442)
T ss_pred             hcCccHHHHHHHHHhcCC------CCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCCCcceEEEecch
Confidence            357888999988888888      8999999999999999999999999999999999999987754   4568999999


Q ss_pred             HHHHHHHHHHHHHhcCC----cEEEeCCCCCC
Q psy2760         247 KALSNQKYRDFRETFQD----VGLIDDLPPVF  274 (333)
Q Consensus       247 raLa~Q~~~~l~~~f~~----vglltGd~~~~  274 (333)
                      |+||-|+.++|...-..    +.++.|+...-
T Consensus        85 rELA~QiaEQF~alGk~l~lK~~vivGG~d~i  116 (442)
T KOG0340|consen   85 RELALQIAEQFIALGKLLNLKVSVIVGGTDMI  116 (442)
T ss_pred             HHHHHHHHHHHHHhcccccceEEEEEccHHHh
Confidence            99999999999764332    67788876643

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.45  E-value=5.8e-13  Score=136.19  Aligned_cols=108  Identities=19%  Similarity=0.154  Sum_probs=83.7

Q ss_pred             CCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC-CCeEEEEcccHHHHHHHHHHHHHhcC----CcEEE
Q psy2760         193 FELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH-KTRTIYTSPIKALSNQKYRDFRETFQ----DVGLI  267 (333)
Q Consensus       193 f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~-g~ral~l~PtraLa~Q~~~~l~~~f~----~vgll  267 (333)
                      +.|+++|.+|+..+..+++.++++|||+|||+++...+...... ..++|+++||++|+.|+.++|++...    .++.+
T Consensus       113 ~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~~~~~~~~~~~vLilvpt~eL~~Q~~~~l~~~~~~~~~~~~~i  192 (501)
T PHA02558        113 IEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLENYEGKVLIIVPTTSLVTQMIDDFVDYRLFPREAMHKI  192 (501)
T ss_pred             CCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHHHHHHhcCCCeEEEEECcHHHHHHHHHHHHHhccccccceeEE
Confidence            47999999999999889999999999999999876544333333 34999999999999999999987432    13344


Q ss_pred             eCCCCCCCCcceEEecc------------CcceEecccccccccc
Q psy2760         268 DDLPPVFPDVEKLLEDL------------NIGGLDELSIHDFNKH  300 (333)
Q Consensus       268 tGd~~~~~~a~ili~t~------------~i~liViDe~H~~~~~  300 (333)
                      .|+........++|+|+            ++.++|+||+|.+...
T Consensus       193 ~~g~~~~~~~~I~VaT~qsl~~~~~~~~~~~~~iIvDEaH~~~~~  237 (501)
T PHA02558        193 YSGTAKDTDAPIVVSTWQSAVKQPKEWFDQFGMVIVDECHLFTGK  237 (501)
T ss_pred             ecCcccCCCCCEEEeeHHHHhhchhhhccccCEEEEEchhcccch
Confidence            45544444567888874            5688999999998653

>KOG0350|consensus

Probab=99.44  E-value=2e-13  Score=136.35  Aligned_cols=114  Identities=18%  Similarity=0.179  Sum_probs=89.4

Q ss_pred             CCCHHHHHHHHHH---------HcCCcEEEEcCCCCcHHHHHHHHHHHHhcC----CCeEEEEcccHHHHHHHHHHHHHh
Q psy2760         194 ELDVFQKQAIIKL---------EEHNHVFVTAHTSAGKTVIAEYAIALSQNH----KTRTIYTSPIKALSNQKYRDFRET  260 (333)
Q Consensus       194 ~l~~~Q~~ai~~l---------~~g~~vlv~apTGSGKTl~~~l~il~~l~~----g~ral~l~PtraLa~Q~~~~l~~~  260 (333)
                      .+.|+|..+++-+         ..+++++|.||||||||++|.+||.+.+..    .-|+++|+|||+|+.|+++.|.+.
T Consensus       159 ~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~LRavVivPtr~L~~QV~~~f~~~  238 (620)
T KOG0350|consen  159 RLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTRELALQVYDTFKRL  238 (620)
T ss_pred             cccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHHHccCCccceEEEEEeeHHHHHHHHHHHHHHh
Confidence            7889999998885         246899999999999999999999987754    368999999999999999999887


Q ss_pred             cCC----cEEEeCCCCCCC------------CcceEEecc----------------CcceEeccccccccccC-cCcccc
Q psy2760         261 FQD----VGLIDDLPPVFP------------DVEKLLEDL----------------NIGGLDELSIHDFNKHL-KFWKPK  307 (333)
Q Consensus       261 f~~----vglltGd~~~~~------------~a~ili~t~----------------~i~liViDe~H~~~~~~-R~~~~~  307 (333)
                      ..+    |+.++|..+...            +..++|.|+                ++-++|+||+..+.+.. -+|-..
T Consensus       239 ~~~tgL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~LrfLVIDEADRll~qsfQ~Wl~~  318 (620)
T KOG0350|consen  239 NSGTGLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNNTKSFDLKHLRFLVIDEADRLLDQSFQEWLDT  318 (620)
T ss_pred             ccCCceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhccCCCCcchhhceEEEechHHHHHHHHHHHHHHH
Confidence            765    566777655421            236888887                46778999998775543 235443

>TIGR00595 priA primosomal protein N'

Probab=99.44  E-value=1.8e-13  Score=140.18  Aligned_cols=119  Identities=17%  Similarity=0.072  Sum_probs=95.1

Q ss_pred             EEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-cEEEeCCCCCC-----------CCcceE
Q psy2760         213 FVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-VGLIDDLPPVF-----------PDVEKL  280 (333)
Q Consensus       213 lv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-vglltGd~~~~-----------~~a~il  280 (333)
                      ++.||||||||++|+.++...+..|.+++|++|+++|+.|++++|++.|+. +.+++|+.+..           ....++
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~g~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IV   80 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVV   80 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEE
Confidence            478999999999998888777888999999999999999999999998875 88898877542           234677


Q ss_pred             Eecc--------CcceEeccccccccccC-cCc-------ccccchhhhhhheeccCcchhhhhhcc
Q psy2760         281 LEDL--------NIGGLDELSIHDFNKHL-KFW-------KPKVQLDDLFDWTMASDATTLEIFTYN  331 (333)
Q Consensus       281 i~t~--------~i~liViDe~H~~~~~~-R~~-------~~~~~l~~l~~l~~~~d~~~~e~~~~~  331 (333)
                      |.|.        +++++|+||.|.+.-.. ++.       +..++....+.++++|+++++|.|...
T Consensus        81 VGTrsalf~p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a~~ra~~~~~~vil~SATPsles~~~~  147 (505)
T TIGR00595        81 IGTRSALFLPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKKFNCPVVLGSATPSLESYHNA  147 (505)
T ss_pred             ECChHHHcCcccCCCEEEEECCCccccccccCCCCcHHHHHHHHHHhcCCCEEEEeCCCCHHHHHHH
Confidence            7764        78999999999875322 232       333444556889999999999998753

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).

>TIGR01054 rgy reverse gyrase

Probab=99.43  E-value=4.7e-13  Score=148.37  Aligned_cols=113  Identities=16%  Similarity=0.051  Sum_probs=88.1

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-------
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-------  263 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-------  263 (333)
                      ..+.|+++|+.+++.++.|++++++||||||||+.++..+......+.+++|++|||+||.|+++.+++.+..       
T Consensus        75 ~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~f~l~~~~~l~~~g~~vLIL~PTreLa~Qi~~~l~~l~~~~~i~~~~  154 (1171)
T TIGR01054        75 VGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTTFGLAMSLFLAKKGKRCYIILPTTLLVIQVAEKISSLAEKAGVGTVN  154 (1171)
T ss_pred             cCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEeCHHHHHHHHHHHHHHHHHhcCCceee
Confidence            3458999999999999999999999999999998443333333456889999999999999999999886542       


Q ss_pred             cEEEeCCCCCCC-----------CcceEEecc------------CcceEeccccccccccCcC
Q psy2760         264 VGLIDDLPPVFP-----------DVEKLLEDL------------NIGGLDELSIHDFNKHLKF  303 (333)
Q Consensus       264 vglltGd~~~~~-----------~a~ili~t~------------~i~liViDe~H~~~~~~R~  303 (333)
                      ++.++|+.+...           ...++|.|+            .+.++|+||+|.+...+|+
T Consensus       155 i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l~~~~~~iVvDEaD~~L~~~k~  217 (1171)
T TIGR01054       155 IGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDELGPKFDFIFVDDVDALLKASKN  217 (1171)
T ss_pred             eeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHhcCCCCEEEEeChHhhhhcccc
Confidence            345678765421           246888876            3669999999999876553

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.

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

Probab=99.42  E-value=7.2e-13  Score=144.21  Aligned_cols=114  Identities=13%  Similarity=0.081  Sum_probs=88.0

Q ss_pred             cCCC-CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEe
Q psy2760         190 TWPF-ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLID  268 (333)
Q Consensus       190 ~~~f-~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vgllt  268 (333)
                      .|+| .|++.|.++|+.++.|+++++++|||+|||++|.+|++..   +..+|||+|+++|+.++...+....-....++
T Consensus       455 ~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~---~GiTLVISPLiSLmqDQV~~L~~~GI~Aa~L~  531 (1195)
T PLN03137        455 VFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC---PGITLVISPLVSLIQDQIMNLLQANIPAASLS  531 (1195)
T ss_pred             HcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc---CCcEEEEeCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            4566 8999999999999999999999999999999999998743   46799999999999988877766333356666


Q ss_pred             CCCCCC-------------CCcceEEecc--------------------CcceEeccccccccccCcCccc
Q psy2760         269 DLPPVF-------------PDVEKLLEDL--------------------NIGGLDELSIHDFNKHLKFWKP  306 (333)
Q Consensus       269 Gd~~~~-------------~~a~ili~t~--------------------~i~liViDe~H~~~~~~R~~~~  306 (333)
                      |+....             ....+++.|+                    .+.++|+||+|.+...+..++.
T Consensus       532 s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~LslIVIDEAHcVSqWGhDFRp  602 (1195)
T PLN03137        532 AGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARFVIDEAHCVSQWGHDFRP  602 (1195)
T ss_pred             CCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhccccceeccCcchhhhhcccchHH
Confidence            765421             2235666654                    2567899999998776544443

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

Probab=99.41  E-value=3.5e-13  Score=139.39  Aligned_cols=135  Identities=18%  Similarity=0.216  Sum_probs=112.3

Q ss_pred             ccCCCCCCHHHHHHHHHHHcC------CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         189 HTWPFELDVFQKQAIIKLEEH------NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       189 ~~~~f~l~~~Q~~ai~~l~~g------~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      +..||.||.-|++++..+..+      .+.++.|..|||||+++.++++.+...|.++..++||--||+|.++.+++.|+
T Consensus       257 ~~LPF~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~G~Q~ALMAPTEILA~QH~~~~~~~l~  336 (677)
T COG1200         257 AALPFKLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEAGYQAALMAPTEILAEQHYESLRKWLE  336 (677)
T ss_pred             HhCCCCccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHcCCeeEEeccHHHHHHHHHHHHHHHhh
Confidence            457999999999999997432      47899999999999999999999999999999999999999999999999888


Q ss_pred             C----cEEEeCCCCC-----------CCCcceEEecc----------CcceEeccccccccccCcCcccccchhhhhhhe
Q psy2760         263 D----VGLIDDLPPV-----------FPDVEKLLEDL----------NIGGLDELSIHDFNKHLKFWKPKVQLDDLFDWT  317 (333)
Q Consensus       263 ~----vglltGd~~~-----------~~~a~ili~t~----------~i~liViDe~H~~~~~~R~~~~~~~l~~l~~l~  317 (333)
                      +    |+++||...-           +.+..++|.|+          +++++|+||-|.|+...|.--+...-. .-..+
T Consensus       337 ~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd~V~F~~LgLVIiDEQHRFGV~QR~~L~~KG~~-~Ph~L  415 (677)
T COG1200         337 PLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQDKVEFHNLGLVIIDEQHRFGVHQRLALREKGEQ-NPHVL  415 (677)
T ss_pred             hcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhcceeecceeEEEEeccccccHHHHHHHHHhCCC-CCcEE
Confidence            5    7889998764           34457888887          789999999999999987644433211 45677


Q ss_pred             eccCcch
Q psy2760         318 MASDATT  324 (333)
Q Consensus       318 ~~~d~~~  324 (333)
                      +++++|+
T Consensus       416 vMTATPI  422 (677)
T COG1200         416 VMTATPI  422 (677)
T ss_pred             EEeCCCc
Confidence            7877764

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.40  E-value=1.3e-12  Score=128.17  Aligned_cols=70  Identities=24%  Similarity=0.255  Sum_probs=58.8

Q ss_pred             HHHHHHHHHHcCCc--EEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC------C--cEEE
Q psy2760         198 FQKQAIIKLEEHNH--VFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ------D--VGLI  267 (333)
Q Consensus       198 ~Q~~ai~~l~~g~~--vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~------~--vgll  267 (333)
                      ||.++++.+.++.+  ++++||||||||++|+++++.   .+.+++|++|+++|++|+++++++.+.      +  +..+
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~---~~~~~~~~~P~~aL~~~~~~~~~~~~~~~~~~~~~~v~~~   77 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLH---GENDTIALYPTNALIEDQTEAIKEFVDVFKPERDVNLLHV   77 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHH---cCCCEEEEeChHHHHHHHHHHHHHHHHhcCCCCCceEEEe
Confidence            69999999977764  889999999999999999874   345789999999999999999988762      2  4556


Q ss_pred             eCC
Q psy2760         268 DDL  270 (333)
Q Consensus       268 tGd  270 (333)
                      +|+
T Consensus        78 ~g~   80 (357)
T TIGR03158        78 SKA   80 (357)
T ss_pred             cCC
Confidence            775

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.

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

Probab=99.40  E-value=8e-13  Score=139.47  Aligned_cols=139  Identities=18%  Similarity=0.132  Sum_probs=115.8

Q ss_pred             CCCHHHHHHHHHHHcC----CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-cEEEe
Q psy2760         194 ELDVFQKQAIIKLEEH----NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-VGLID  268 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g----~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-vgllt  268 (333)
                      .+++-|..|+..+...    ...++.+.||||||.+|+-+|...+..|+.+|+++|.++|..|+..+|+.+|+. +++++
T Consensus       198 ~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlH  277 (730)
T COG1198         198 ALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLH  277 (730)
T ss_pred             ccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhc
Confidence            6899999999997433    788999999999999999999999999999999999999999999999999996 89999


Q ss_pred             CCCCCC-----------CCcceEEecc--------CcceEecccccccc-ccCcCcccc-------cchhhhhhheeccC
Q psy2760         269 DLPPVF-----------PDVEKLLEDL--------NIGGLDELSIHDFN-KHLKFWKPK-------VQLDDLFDWTMASD  321 (333)
Q Consensus       269 Gd~~~~-----------~~a~ili~t~--------~i~liViDe~H~~~-~~~R~~~~~-------~~l~~l~~l~~~~d  321 (333)
                      ++++..           .++++++.|-        ++++||+||-|.-. ...+++++.       ++-...+.++|+|+
T Consensus       278 S~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF~Pf~~LGLIIvDEEHD~sYKq~~~prYhARdvA~~Ra~~~~~pvvLgSA  357 (730)
T COG1198         278 SGLSPGERYRVWRRARRGEARVVIGTRSALFLPFKNLGLIIVDEEHDSSYKQEDGPRYHARDVAVLRAKKENAPVVLGSA  357 (730)
T ss_pred             ccCChHHHHHHHHHHhcCCceEEEEechhhcCchhhccEEEEeccccccccCCcCCCcCHHHHHHHHHHHhCCCEEEecC
Confidence            888753           3445666653        89999999999542 222344443       34466688999999


Q ss_pred             cchhhhhhccc
Q psy2760         322 ATTLEIFTYNK  332 (333)
Q Consensus       322 ~~~~e~~~~~~  332 (333)
                      +||+|.|++.+
T Consensus       358 TPSLES~~~~~  368 (730)
T COG1198         358 TPSLESYANAE  368 (730)
T ss_pred             CCCHHHHHhhh
Confidence            99999998864

>PRK14701 reverse gyrase; Provisional

Probab=99.40  E-value=1.2e-12  Score=148.43  Aligned_cols=114  Identities=14%  Similarity=0.083  Sum_probs=91.0

Q ss_pred             ccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-----
Q psy2760         189 HTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-----  263 (333)
Q Consensus       189 ~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-----  263 (333)
                      ..++|.|+++|+++++.+++|+++++.||||||||+++..+.+....+|.++++++||++|+.|+++.++.....     
T Consensus        74 ~~~G~~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~~~g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v  153 (1638)
T PRK14701         74 KITGFEFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLALKGKKCYIILPTTLLVKQTVEKIESFCEKANLDV  153 (1638)
T ss_pred             HhhCCCCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHhcCCeEEEEECHHHHHHHHHHHHHHHHhhcCCce
Confidence            345678999999999999999999999999999999766665555556789999999999999999999875432     


Q ss_pred             -cEEEeCCCCCCC-----------CcceEEecc-------------CcceEeccccccccccCc
Q psy2760         264 -VGLIDDLPPVFP-----------DVEKLLEDL-------------NIGGLDELSIHDFNKHLK  302 (333)
Q Consensus       264 -vglltGd~~~~~-----------~a~ili~t~-------------~i~liViDe~H~~~~~~R  302 (333)
                       +..++|+.+...           ...+++.|+             ++.++++||+|.+...++
T Consensus       154 ~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l~~~~i~~iVVDEAD~ml~~~k  217 (1638)
T PRK14701        154 RLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEMKHLKFDFIFVDDVDAFLKASK  217 (1638)
T ss_pred             eEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHHhhCCCCEEEEECceecccccc
Confidence             355778765431           246888876             367899999998875444

>KOG0335|consensus

Probab=99.37  E-value=6.1e-13  Score=133.43  Aligned_cols=109  Identities=17%  Similarity=0.039  Sum_probs=87.0

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc-------------CCCeEEEEcccHHHHHHHHHHHHHh
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN-------------HKTRTIYTSPIKALSNQKYRDFRET  260 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~-------------~g~ral~l~PtraLa~Q~~~~l~~~  260 (333)
                      .++|+|+-+|+.+..|+++++||+||||||.+|++|++..+.             ..+++++++|||+||.|++.+-++.
T Consensus        96 ~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~Qi~nea~k~  175 (482)
T KOG0335|consen   96 KPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALILAPTRELVDQIYNEARKF  175 (482)
T ss_pred             CCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCCCCCCceEEEeCcHHHhhHHHHHHHhh
Confidence            799999999999999999999999999999999999984431             1378999999999999999998774


Q ss_pred             cCC----cEEEeCCCCCCCC-------cceEEecc---------------CcceEeccccccccc-cCc
Q psy2760         261 FQD----VGLIDDLPPVFPD-------VEKLLEDL---------------NIGGLDELSIHDFNK-HLK  302 (333)
Q Consensus       261 f~~----vglltGd~~~~~~-------a~ili~t~---------------~i~liViDe~H~~~~-~~R  302 (333)
                      ...    .+...|+.+...+       -.++++|+               ++.++|+||+....+ .+.
T Consensus       176 ~~~s~~~~~~~ygg~~~~~q~~~~~~gcdIlvaTpGrL~d~~e~g~i~l~~~k~~vLDEADrMlD~mgF  244 (482)
T KOG0335|consen  176 SYLSGMKSVVVYGGTDLGAQLRFIKRGCDILVATPGRLKDLIERGKISLDNCKFLVLDEADRMLDEMGF  244 (482)
T ss_pred             cccccceeeeeeCCcchhhhhhhhccCccEEEecCchhhhhhhcceeehhhCcEEEecchHHhhhhccc
Confidence            332    4556666544322       35777776               577899999997765 443

>KOG0346|consensus

Probab=99.36  E-value=9.1e-13  Score=130.06  Aligned_cols=124  Identities=15%  Similarity=0.065  Sum_probs=93.5

Q ss_pred             ccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh---------cCCCeEE
Q psy2760         171 LDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ---------NHKTRTI  241 (333)
Q Consensus       171 ~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l---------~~g~ral  241 (333)
                      .+|.+.+......+|..      .|+-+|..||+.+++|++++..|.||||||.+|++|+++.+         ..+..++
T Consensus        24 ~gLD~RllkAi~~lG~e------kpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~   97 (569)
T KOG0346|consen   24 FGLDSRLLKAITKLGWE------KPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAV   97 (569)
T ss_pred             hCCCHHHHHHHHHhCcC------CcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccceeE
Confidence            45667777777777777      89999999999999999999999999999999999998543         3467899


Q ss_pred             EEcccHHHHHHHHHHHHHhcCC----c--EEEeCCCCCC-------CCcceEEecc----------------CcceEecc
Q psy2760         242 YTSPIKALSNQKYRDFRETFQD----V--GLIDDLPPVF-------PDVEKLLEDL----------------NIGGLDEL  292 (333)
Q Consensus       242 ~l~PtraLa~Q~~~~l~~~f~~----v--glltGd~~~~-------~~a~ili~t~----------------~i~liViD  292 (333)
                      +++|||+||+|++..+.+.-..    +  .-++.+.+..       ..-.++|.|+                .+.++|+|
T Consensus        98 iLvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~~~~~~~l~~LVvD  177 (569)
T KOG0346|consen   98 ILVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGVLEYLDSLSFLVVD  177 (569)
T ss_pred             EEechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhccchhhhheeeEEec
Confidence            9999999999999887664321    1  1122222211       2235777776                46789999


Q ss_pred             cccccccc
Q psy2760         293 SIHDFNKH  300 (333)
Q Consensus       293 e~H~~~~~  300 (333)
                      |+..+-+-
T Consensus       178 EADLllsf  185 (569)
T KOG0346|consen  178 EADLLLSF  185 (569)
T ss_pred             hhhhhhhc
Confidence            99876543

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.36  E-value=4.6e-12  Score=109.27  Aligned_cols=130  Identities=19%  Similarity=0.111  Sum_probs=95.5

Q ss_pred             CCCCHHHHHHHHHHHcC-CcEEEEcCCCCcHHHHHHHHHHHHhcCC--CeEEEEcccHHHHHHHHHHHHHhcCC-----c
Q psy2760         193 FELDVFQKQAIIKLEEH-NHVFVTAHTSAGKTVIAEYAIALSQNHK--TRTIYTSPIKALSNQKYRDFRETFQD-----V  264 (333)
Q Consensus       193 f~l~~~Q~~ai~~l~~g-~~vlv~apTGSGKTl~~~l~il~~l~~g--~ral~l~PtraLa~Q~~~~l~~~f~~-----v  264 (333)
                      ..++++|.+++..+... +++++++|||+|||.++..+++.....+  .+++|++|+++++.|+..++.+.+..     .
T Consensus         7 ~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~~~~~l~~~p~~~~~~~~~~~~~~~~~~~~~~~~   86 (201)
T smart00487        7 EPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAEQWAEELKKLGPSLGLKVV   86 (201)
T ss_pred             CCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccCCCcEEEEeCCHHHHHHHHHHHHHHhccCCeEEE
Confidence            37899999999999888 9999999999999999988888766554  78999999999999999999887643     3


Q ss_pred             EEEeCCCC------CCCCc-ceEEecc---------------CcceEeccccccccccCcCcccccchhh----hhhhee
Q psy2760         265 GLIDDLPP------VFPDV-EKLLEDL---------------NIGGLDELSIHDFNKHLKFWKPKVQLDD----LFDWTM  318 (333)
Q Consensus       265 glltGd~~------~~~~a-~ili~t~---------------~i~liViDe~H~~~~~~R~~~~~~~l~~----l~~l~~  318 (333)
                      ..+.|...      ..... .+++.|+               .+.++|+||+|++....+...+.. +++    ....++
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~~~~~~~~~iIiDE~h~~~~~~~~~~~~~-~~~~~~~~~~~v~  165 (201)
T smart00487       87 GLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEK-LLKLLPKNVQLLL  165 (201)
T ss_pred             EEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCCcCHhHCCEEEEECHHHHhcCCcHHHHHH-HHHhCCccceEEE
Confidence            33444332      12222 6677663               345899999999986433333332 223    355677


Q ss_pred             ccCcc
Q psy2760         319 ASDAT  323 (333)
Q Consensus       319 ~~d~~  323 (333)
                      +++.+
T Consensus       166 ~saT~  170 (201)
T smart00487      166 LSATP  170 (201)
T ss_pred             EecCC
Confidence            77766

>KOG0333|consensus

Probab=99.33  E-value=3.8e-12  Score=127.90  Aligned_cols=130  Identities=15%  Similarity=0.052  Sum_probs=104.8

Q ss_pred             CcccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHH---------
Q psy2760         163 TQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALS---------  233 (333)
Q Consensus       163 ~~~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~---------  233 (333)
                      +...|.+.. ++..+.......+..      .|+|+|++|++..++.+++++.|.||||||++|.+|++..         
T Consensus       243 plrnwEE~~-~P~e~l~~I~~~~y~------eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~  315 (673)
T KOG0333|consen  243 PLRNWEESG-FPLELLSVIKKPGYK------EPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMAR  315 (673)
T ss_pred             cccChhhcC-CCHHHHHHHHhcCCC------CCchHHHhhccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCcch
Confidence            788898865 898888888887777      8999999999999999999999999999999999998732         


Q ss_pred             ---hcCCCeEEEEcccHHHHHHHHHHHHHhcCC-----cEEEeCCCCCCCC-------cceEEecc--------------
Q psy2760         234 ---QNHKTRTIYTSPIKALSNQKYRDFRETFQD-----VGLIDDLPPVFPD-------VEKLLEDL--------------  284 (333)
Q Consensus       234 ---l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-----vglltGd~~~~~~-------a~ili~t~--------------  284 (333)
                         ...|+++++++|||+|++|+..+-.+ |+.     +..+.|+.+...+       ..++++|+              
T Consensus       316 ~en~~~gpyaiilaptReLaqqIeeEt~k-f~~~lg~r~vsvigg~s~EEq~fqls~gceiviatPgrLid~Lenr~lvl  394 (673)
T KOG0333|consen  316 LENNIEGPYAIILAPTRELAQQIEEETNK-FGKPLGIRTVSVIGGLSFEEQGFQLSMGCEIVIATPGRLIDSLENRYLVL  394 (673)
T ss_pred             hhhcccCceeeeechHHHHHHHHHHHHHH-hcccccceEEEEecccchhhhhhhhhccceeeecCchHHHHHHHHHHHHh
Confidence               13588999999999999999988766 442     4446677766543       46777777              


Q ss_pred             -CcceEecccccccccc
Q psy2760         285 -NIGGLDELSIHDFNKH  300 (333)
Q Consensus       285 -~i~liViDe~H~~~~~  300 (333)
                       ....+|.||+...-+.
T Consensus       395 ~qctyvvldeadrmiDm  411 (673)
T KOG0333|consen  395 NQCTYVVLDEADRMIDM  411 (673)
T ss_pred             ccCceEeccchhhhhcc
Confidence             3566788888765544

>KOG0334|consensus

Probab=99.31  E-value=3.4e-12  Score=136.25  Aligned_cols=129  Identities=18%  Similarity=0.132  Sum_probs=99.5

Q ss_pred             CcccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh--------
Q psy2760         163 TQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ--------  234 (333)
Q Consensus       163 ~~~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l--------  234 (333)
                      +...|... +++..+....++++..      .++++|.+|||++..|++|++.|-||||||++|++|++.+.        
T Consensus       363 pv~sW~q~-gl~~~il~tlkkl~y~------k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~~~~  435 (997)
T KOG0334|consen  363 PVTSWTQC-GLSSKILETLKKLGYE------KPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEE  435 (997)
T ss_pred             ccchHhhC-CchHHHHHHHHHhcCC------CCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCChhh
Confidence            66778775 5677777766666665      89999999999999999999999999999999999998543        


Q ss_pred             cCCCeEEEEcccHHHHHHHHHHHHHhcCC----cEEEeCCCCCC-------CCcceEEecc------------------C
Q psy2760         235 NHKTRTIYTSPIKALSNQKYRDFRETFQD----VGLIDDLPPVF-------PDVEKLLEDL------------------N  285 (333)
Q Consensus       235 ~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~~~-------~~a~ili~t~------------------~  285 (333)
                      ..|+-+++++|||+|+.|+++.++.....    +..+.|+..+.       ..++++|+|+                  .
T Consensus       436 gdGPi~li~aPtrela~QI~r~~~kf~k~l~ir~v~vygg~~~~~qiaelkRg~eIvV~tpGRmiD~l~~n~grvtnlrR  515 (997)
T KOG0334|consen  436 GDGPIALILAPTRELAMQIHREVRKFLKLLGIRVVCVYGGSGISQQIAELKRGAEIVVCTPGRMIDILCANSGRVTNLRR  515 (997)
T ss_pred             CCCceEEEEcCCHHHHHHHHHHHHHHHhhcCceEEEecCCccHHHHHHHHhcCCceEEeccchhhhhHhhcCCccccccc
Confidence            35888999999999999999988764332    33345554432       2267888876                  2


Q ss_pred             cceEecccccccc
Q psy2760         286 IGGLDELSIHDFN  298 (333)
Q Consensus       286 i~liViDe~H~~~  298 (333)
                      +-++|.||+....
T Consensus       516 ~t~lv~deaDrmf  528 (997)
T KOG0334|consen  516 VTYLVLDEADRMF  528 (997)
T ss_pred             cceeeechhhhhh
Confidence            3467788887555

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

Probab=99.27  E-value=2.6e-11  Score=122.37  Aligned_cols=108  Identities=22%  Similarity=0.254  Sum_probs=86.8

Q ss_pred             CCCCCCHHHHHHHHHHHc----CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC---
Q psy2760         191 WPFELDVFQKQAIIKLEE----HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD---  263 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~----g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~---  263 (333)
                      +.+.++++|.+|+..+..    ++..++++|||+|||.++..++......   ++||+|+++|+.|+.+++.+.+..   
T Consensus        33 ~~~~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~~~~---~Lvlv~~~~L~~Qw~~~~~~~~~~~~~  109 (442)
T COG1061          33 FEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELKRS---TLVLVPTKELLDQWAEALKKFLLLNDE  109 (442)
T ss_pred             cCCCCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHhcCC---EEEEECcHHHHHHHHHHHHHhcCCccc
Confidence            345799999999999866    8999999999999999999887654433   999999999999999888776653   


Q ss_pred             cEEEeCCCCCCCCcceEEecc---------------CcceEeccccccccccC
Q psy2760         264 VGLIDDLPPVFPDVEKLLEDL---------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       264 vglltGd~~~~~~a~ili~t~---------------~i~liViDe~H~~~~~~  301 (333)
                      +|.+.|+........+++.|.               ...++|+||+|......
T Consensus       110 ~g~~~~~~~~~~~~~i~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~~a~~  162 (442)
T COG1061         110 IGIYGGGEKELEPAKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAPS  162 (442)
T ss_pred             cceecCceeccCCCcEEEEEhHHHhhhhhhhhhcccccCEEEEEccccCCcHH
Confidence            688877755433245666654               37889999999998654

>PRK13766 Hef nuclease; Provisional

Probab=99.26  E-value=2.6e-11  Score=129.72  Aligned_cols=106  Identities=18%  Similarity=0.154  Sum_probs=87.0

Q ss_pred             CCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh-cCCCeEEEEcccHHHHHHHHHHHHHhcC----CcEEE
Q psy2760         193 FELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ-NHKTRTIYTSPIKALSNQKYRDFRETFQ----DVGLI  267 (333)
Q Consensus       193 f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l-~~g~ral~l~PtraLa~Q~~~~l~~~f~----~vgll  267 (333)
                      +.++++|.+++..++.+ ++++++|||+|||+++.+++...+ ..+.++||++||++|+.|+.+.+++.++    .+..+
T Consensus        14 ~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~   92 (773)
T PRK13766         14 IEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLHKKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVF   92 (773)
T ss_pred             CCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHHhCCCeEEEEeCcHHHHHHHHHHHHHHhCCCCceEEEE
Confidence            47899999999887776 999999999999999988877544 4578999999999999999999988664    36778


Q ss_pred             eCCCCCCC------CcceEEecc---------------CcceEeccccccccc
Q psy2760         268 DDLPPVFP------DVEKLLEDL---------------NIGGLDELSIHDFNK  299 (333)
Q Consensus       268 tGd~~~~~------~a~ili~t~---------------~i~liViDe~H~~~~  299 (333)
                      +|+.+...      ...+++.|+               ++.++|+||+|....
T Consensus        93 ~g~~~~~~r~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~liVvDEaH~~~~  145 (773)
T PRK13766         93 TGEVSPEKRAELWEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVG  145 (773)
T ss_pred             eCCCCHHHHHHHHhCCCEEEECHHHHHHHHHcCCCChhhCcEEEEECCccccc
Confidence            88876432      346778775               467899999998754

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.25  E-value=9.2e-12  Score=139.69  Aligned_cols=97  Identities=23%  Similarity=0.210  Sum_probs=76.5

Q ss_pred             EEcCCCCcHHHHHHHHHHHHhc-------------CCCeEEEEcccHHHHHHHHHHHHHh----------cC----C--c
Q psy2760         214 VTAHTSAGKTVIAEYAIALSQN-------------HKTRTIYTSPIKALSNQKYRDFRET----------FQ----D--V  264 (333)
Q Consensus       214 v~apTGSGKTl~~~l~il~~l~-------------~g~ral~l~PtraLa~Q~~~~l~~~----------f~----~--v  264 (333)
                      |+||||||||++|++|++..+.             ++.++|||+|+|||++|+++.|+..          ++    +  +
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            5899999999999999884431             3578999999999999999988641          11    2  7


Q ss_pred             EEEeCCCCCCC-------CcceEEecc----------------CcceEeccccccccccCcCcccccch
Q psy2760         265 GLIDDLPPVFP-------DVEKLLEDL----------------NIGGLDELSIHDFNKHLKFWKPKVQL  310 (333)
Q Consensus       265 glltGd~~~~~-------~a~ili~t~----------------~i~liViDe~H~~~~~~R~~~~~~~l  310 (333)
                      ++++||++...       ...++|.|+                ++.++|+||+|.+.+..||......+
T Consensus        81 ~vrtGDt~~~eR~rll~~ppdILVTTPEsL~~LLtsk~r~~L~~Vr~VIVDE~H~L~g~kRG~~Lel~L  149 (1490)
T PRK09751         81 GIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARETLRGVETVIIDEVHAVAGSKRGAHLALSL  149 (1490)
T ss_pred             EEEECCCCHHHHHHHhcCCCCEEEecHHHHHHHHhhhhhhhhccCCEEEEecHHHhcccccccHHHHHH
Confidence            88999987643       236888876                57899999999999888997765533

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.24  E-value=1.1e-11  Score=120.53  Aligned_cols=112  Identities=19%  Similarity=0.104  Sum_probs=79.3

Q ss_pred             cEEEEcCCCCcHHHHHHHHHHHHh--cCCCeEEEEcccHHHHHHHHHHHHHhcCC-cEEEeCCCCC--------------
Q psy2760         211 HVFVTAHTSAGKTVIAEYAIALSQ--NHKTRTIYTSPIKALSNQKYRDFRETFQD-VGLIDDLPPV--------------  273 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~il~~l--~~g~ral~l~PtraLa~Q~~~~l~~~f~~-vglltGd~~~--------------  273 (333)
                      +++++||||||||++|+.+++...  ..+.+++|++|+++|+.|++++++..|+. +++++|+...              
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~~~~~ii~v~P~~~L~~q~~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQKADRVIIALPTRATINAMYRRAKELFGSNLGLLHSSSSFKRIKEMGDSEEFEH   80 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhCCCCeEEEEeehHHHHHHHHHHHHHHhCcccEEeeccHHHHHHhccCCchhHHH
Confidence            479999999999999999998655  45679999999999999999999998874 6766654321              


Q ss_pred             -------C----CCcceEEeccC---------------------cceEeccccccccccCcCcccccchhh-----hhhh
Q psy2760         274 -------F----PDVEKLLEDLN---------------------IGGLDELSIHDFNKHLKFWKPKVQLDD-----LFDW  316 (333)
Q Consensus       274 -------~----~~a~ili~t~~---------------------i~liViDe~H~~~~~~R~~~~~~~l~~-----l~~l  316 (333)
                             +    ....++++|++                     ..++|+||+|.+....++.  ...+++     ..+.
T Consensus        81 ~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~~~~~--l~~~l~~l~~~~~~~  158 (358)
T TIGR01587        81 LFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYTLAL--ILAVLEVLKDNDVPI  158 (358)
T ss_pred             HHHHHhhchhhhhhCCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHHHHHH--HHHHHHHHHHcCCCE
Confidence                   0    12346666541                     1579999999998754432  111111     2456


Q ss_pred             eeccCcch
Q psy2760         317 TMASDATT  324 (333)
Q Consensus       317 ~~~~d~~~  324 (333)
                      +++|++..
T Consensus       159 i~~SATlp  166 (358)
T TIGR01587       159 LLMSATLP  166 (358)
T ss_pred             EEEecCch
Confidence            77777644

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.

>KOG0354|consensus

Probab=99.23  E-value=3e-11  Score=126.67  Aligned_cols=106  Identities=19%  Similarity=0.227  Sum_probs=83.1

Q ss_pred             CCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh--cCCCeEEEEcccHHHHHHHHHHHHHhcCC---cEEE
Q psy2760         193 FELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ--NHKTRTIYTSPIKALSNQKYRDFRETFQD---VGLI  267 (333)
Q Consensus       193 f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l--~~g~ral~l~PtraLa~Q~~~~l~~~f~~---vgll  267 (333)
                      +.++.+|.+....++ |+|++|++|||+|||++|...+..++  .++.++||++|++-|+.|+...+...+-+   .+.+
T Consensus        61 ~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~~KiVF~aP~~pLv~QQ~a~~~~~~~~~~~T~~l  139 (746)
T KOG0354|consen   61 LELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPKGKVVFLAPTRPLVNQQIACFSIYLIPYSVTGQL  139 (746)
T ss_pred             ccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCcceEEEeeCCchHHHHHHHHHhhccCcccceeec
Confidence            478999999999988 99999999999999999999988665  46789999999999999999777653322   3444


Q ss_pred             eCCCCCCCC------cceEEecc----------------CcceEeccccccccc
Q psy2760         268 DDLPPVFPD------VEKLLEDL----------------NIGGLDELSIHDFNK  299 (333)
Q Consensus       268 tGd~~~~~~------a~ili~t~----------------~i~liViDe~H~~~~  299 (333)
                      +|..+....      .++++.|+                .+.++|+||+|+-..
T Consensus       140 ~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra~k  193 (746)
T KOG0354|consen  140 GDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRTSK  193 (746)
T ss_pred             cCccCCCchhhhhcccceEEeChHhhhhhcccccccccceEEEEEEcccccccc
Confidence            443443332      25666665                488999999998543

>KOG0336|consensus

Probab=99.14  E-value=6.3e-11  Score=116.44  Aligned_cols=122  Identities=16%  Similarity=0.052  Sum_probs=94.5

Q ss_pred             ChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHH---------hcCCCeEEEEc
Q psy2760         174 SKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALS---------QNHKTRTIYTS  244 (333)
Q Consensus       174 ~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~---------l~~g~ral~l~  244 (333)
                      .+.+..-.++.|++      .|+|+|.||.|.+++|.++++.|-||+|||++|++|-+.+         ...+.++++++
T Consensus       228 ~pevmenIkK~GFq------KPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~  301 (629)
T KOG0336|consen  228 YPEVMENIKKTGFQ------KPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLT  301 (629)
T ss_pred             hHHHHHHHHhccCC------CCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccCCCceEEEe
Confidence            44555556667777      8999999999999999999999999999999999986632         24578899999


Q ss_pred             ccHHHHHHHHHHHHHh-cCC---cEEEeCCCCCC------CCcceEEecc---------------CcceEeccccccccc
Q psy2760         245 PIKALSNQKYRDFRET-FQD---VGLIDDLPPVF------PDVEKLLEDL---------------NIGGLDELSIHDFNK  299 (333)
Q Consensus       245 PtraLa~Q~~~~l~~~-f~~---vglltGd~~~~------~~a~ili~t~---------------~i~liViDe~H~~~~  299 (333)
                      |||+|+.|+.....+. +..   ++++.|+....      ...+++++|+               ++.++|+||+...-+
T Consensus       302 ptreLalqie~e~~kysyng~ksvc~ygggnR~eqie~lkrgveiiiatPgrlndL~~~n~i~l~siTYlVlDEADrMLD  381 (629)
T KOG0336|consen  302 PTRELALQIEGEVKKYSYNGLKSVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINLASITYLVLDEADRMLD  381 (629)
T ss_pred             ccHHHHHHHHhHHhHhhhcCcceEEEecCCCchhHHHHHhcCceEEeeCCchHhhhhhcCeeeeeeeEEEEecchhhhhc
Confidence            9999999999776542 222   67666654321      2346777776               578899999998877


Q ss_pred             cC
Q psy2760         300 HL  301 (333)
Q Consensus       300 ~~  301 (333)
                      ++
T Consensus       382 Mg  383 (629)
T KOG0336|consen  382 MG  383 (629)
T ss_pred             cc
Confidence            65

>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=99.13  E-value=3.1e-10  Score=98.22  Aligned_cols=67  Identities=28%  Similarity=0.415  Sum_probs=55.5

Q ss_pred             CCCCHHHHHHHHHHH-------cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         193 FELDVFQKQAIIKLE-------EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       193 f~l~~~Q~~ai~~l~-------~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      |.|+++|.+|+..+.       ..+++++.+|||||||.++...+.....   ++++++|++.|+.|....|.....
T Consensus         2 ~~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~---~~l~~~p~~~l~~Q~~~~~~~~~~   75 (184)
T PF04851_consen    2 YKLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELAR---KVLIVAPNISLLEQWYDEFDDFGS   75 (184)
T ss_dssp             -EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHC---EEEEEESSHHHHHHHHHHHHHHST
T ss_pred             CCCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcccc---ceeEecCHHHHHHHHHHHHHHhhh
Confidence            468999999999964       3689999999999999999976665544   899999999999999999955443

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 ....

>KOG0337|consensus

Probab=99.12  E-value=7.1e-11  Score=116.34  Aligned_cols=127  Identities=14%  Similarity=0.094  Sum_probs=95.1

Q ss_pred             ccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc----CCCeEEEEccc
Q psy2760         171 LDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN----HKTRTIYTSPI  246 (333)
Q Consensus       171 ~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~----~g~ral~l~Pt  246 (333)
                      .+|+..+...+.+.++.      .|+|+|+.++|.++++++++..|-||||||.+|++|++..+.    .|.|+++++||
T Consensus        26 mgL~~~v~raI~kkg~~------~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~Ralilspt   99 (529)
T KOG0337|consen   26 MGLDYKVLRAIHKKGFN------TPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALILSPT   99 (529)
T ss_pred             cCCCHHHHHHHHHhhcC------CCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhccccccceeeccCc
Confidence            45666666655565666      799999999999999999999999999999999999996653    45699999999


Q ss_pred             HHHHHHHHHHHHHhcCC-----cEEEeCCCCC-------CCCcceEEecc---------------CcceEeccccccccc
Q psy2760         247 KALSNQKYRDFRETFQD-----VGLIDDLPPV-------FPDVEKLLEDL---------------NIGGLDELSIHDFNK  299 (333)
Q Consensus       247 raLa~Q~~~~l~~~f~~-----vglltGd~~~-------~~~a~ili~t~---------------~i~liViDe~H~~~~  299 (333)
                      |+|+.|..+.+++ ++.     ..++.|+-++       +.+..++++|+               .+.++|.||+..+..
T Consensus       100 reLa~qtlkvvkd-lgrgt~lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~vem~l~l~sveyVVfdEadrlfe  178 (529)
T KOG0337|consen  100 RELALQTLKVVKD-LGRGTKLRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEADRLFE  178 (529)
T ss_pred             HHHHHHHHHHHHH-hccccchhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehheeccccceeeeeehhhhHHHh
Confidence            9999999998876 443     3334444443       22345667665               456677788876654


Q ss_pred             cCcCccc
Q psy2760         300 HLKFWKP  306 (333)
Q Consensus       300 ~~R~~~~  306 (333)
                      .  ||+.
T Consensus       179 m--gfqe  183 (529)
T KOG0337|consen  179 M--GFQE  183 (529)
T ss_pred             h--hhHH
Confidence            3  4543

>KOG0344|consensus

Probab=99.12  E-value=1.4e-10  Score=118.00  Aligned_cols=94  Identities=26%  Similarity=0.285  Sum_probs=76.4

Q ss_pred             CCcccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh-------
Q psy2760         162 VTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ-------  234 (333)
Q Consensus       162 ~~~~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l-------  234 (333)
                      .+|..+......+..+.+-+...++.      .|+++|.+|++.+..+++++.|||||||||++|.+|++..+       
T Consensus       132 ~~f~~lt~~~~~~~~ll~nl~~~~F~------~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~  205 (593)
T KOG0344|consen  132 LSFSDLTYDYSMNKRLLENLQELGFD------EPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQEK  205 (593)
T ss_pred             ccccccchhhhhcHHHHHhHhhCCCC------CCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhhccc
Confidence            35555555555566665554444444      89999999999999999999999999999999999999654       


Q ss_pred             -cCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy2760         235 -NHKTRTIYTSPIKALSNQKYRDFRETF  261 (333)
Q Consensus       235 -~~g~ral~l~PtraLa~Q~~~~l~~~f  261 (333)
                       ..|-+++++.|||+|++|+++++++..
T Consensus       206 ~~~gl~a~Il~ptreLa~Qi~re~~k~~  233 (593)
T KOG0344|consen  206 HKVGLRALILSPTRELAAQIYREMRKYS  233 (593)
T ss_pred             CccceEEEEecchHHHHHHHHHHHHhcC
Confidence             235789999999999999999998855

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.11  E-value=3.9e-10  Score=91.61  Aligned_cols=95  Identities=19%  Similarity=0.171  Sum_probs=73.0

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhc--CCCeEEEEcccHHHHHHHHHHHHHhcC---CcEEEeCCCCCC-------CCc
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQN--HKTRTIYTSPIKALSNQKYRDFRETFQ---DVGLIDDLPPVF-------PDV  277 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~--~g~ral~l~PtraLa~Q~~~~l~~~f~---~vglltGd~~~~-------~~a  277 (333)
                      +++++.+|||+|||.++...+.....  ...+++|++|+++++.|..+.+...+.   .+..+.+.....       ...
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~p~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKVGYLIGGTSIKQQEKLLSGKT   80 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhcccCCCEEEEcCcHHHHHHHHHHHHHHhhCCcEEEEEecCcchhHHHHHhcCCC
Confidence            47899999999999999988875553  568999999999999999999888764   266666654433       344


Q ss_pred             ceEEecc---------------CcceEeccccccccccCcCc
Q psy2760         278 EKLLEDL---------------NIGGLDELSIHDFNKHLKFW  304 (333)
Q Consensus       278 ~ili~t~---------------~i~liViDe~H~~~~~~R~~  304 (333)
                      .++++|.               ...++++||+|.+.......
T Consensus        81 ~i~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~  122 (144)
T cd00046          81 DIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGL  122 (144)
T ss_pred             CEEEECcHHHHHHHHcCCcchhcCCEEEEeCHHHHhhcchHH
Confidence            5666654               36789999999998775433

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

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

Probab=99.10  E-value=2.4e-10  Score=114.86  Aligned_cols=103  Identities=18%  Similarity=0.129  Sum_probs=85.4

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc-CCCeEEEEcccHHHHHHHHHHHHHhcC----CcEEEe
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN-HKTRTIYTSPIKALSNQKYRDFRETFQ----DVGLID  268 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~-~g~ral~l~PtraLa~Q~~~~l~~~f~----~vgllt  268 (333)
                      +++.+|.......+.+ |.|++.|||-|||.++.+-+...+. .++++|+++||+-|+.|+.+.+++.++    .++.+|
T Consensus        15 e~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~~~kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~i~~lt   93 (542)
T COG1111          15 EPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWFGGKVLFLAPTKPLVLQHAEFCRKVTGIPEDEIAALT   93 (542)
T ss_pred             cHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhcCCeEEEecCCchHHHHHHHHHHHHhCCChhheeeec
Confidence            5788888877766554 9999999999999999998885553 334899999999999999999988775    288999


Q ss_pred             CCCCCCC------CcceEEecc---------------CcceEeccccccc
Q psy2760         269 DLPPVFP------DVEKLLEDL---------------NIGGLDELSIHDF  297 (333)
Q Consensus       269 Gd~~~~~------~a~ili~t~---------------~i~liViDe~H~~  297 (333)
                      |..+.+.      .++++++|+               +++++|.||+|.-
T Consensus        94 Gev~p~~R~~~w~~~kVfvaTPQvveNDl~~Grid~~dv~~lifDEAHRA  143 (542)
T COG1111          94 GEVRPEEREELWAKKKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHRA  143 (542)
T ss_pred             CCCChHHHHHHHhhCCEEEeccHHHHhHHhcCccChHHceEEEechhhhc
Confidence            9988763      357888887               6899999999975

>KOG0953|consensus

Probab=99.09  E-value=7.6e-11  Score=119.36  Aligned_cols=121  Identities=17%  Similarity=0.159  Sum_probs=97.5

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEeCCCCCCCC--------cce
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPD--------VEK  279 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vglltGd~~~~~~--------a~i  279 (333)
                      +.+-++-+|||.||||.-++    +.+....+++|..|.|-||+++++++.+.--.+.++||.-.....        ..|
T Consensus       190 ~RkIi~H~GPTNSGKTy~AL----qrl~~aksGvycGPLrLLA~EV~~r~na~gipCdL~TGeE~~~~~~~~~~a~hvSc  265 (700)
T KOG0953|consen  190 RRKIIMHVGPTNSGKTYRAL----QRLKSAKSGVYCGPLRLLAHEVYDRLNALGIPCDLLTGEERRFVLDNGNPAQHVSC  265 (700)
T ss_pred             hheEEEEeCCCCCchhHHHH----HHHhhhccceecchHHHHHHHHHHHhhhcCCCccccccceeeecCCCCCcccceEE
Confidence            45667889999999998765    455666789999999999999999998855568899997543211        246


Q ss_pred             EEecc----CcceEeccccccccccCcCcccccch----------------hhhhhheeccCcchhhhhhccc
Q psy2760         280 LLEDL----NIGGLDELSIHDFNKHLKFWKPKVQL----------------DDLFDWTMASDATTLEIFTYNK  332 (333)
Q Consensus       280 li~t~----~i~liViDe~H~~~~~~R~~~~~~~l----------------~~l~~l~~~~d~~~~e~~~~~~  332 (333)
                      +|.+.    .....|+||+++..+++|||+|..++                +.+++.++...-+.+|+++|-|
T Consensus       266 TVEM~sv~~~yeVAViDEIQmm~Dp~RGwAWTrALLGl~AdEiHLCGepsvldlV~~i~k~TGd~vev~~YeR  338 (700)
T KOG0953|consen  266 TVEMVSVNTPYEVAVIDEIQMMRDPSRGWAWTRALLGLAADEIHLCGEPSVLDLVRKILKMTGDDVEVREYER  338 (700)
T ss_pred             EEEEeecCCceEEEEehhHHhhcCcccchHHHHHHHhhhhhhhhccCCchHHHHHHHHHhhcCCeeEEEeecc
Confidence            66644    45778999999999999999998766                6778889999999999999976

>KOG0339|consensus

Probab=99.08  E-value=1.5e-10  Score=116.16  Aligned_cols=107  Identities=14%  Similarity=0.089  Sum_probs=86.2

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh--------cCCCeEEEEcccHHHHHHHHHHHHHhcCC-c
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ--------NHKTRTIYTSPIKALSNQKYRDFRETFQD-V  264 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l--------~~g~ral~l~PtraLa~Q~~~~l~~~f~~-v  264 (333)
                      .++++|-++++..+.|++++..|-||||||.+|..|++.+.        ..|+-++|++|||+||.|++.+.++ |++ +
T Consensus       245 kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL~~g~gPi~vilvPTrela~Qi~~eaKk-f~K~y  323 (731)
T KOG0339|consen  245 KPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVILVPTRELASQIFSEAKK-FGKAY  323 (731)
T ss_pred             cCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhhcCCCCCeEEEEeccHHHHHHHHHHHHH-hhhhc
Confidence            79999999999999999999999999999999999988432        4578899999999999999999866 643 2


Q ss_pred             ----EEEeCCCCCC-------CCcceEEecc---------------CcceEeccccccccccC
Q psy2760         265 ----GLIDDLPPVF-------PDVEKLLEDL---------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       265 ----glltGd~~~~-------~~a~ili~t~---------------~i~liViDe~H~~~~~~  301 (333)
                          ..+.|+.+..       ..++++|+|+               ++.++|+||+...-+.+
T Consensus       324 gl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~rvS~LV~DEadrmfdmG  386 (731)
T KOG0339|consen  324 GLRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDMVKMKATNLSRVSYLVLDEADRMFDMG  386 (731)
T ss_pred             cceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHHHHhhcccceeeeEEEEechhhhhccc
Confidence                2244544432       3457888887               57889999998765553

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.06  E-value=3.1e-10  Score=121.83  Aligned_cols=94  Identities=12%  Similarity=0.122  Sum_probs=78.3

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC----cEE
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD----VGL  266 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vgl  266 (333)
                      .||.++|+|.|+++.+..++++++.++||+|||++|.+|++.....+..+++|+||++||.|..+.+...+..    ++.
T Consensus        89 ~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g~~v~IVTpTrELA~Qdae~m~~L~k~lGLsV~~  168 (970)
T PRK12899         89 QQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTGKPVHLVTVNDYLAQRDCEWVGSVLRWLGLTTGV  168 (970)
T ss_pred             CCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhcCCeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEE
Confidence            4677899999999999999999999999999999999999966655667999999999999999988776542    677


Q ss_pred             EeCCCCCCCC-----cceEEecc
Q psy2760         267 IDDLPPVFPD-----VEKLLEDL  284 (333)
Q Consensus       267 ltGd~~~~~~-----a~ili~t~  284 (333)
                      +.|+.....+     ..++++|+
T Consensus       169 i~GG~~~~eq~~~y~~DIVygTP  191 (970)
T PRK12899        169 LVSGSPLEKRKEIYQCDVVYGTA  191 (970)
T ss_pred             EeCCCCHHHHHHHcCCCEEEECC
Confidence            8888776432     35666666

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

Probab=99.06  E-value=1.8e-10  Score=123.29  Aligned_cols=134  Identities=9%  Similarity=0.014  Sum_probs=88.9

Q ss_pred             CCCCCHHHHHHHHHHHcCC-cEEEEcCCCCcHHHHHHHHHH---HHhcCCCeEEEEcccHHHHHHHHHHHHHhcC-----
Q psy2760         192 PFELDVFQKQAIIKLEEHN-HVFVTAHTSAGKTVIAEYAIA---LSQNHKTRTIYTSPIKALSNQKYRDFRETFQ-----  262 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~g~-~vlv~apTGSGKTl~~~l~il---~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~-----  262 (333)
                      +|.|+|+|.++++.+..|+ ++++++|||||||.++....+   .......+.+|++|||+||.|+++.+.+...     
T Consensus        13 G~~PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~~~~~~~~~rLv~~vPtReLa~Qi~~~~~~~~k~l~~~   92 (844)
T TIGR02621        13 GYSPFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAVEIGAKVPRRLVYVVNRRTVVDQVTEEAEKIGERLPDV   92 (844)
T ss_pred             CCCCCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccccccccccceEEEeCchHHHHHHHHHHHHHHHHHhccc
Confidence            4569999999999999998 677889999999996543222   1112234677788999999999988766332     


Q ss_pred             --------------------C--cEEEeCCCCCCCC-------cceEEecc---------------------------Cc
Q psy2760         263 --------------------D--VGLIDDLPPVFPD-------VEKLLEDL---------------------------NI  286 (333)
Q Consensus       263 --------------------~--vglltGd~~~~~~-------a~ili~t~---------------------------~i  286 (333)
                                          +  +..++|+...+.+       ..++|+|.                           ++
T Consensus        93 ~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~D~i~sr~L~~gYg~~~~~~pi~ag~L~~v  172 (844)
T TIGR02621        93 PEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHRPAVIVGTVDMIGSRLLFSGYGCGFKSRPLHAGFLGQD  172 (844)
T ss_pred             chhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCCCcEEEECHHHHcCCccccccccccccccchhhhhccc
Confidence                                1  4567888776432       24667664                           25


Q ss_pred             ceEeccccccccccCcCcccccchhhh---------hhheeccCcchhhhh
Q psy2760         287 GGLDELSIHDFNKHLKFWKPKVQLDDL---------FDWTMASDATTLEIF  328 (333)
Q Consensus       287 ~liViDe~H~~~~~~R~~~~~~~l~~l---------~~l~~~~d~~~~e~~  328 (333)
                      .++|+||+| .. .+ +.....+++..         .+.+++|++..-++.
T Consensus       173 ~~LVLDEAD-Ld-~g-F~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~  220 (844)
T TIGR02621       173 ALIVHDEAH-LE-PA-FQELLKQIMNEQQRPPDFLPLRVVELTATSRTDGP  220 (844)
T ss_pred             eEEEEehhh-hc-cc-cHHHHHHHHHhcccCcccccceEEEEecCCCccHH
Confidence            678999999 32 22 22222223331         246778887665544

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.

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.05  E-value=8.9e-10  Score=116.40  Aligned_cols=128  Identities=12%  Similarity=0.024  Sum_probs=87.0

Q ss_pred             HHHHHHHHHHHcCCcEEEEcCCCCcHHHH---------HHHHHHHHh---c---CCCeEEEEcccHHHHHHHHHHHHHhc
Q psy2760         197 VFQKQAIIKLEEHNHVFVTAHTSAGKTVI---------AEYAIALSQ---N---HKTRTIYTSPIKALSNQKYRDFRETF  261 (333)
Q Consensus       197 ~~Q~~ai~~l~~g~~vlv~apTGSGKTl~---------~~l~il~~l---~---~g~ral~l~PtraLa~Q~~~~l~~~f  261 (333)
                      .+|.++++.+.+|++++++|+||||||.+         |+++.+..+   .   .+.++++++|||+||.|+..++.+..
T Consensus       167 ~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~~v  246 (675)
T PHA02653        167 DVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLKSL  246 (675)
T ss_pred             HHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHHHh
Confidence            47788888899999999999999999997         333333222   2   35689999999999999999987644


Q ss_pred             CC-------cEEEeCCCCCC------CCcceEEecc--------CcceEeccccccccccCcCcccc-cch-hhhhhhee
Q psy2760         262 QD-------VGLIDDLPPVF------PDVEKLLEDL--------NIGGLDELSIHDFNKHLKFWKPK-VQL-DDLFDWTM  318 (333)
Q Consensus       262 ~~-------vglltGd~~~~------~~a~ili~t~--------~i~liViDe~H~~~~~~R~~~~~-~~l-~~l~~l~~  318 (333)
                      +.       +.+..|+....      ....++++|.        ++.++|+||+|.....+...-.. ..+ .+..+.++
T Consensus       247 g~~~~~g~~v~v~~Gg~~~~~~~t~~k~~~Ilv~T~~L~l~~L~~v~~VVIDEaHEr~~~~DllL~llk~~~~~~rq~IL  326 (675)
T PHA02653        247 GFDEIDGSPISLKYGSIPDELINTNPKPYGLVFSTHKLTLNKLFDYGTVIIDEVHEHDQIGDIIIAVARKHIDKIRSLFL  326 (675)
T ss_pred             CccccCCceEEEEECCcchHHhhcccCCCCEEEEeCcccccccccCCEEEccccccCccchhHHHHHHHHhhhhcCEEEE
Confidence            32       46677876521      1235677764        46889999999976654211000 000 11236788


Q ss_pred             ccCcch
Q psy2760         319 ASDATT  324 (333)
Q Consensus       319 ~~d~~~  324 (333)
                      +|++-.
T Consensus       327 mSATl~  332 (675)
T PHA02653        327 MTATLE  332 (675)
T ss_pred             EccCCc
Confidence            888763

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.03  E-value=1.6e-09  Score=114.77  Aligned_cols=106  Identities=10%  Similarity=0.058  Sum_probs=81.7

Q ss_pred             CCCCCHHHHHHHHHHH-cC--CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC----Cc
Q psy2760         192 PFELDVFQKQAIIKLE-EH--NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ----DV  264 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~-~g--~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~----~v  264 (333)
                      .+.++++|.+|+..+. .|  ++.++++|||+|||++++.++...   +.++||++|+..|++|+.++|.+.+.    .+
T Consensus       253 ~~~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~l---~k~tLILvps~~Lv~QW~~ef~~~~~l~~~~I  329 (732)
T TIGR00603       253 TTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTV---KKSCLVLCTSAVSVEQWKQQFKMWSTIDDSQI  329 (732)
T ss_pred             CCCcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHHh---CCCEEEEeCcHHHHHHHHHHHHHhcCCCCceE
Confidence            3589999999999974 44  478999999999999998766432   46799999999999999999987542    27


Q ss_pred             EEEeCCCCCCC--CcceEEecc-----------------------CcceEecccccccccc
Q psy2760         265 GLIDDLPPVFP--DVEKLLEDL-----------------------NIGGLDELSIHDFNKH  300 (333)
Q Consensus       265 glltGd~~~~~--~a~ili~t~-----------------------~i~liViDe~H~~~~~  300 (333)
                      +.++|+.....  ...++|.|.                       ..+++|+||+|.+...
T Consensus       330 ~~~tg~~k~~~~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lpA~  390 (732)
T TIGR00603       330 CRFTSDAKERFHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPAA  390 (732)
T ss_pred             EEEecCcccccccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccccHH
Confidence            88888765432  245666654                       2458999999988543

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).

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.00  E-value=1.5e-09  Score=115.88  Aligned_cols=92  Identities=15%  Similarity=0.095  Sum_probs=75.9

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC----cEE
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD----VGL  266 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vgl  266 (333)
                      ++..|++.|..+...+.+|+  ++.+.||+|||++|.+|++.....|.++.+++||+.||.|.++.+...+..    +++
T Consensus        75 ~g~~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~G~~v~VvTpt~~LA~qd~e~~~~l~~~lGl~v~~  152 (790)
T PRK09200         75 LGMRPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNALEGKGVHLITVNDYLAKRDAEEMGQVYEFLGLTVGL  152 (790)
T ss_pred             hCCCCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHcCCCeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEE
Confidence            45568999999988888887  999999999999999999866667999999999999999999998886653    788


Q ss_pred             EeCCCC-CC-----CCcceEEecc
Q psy2760         267 IDDLPP-VF-----PDVEKLLEDL  284 (333)
Q Consensus       267 ltGd~~-~~-----~~a~ili~t~  284 (333)
                      ++|+.+ ..     ....++++|+
T Consensus       153 i~g~~~~~~~r~~~y~~dIvygT~  176 (790)
T PRK09200        153 NFSDIDDASEKKAIYEADIIYTTN  176 (790)
T ss_pred             EeCCCCcHHHHHHhcCCCEEEECC
Confidence            888877 21     2345666664

>KOG0951|consensus

Probab=98.98  E-value=1.1e-09  Score=118.69  Aligned_cols=112  Identities=18%  Similarity=0.153  Sum_probs=87.9

Q ss_pred             CCCHHHHHHHHHHH-cCCcEEEEcCCCCcHHHHHHHHHHHHhcC-----------CCeEEEEcccHHHHHHHHHHHHHhc
Q psy2760         194 ELDVFQKQAIIKLE-EHNHVFVTAHTSAGKTVIAEYAIALSQNH-----------KTRTIYTSPIKALSNQKYRDFRETF  261 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~-~g~~vlv~apTGSGKTl~~~l~il~~l~~-----------g~ral~l~PtraLa~Q~~~~l~~~f  261 (333)
                      .|+++|......++ ...|+++|||||+|||.++++.|++.+..           ..+++|++|+++|++++...|.+++
T Consensus       309 sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLvqE~VgsfSkRl  388 (1674)
T KOG0951|consen  309 SLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALVQEMVGSFSKRL  388 (1674)
T ss_pred             hhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeHHHHHHHHHHHHHhhc
Confidence            58999999999864 55699999999999999999999965532           2479999999999999999999998


Q ss_pred             CC----cEEEeCCCCCCC----CcceEEecc-----------------CcceEeccccccccccCcCccc
Q psy2760         262 QD----VGLIDDLPPVFP----DVEKLLEDL-----------------NIGGLDELSIHDFNKHLKFWKP  306 (333)
Q Consensus       262 ~~----vglltGd~~~~~----~a~ili~t~-----------------~i~liViDe~H~~~~~~R~~~~  306 (333)
                      .+    |+-+|||.+...    ...++++|+                 -+.++++||+|+..+. ||-.-
T Consensus       389 a~~GI~V~ElTgD~~l~~~qieeTqVIV~TPEK~DiITRk~gdraY~qlvrLlIIDEIHLLhDd-RGpvL  457 (1674)
T KOG0951|consen  389 APLGITVLELTGDSQLGKEQIEETQVIVTTPEKWDIITRKSGDRAYEQLVRLLIIDEIHLLHDD-RGPVL  457 (1674)
T ss_pred             cccCcEEEEecccccchhhhhhcceeEEeccchhhhhhcccCchhHHHHHHHHhhhhhhhcccc-cchHH
Confidence            86    566899977543    346777766                 1456778999987533 55443

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=98.97  E-value=3.3e-09  Score=114.38  Aligned_cols=129  Identities=15%  Similarity=0.141  Sum_probs=88.9

Q ss_pred             HHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-----cEEEeCCC-
Q psy2760         198 FQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-----VGLIDDLP-  271 (333)
Q Consensus       198 ~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-----vglltGd~-  271 (333)
                      +-.+.+..+.++++++++||||||||.++.++++.....+.+++++.|||++|.|+.+++.+.++.     ||..+++. 
T Consensus         9 ~~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~~~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VGy~vr~~~   88 (812)
T PRK11664          9 VLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGINGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVGYRMRAES   88 (812)
T ss_pred             HHHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCCcCCeEEEECChHHHHHHHHHHHHHHhCcccCceEEEEecCcc
Confidence            334555667788999999999999999999998865544568999999999999999999766542     55555443 


Q ss_pred             CCCCCcceEEecc--------------CcceEeccccccccccCcC-cccccc----hhhhhhheeccCcchhh
Q psy2760         272 PVFPDVEKLLEDL--------------NIGGLDELSIHDFNKHLKF-WKPKVQ----LDDLFDWTMASDATTLE  326 (333)
Q Consensus       272 ~~~~~a~ili~t~--------------~i~liViDe~H~~~~~~R~-~~~~~~----l~~l~~l~~~~d~~~~e  326 (333)
                      ....+..++++|.              ++.++|+||+|...-.... ......    +-...+++++|++-..+
T Consensus        89 ~~~~~t~I~v~T~G~Llr~l~~d~~L~~v~~IIlDEaHER~l~~Dl~L~ll~~i~~~lr~~lqlilmSATl~~~  162 (812)
T PRK11664         89 KVGPNTRLEVVTEGILTRMIQRDPELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDDLKLLIMSATLDND  162 (812)
T ss_pred             ccCCCCcEEEEChhHHHHHHhhCCCcCcCcEEEEcCCCccccccchHHHHHHHHHHhCCccceEEEEecCCCHH
Confidence            3444456777775              5789999999974322111 111100    11235678888775544

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=98.97  E-value=4.1e-09  Score=113.68  Aligned_cols=130  Identities=15%  Similarity=0.055  Sum_probs=89.2

Q ss_pred             HHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-----cEEEeC-CC
Q psy2760         198 FQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-----VGLIDD-LP  271 (333)
Q Consensus       198 ~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-----vglltG-d~  271 (333)
                      +-.+.+..+..+.+++++|+||||||.++..+++.....+.+++++.|+|++|.|+.+++.+.++.     ||...+ +.
T Consensus         6 ~~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~~~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~VGy~vr~~~   85 (819)
T TIGR01970         6 VLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGIGGKIIMLEPRRLAARSAAQRLASQLGEAVGQTVGYRVRGEN   85 (819)
T ss_pred             HHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhccCCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEEEEEEcccc
Confidence            334555667788999999999999999999999876656679999999999999999999766652     444333 33


Q ss_pred             CCCCCcceEEecc--------------CcceEecccccccc-ccCcCcccccc----hhhhhhheeccCcchhhh
Q psy2760         272 PVFPDVEKLLEDL--------------NIGGLDELSIHDFN-KHLKFWKPKVQ----LDDLFDWTMASDATTLEI  327 (333)
Q Consensus       272 ~~~~~a~ili~t~--------------~i~liViDe~H~~~-~~~R~~~~~~~----l~~l~~l~~~~d~~~~e~  327 (333)
                      ......++.++|.              ++.++|+||+|... ....+......    +-...+++++|++-.-+.
T Consensus        86 ~~s~~t~I~v~T~G~Llr~l~~d~~L~~v~~VIiDEaHER~L~~Dl~L~ll~~i~~~lr~dlqlIlmSATl~~~~  160 (819)
T TIGR01970        86 KVSRRTRLEVVTEGILTRMIQDDPELDGVGALIFDEFHERSLDADLGLALALDVQSSLREDLKILAMSATLDGER  160 (819)
T ss_pred             ccCCCCcEEEECCcHHHHHHhhCcccccCCEEEEeccchhhhccchHHHHHHHHHHhcCCCceEEEEeCCCCHHH
Confidence            3334456777775              57899999999532 11112211111    112356788887655443

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.

>KOG0341|consensus

Probab=98.96  E-value=5e-11  Score=116.48  Aligned_cols=99  Identities=18%  Similarity=0.159  Sum_probs=78.8

Q ss_pred             CChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHH-HH----------hcCCCeEE
Q psy2760         173 VSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIA-LS----------QNHKTRTI  241 (333)
Q Consensus       173 L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il-~~----------l~~g~ral  241 (333)
                      .+.++.++++..|+.      .|+|+|.|-+|.+++|++.+..|-||||||++|.+|++ .+          ...|+-.+
T Consensus       177 FP~~~L~~lk~KGI~------~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~gL  250 (610)
T KOG0341|consen  177 FPKPLLRGLKKKGIV------HPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGL  250 (610)
T ss_pred             CCHHHHHHHHhcCCC------CCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCCCeeE
Confidence            345566666666776      89999999999999999999999999999999999876 22          24688999


Q ss_pred             EEcccHHHHHHHHHHHHHhcC---C-------cEEEeCCCCCCCCc
Q psy2760         242 YTSPIKALSNQKYRDFRETFQ---D-------VGLIDDLPPVFPDV  277 (333)
Q Consensus       242 ~l~PtraLa~Q~~~~l~~~f~---~-------vglltGd~~~~~~a  277 (333)
                      +++|.|+||.|++.-+...+.   .       .++..|+.....+.
T Consensus       251 iicPSRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql  296 (610)
T KOG0341|consen  251 IICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQL  296 (610)
T ss_pred             EEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHH
Confidence            999999999999976655332   1       36677887776543

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=98.96  E-value=2.2e-09  Score=113.59  Aligned_cols=107  Identities=13%  Similarity=-0.042  Sum_probs=85.6

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC----cEE
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD----VGL  266 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vgl  266 (333)
                      ++..|++.|..+...+..|+  +..++||+|||++|.+|++.....|.++.+++||+.||.|.++.+...+..    ++.
T Consensus        53 lg~~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~G~~V~VvTpt~~LA~qdae~~~~l~~~LGLsv~~  130 (745)
T TIGR00963        53 LGMRPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALTGKGVHVVTVNDYLAQRDAEWMGQVYRFLGLSVGL  130 (745)
T ss_pred             hCCCccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHhCCCEEEEcCCHHHHHHHHHHHHHHhccCCCeEEE
Confidence            45578899998888888776  899999999999999998644445778999999999999999999887764    688


Q ss_pred             EeCCCCCCC-----CcceEEecc----------------------CcceEeccccccccc
Q psy2760         267 IDDLPPVFP-----DVEKLLEDL----------------------NIGGLDELSIHDFNK  299 (333)
Q Consensus       267 ltGd~~~~~-----~a~ili~t~----------------------~i~liViDe~H~~~~  299 (333)
                      ++|+.....     ...+++.|+                      ++.++|+||.|.+..
T Consensus       131 i~g~~~~~~r~~~y~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs~LI  190 (745)
T TIGR00963       131 ILSGMSPEERREAYACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDSILI  190 (745)
T ss_pred             EeCCCCHHHHHHhcCCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHHHHhH
Confidence            888866432     235777765                      356788999998765

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.

>PRK09694 helicase Cas3; Provisional

Probab=98.95  E-value=3.9e-09  Score=114.28  Aligned_cols=80  Identities=16%  Similarity=0.090  Sum_probs=62.5

Q ss_pred             CCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc--CCCeEEEEcccHHHHHHHHHHHHH----hcCC--
Q psy2760         192 PFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN--HKTRTIYTSPIKALSNQKYRDFRE----TFQD--  263 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~--~g~ral~l~PtraLa~Q~~~~l~~----~f~~--  263 (333)
                      .+.|+|+|+.+......+..+++.||||+|||.+++.++.....  ...+++|..||+++++|+++++++    .|+.  
T Consensus       284 ~~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~~~~~~~gi~~aLPT~Atan~m~~Rl~~~~~~~f~~~~  363 (878)
T PRK09694        284 GYQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLIDQGLADSIIFALPTQATANAMLSRLEALASKLFPSPN  363 (878)
T ss_pred             CCCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHHHhCCCCeEEEECcHHHHHHHHHHHHHHHHHHhcCCCc
Confidence            35899999987544445678999999999999999887764433  346899999999999999999864    4442  


Q ss_pred             cEEEeCCC
Q psy2760         264 VGLIDDLP  271 (333)
Q Consensus       264 vglltGd~  271 (333)
                      +.+.+|..
T Consensus       364 v~L~Hg~a  371 (878)
T PRK09694        364 LILAHGNS  371 (878)
T ss_pred             eEeecCcc
Confidence            77777654

>KOG0326|consensus

Probab=98.94  E-value=3e-10  Score=108.89  Aligned_cols=108  Identities=14%  Similarity=0.050  Sum_probs=86.7

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcccHHHHHHHHHHHHHhcCC----cEE
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSPIKALSNQKYRDFRETFQD----VGL  266 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~PtraLa~Q~~~~l~~~f~~----vgl  266 (333)
                      .|.|+|.++||.++.|++++..|..|.|||.+|.+|++....   ...++++++|||+||.|+.+..++.-..    +-+
T Consensus       107 kPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPtrelALQtSqvc~~lskh~~i~vmv  186 (459)
T KOG0326|consen  107 KPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPTRELALQTSQVCKELSKHLGIKVMV  186 (459)
T ss_pred             CCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCccccceeEEEEeecchhhHHHHHHHHHHhcccCeEEEE
Confidence            599999999999999999999999999999999999996654   3468999999999999998877664332    566


Q ss_pred             EeCCCCCCCC-------cceEEecc---------------CcceEeccccccccccC
Q psy2760         267 IDDLPPVFPD-------VEKLLEDL---------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       267 ltGd~~~~~~-------a~ili~t~---------------~i~liViDe~H~~~~~~  301 (333)
                      .||+++...+       ..++|.|+               +...+|.||+.++-+..
T Consensus       187 ttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~KgVa~ls~c~~lV~DEADKlLs~~  243 (459)
T KOG0326|consen  187 TTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKKGVADLSDCVILVMDEADKLLSVD  243 (459)
T ss_pred             ecCCcccccceeeecCceEEEEcCChhHHHHHhcccccchhceEEEechhhhhhchh
Confidence            7898876533       24566665               45668889988876654

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=98.92  E-value=3.8e-09  Score=110.82  Aligned_cols=92  Identities=12%  Similarity=-0.017  Sum_probs=78.0

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC----cEE
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD----VGL  266 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vgl  266 (333)
                      .+..|+++|..+++.++.|+  ++.+.||+|||++|.+|++.....|.++++++||++||.|.++.+...+..    ++.
T Consensus       100 lg~~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~G~~v~VvTptreLA~qdae~~~~l~~~lGlsv~~  177 (656)
T PRK12898        100 LGQRHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAALAGLPVHVITVNDYLAERDAELMRPLYEALGLTVGC  177 (656)
T ss_pred             hCCCCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhcCCeEEEEcCcHHHHHHHHHHHHHHHhhcCCEEEE
Confidence            45579999999999999998  899999999999999999988778899999999999999999999876642    788


Q ss_pred             EeCCCCCC-----CCcceEEecc
Q psy2760         267 IDDLPPVF-----PDVEKLLEDL  284 (333)
Q Consensus       267 ltGd~~~~-----~~a~ili~t~  284 (333)
                      ++|+.+..     ....+++.|.
T Consensus       178 i~gg~~~~~r~~~y~~dIvygT~  200 (656)
T PRK12898        178 VVEDQSPDERRAAYGADITYCTN  200 (656)
T ss_pred             EeCCCCHHHHHHHcCCCEEEECC
Confidence            88886542     2345667665

>KOG4284|consensus

Probab=98.90  E-value=9.4e-10  Score=113.13  Aligned_cols=128  Identities=12%  Similarity=0.026  Sum_probs=100.0

Q ss_pred             CcccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc---CCCe
Q psy2760         163 TQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN---HKTR  239 (333)
Q Consensus       163 ~~~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~---~g~r  239 (333)
                      .|+++..+.    .+..++++.++.      .++++|..|||.++.+.+++|.|..|.|||++|-.+++..+.   ....
T Consensus        26 ~fe~l~l~r----~vl~glrrn~f~------~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q   95 (980)
T KOG4284|consen   26 GFEQLALWR----EVLLGLRRNAFA------LPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQ   95 (980)
T ss_pred             CHHHHHHHH----HHHHHHHhhccc------CCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcccCcce
Confidence            566665554    455555554444      699999999999999999999999999999999887776553   4578


Q ss_pred             EEEEcccHHHHHHHHHHHHHhcCC-----cEEEeCCCCCCC------CcceEEecc---------------CcceEeccc
Q psy2760         240 TIYTSPIKALSNQKYRDFRETFQD-----VGLIDDLPPVFP------DVEKLLEDL---------------NIGGLDELS  293 (333)
Q Consensus       240 al~l~PtraLa~Q~~~~l~~~f~~-----vglltGd~~~~~------~a~ili~t~---------------~i~liViDe  293 (333)
                      +++++|||++|-|+...+.+....     +.++.||+....      +.+++|.|+               .+-++|+||
T Consensus        96 ~~Iv~PTREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rlk~~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDE  175 (980)
T KOG4284|consen   96 KVIVTPTREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRLKQTRIVIGTPGRIAQLVELGAMNMSHVRLFVLDE  175 (980)
T ss_pred             eEEEecchhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhhhhceEEecCchHHHHHHHhcCCCccceeEEEecc
Confidence            999999999999999999876542     778889876543      235777776               567889999


Q ss_pred             ccccccc
Q psy2760         294 IHDFNKH  300 (333)
Q Consensus       294 ~H~~~~~  300 (333)
                      +.++...
T Consensus       176 ADkL~~t  182 (980)
T KOG4284|consen  176 ADKLMDT  182 (980)
T ss_pred             HHhhhch
Confidence            9887653

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=98.86  E-value=7.8e-09  Score=109.92  Aligned_cols=102  Identities=13%  Similarity=0.027  Sum_probs=72.8

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC----cEEEeC
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD----VGLIDD  269 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vglltG  269 (333)
                      .|++.|......+..|  .++.++||+|||++|.+|++.....|..+++++|+++||.|..+.+...+..    ++...+
T Consensus        70 rpydVQlig~l~l~~G--~Iaem~TGeGKTLta~Lpa~l~aL~g~~V~VVTpn~yLA~Rdae~m~~l~~~LGLsv~~~~~  147 (762)
T TIGR03714        70 FPYDVQVLGAIVLHQG--NIAEMKTGEGKTLTATMPLYLNALTGKGAMLVTTNDYLAKRDAEEMGPVYEWLGLTVSLGVV  147 (762)
T ss_pred             CccHHHHHHHHHhcCC--ceeEecCCcchHHHHHHHHHHHhhcCCceEEeCCCHHHHHHHHHHHHHHHhhcCCcEEEEEC
Confidence            3444444444444555  6999999999999999998766667888999999999999999888665432    666655


Q ss_pred             CCC---CC-------CCcceEEecc----------------------CcceEeccccccc
Q psy2760         270 LPP---VF-------PDVEKLLEDL----------------------NIGGLDELSIHDF  297 (333)
Q Consensus       270 d~~---~~-------~~a~ili~t~----------------------~i~liViDe~H~~  297 (333)
                      +..   ..       ....++++|+                      ++.++|+||+|.+
T Consensus       148 ~s~~~~~~~~~rr~~y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDsI  207 (762)
T TIGR03714       148 DDPDEEYDANEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDSV  207 (762)
T ss_pred             CCCccccCHHHHHHhCCCCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhhH
Confidence            411   11       2345777765                      2346888998876

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.

>PRK14873 primosome assembly protein PriA; Provisional

Probab=98.86  E-value=4.8e-09  Score=110.78  Aligned_cols=115  Identities=9%  Similarity=-0.081  Sum_probs=91.9

Q ss_pred             CCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC-C-cEEEeCCCCCC-----------CCcceEEec
Q psy2760         217 HTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ-D-VGLIDDLPPVF-----------PDVEKLLED  283 (333)
Q Consensus       217 pTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~-~-vglltGd~~~~-----------~~a~ili~t  283 (333)
                      .+|||||.+|+-.+...+..|+++|+++|..+|+.|+.++|+++|+ . +.+++++.+..           .+..++|.|
T Consensus       168 ~~GSGKTevyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~~~IViGt  247 (665)
T PRK14873        168 LPGEDWARRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQARVVVGT  247 (665)
T ss_pred             CCCCcHHHHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCCCcEEEEc
Confidence            3599999999999999999999999999999999999999999997 4 88899887643           334677776


Q ss_pred             c--------CcceEecccccccc-ccC-------cCcccccchhhhhhheeccCcchhhhhhcc
Q psy2760         284 L--------NIGGLDELSIHDFN-KHL-------KFWKPKVQLDDLFDWTMASDATTLEIFTYN  331 (333)
Q Consensus       284 ~--------~i~liViDe~H~~~-~~~-------R~~~~~~~l~~l~~l~~~~d~~~~e~~~~~  331 (333)
                      -        ++++||+||-|.-. ...       |..+..++-...+.++++|+++|+|.|.+.
T Consensus       248 RSAvFaP~~~LgLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra~~~~~~lvLgSaTPSles~~~~  311 (665)
T PRK14873        248 RSAVFAPVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAHQHGCALLIGGHARTAEAQALV  311 (665)
T ss_pred             ceeEEeccCCCCEEEEEcCCchhhcCCCCCCccHHHHHHHHHHHcCCcEEEECCCCCHHHHHHH
Confidence            4        78999999999542 122       223333444567889999999999999753

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

Probab=98.85  E-value=5e-09  Score=108.47  Aligned_cols=114  Identities=14%  Similarity=0.125  Sum_probs=87.7

Q ss_pred             CCC-CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEeC
Q psy2760         191 WPF-ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDD  269 (333)
Q Consensus       191 ~~f-~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vglltG  269 (333)
                      |+| .|++-|.++|..+.+|+++++..|||+||+++|.+|.+..   .+-+|+|+|..+|...+.+.++..--.+..+.+
T Consensus        13 fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~---~G~TLVVSPLiSLM~DQV~~l~~~Gi~A~~lnS   89 (590)
T COG0514          13 FGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL---EGLTLVVSPLISLMKDQVDQLEAAGIRAAYLNS   89 (590)
T ss_pred             hCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc---CCCEEEECchHHHHHHHHHHHHHcCceeehhhc
Confidence            455 7899999999999999999999999999999999998644   347899999999999999999774323444554


Q ss_pred             CCCCCCC-----------cceEEecc---------------CcceEeccccccccccCcCcccc
Q psy2760         270 LPPVFPD-----------VEKLLEDL---------------NIGGLDELSIHDFNKHLKFWKPK  307 (333)
Q Consensus       270 d~~~~~~-----------a~ili~t~---------------~i~liViDe~H~~~~~~R~~~~~  307 (333)
                      .++....           -.++.-.+               .+.++++||+|.+...+-.||..
T Consensus        90 ~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~L~~~~i~l~vIDEAHCiSqWGhdFRP~  153 (590)
T COG0514          90 TLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPD  153 (590)
T ss_pred             ccCHHHHHHHHHHHhcCceeEEEECchhhcChHHHHHHHhCCCceEEechHHHHhhcCCccCHh
Confidence            4443211           12222222               78999999999999887677764

>KOG0328|consensus

Probab=98.77  E-value=7.8e-09  Score=97.90  Aligned_cols=108  Identities=15%  Similarity=0.085  Sum_probs=82.4

Q ss_pred             CCC-CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcccHHHHHHHHHHHHHhcCC---
Q psy2760         191 WPF-ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSPIKALSNQKYRDFRETFQD---  263 (333)
Q Consensus       191 ~~f-~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~PtraLa~Q~~~~l~~~f~~---  263 (333)
                      ++| .|..+|++|++.++.|++|++.|..|.|||..|-+.+++...   +..++++++|||+||.|+.+.+...-..   
T Consensus        45 yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~lilsPTRELa~Qi~~vi~alg~~mnv  124 (400)
T KOG0328|consen   45 YGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDISVRETQALILSPTRELAVQIQKVILALGDYMNV  124 (400)
T ss_pred             hccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccccceeeEEEecChHHHHHHHHHHHHHhcccccc
Confidence            455 899999999999999999999999999999999988886654   3467999999999999999998774332   


Q ss_pred             -cEEEeCCCCCCC-------CcceEEecc---------------CcceEecccccccc
Q psy2760         264 -VGLIDDLPPVFP-------DVEKLLEDL---------------NIGGLDELSIHDFN  298 (333)
Q Consensus       264 -vglltGd~~~~~-------~a~ili~t~---------------~i~liViDe~H~~~  298 (333)
                       +....|+.+...       ...++..|+               ++-++|.||..-.-
T Consensus       125 q~hacigg~n~gedikkld~G~hvVsGtPGrv~dmikr~~L~tr~vkmlVLDEaDemL  182 (400)
T KOG0328|consen  125 QCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVLDMIKRRSLRTRAVKMLVLDEADEML  182 (400)
T ss_pred             eEEEEecCCccchhhhhhcccceEeeCCCchHHHHHHhccccccceeEEEeccHHHHH
Confidence             444667666322       223344443               56778888877543

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

Probab=98.76  E-value=3.6e-08  Score=109.47  Aligned_cols=105  Identities=16%  Similarity=0.130  Sum_probs=73.8

Q ss_pred             CCCCHHHHHHHHHHH-----cCCcEEEEcCCCCcHHHHHHHHHHHHh--cCCCeEEEEcccHHHHHHHHHHHHHhcCCcE
Q psy2760         193 FELDVFQKQAIIKLE-----EHNHVFVTAHTSAGKTVIAEYAIALSQ--NHKTRTIYTSPIKALSNQKYRDFRETFQDVG  265 (333)
Q Consensus       193 f~l~~~Q~~ai~~l~-----~g~~vlv~apTGSGKTl~~~l~il~~l--~~g~ral~l~PtraLa~Q~~~~l~~~f~~vg  265 (333)
                      +.++++|.+|+..+.     ..++++++++||||||.++...+...+  ....|+||++|+++|+.|..+.|.......+
T Consensus       412 ~~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~li~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~~~~~  491 (1123)
T PRK11448        412 LGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALMYRLLKAKRFRRILFLVDRSALGEQAEDAFKDTKIEGD  491 (1123)
T ss_pred             CCCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHHHHHHHHhcCccCeEEEEecHHHHHHHHHHHHHhcccccc
Confidence            478999999998752     346899999999999998766554333  3457999999999999999999977422111


Q ss_pred             -----EE--e--CCCCCCCCcceEEecc--------------------CcceEeccccccc
Q psy2760         266 -----LI--D--DLPPVFPDVEKLLEDL--------------------NIGGLDELSIHDF  297 (333)
Q Consensus       266 -----ll--t--Gd~~~~~~a~ili~t~--------------------~i~liViDe~H~~  297 (333)
                           +.  .  ++........++++|.                    ...+||+||+|.-
T Consensus       492 ~~~~~i~~i~~L~~~~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs  552 (1123)
T PRK11448        492 QTFASIYDIKGLEDKFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRG  552 (1123)
T ss_pred             cchhhhhchhhhhhhcccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCC
Confidence                 11  1  1222233456666654                    1348899999984

>KOG0949|consensus

Probab=98.76  E-value=1.5e-08  Score=108.19  Aligned_cols=117  Identities=24%  Similarity=0.226  Sum_probs=93.1

Q ss_pred             CCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc--CCCeEEEEcccHHHHHHHHHHHHHhcCC------
Q psy2760         192 PFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN--HKTRTIYTSPIKALSNQKYRDFRETFQD------  263 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~--~g~ral~l~PtraLa~Q~~~~l~~~f~~------  263 (333)
                      .|.|+.||++.+..+..+.++++.|||++|||.+..++|...++  ...-+||++||++|++|+...+..+|..      
T Consensus       509 dF~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfisfY~iEKVLResD~~VVIyvaPtKaLVnQvsa~VyaRF~~~t~~rg  588 (1330)
T KOG0949|consen  509 DFCPDEWQRELLDSVDRNESAVIVAPTSAGKTFISFYAIEKVLRESDSDVVIYVAPTKALVNQVSANVYARFDTKTFLRG  588 (1330)
T ss_pred             ccCCcHHHHHHhhhhhcccceEEEeeccCCceeccHHHHHHHHhhcCCCEEEEecchHHHhhhhhHHHHHhhccCccccc
Confidence            48999999999999999999999999999999999999986654  4567999999999999999999888832      


Q ss_pred             ---cEEEeCCCCCCCCc-ceEEecc------------------CcceEeccccccccccCcCccccc
Q psy2760         264 ---VGLIDDLPPVFPDV-EKLLEDL------------------NIGGLDELSIHDFNKHLKFWKPKV  308 (333)
Q Consensus       264 ---vglltGd~~~~~~a-~ili~t~------------------~i~liViDe~H~~~~~~R~~~~~~  308 (333)
                         .|.+|-+.++++-. ++++..+                  .|-.+|.||+|.++...-+.-|+.
T Consensus       589 ~sl~g~ltqEYsinp~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~ed~l~~Eq  655 (1330)
T KOG0949|consen  589 VSLLGDLTQEYSINPWNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNEEDGLLWEQ  655 (1330)
T ss_pred             hhhHhhhhHHhcCCchhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhccccccchHHHH
Confidence               35566666666432 2333322                  577889999999997765655543

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=98.75  E-value=3.4e-08  Score=94.60  Aligned_cols=71  Identities=17%  Similarity=0.215  Sum_probs=59.3

Q ss_pred             cCCCCCCHHHHHHHHH----HHcCCcEEEEcCCCCcHHHHHHHHHHH-HhcCCC-----eEEEEcccHHHHHHHHHHHHH
Q psy2760         190 TWPFELDVFQKQAIIK----LEEHNHVFVTAHTSAGKTVIAEYAIAL-SQNHKT-----RTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       190 ~~~f~l~~~Q~~ai~~----l~~g~~vlv~apTGSGKTl~~~l~il~-~l~~g~-----ral~l~PtraLa~Q~~~~l~~  259 (333)
                      .|||.+++.|.+.+..    +..|.++++.||||+|||++++.|++. ....+.     +++|.++|.++..|....+++
T Consensus         4 ~FPy~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~   83 (289)
T smart00488        4 YFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRK   83 (289)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHh
Confidence            3899999999996555    578999999999999999999999873 333233     899999999999999888876


Q ss_pred             h
Q psy2760         260 T  260 (333)
Q Consensus       260 ~  260 (333)
                      .
T Consensus        84 ~   84 (289)
T smart00488       84 L   84 (289)
T ss_pred             c
Confidence            4

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=98.75  E-value=3.4e-08  Score=94.60  Aligned_cols=71  Identities=17%  Similarity=0.215  Sum_probs=59.3

Q ss_pred             cCCCCCCHHHHHHHHH----HHcCCcEEEEcCCCCcHHHHHHHHHHH-HhcCCC-----eEEEEcccHHHHHHHHHHHHH
Q psy2760         190 TWPFELDVFQKQAIIK----LEEHNHVFVTAHTSAGKTVIAEYAIAL-SQNHKT-----RTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       190 ~~~f~l~~~Q~~ai~~----l~~g~~vlv~apTGSGKTl~~~l~il~-~l~~g~-----ral~l~PtraLa~Q~~~~l~~  259 (333)
                      .|||.+++.|.+.+..    +..|.++++.||||+|||++++.|++. ....+.     +++|.++|.++..|....+++
T Consensus         4 ~FPy~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~   83 (289)
T smart00489        4 YFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRK   83 (289)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHh
Confidence            3899999999996555    578999999999999999999999873 333233     899999999999999888876


Q ss_pred             h
Q psy2760         260 T  260 (333)
Q Consensus       260 ~  260 (333)
                      .
T Consensus        84 ~   84 (289)
T smart00489       84 L   84 (289)
T ss_pred             c
Confidence            4

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

Probab=98.70  E-value=8.6e-08  Score=92.99  Aligned_cols=131  Identities=18%  Similarity=0.135  Sum_probs=104.6

Q ss_pred             CCCHHHHHHHHHH----HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC--cEEE
Q psy2760         194 ELDVFQKQAIIKL----EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD--VGLI  267 (333)
Q Consensus       194 ~l~~~Q~~ai~~l----~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~--vgll  267 (333)
                      .+++.|+.+-..+    .+.++.++.|.||||||..-.-+|.++++.|.++.+.+|....+.+++.+++..|++  +.++
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEMif~~i~~al~~G~~vciASPRvDVclEl~~Rlk~aF~~~~I~~L  176 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMIFQGIEQALNQGGRVCIASPRVDVCLELYPRLKQAFSNCDIDLL  176 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhhHHHHHHHHhcCCeEEEecCcccchHHHHHHHHHhhccCCeeeE
Confidence            7999999987764    678899999999999999999999999999999999999999999999999999985  7889


Q ss_pred             eCCCCCCCCcceEEecc--------CcceEecccccccc---ccCcCcccccchhhhhhheeccCcch
Q psy2760         268 DDLPPVFPDVEKLLEDL--------NIGGLDELSIHDFN---KHLKFWKPKVQLDDLFDWTMASDATT  324 (333)
Q Consensus       268 tGd~~~~~~a~ili~t~--------~i~liViDe~H~~~---~~~R~~~~~~~l~~l~~l~~~~d~~~  324 (333)
                      .|+.....++..+|+|+        ...++++||..-|.   +..-.++-..+.-..-..+.++++++
T Consensus       177 yg~S~~~fr~plvVaTtHQLlrFk~aFD~liIDEVDAFP~~~d~~L~~Av~~ark~~g~~IylTATp~  244 (441)
T COG4098         177 YGDSDSYFRAPLVVATTHQLLRFKQAFDLLIIDEVDAFPFSDDQSLQYAVKKARKKEGATIYLTATPT  244 (441)
T ss_pred             ecCCchhccccEEEEehHHHHHHHhhccEEEEeccccccccCCHHHHHHHHHhhcccCceEEEecCCh
Confidence            99999888899999987        56788889888764   22212222222222333556666655

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

Probab=98.68  E-value=7e-08  Score=103.75  Aligned_cols=112  Identities=16%  Similarity=0.132  Sum_probs=85.2

Q ss_pred             ccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcE-
Q psy2760         187 MAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVG-  265 (333)
Q Consensus       187 ~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vg-  265 (333)
                      +.+..+|.|+..|+-+...+..|++.-+.||||.|||...++..+....+|.|++|++||+.|+.|+++++.+.....+ 
T Consensus        75 F~k~~G~~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a~kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~  154 (1187)
T COG1110          75 FKKATGFRPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLAKKGKRVYIIVPTTTLVRQVYERLKKFAEDAGS  154 (1187)
T ss_pred             HHHhhCCCchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEecCHHHHHHHHHHHHHHHhhcCC
Confidence            3445566899999999999999999999999999999998887777777889999999999999999999977442221 


Q ss_pred             -----EEeCCCCCC-----------CCcceEEecc-------------CcceEecccccccc
Q psy2760         266 -----LIDDLPPVF-----------PDVEKLLEDL-------------NIGGLDELSIHDFN  298 (333)
Q Consensus       266 -----lltGd~~~~-----------~~a~ili~t~-------------~i~liViDe~H~~~  298 (333)
                           +++|..+..           .+.+++|.|.             ...++.+|-..-+-
T Consensus       155 ~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~L~~~kFdfifVDDVDA~L  216 (1187)
T COG1110         155 LDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEELSKLKFDFIFVDDVDAIL  216 (1187)
T ss_pred             cceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHHhcccCCCEEEEccHHHHH
Confidence                 155654432           2346777775             34555566555443

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=98.66  E-value=6.9e-08  Score=103.89  Aligned_cols=93  Identities=16%  Similarity=0.071  Sum_probs=72.9

Q ss_pred             cCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC----cE
Q psy2760         190 TWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD----VG  265 (333)
Q Consensus       190 ~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vg  265 (333)
                      .++..++..|...--.+..|+  +..++||+|||++|.+|++.....|..+.+++||+.||.|.++.+...+..    ++
T Consensus        78 ~lg~~~ydvQliGg~~Lh~G~--Iaem~TGeGKTL~a~Lpa~~~al~G~~V~VvTpn~yLA~qd~e~m~~l~~~lGLtv~  155 (896)
T PRK13104         78 TLGLRHFDVQLIGGMVLHEGN--IAEMRTGEGKTLVATLPAYLNAISGRGVHIVTVNDYLAKRDSQWMKPIYEFLGLTVG  155 (896)
T ss_pred             HcCCCcchHHHhhhhhhccCc--cccccCCCCchHHHHHHHHHHHhcCCCEEEEcCCHHHHHHHHHHHHHHhcccCceEE
Confidence            344567778877666666665  779999999999999999866666788999999999999999999887653    78


Q ss_pred             EEeCCCCCCC-----CcceEEecc
Q psy2760         266 LIDDLPPVFP-----DVEKLLEDL  284 (333)
Q Consensus       266 lltGd~~~~~-----~a~ili~t~  284 (333)
                      +++|+.....     ...++++|+
T Consensus       156 ~i~gg~~~~~r~~~y~~dIvygT~  179 (896)
T PRK13104        156 VIYPDMSHKEKQEAYKADIVYGTN  179 (896)
T ss_pred             EEeCCCCHHHHHHHhCCCEEEECC
Confidence            8888866432     246777766

>KOG0352|consensus

Probab=98.65  E-value=6.9e-08  Score=95.82  Aligned_cols=110  Identities=18%  Similarity=0.166  Sum_probs=80.9

Q ss_pred             CCHHHHHHHHHH-HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEe-----
Q psy2760         195 LDVFQKQAIIKL-EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLID-----  268 (333)
Q Consensus       195 l~~~Q~~ai~~l-~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vgllt-----  268 (333)
                      -++.|.+|+.++ ....+|.|+.|||+||+++|.+|.+.+   +.-.|+++|..||+..+.++|.++--.+.-+.     
T Consensus        21 Ks~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~---~gITIV~SPLiALIkDQiDHL~~LKVp~~SLNSKlSt   97 (641)
T KOG0352|consen   21 KSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH---GGITIVISPLIALIKDQIDHLKRLKVPCESLNSKLST   97 (641)
T ss_pred             cChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHh---CCeEEEehHHHHHHHHHHHHHHhcCCchhHhcchhhH
Confidence            488999999996 777899999999999999999997644   34788999999999999999876322232222     


Q ss_pred             -------CCCCC-CCCcceEEecc-------------------CcceEeccccccccccCcCcccc
Q psy2760         269 -------DLPPV-FPDVEKLLEDL-------------------NIGGLDELSIHDFNKHLKFWKPK  307 (333)
Q Consensus       269 -------Gd~~~-~~~a~ili~t~-------------------~i~liViDe~H~~~~~~R~~~~~  307 (333)
                             +|+.. .++..++.-|+                   -+.++++||+|.+...+..++..
T Consensus        98 ~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHCVSQWGHDFRPD  163 (641)
T KOG0352|consen   98 VERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHCVSQWGHDFRPD  163 (641)
T ss_pred             HHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHHHhhhceeeeEEechhhhHhhhccccCcc
Confidence                   22221 12223333333                   36889999999999887777764

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

Probab=98.63  E-value=1.4e-07  Score=102.54  Aligned_cols=65  Identities=17%  Similarity=0.097  Sum_probs=56.1

Q ss_pred             CCCCCCHHHHHHHHH----HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHH
Q psy2760         191 WPFELDVFQKQAIIK----LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYR  255 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~----l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~  255 (333)
                      .+|++++.|.+++..    +..++++++.||||+|||++|++|++.....+.+++|.+||++|..|+..
T Consensus       242 ~~~~~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~~~~~vvi~t~t~~Lq~Ql~~  310 (850)
T TIGR01407       242 LGLEYRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAITEKPVVISTNTKVLQSQLLE  310 (850)
T ss_pred             cCCccCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhcCCCeEEEEeCcHHHHHHHHH
Confidence            456889999987774    56889999999999999999999987654467899999999999999875

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.

>KOG0951|consensus

Probab=98.62  E-value=4.4e-08  Score=106.66  Aligned_cols=107  Identities=19%  Similarity=0.335  Sum_probs=90.5

Q ss_pred             CCCHHHHHHHHHH-HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-----cEEE
Q psy2760         194 ELDVFQKQAIIKL-EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-----VGLI  267 (333)
Q Consensus       194 ~l~~~Q~~ai~~l-~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-----vgll  267 (333)
                      .++++|.|+++.+ ..++++++++|+|||||.++.++++. ...-.+++|++|..+.+..+++.|.++|+.     +..+
T Consensus      1143 ~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~-~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~~G~~~~~l 1221 (1674)
T KOG0951|consen 1143 DFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR-PDTIGRAVYIAPLEEIADEQYRDWEKKFSKLLGLRIVKL 1221 (1674)
T ss_pred             ccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC-CccceEEEEecchHHHHHHHHHHHHHhhccccCceEEec
Confidence            4599999999997 88899999999999999999999876 445578999999999999999999999986     4557


Q ss_pred             eCCCCCCC----CcceEEecc----------CcceEeccccccccccC
Q psy2760         268 DDLPPVFP----DVEKLLEDL----------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       268 tGd~~~~~----~a~ili~t~----------~i~liViDe~H~~~~~~  301 (333)
                      +|+.+.+.    .+.+++.|+          .+.+++.|+.|+.++..
T Consensus      1222 ~ge~s~~lkl~~~~~vii~tpe~~d~lq~iQ~v~l~i~d~lh~igg~~ 1269 (1674)
T KOG0951|consen 1222 TGETSLDLKLLQKGQVIISTPEQWDLLQSIQQVDLFIVDELHLIGGVY 1269 (1674)
T ss_pred             CCccccchHHhhhcceEEechhHHHHHhhhhhcceEeeehhhhhcccC
Confidence            88877653    357888887          46889999999998443

>KOG0332|consensus

Probab=98.61  E-value=1.7e-07  Score=91.73  Aligned_cols=103  Identities=14%  Similarity=0.043  Sum_probs=76.3

Q ss_pred             CCCHHHHHHHHHHH--cCCcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcccHHHHHHHHHHHHHhcCCcEE--
Q psy2760         194 ELDVFQKQAIIKLE--EHNHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSPIKALSNQKYRDFRETFQDVGL--  266 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~--~g~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~PtraLa~Q~~~~l~~~f~~vgl--  266 (333)
                      .|+.+|..|+|.++  -.+|++..+..|+|||.+|.+.++....   ..+.++.++|||+||.|+.+.+.+.-+..++  
T Consensus       112 kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~~~~PQ~iCLaPtrELA~Q~~eVv~eMGKf~~ita  191 (477)
T KOG0332|consen  112 KPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPDVVVPQCICLAPTRELAPQTGEVVEEMGKFTELTA  191 (477)
T ss_pred             CcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCccccCCCceeeCchHHHHHHHHHHHHHhcCceeeeE
Confidence            69999999999974  5579999999999999999999996553   3577899999999999999999874322211  


Q ss_pred             ---EeCCCCCC---CCcceEEecc----------------CcceEecccccc
Q psy2760         267 ---IDDLPPVF---PDVEKLLEDL----------------NIGGLDELSIHD  296 (333)
Q Consensus       267 ---ltGd~~~~---~~a~ili~t~----------------~i~liViDe~H~  296 (333)
                         +-|....+   ..+++++.|+                .+-.++.||+..
T Consensus       192 ~yair~sk~~rG~~i~eqIviGTPGtv~Dlm~klk~id~~kikvfVlDEAD~  243 (477)
T KOG0332|consen  192 SYAIRGSKAKRGNKLTEQIVIGTPGTVLDLMLKLKCIDLEKIKVFVLDEADV  243 (477)
T ss_pred             EEEecCcccccCCcchhheeeCCCccHHHHHHHHHhhChhhceEEEecchhh
Confidence               22221111   1245677765                456788899874

>KOG0327|consensus

Probab=98.56  E-value=5.7e-08  Score=95.00  Aligned_cols=83  Identities=20%  Similarity=0.231  Sum_probs=67.9

Q ss_pred             CCC-CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcccHHHHHHHHHHHHHhcCC---
Q psy2760         191 WPF-ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSPIKALSNQKYRDFRETFQD---  263 (333)
Q Consensus       191 ~~f-~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~PtraLa~Q~~~~l~~~f~~---  263 (333)
                      ++| .|+.+|++||.++..|.|+.+.+.+|+|||.+|..++++...   +...|++++|+|+||.|+.......+..   
T Consensus        44 yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~ke~qalilaPtreLa~qi~~v~~~lg~~~~~  123 (397)
T KOG0327|consen   44 YGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAPTRELAQQIQKVVRALGDHMDV  123 (397)
T ss_pred             hccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcchHHHHHHHhcchHHHHHHHHHHHHhhhcccce
Confidence            455 899999999999999999999999999999999999987643   3467999999999999999777664432   


Q ss_pred             -cEEEeCCCCC
Q psy2760         264 -VGLIDDLPPV  273 (333)
Q Consensus       264 -vglltGd~~~  273 (333)
                       +....|+...
T Consensus       124 ~v~~~igg~~~  134 (397)
T KOG0327|consen  124 SVHACIGGTNV  134 (397)
T ss_pred             eeeeecCcccc
Confidence             3445555544

>KOG0950|consensus

Probab=98.52  E-value=1.4e-07  Score=100.87  Aligned_cols=115  Identities=17%  Similarity=0.149  Sum_probs=90.9

Q ss_pred             CCCHHHHHHHHH--HHcCCcEEEEcCCCCcHHHHHHHHHHH-HhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEE----
Q psy2760         194 ELDVFQKQAIIK--LEEHNHVFVTAHTSAGKTVIAEYAIAL-SQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGL----  266 (333)
Q Consensus       194 ~l~~~Q~~ai~~--l~~g~~vlv~apTGSGKTl~~~l~il~-~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vgl----  266 (333)
                      .++.||.+++..  +++++|.+..+||+.|||+++.+.++. .+..++.++++.|..+-+.+....+...+-+.|+    
T Consensus       223 ~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~rr~~llilp~vsiv~Ek~~~l~~~~~~~G~~ve~  302 (1008)
T KOG0950|consen  223 KLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCRRRNVLLILPYVSIVQEKISALSPFSIDLGFPVEE  302 (1008)
T ss_pred             HHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHHhhceeEecceeehhHHHHhhhhhhccccCCcchh
Confidence            789999999765  789999999999999999999998874 4566778999999999999998888765444333    


Q ss_pred             EeCCCC---CCCCcceEEecc-----------------CcceEeccccccccccCcCccccc
Q psy2760         267 IDDLPP---VFPDVEKLLEDL-----------------NIGGLDELSIHDFNKHLKFWKPKV  308 (333)
Q Consensus       267 ltGd~~---~~~~a~ili~t~-----------------~i~liViDe~H~~~~~~R~~~~~~  308 (333)
                      +.|...   ......+.++|.                 .++.+|+||.|++++.+||.-.+.
T Consensus       303 y~g~~~p~~~~k~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~~rg~~lE~  364 (1008)
T KOG0950|consen  303 YAGRFPPEKRRKRESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDKGRGAILEL  364 (1008)
T ss_pred             hcccCCCCCcccceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeeccccchHHHH
Confidence            334433   333445666664                 478999999999999999987654

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

Probab=98.41  E-value=8.1e-07  Score=94.26  Aligned_cols=68  Identities=15%  Similarity=0.192  Sum_probs=55.6

Q ss_pred             CCCHHHHHHHHHH----Hc------CCcEEEEcCCCCcHHHHHHHHHHHHh--cCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy2760         194 ELDVFQKQAIIKL----EE------HNHVFVTAHTSAGKTVIAEYAIALSQ--NHKTRTIYTSPIKALSNQKYRDFRETF  261 (333)
Q Consensus       194 ~l~~~Q~~ai~~l----~~------g~~vlv~apTGSGKTl~~~l~il~~l--~~g~ral~l~PtraLa~Q~~~~l~~~f  261 (333)
                      .++.+|..|+..+    ..      .+..++..+||||||+++...+....  ....++|+|+|+++|..|+.+.|....
T Consensus       238 ~~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~~~~~~~~vl~lvdR~~L~~Q~~~~f~~~~  317 (667)
T TIGR00348       238 YQRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKALELLKNPKVFFVVDRRELDYQLMKEFQSLQ  317 (667)
T ss_pred             ehHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHHhhcCCCeEEEEECcHHHHHHHHHHHHhhC
Confidence            4789999999884    22      35899999999999999877665432  456799999999999999999998744

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

>KOG0329|consensus

Probab=98.41  E-value=1.9e-07  Score=87.57  Aligned_cols=104  Identities=13%  Similarity=0.080  Sum_probs=84.1

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC---CCeEEEEcccHHHHHHHHHHHHHhcC----C--c
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH---KTRTIYTSPIKALSNQKYRDFRETFQ----D--V  264 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~---g~ral~l~PtraLa~Q~~~~l~~~f~----~--v  264 (333)
                      .|...|.++||...-|.+++..|..|-|||.+|.++-++.+.+   ...+++++.||+||-|+..++.+ |+    +  +
T Consensus        64 hpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtrelafqi~~ey~r-fskymP~vkv  142 (387)
T KOG0329|consen   64 HPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTRELAFQISKEYER-FSKYMPSVKV  142 (387)
T ss_pred             CchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCCCCeEEEEEEeccHHHHHHHHHHHHH-HHhhCCCceE
Confidence            7999999999999999999999999999999999998877643   34688899999999999877633 54    3  7


Q ss_pred             EEEeCCCCCCCCc-------ceEEecc---------------CcceEecccccccc
Q psy2760         265 GLIDDLPPVFPDV-------EKLLEDL---------------NIGGLDELSIHDFN  298 (333)
Q Consensus       265 glltGd~~~~~~a-------~ili~t~---------------~i~liViDe~H~~~  298 (333)
                      .++.||..+....       .+.+.|+               ++-.+++||+.+.-
T Consensus       143 aVFfGG~~Ikkdee~lk~~PhivVgTPGrilALvr~k~l~lk~vkhFvlDEcdkml  198 (387)
T KOG0329|consen  143 SVFFGGLFIKKDEELLKNCPHIVVGTPGRILALVRNRSLNLKNVKHFVLDECDKML  198 (387)
T ss_pred             EEEEcceeccccHHHHhCCCeEEEcCcHHHHHHHHhccCchhhcceeehhhHHHHH
Confidence            8899999887654       3555555               45677888887553

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=98.40  E-value=1.4e-06  Score=94.43  Aligned_cols=62  Identities=21%  Similarity=0.186  Sum_probs=53.8

Q ss_pred             CCCCCHHHHHHHHH----HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHH
Q psy2760         192 PFELDVFQKQAIIK----LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKY  254 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~----l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~  254 (333)
                      +|+.++-|.+....    +..+.++++.|+||+|||++|++|++... .+.++++.+||++|++|+.
T Consensus       243 ~~e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~-~~~~vvI~t~T~~Lq~Ql~  308 (820)
T PRK07246        243 GLEERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS-DQRQIIVSVPTKILQDQIM  308 (820)
T ss_pred             CCccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc-CCCcEEEEeCcHHHHHHHH
Confidence            47899999996655    46788999999999999999999987643 4688999999999999995

>KOG0351|consensus

Probab=98.39  E-value=2.7e-07  Score=100.40  Aligned_cols=113  Identities=14%  Similarity=0.107  Sum_probs=84.5

Q ss_pred             CCC-CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEeC
Q psy2760         191 WPF-ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDD  269 (333)
Q Consensus       191 ~~f-~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vglltG  269 (333)
                      |+. .+++-|.+||...+.|++++|..|||+||+++|.+|.+..   ++-.|+|+|..+|.+.+...+....=....++|
T Consensus       260 Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~---~gitvVISPL~SLm~DQv~~L~~~~I~a~~L~s  336 (941)
T KOG0351|consen  260 FGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLL---GGVTVVISPLISLMQDQVTHLSKKGIPACFLSS  336 (941)
T ss_pred             hccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeecccccc---CCceEEeccHHHHHHHHHHhhhhcCcceeeccc
Confidence            444 7899999999999999999999999999999999987532   347889999999999999988443323455666


Q ss_pred             CCCCCC-------------CcceEEecc-----------------C---cceEeccccccccccCcCccc
Q psy2760         270 LPPVFP-------------DVEKLLEDL-----------------N---IGGLDELSIHDFNKHLKFWKP  306 (333)
Q Consensus       270 d~~~~~-------------~a~ili~t~-----------------~---i~liViDe~H~~~~~~R~~~~  306 (333)
                      ++....             .-.++..|+                 .   +.++|+||+|.+...+..+|.
T Consensus       337 ~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCVSqWgHdFRp  406 (941)
T KOG0351|consen  337 IQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCVSQWGHDFRP  406 (941)
T ss_pred             cccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHhhhhcccccH
Confidence            655421             112232232                 2   789999999998877655554

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

Probab=98.38  E-value=9.4e-07  Score=92.95  Aligned_cols=55  Identities=20%  Similarity=0.215  Sum_probs=47.5

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHHHHHHHHhc--CCCeEEEEcccHHHHHHHHHHHHHh
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAEYAIALSQN--HKTRTIYTSPIKALSNQKYRDFRET  260 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~l~il~~l~--~g~ral~l~PtraLa~Q~~~~l~~~  260 (333)
                      +.+++.+++.||||+|||++|++|++....  .+.+++|++||++|+.|+.+.+...
T Consensus        13 l~~~~~lliEA~TGtGKTlAYLlpal~~~~~~~~~rvlIstpT~~Lq~Ql~~~l~~l   69 (636)
T TIGR03117        13 LRQKRIGMLEASTGVGKTLAMIMAALTMLKERPDQKIAIAVPTLALMGQLWSELERL   69 (636)
T ss_pred             HhcCCeEEEEcCCCCcHHHHHHHHHHHHHHhccCceEEEECCcHHHHHHHHHHHHHH
Confidence            477889999999999999999999875433  4789999999999999999877643

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.

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=98.36  E-value=7.6e-07  Score=95.66  Aligned_cols=92  Identities=14%  Similarity=0.011  Sum_probs=71.5

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC----cEE
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD----VGL  266 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vgl  266 (333)
                      ++..+++.|.-..-.+..|+  +..+.||+|||+++.+|++.....|..+-+++||..||.|.++.+...|..    +++
T Consensus        78 lg~~~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL~G~~V~IvTpn~yLA~rd~e~~~~l~~~LGlsv~~  155 (830)
T PRK12904         78 LGMRHFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNALTGKGVHVVTVNDYLAKRDAEWMGPLYEFLGLSVGV  155 (830)
T ss_pred             hCCCCCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHHcCCCEEEEecCHHHHHHHHHHHHHHHhhcCCeEEE
Confidence            44567888887777777775  889999999999999998633335667889999999999999999887763    788


Q ss_pred             EeCCCCCCC-----CcceEEecc
Q psy2760         267 IDDLPPVFP-----DVEKLLEDL  284 (333)
Q Consensus       267 ltGd~~~~~-----~a~ili~t~  284 (333)
                      ++|+.+...     ...+++.|+
T Consensus       156 i~~~~~~~er~~~y~~dI~ygT~  178 (830)
T PRK12904        156 ILSGMSPEERREAYAADITYGTN  178 (830)
T ss_pred             EcCCCCHHHHHHhcCCCeEEECC
Confidence            888876542     235666665

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=98.33  E-value=1.3e-06  Score=93.71  Aligned_cols=70  Identities=26%  Similarity=0.286  Sum_probs=57.7

Q ss_pred             CCCHHHHHHHHHHH---cCC-cEEEEcCCCCcHHHHHHHHHHHHhc----CCCeEEEEcccHHHHHHHHHHHHHhcCC
Q psy2760         194 ELDVFQKQAIIKLE---EHN-HVFVTAHTSAGKTVIAEYAIALSQN----HKTRTIYTSPIKALSNQKYRDFRETFQD  263 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~---~g~-~vlv~apTGSGKTl~~~l~il~~l~----~g~ral~l~PtraLa~Q~~~~l~~~f~~  263 (333)
                      ...+.|..++..+.   ... .+++.||||+|||++++........    ...|++|+.|+|++++++++++++.++.
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~~~  272 (733)
T COG1203         195 EGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGL  272 (733)
T ss_pred             hhhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHHHHHHHHHHHhhhcc
Confidence            45888999988852   334 7889999999999999987774433    4789999999999999999999987664

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

Probab=98.33  E-value=1.9e-06  Score=91.40  Aligned_cols=102  Identities=21%  Similarity=0.174  Sum_probs=73.9

Q ss_pred             CCCHHHHHHHHHH----Hc-CCcEEEEcCCCCcHHHHHHHHHHHHhc--CCCeEEEEcccHHHHHHHHHHHHHhcCC---
Q psy2760         194 ELDVFQKQAIIKL----EE-HNHVFVTAHTSAGKTVIAEYAIALSQN--HKTRTIYTSPIKALSNQKYRDFRETFQD---  263 (333)
Q Consensus       194 ~l~~~Q~~ai~~l----~~-g~~vlv~apTGSGKTl~~~l~il~~l~--~g~ral~l~PtraLa~Q~~~~l~~~f~~---  263 (333)
                      .++.+|..||..+    .. .+.+|+++.||+|||..++.-|....+  .-+|+||++-+++|+.|-+..|...++.   
T Consensus       165 ~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTAiaii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P~~~~  244 (875)
T COG4096         165 GPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTAIAIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLPFGTK  244 (875)
T ss_pred             cchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeHHHHHHHHHhcchhheeeEEechHHHHHHHHHHHHHhCCCccc
Confidence            6899999999884    33 346899999999999998876665443  3479999999999999999999886664   


Q ss_pred             cEEEeCCCCCCCCcceEEecc--------------------CcceEecccccc
Q psy2760         264 VGLIDDLPPVFPDVEKLLEDL--------------------NIGGLDELSIHD  296 (333)
Q Consensus       264 vglltGd~~~~~~a~ili~t~--------------------~i~liViDe~H~  296 (333)
                      +..+++- ......++-++|.                    ...+||+||+|.
T Consensus       245 ~n~i~~~-~~~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHR  296 (875)
T COG4096         245 MNKIEDK-KGDTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHR  296 (875)
T ss_pred             eeeeecc-cCCcceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhh
Confidence            3333322 2222223333332                    367899999995

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

Probab=98.28  E-value=2.7e-07  Score=79.94  Aligned_cols=114  Identities=11%  Similarity=0.060  Sum_probs=68.0

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHH-HHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEeCCC--CCCCCcceEEecc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIA-LSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLP--PVFPDVEKLLEDL  284 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il-~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vglltGd~--~~~~~a~ili~t~  284 (333)
                      .|+--++-.++|+|||.-.+-.++ .++..+.|+|++.|||.++..+.+.++..  ++..-+.-.  ......-+.+++.
T Consensus         3 kg~~~~~d~hpGaGKTr~vlp~~~~~~i~~~~rvLvL~PTRvva~em~~aL~~~--~~~~~t~~~~~~~~g~~~i~vMc~   80 (148)
T PF07652_consen    3 KGELTVLDLHPGAGKTRRVLPEIVREAIKRRLRVLVLAPTRVVAEEMYEALKGL--PVRFHTNARMRTHFGSSIIDVMCH   80 (148)
T ss_dssp             TTEEEEEE--TTSSTTTTHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHTTTS--SEEEESTTSS----SSSSEEEEEH
T ss_pred             CCceeEEecCCCCCCcccccHHHHHHHHHccCeEEEecccHHHHHHHHHHHhcC--CcccCceeeeccccCCCccccccc
Confidence            355668899999999997666554 67889999999999999999999998642  122211100  1122233444432


Q ss_pred             --------------CcceEeccccccccccC---cCcccccchhhhhhheeccCcc
Q psy2760         285 --------------NIGGLDELSIHDFNKHL---KFWKPKVQLDDLFDWTMASDAT  323 (333)
Q Consensus       285 --------------~i~liViDe~H~~~~~~---R~~~~~~~l~~l~~l~~~~d~~  323 (333)
                                    +..++|+||+|.-+..+   |+|-...+..-..+++.+++.|
T Consensus        81 at~~~~~~~p~~~~~yd~II~DEcH~~Dp~sIA~rg~l~~~~~~g~~~~i~mTATP  136 (148)
T PF07652_consen   81 ATYGHFLLNPCRLKNYDVIIMDECHFTDPTSIAARGYLRELAESGEAKVIFMTATP  136 (148)
T ss_dssp             HHHHHHHHTSSCTTS-SEEEECTTT--SHHHHHHHHHHHHHHHTTS-EEEEEESS-
T ss_pred             HHHHHHhcCcccccCccEEEEeccccCCHHHHhhheeHHHhhhccCeeEEEEeCCC
Confidence                          67889999999876553   6655544333335667777665

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 ....

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=98.20  E-value=6.8e-06  Score=90.32  Aligned_cols=71  Identities=17%  Similarity=0.257  Sum_probs=59.0

Q ss_pred             CCCCCHHHHHHHHH----HHcCCcEEEEcCCCCcHHHHHHHHHHH-HhcCCCeEEEEcccHHHHHHHHH----HHHHhcC
Q psy2760         192 PFELDVFQKQAIIK----LEEHNHVFVTAHTSAGKTVIAEYAIAL-SQNHKTRTIYTSPIKALSNQKYR----DFRETFQ  262 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~----l~~g~~vlv~apTGSGKTl~~~l~il~-~l~~g~ral~l~PtraLa~Q~~~----~l~~~f~  262 (333)
                      .|++++-|.+.+..    +..++++++.||||+|||++|++|.+. +...+.+++|-++|++|.+|+..    .+++.++
T Consensus       255 ~~e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~~~~~vvIsT~T~~LQ~Ql~~kDiP~L~~~~~  334 (928)
T PRK08074        255 KYEKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKKKEEPVVISTYTIQLQQQLLEKDIPLLQKIFP  334 (928)
T ss_pred             CCcCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhccCCeEEEEcCCHHHHHHHHHhhHHHHHHHcC
Confidence            46899999997766    367889999999999999999998874 45578999999999999999875    3455443

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=98.18  E-value=1e-05  Score=88.76  Aligned_cols=131  Identities=16%  Similarity=0.112  Sum_probs=86.7

Q ss_pred             CCCCHHHHHHHHHHH--cCCcEEEEcCCCCcHHHHHHHHHHHHhc--CCCeEEEEcccHHHHHHHHHHHHHhcCC-cEEE
Q psy2760         193 FELDVFQKQAIIKLE--EHNHVFVTAHTSAGKTVIAEYAIALSQN--HKTRTIYTSPIKALSNQKYRDFRETFQD-VGLI  267 (333)
Q Consensus       193 f~l~~~Q~~ai~~l~--~g~~vlv~apTGSGKTl~~~l~il~~l~--~g~ral~l~PtraLa~Q~~~~l~~~f~~-vgll  267 (333)
                      ..|.|||..++..+.  ....++++-..|-|||.-+.+.+...+.  ...++|+|+|. .|..|+..++.++|.- +.++
T Consensus       151 ~~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g~~~rvLIVvP~-sL~~QW~~El~~kF~l~~~i~  229 (956)
T PRK04914        151 ASLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTGRAERVLILVPE-TLQHQWLVEMLRRFNLRFSLF  229 (956)
T ss_pred             CCCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcCCCCcEEEEcCH-HHHHHHHHHHHHHhCCCeEEE
Confidence            469999999987763  3347899999999999998765543333  33689999998 8999999999888863 5555


Q ss_pred             eCCCC---------CCCCcceEEecc----------------CcceEeccccccccc----cCcCcccccchhhhh-hhe
Q psy2760         268 DDLPP---------VFPDVEKLLEDL----------------NIGGLDELSIHDFNK----HLKFWKPKVQLDDLF-DWT  317 (333)
Q Consensus       268 tGd~~---------~~~~a~ili~t~----------------~i~liViDe~H~~~~----~~R~~~~~~~l~~l~-~l~  317 (333)
                      .++..         .-....++|++.                ...++|+||+|++..    +++.|+....+.+.+ ..+
T Consensus       230 ~~~~~~~~~~~~~~pf~~~~~vI~S~~~l~~~~~~~~~l~~~~wdlvIvDEAH~lk~~~~~~s~~y~~v~~La~~~~~~L  309 (956)
T PRK04914        230 DEERYAEAQHDADNPFETEQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHHLVWSEEAPSREYQVVEQLAEVIPGVL  309 (956)
T ss_pred             cCcchhhhcccccCccccCcEEEEEHHHhhhCHHHHHHHhhcCCCEEEEechhhhccCCCCcCHHHHHHHHHhhccCCEE
Confidence            43321         111234555533                347899999999862    233333222222222 256


Q ss_pred             eccCcch
Q psy2760         318 MASDATT  324 (333)
Q Consensus       318 ~~~d~~~  324 (333)
                      +.+++|.
T Consensus       310 LLTATP~  316 (956)
T PRK04914        310 LLTATPE  316 (956)
T ss_pred             EEEcCcc
Confidence            6777764

>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=98.18  E-value=6.2e-06  Score=77.12  Aligned_cols=90  Identities=16%  Similarity=0.173  Sum_probs=59.9

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHh--cCC---CeEEEEcccHHHHHHHHHHHHHhcC--C--cEEEeCCC-------
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQ--NHK---TRTIYTSPIKALSNQKYRDFRETFQ--D--VGLIDDLP-------  271 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l--~~g---~ral~l~PtraLa~Q~~~~l~~~f~--~--vglltGd~-------  271 (333)
                      ..+.++++-..|+|||..++..+....  .+.   .++|+|+|. ++..|+.+++.+.+.  .  +..+.|+.       
T Consensus        24 ~~~g~lL~de~GlGKT~~~i~~~~~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~~~~~~~~~v~~~~~~~~~~~~~~  102 (299)
T PF00176_consen   24 PPRGGLLADEMGLGKTITAIALISYLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEKWFDPDSLRVIIYDGDSERRRLSK  102 (299)
T ss_dssp             TT-EEEE---TTSSHHHHHHHHHHHHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHHHSGT-TS-EEEESSSCHHHHTTS
T ss_pred             CCCCEEEEECCCCCchhhhhhhhhhhhhccccccccceeEeecc-chhhhhhhhhccccccccccccccccccccccccc
Confidence            446889999999999999887765322  122   259999999 888999999988773  2  56666665       


Q ss_pred             CCCCCcceEEecc------------------CcceEecccccccc
Q psy2760         272 PVFPDVEKLLEDL------------------NIGGLDELSIHDFN  298 (333)
Q Consensus       272 ~~~~~a~ili~t~------------------~i~liViDe~H~~~  298 (333)
                      .......+++.+.                  +..++|+||.|.+.
T Consensus       103 ~~~~~~~vvi~ty~~~~~~~~~~~~~~l~~~~~~~vIvDEaH~~k  147 (299)
T PF00176_consen  103 NQLPKYDVVITTYETLRKARKKKDKEDLKQIKWDRVIVDEAHRLK  147 (299)
T ss_dssp             SSCCCSSEEEEEHHHHH--TSTHTTHHHHTSEEEEEEETTGGGGT
T ss_pred             cccccceeeeccccccccccccccccccccccceeEEEecccccc
Confidence            2233345666654                  35669999999994

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.

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=98.06  E-value=2.2e-05  Score=88.08  Aligned_cols=130  Identities=15%  Similarity=0.097  Sum_probs=77.3

Q ss_pred             CHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHH-HHhcCCC--eEEEEcc----cHHHHHHHHHHHHHhcCC-cEEE
Q psy2760         196 DVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIA-LSQNHKT--RTIYTSP----IKALSNQKYRDFRETFQD-VGLI  267 (333)
Q Consensus       196 ~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il-~~l~~g~--ral~l~P----traLa~Q~~~~l~~~f~~-vgll  267 (333)
                      +.+-.+.+..+..+..++++|+||||||.  .+|.+ .....+.  ++++.-|    +++||.++.+++...++. ||.-
T Consensus        76 ~~~r~~Il~ai~~~~VviI~GeTGSGKTT--qlPq~lle~g~g~~g~I~~TQPRRlAArsLA~RVA~El~~~lG~~VGY~  153 (1294)
T PRK11131         76 SQKKQDILEAIRDHQVVIVAGETGSGKTT--QLPKICLELGRGVKGLIGHTQPRRLAARTVANRIAEELETELGGCVGYK  153 (1294)
T ss_pred             HHHHHHHHHHHHhCCeEEEECCCCCCHHH--HHHHHHHHcCCCCCCceeeCCCcHHHHHHHHHHHHHHHhhhhcceecee
Confidence            44444555667778888999999999999  46643 3333332  3344446    578888888888765654 4442


Q ss_pred             e-CCCCCCCCcceEEecc--------------CcceEeccccccccccCcCcc--cccchh---hhhhheeccCcchhhh
Q psy2760         268 D-DLPPVFPDVEKLLEDL--------------NIGGLDELSIHDFNKHLKFWK--PKVQLD---DLFDWTMASDATTLEI  327 (333)
Q Consensus       268 t-Gd~~~~~~a~ili~t~--------------~i~liViDe~H~~~~~~R~~~--~~~~l~---~l~~l~~~~d~~~~e~  327 (333)
                      + .+.+......++++|.              ++.++|+||+|...-.. ++.  ....++   ...+++++|++-..|-
T Consensus       154 vrf~~~~s~~t~I~v~TpG~LL~~l~~d~~Ls~~~~IIIDEAHERsLn~-DfLLg~Lk~lL~~rpdlKvILmSATid~e~  232 (1294)
T PRK11131        154 VRFNDQVSDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNI-DFILGYLKELLPRRPDLKVIITSATIDPER  232 (1294)
T ss_pred             ecCccccCCCCCEEEEChHHHHHHHhcCCccccCcEEEecCcccccccc-chHHHHHHHhhhcCCCceEEEeeCCCCHHH
Confidence            2 1223334556777775              56789999999522111 110  011111   1246788887765554


Q ss_pred             h
Q psy2760         328 F  328 (333)
Q Consensus       328 ~  328 (333)
                      |
T Consensus       233 f  233 (1294)
T PRK11131        233 F  233 (1294)
T ss_pred             H
Confidence            3

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.05  E-value=1.1e-05  Score=86.15  Aligned_cols=70  Identities=20%  Similarity=0.278  Sum_probs=60.5

Q ss_pred             cCCCCC-CHHHHHHHHH----HHcCCcEEEEcCCCCcHHHHHHHHHHHHhc-CC--CeEEEEcccHHHHHHHHHHHHH
Q psy2760         190 TWPFEL-DVFQKQAIIK----LEEHNHVFVTAHTSAGKTVIAEYAIALSQN-HK--TRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       190 ~~~f~l-~~~Q~~ai~~----l~~g~~vlv~apTGSGKTl~~~l~il~~l~-~g--~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      .|||.+ +|.|.+.+..    +..+.++++.+|||+|||++.+.+.+.... .+  .+++|.+.|..-..|..+++++
T Consensus         5 ~FPy~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~sRThsQl~q~i~Elk~   82 (705)
T TIGR00604         5 YFPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRK   82 (705)
T ss_pred             ecCCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhccccccEEEEcccchHHHHHHHHHHh
Confidence            489965 9999998877    478899999999999999999998885433 33  7999999999999999999987

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).

>KOG0353|consensus

Probab=98.05  E-value=1.5e-05  Score=78.50  Aligned_cols=111  Identities=11%  Similarity=0.110  Sum_probs=81.0

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEeCCCCC
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPV  273 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vglltGd~~~  273 (333)
                      .++|.|..+|.....|+++++..|||.||+++|.+|.+.   ..+-+++++|..+|+..+.-+++..--+...+....+.
T Consensus        94 kfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~---adg~alvi~plislmedqil~lkqlgi~as~lnanssk  170 (695)
T KOG0353|consen   94 KFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALC---ADGFALVICPLISLMEDQILQLKQLGIDASMLNANSSK  170 (695)
T ss_pred             hcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHh---cCCceEeechhHHHHHHHHHHHHHhCcchhhccCcccH
Confidence            689999999999999999999999999999999999764   34558999999999999998987732222223222221


Q ss_pred             -------------CCCcceEEecc--------------------CcceEeccccccccccCcCcccc
Q psy2760         274 -------------FPDVEKLLEDL--------------------NIGGLDELSIHDFNKHLKFWKPK  307 (333)
Q Consensus       274 -------------~~~a~ili~t~--------------------~i~liViDe~H~~~~~~R~~~~~  307 (333)
                                   +..-+++..|+                    -+.++-+||.|.....+..++..
T Consensus       171 e~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~~~iaidevhccsqwghdfr~d  237 (695)
T KOG0353|consen  171 EEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFFKLIAIDEVHCCSQWGHDFRPD  237 (695)
T ss_pred             HHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhcceeEEEeecceeehhhhCcccCcc
Confidence                         11112333333                    24567789999888777666664

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=98.05  E-value=1.6e-05  Score=71.17  Aligned_cols=66  Identities=20%  Similarity=0.255  Sum_probs=52.6

Q ss_pred             CCCHHHHHHHHHHHcCCc-EEEEcCCCCcHHHHHHHHHHHH--------hcCCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         194 ELDVFQKQAIIKLEEHNH-VFVTAHTSAGKTVIAEYAIALS--------QNHKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~-vlv~apTGSGKTl~~~l~il~~--------l~~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      .+++.|.+|+..++.... .+|.||.|+|||.+....+...        ...+.++++++|+.+-++++.+++.+
T Consensus         1 ~ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    1 KLNESQREAIQSALSSNGITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             ---HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            378999999999988887 9999999999996655544444        56788999999999999999999977

>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

Probab=98.03  E-value=1.4e-05  Score=84.25  Aligned_cols=68  Identities=19%  Similarity=0.195  Sum_probs=57.7

Q ss_pred             CCCCCHHHHHHHHHH----HcCCcEEEEcCCCCcHHHHHHHHHH-HHhcCCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         192 PFELDVFQKQAIIKL----EEHNHVFVTAHTSAGKTVIAEYAIA-LSQNHKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l----~~g~~vlv~apTGSGKTl~~~l~il-~~l~~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      +|++++.|.+++..+    ..++.+++.||||+|||++++.|++ .+...+.++++.++|++|-.|..++...
T Consensus        13 ~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~~~~viist~t~~lq~q~~~~~~~   85 (654)
T COG1199          13 GFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKKVIISTRTKALQEQLLEEDLP   85 (654)
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHcCCcEEEECCCHHHHHHHHHhhcc
Confidence            459999999998763    5666799999999999999999887 4556678999999999999999977544

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=98.03  E-value=1.7e-05  Score=85.64  Aligned_cols=93  Identities=14%  Similarity=0.043  Sum_probs=70.7

Q ss_pred             cCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC----cE
Q psy2760         190 TWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD----VG  265 (333)
Q Consensus       190 ~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vg  265 (333)
                      .++..+++.|.-.--.+.+|+  +..++||.|||++|.+|++.....|..+.+|+|++.||.|..+.+...|..    ||
T Consensus        78 ~lgm~~ydVQliGgl~L~~G~--IaEm~TGEGKTL~a~lp~~l~al~g~~VhIvT~ndyLA~RD~e~m~~l~~~lGlsv~  155 (908)
T PRK13107         78 VFEMRHFDVQLLGGMVLDSNR--IAEMRTGEGKTLTATLPAYLNALTGKGVHVITVNDYLARRDAENNRPLFEFLGLTVG  155 (908)
T ss_pred             HhCCCcCchHHhcchHhcCCc--cccccCCCCchHHHHHHHHHHHhcCCCEEEEeCCHHHHHHHHHHHHHHHHhcCCeEE
Confidence            445567778876655566665  779999999999999999877777888999999999999999888776653    67


Q ss_pred             EEeCCCCCCC-----CcceEEecc
Q psy2760         266 LIDDLPPVFP-----DVEKLLEDL  284 (333)
Q Consensus       266 lltGd~~~~~-----~a~ili~t~  284 (333)
                      .++|+.....     ...++..|.
T Consensus       156 ~i~~~~~~~~r~~~Y~~dI~YgT~  179 (908)
T PRK13107        156 INVAGLGQQEKKAAYNADITYGTN  179 (908)
T ss_pred             EecCCCCHHHHHhcCCCCeEEeCC
Confidence            7777765422     345666665

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.02  E-value=1.9e-05  Score=85.48  Aligned_cols=105  Identities=13%  Similarity=0.076  Sum_probs=81.2

Q ss_pred             CCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC----cEEE
Q psy2760         192 PFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD----VGLI  267 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vgll  267 (333)
                      +..++..|...--.+..|+  +....||+|||+++.+|++.....|..+.+++|+--||.|-++.+...|..    ||++
T Consensus        80 Gm~~ydVQliGg~~Lh~G~--iaEM~TGEGKTLvA~l~a~l~al~G~~VhvvT~ndyLA~RD~e~m~~l~~~lGl~v~~i  157 (913)
T PRK13103         80 GMRHFDVQLIGGMTLHEGK--IAEMRTGEGKTLVGTLAVYLNALSGKGVHVVTVNDYLARRDANWMRPLYEFLGLSVGIV  157 (913)
T ss_pred             CCCcchhHHHhhhHhccCc--cccccCCCCChHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHHHhcccCCEEEEE
Confidence            4467788876666666664  668999999999999999888888999999999999999999999888764    7778


Q ss_pred             eCCCCCCC-----CcceEEecc----------------------CcceEecccccccc
Q psy2760         268 DDLPPVFP-----DVEKLLEDL----------------------NIGGLDELSIHDFN  298 (333)
Q Consensus       268 tGd~~~~~-----~a~ili~t~----------------------~i~liViDe~H~~~  298 (333)
                      +|+.+...     ...++..|.                      +..+.++||.|.+-
T Consensus       158 ~~~~~~~err~~Y~~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDsiL  215 (913)
T PRK13103        158 TPFQPPEEKRAAYAADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDSIL  215 (913)
T ss_pred             CCCCCHHHHHHHhcCCEEEEcccccccchhhccceechhhhcccccceeEechhhhee
Confidence            88765432     234555554                      45668888888764

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.00  E-value=1.7e-05  Score=84.67  Aligned_cols=63  Identities=22%  Similarity=0.205  Sum_probs=54.0

Q ss_pred             CCCCCHHHHHHHHHH----Hc-----CCcEEEEcCCCCcHHHHHHHHHH-HHhcCCCeEEEEcccHHHHHHHH
Q psy2760         192 PFELDVFQKQAIIKL----EE-----HNHVFVTAHTSAGKTVIAEYAIA-LSQNHKTRTIYTSPIKALSNQKY  254 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l----~~-----g~~vlv~apTGSGKTl~~~l~il-~~l~~g~ral~l~PtraLa~Q~~  254 (333)
                      +|+.++-|.+.+..+    ..     ++.+++-||||.|||++|++|.+ .+...+.++||-+.|++|-+|+.
T Consensus        23 ~~e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~~~k~vVIST~T~~LQeQL~   95 (697)
T PRK11747         23 GFIPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARAEKKKLVISTATVALQEQLV   95 (697)
T ss_pred             CCCcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHHcCCeEEEEcCCHHHHHHHH
Confidence            378999999987764    33     47899999999999999999876 45668899999999999999997

>KOG0952|consensus

Probab=97.97  E-value=1.9e-06  Score=93.12  Aligned_cols=108  Identities=19%  Similarity=0.230  Sum_probs=76.6

Q ss_pred             CCCHHHHHHHHHH-HcCCcEEEEcCCCCcHHHHHHHHHHHHh--cCCCeEEEEcccHHHHHHHHHHHHHhcCC----cEE
Q psy2760         194 ELDVFQKQAIIKL-EEHNHVFVTAHTSAGKTVIAEYAIALSQ--NHKTRTIYTSPIKALSNQKYRDFRETFQD----VGL  266 (333)
Q Consensus       194 ~l~~~Q~~ai~~l-~~g~~vlv~apTGSGKTl~~~l~il~~l--~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vgl  266 (333)
                      .++|.|.+.|..+ ....++++.+|||||||++|..+++..+  .++.+++|++|.++|+.....+|.+++..    ++-
T Consensus       927 ~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~p~~kvvyIap~kalvker~~Dw~~r~~~~g~k~ie 1006 (1230)
T KOG0952|consen  927 YFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYYPGSKVVYIAPDKALVKERSDDWSKRDELPGIKVIE 1006 (1230)
T ss_pred             ccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccCCCccEEEEcCCchhhcccccchhhhcccCCceeEe
Confidence            3566777766664 5667899999999999999999999765  45789999999999999999999887753    566


Q ss_pred             EeCCCCCCCCcceEEeccCcceEeccccccccccCcCcccc
Q psy2760         267 IDDLPPVFPDVEKLLEDLNIGGLDELSIHDFNKHLKFWKPK  307 (333)
Q Consensus       267 ltGd~~~~~~a~ili~t~~i~liViDe~H~~~~~~R~~~~~  307 (333)
                      ++|+...+..+   +.-   .-+++..+|.|++..|.|...
T Consensus      1007 ~tgd~~pd~~~---v~~---~~~~ittpek~dgi~Rsw~~r 1041 (1230)
T KOG0952|consen 1007 LTGDVTPDVKA---VRE---ADIVITTPEKWDGISRSWQTR 1041 (1230)
T ss_pred             ccCccCCChhh---eec---CceEEcccccccCccccccch
Confidence            78877655322   111   112244455555555555443

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=97.94  E-value=2.5e-05  Score=83.85  Aligned_cols=83  Identities=20%  Similarity=0.096  Sum_probs=70.1

Q ss_pred             cCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC----cE
Q psy2760         190 TWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD----VG  265 (333)
Q Consensus       190 ~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vg  265 (333)
                      .++..+++.|.-+.-.+..|+  +....||+|||+++.+|+......|..+-+++|+--||.|-++.+...|..    ||
T Consensus        76 ~~g~~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~G~~v~vvT~neyLA~Rd~e~~~~~~~~LGl~vg  153 (796)
T PRK12906         76 VLGLRPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALTGKGVHVVTVNEYLSSRDATEMGELYRWLGLTVG  153 (796)
T ss_pred             HhCCCCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHcCCCeEEEeccHHHHHhhHHHHHHHHHhcCCeEE
Confidence            345568888888877778887  889999999999999999888888999999999999999999998887763    78


Q ss_pred             EEeCCCCCC
Q psy2760         266 LIDDLPPVF  274 (333)
Q Consensus       266 lltGd~~~~  274 (333)
                      +++|+.+..
T Consensus       154 ~i~~~~~~~  162 (796)
T PRK12906        154 LNLNSMSPD  162 (796)
T ss_pred             EeCCCCCHH
Confidence            888876543

>PF13245 AAA_19: Part of AAA domain

Probab=97.94  E-value=3.4e-05  Score=59.65  Aligned_cols=49  Identities=18%  Similarity=0.185  Sum_probs=38.9

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcC----CCeEEEEcccHHHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNH----KTRTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~----g~ral~l~PtraLa~Q~~~~l  257 (333)
                      +.-++|.||.|||||......+......    +.++++++|++..++++.+++
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCHHHHHHHHHHH
Confidence            4445669999999997776666544432    789999999999999998887

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=97.80  E-value=8.3e-05  Score=79.01  Aligned_cols=82  Identities=17%  Similarity=0.103  Sum_probs=69.4

Q ss_pred             cCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC----cE
Q psy2760         190 TWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD----VG  265 (333)
Q Consensus       190 ~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vg  265 (333)
                      .++..++..|.-....+++|+  +....||+|||+++.+|+......|..+.+++|+--||.|-++.+...|..    +|
T Consensus        74 ~lg~r~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL~G~~VhvvT~NdyLA~RDae~m~~ly~~LGLsvg  151 (764)
T PRK12326         74 TLGLRPFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYALQGRRVHVITVNDYLARRDAEWMGPLYEALGLTVG  151 (764)
T ss_pred             HcCCCcchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHcCCCeEEEcCCHHHHHHHHHHHHHHHHhcCCEEE
Confidence            345578899988888888885  669999999999999998877788999999999999999999998887763    78


Q ss_pred             EEeCCCCC
Q psy2760         266 LIDDLPPV  273 (333)
Q Consensus       266 lltGd~~~  273 (333)
                      +++++.+.
T Consensus       152 ~i~~~~~~  159 (764)
T PRK12326        152 WITEESTP  159 (764)
T ss_pred             EECCCCCH
Confidence            78877654

>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=97.68  E-value=0.00011  Score=68.93  Aligned_cols=65  Identities=22%  Similarity=0.180  Sum_probs=52.0

Q ss_pred             CCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC----CCeEEEEcccHHHHHHHHHHHHHhc
Q psy2760         195 LDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH----KTRTIYTSPIKALSNQKYRDFRETF  261 (333)
Q Consensus       195 l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~----g~ral~l~PtraLa~Q~~~~l~~~f  261 (333)
                      |++-|.+++..  ...+++|.|+.|||||.+...-++..+..    ..+++++++|++.+.++..++.+.+
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~aa~e~~~ri~~~l   69 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNAAAQEMRERIRELL   69 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHHHHHHHHHHHHHhc
Confidence            57789988877  67899999999999999988877655433    3679999999999999999998754

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 ....

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=97.57  E-value=0.00029  Score=79.36  Aligned_cols=97  Identities=13%  Similarity=0.045  Sum_probs=63.2

Q ss_pred             HHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHH-HhcCC--CeEEEEcccHHHHHHHHHHHHHhcCC-cEEEeC----
Q psy2760         198 FQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIAL-SQNHK--TRTIYTSPIKALSNQKYRDFRETFQD-VGLIDD----  269 (333)
Q Consensus       198 ~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~-~l~~g--~ral~l~PtraLa~Q~~~~l~~~f~~-vglltG----  269 (333)
                      +..+.+..+..+..++++|+||||||..  +|.+. ....+  .++++.-|.|--|..+.+++.+.++. +|...|    
T Consensus        71 ~~~~Il~~l~~~~vvii~g~TGSGKTTq--lPq~lle~~~~~~~~I~~tQPRRlAA~svA~RvA~elg~~lG~~VGY~vR  148 (1283)
T TIGR01967        71 KREDIAEAIAENQVVIIAGETGSGKTTQ--LPKICLELGRGSHGLIGHTQPRRLAARTVAQRIAEELGTPLGEKVGYKVR  148 (1283)
T ss_pred             HHHHHHHHHHhCceEEEeCCCCCCcHHH--HHHHHHHcCCCCCceEecCCccHHHHHHHHHHHHHHhCCCcceEEeeEEc
Confidence            3345556677788899999999999994  45442 22222  35555678887777777777666653 444333    


Q ss_pred             -CCCCCCCcceEEecc--------------CcceEecccccc
Q psy2760         270 -LPPVFPDVEKLLEDL--------------NIGGLDELSIHD  296 (333)
Q Consensus       270 -d~~~~~~a~ili~t~--------------~i~liViDe~H~  296 (333)
                       +........+.++|.              ++.++|+||+|.
T Consensus       149 ~~~~~s~~T~I~~~TdGiLLr~l~~d~~L~~~~~IIIDEaHE  190 (1283)
T TIGR01967       149 FHDQVSSNTLVKLMTDGILLAETQQDRFLSRYDTIIIDEAHE  190 (1283)
T ss_pred             CCcccCCCceeeeccccHHHHHhhhCcccccCcEEEEcCcch
Confidence             333344455666664              578899999994

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.

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=97.57  E-value=0.00026  Score=78.37  Aligned_cols=106  Identities=9%  Similarity=0.032  Sum_probs=75.5

Q ss_pred             CCCHHHHHHHHHH----HcCCcEEEEcCCCCcHHHHHHHHHHHH--h-cCCCeEEEEcccHHHHHHHHHHHHHhcCC--c
Q psy2760         194 ELDVFQKQAIIKL----EEHNHVFVTAHTSAGKTVIAEYAIALS--Q-NHKTRTIYTSPIKALSNQKYRDFRETFQD--V  264 (333)
Q Consensus       194 ~l~~~Q~~ai~~l----~~g~~vlv~apTGSGKTl~~~l~il~~--l-~~g~ral~l~PtraLa~Q~~~~l~~~f~~--v  264 (333)
                      .|++||.+++.-+    ..|.+.+++=..|.|||+.++..+...  . ....++|+|+|. +|..|+.+++.+.++.  +
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaIalL~~L~~~~~~~gp~LIVvP~-SlL~nW~~Ei~kw~p~l~v  247 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPK-STLGNWMNEIRRFCPVLRA  247 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHHHHHHHHHHhcCCCCCEEEEeCh-HHHHHHHHHHHHHCCCCce
Confidence            6899999998765    467889999999999999765544322  2 223578999997 7778899999886654  5


Q ss_pred             EEEeCCCCC----------CCCcceEEecc-------------CcceEecccccccccc
Q psy2760         265 GLIDDLPPV----------FPDVEKLLEDL-------------NIGGLDELSIHDFNKH  300 (333)
Q Consensus       265 glltGd~~~----------~~~a~ili~t~-------------~i~liViDe~H~~~~~  300 (333)
                      ..++|+...          .....+++.+.             ...++|+||+|.+...
T Consensus       248 ~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~~~L~k~~W~~VIvDEAHrIKN~  306 (1033)
T PLN03142        248 VKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKTALKRFSWRYIIIDEAHRIKNE  306 (1033)
T ss_pred             EEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHHHHhccCCCCEEEEcCccccCCH
Confidence            666775421          11234555543             3468999999998764

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

Probab=97.53  E-value=0.00017  Score=73.90  Aligned_cols=69  Identities=32%  Similarity=0.391  Sum_probs=56.1

Q ss_pred             CCCCCHHHHHHHHHH----H-cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC
Q psy2760         192 PFELDVFQKQAIIKL----E-EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD  263 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l----~-~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~  263 (333)
                      +|.|...|-+||..+    . ..+.-.+-|.||||||....-.|...   +..+++++|.+.||.|.+.+|++.|++
T Consensus        10 ~f~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~AnVI~~~---~rPtLV~AhNKTLAaQLy~Efk~fFP~   83 (663)
T COG0556          10 PFKPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTMANVIAKV---QRPTLVLAHNKTLAAQLYSEFKEFFPE   83 (663)
T ss_pred             CCCCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHHHHHHHHh---CCCeEEEecchhHHHHHHHHHHHhCcC
Confidence            567888899999885    2 33577889999999998766555433   345899999999999999999999985

>COG4889 Predicted helicase [General function prediction only]

Probab=97.42  E-value=0.00073  Score=72.70  Aligned_cols=67  Identities=19%  Similarity=0.198  Sum_probs=49.7

Q ss_pred             CCCCCHHHHHHHHHHHcC----CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHh
Q psy2760         192 PFELDVFQKQAIIKLEEH----NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRET  260 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~g----~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~  260 (333)
                      |..|+|||++|+....+|    ..-=+....|.|||..++--... +. ..++||++|..+|..|.++.|...
T Consensus       159 ~kk~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTsLkisEa-la-~~~iL~LvPSIsLLsQTlrew~~~  229 (1518)
T COG4889         159 PKKPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSLKISEA-LA-AARILFLVPSISLLSQTLREWTAQ  229 (1518)
T ss_pred             CCCCChhHHHHHHHHHhhcccccCCcEEEecCCCccchHHHHHHH-Hh-hhheEeecchHHHHHHHHHHHhhc
Confidence            558999999999996332    22233445689999998764432 22 278999999999999999999764

>TIGR00376 DNA helicase, putative

Probab=97.36  E-value=0.00072  Score=71.69  Aligned_cols=67  Identities=16%  Similarity=0.125  Sum_probs=58.0

Q ss_pred             CCCHHHHHHHHHHHcC-CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHh
Q psy2760         194 ELDVFQKQAIIKLEEH-NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRET  260 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g-~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~  260 (333)
                      .+++.|++|+..+... ..+++.||+|+|||.+....+......|.++++++||..-++++.+++.+.
T Consensus       157 ~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~~g~~VLv~a~sn~Avd~l~e~l~~~  224 (637)
T TIGR00376       157 NLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVKRGLRVLVTAPSNIAVDNLLERLALC  224 (637)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEEcCcHHHHHHHHHHHHhC
Confidence            6899999999997655 688999999999998877666666677889999999999999999999763

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.

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=97.25  E-value=0.0013  Score=59.45  Aligned_cols=63  Identities=14%  Similarity=0.137  Sum_probs=45.7

Q ss_pred             CCHHHHHHHHHHH-cC-CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHH
Q psy2760         195 LDVFQKQAIIKLE-EH-NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       195 l~~~Q~~ai~~l~-~g-~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l  257 (333)
                      |++-|++|+..+. ++ +-+++.||.|+|||.+...........+.++++++||...+..+.+..
T Consensus         2 L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l~~~~~~~~~~g~~v~~~apT~~Aa~~L~~~~   66 (196)
T PF13604_consen    2 LNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLLKALAEALEAAGKRVIGLAPTNKAAKELREKT   66 (196)
T ss_dssp             S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHHHHHHHHHHhCCCeEEEECCcHHHHHHHHHhh
Confidence            7889999999984 44 357788999999998754433333456789999999988888866653

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.15  E-value=0.00097  Score=71.65  Aligned_cols=64  Identities=23%  Similarity=0.179  Sum_probs=48.7

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCC--CeEEEEcccHHHHHHHH
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHK--TRTIYTSPIKALSNQKY  254 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g--~ral~l~PtraLa~Q~~  254 (333)
                      .++.+++.|++|+..+..++.+++.|+.|+|||.+....+......+  .+++.++||-.-|..+.
T Consensus       320 ~~~~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~  385 (720)
T TIGR01448       320 LRKGLSEEQKQALDTAIQHKVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAAPTGRAAKRLG  385 (720)
T ss_pred             cCCCCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCceEEEEeCchHHHHHHH
Confidence            45689999999999998888999999999999987643332222234  67888999976665444

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.

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

Probab=97.10  E-value=0.0031  Score=68.57  Aligned_cols=134  Identities=13%  Similarity=0.071  Sum_probs=83.3

Q ss_pred             CHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHH-hcCCCeEEEEcccHHHHHHHHHHHHHhcCC-----cEE-Ee
Q psy2760         196 DVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALS-QNHKTRTIYTSPIKALSNQKYRDFRETFQD-----VGL-ID  268 (333)
Q Consensus       196 ~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~-l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-----vgl-lt  268 (333)
                      +....+.+..+.++.-++++|+||||||.-.=.-++.. ...+.++.+.-|.|-=|..+.+++.+.++.     ||- +.
T Consensus        52 ~~~~~~i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~VGY~iR  131 (845)
T COG1643          52 TAVRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGLGIAGKIGCTQPRRLAARSVAERVAEELGEKLGETVGYSIR  131 (845)
T ss_pred             HHHHHHHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhcccCCeEEecCchHHHHHHHHHHHHHHhCCCcCceeeEEEE
Confidence            44455566667888999999999999998654444432 244557777789988788888888777764     333 23


Q ss_pred             CCCCCCCCcceEEecc--------------CcceEeccccccccccC---cCccccc-chhh-hhhheeccCcchhhhhh
Q psy2760         269 DLPPVFPDVEKLLEDL--------------NIGGLDELSIHDFNKHL---KFWKPKV-QLDD-LFDWTMASDATTLEIFT  329 (333)
Q Consensus       269 Gd~~~~~~a~ili~t~--------------~i~liViDe~H~~~~~~---R~~~~~~-~l~~-l~~l~~~~d~~~~e~~~  329 (333)
                      .+.....+.++-++|-              .+.++++||+|.-.-..   =|.-..+ ...+ -++++++|++=--|-|+
T Consensus       132 fe~~~s~~Trik~mTdGiLlrei~~D~~Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DLKiIimSATld~~rfs  211 (845)
T COG1643         132 FESKVSPRTRIKVMTDGILLREIQNDPLLSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLIIMSATLDAERFS  211 (845)
T ss_pred             eeccCCCCceeEEeccHHHHHHHhhCcccccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCceEEEEecccCHHHHH
Confidence            4545555566666653              57889999999643221   0111111 0111 26778887764444443

>KOG1123|consensus

Probab=97.09  E-value=0.00061  Score=69.48  Aligned_cols=102  Identities=13%  Similarity=0.112  Sum_probs=75.8

Q ss_pred             CCCHHHHHHHHHHHcC---CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-----cE
Q psy2760         194 ELDVFQKQAIIKLEEH---NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-----VG  265 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g---~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-----vg  265 (333)
                      .++|+|...+..+..+   ++-++..|.|+|||++..-++.   .-..++|+++..---+.|+..+|.. +..     ++
T Consensus       302 ~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~---tikK~clvLcts~VSVeQWkqQfk~-wsti~d~~i~  377 (776)
T KOG1123|consen  302 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAAC---TIKKSCLVLCTSAVSVEQWKQQFKQ-WSTIQDDQIC  377 (776)
T ss_pred             ccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeee---eecccEEEEecCccCHHHHHHHHHh-hcccCccceE
Confidence            6799999999998433   5789999999999998766542   2245688888888888998888855 542     89


Q ss_pred             EEeCCCCCCCC--cceEEecc-----------------------CcceEeccccccccc
Q psy2760         266 LIDDLPPVFPD--VEKLLEDL-----------------------NIGGLDELSIHDFNK  299 (333)
Q Consensus       266 lltGd~~~~~~--a~ili~t~-----------------------~i~liViDe~H~~~~  299 (333)
                      .+|++.+....  +.++|.|.                       .-++++.||.|-+..
T Consensus       378 rFTsd~Ke~~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvvPA  436 (776)
T KOG1123|consen  378 RFTSDAKERFPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVVPA  436 (776)
T ss_pred             EeeccccccCCCCCcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccchH
Confidence            99999876433  44566553                       357788888887643

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

Probab=97.06  E-value=0.001  Score=65.26  Aligned_cols=90  Identities=12%  Similarity=0.091  Sum_probs=58.8

Q ss_pred             cEEEEcCCCCcHHHHHHHHHHHH--hcCCCeEEEEcccHHHHHHHHHHHHHhc-CC-c-EEEeCCCC-CCCCcceEEecc
Q psy2760         211 HVFVTAHTSAGKTVIAEYAIALS--QNHKTRTIYTSPIKALSNQKYRDFRETF-QD-V-GLIDDLPP-VFPDVEKLLEDL  284 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~il~~--l~~g~ral~l~PtraLa~Q~~~~l~~~f-~~-v-glltGd~~-~~~~a~ili~t~  284 (333)
                      -++|.|..|||||++++..+...  ...+.+++|+++..+|...+.+.+.+.. .. . ..+..-.. ++.-........
T Consensus         3 v~~I~G~aGTGKTvla~~l~~~l~~~~~~~~~~~l~~n~~l~~~l~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~   82 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALNLAKELQNSEEGKKVLYLCGNHPLRNKLREQLAKKYNPKLKKSDFRKPTSFINNYSESDKEKN   82 (352)
T ss_pred             EEEEEecCCcCHHHHHHHHHHHhhccccCCceEEEEecchHHHHHHHHHhhhcccchhhhhhhhhHHHHhhcccccccCC
Confidence            57899999999999998766655  5678899999999999999988887654 11 0 00000000 000000001123


Q ss_pred             CcceEecccccccccc
Q psy2760         285 NIGGLDELSIHDFNKH  300 (333)
Q Consensus       285 ~i~liViDe~H~~~~~  300 (333)
                      ...++++||+|.+...
T Consensus        83 ~~DviivDEAqrl~~~   98 (352)
T PF09848_consen   83 KYDVIIVDEAQRLRTK   98 (352)
T ss_pred             cCCEEEEehhHhhhhc
Confidence            5678899999998773

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

>KOG1803|consensus

Probab=97.03  E-value=0.0015  Score=67.78  Aligned_cols=68  Identities=16%  Similarity=0.173  Sum_probs=59.0

Q ss_pred             CCCCCCHHHHHHHHHHHcC-CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHH
Q psy2760         191 WPFELDVFQKQAIIKLEEH-NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFR  258 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g-~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~  258 (333)
                      ++..+++.|++|+..+... .-.++.||+|.|||.....-|.+....+.++++++||+.-++-+.+++.
T Consensus       182 ~~~~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk~~k~VLVcaPSn~AVdNiverl~  250 (649)
T KOG1803|consen  182 FNKNLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQKKRVLVCAPSNVAVDNIVERLT  250 (649)
T ss_pred             CCccccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHHcCCeEEEEcCchHHHHHHHHHhc
Confidence            4558999999999997655 5668899999999999888888899999999999999998888888653

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

Probab=96.84  E-value=0.0049  Score=58.70  Aligned_cols=82  Identities=20%  Similarity=0.215  Sum_probs=60.6

Q ss_pred             cCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC----CcE
Q psy2760         190 TWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ----DVG  265 (333)
Q Consensus       190 ~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~----~vg  265 (333)
                      ..++.|++.|..+.-.+..|+  ++...||-|||+++.++.....-.|..|-+++...-||..=++.+...|.    .+|
T Consensus        73 ~~g~~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~G~~V~vvT~NdyLA~RD~~~~~~~y~~LGlsv~  150 (266)
T PF07517_consen   73 TLGLRPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQGKGVHVVTSNDYLAKRDAEEMRPFYEFLGLSVG  150 (266)
T ss_dssp             HTS----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTTSS-EEEEESSHHHHHHHHHHHHHHHHHTT--EE
T ss_pred             HcCCcccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHhcCCcEEEeccHHHhhccHHHHHHHHHHhhhccc
Confidence            345578888988887787776  88999999999999887765555788899999999999888877766554    278


Q ss_pred             EEeCCCCC
Q psy2760         266 LIDDLPPV  273 (333)
Q Consensus       266 lltGd~~~  273 (333)
                      ..+++.+.
T Consensus       151 ~~~~~~~~  158 (266)
T PF07517_consen  151 IITSDMSS  158 (266)
T ss_dssp             EEETTTEH
T ss_pred             cCccccCH
Confidence            88877653

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 ....

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=96.72  E-value=0.0048  Score=61.02  Aligned_cols=105  Identities=15%  Similarity=0.123  Sum_probs=65.3

Q ss_pred             CCHHHHHHHHHH------HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHH--HHHHHHhcCCcEE
Q psy2760         195 LDVFQKQAIIKL------EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQK--YRDFRETFQDVGL  266 (333)
Q Consensus       195 l~~~Q~~ai~~l------~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~--~~~l~~~f~~vgl  266 (333)
                      |++-|++++..+      ..+.++++.|+-|+|||.+.-..+-.....+..+++++||-.=|.-+  -..+...|+ +++
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~~i~~~~~~~~~~~~~~a~tg~AA~~i~~G~T~hs~f~-i~~   80 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLIKAIIDYLRSRGKKVLVTAPTGIAAFNIPGGRTIHSFFG-IPI   80 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHHHHHHHHhccccceEEEecchHHHHHhccCCcchHHhcC-ccc
Confidence            788999998887      78899999999999999887655444445567899999996555444  234444443 111


Q ss_pred             EeCCCC---CCCCcceEEeccCcceEecccccccccc
Q psy2760         267 IDDLPP---VFPDVEKLLEDLNIGGLDELSIHDFNKH  300 (333)
Q Consensus       267 ltGd~~---~~~~a~ili~t~~i~liViDe~H~~~~~  300 (333)
                      -.....   ........-.-....++++||+-++...
T Consensus        81 ~~~~~~~~~~~~~~~~~~~l~~~~~lIiDEism~~~~  117 (364)
T PF05970_consen   81 NNNEKSQCKISKNSRLRERLRKADVLIIDEISMVSAD  117 (364)
T ss_pred             cccccccccccccchhhhhhhhheeeecccccchhHH
Confidence            111100   0000011111125678889999987644

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=96.62  E-value=0.0081  Score=64.00  Aligned_cols=69  Identities=32%  Similarity=0.412  Sum_probs=55.3

Q ss_pred             CCCCCHHHHHHHHHH----HcC-CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC
Q psy2760         192 PFELDVFQKQAIIKL----EEH-NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD  263 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l----~~g-~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~  263 (333)
                      ||.|...|.++|..+    ..| ++.++.|.||||||+.....+. .  .+..+|+|+|.+.+|.|++++|+..|++
T Consensus         7 ~~~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~a~~~~-~--~~~p~Lvi~~n~~~A~ql~~el~~f~p~   80 (655)
T TIGR00631         7 PFQPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMANVIA-Q--VNRPTLVIAHNKTLAAQLYNEFKEFFPE   80 (655)
T ss_pred             CCCCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHHHHHHH-H--hCCCEEEEECCHHHHHHHHHHHHHhCCC
Confidence            678999999999886    233 3677999999999988654332 2  3456999999999999999999998775

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

>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=96.56  E-value=0.0044  Score=56.84  Aligned_cols=54  Identities=26%  Similarity=0.182  Sum_probs=40.0

Q ss_pred             CCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCC--CeEEEEcccHH
Q psy2760         195 LDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHK--TRTIYTSPIKA  248 (333)
Q Consensus       195 l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g--~ral~l~Ptra  248 (333)
                      .+..|+.++..+.....+++.||.|+|||+.+..+.+..+..+  .+++|+-|..+
T Consensus         5 ~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~   60 (205)
T PF02562_consen    5 KNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVE   60 (205)
T ss_dssp             -SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--
T ss_pred             CCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCC
Confidence            5889999999999888999999999999999999887655444  47888877754

; GO: 0005524 ATP binding; PDB: 3B85_A.

>KOG0920|consensus

Probab=96.49  E-value=0.017  Score=63.22  Aligned_cols=135  Identities=14%  Similarity=0.094  Sum_probs=88.1

Q ss_pred             CHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHH---HhcCCCeEEEEcccHHHHHHHHHHHHH-hcCC----cEEE
Q psy2760         196 DVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIAL---SQNHKTRTIYTSPIKALSNQKYRDFRE-TFQD----VGLI  267 (333)
Q Consensus       196 ~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~---~l~~g~ral~l~PtraLa~Q~~~~l~~-~f~~----vgll  267 (333)
                      +..+.+.+..+.++..++++|.||+|||.=.---|+.   ......++++.-|.|--|-.+++++.. ++..    ||--
T Consensus       175 ~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsvAeRVa~ER~~~~g~~VGYq  254 (924)
T KOG0920|consen  175 YKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISVAERVAKERGESLGEEVGYQ  254 (924)
T ss_pred             HHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcCCCCeEEecCCchHHHHHHHHHHHHHhccccCCeeeEE
Confidence            6778888888999999999999999999864443442   122445677778998888888877644 3322    3332


Q ss_pred             eC-CCCCCCCcceEEecc--------------CcceEeccccccccccCcCccccc----chhhhhhheeccCcchhhhh
Q psy2760         268 DD-LPPVFPDVEKLLEDL--------------NIGGLDELSIHDFNKHLKFWKPKV----QLDDLFDWTMASDATTLEIF  328 (333)
Q Consensus       268 tG-d~~~~~~a~ili~t~--------------~i~liViDe~H~~~~~~R~~~~~~----~l~~l~~l~~~~d~~~~e~~  328 (333)
                      .+ +.....+..++.+|+              ++.++|+||+|--+..+=+.-.-.    ...--++++++|++--.|.|
T Consensus       255 vrl~~~~s~~t~L~fcTtGvLLr~L~~~~~l~~vthiivDEVHER~i~~DflLi~lk~lL~~~p~LkvILMSAT~dae~f  334 (924)
T KOG0920|consen  255 VRLESKRSRETRLLFCTTGVLLRRLQSDPTLSGVTHIIVDEVHERSINTDFLLILLKDLLPRNPDLKVILMSATLDAELF  334 (924)
T ss_pred             EeeecccCCceeEEEecHHHHHHHhccCcccccCceeeeeeEEEccCCcccHHHHHHHHhhhCCCceEEEeeeecchHHH
Confidence            22 222233356666665              678899999998665542221111    01123678899998888887


Q ss_pred             hc
Q psy2760         329 TY  330 (333)
Q Consensus       329 ~~  330 (333)
                      +.
T Consensus       335 s~  336 (924)
T KOG0920|consen  335 SD  336 (924)
T ss_pred             HH
Confidence            64

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=96.44  E-value=0.0055  Score=66.54  Aligned_cols=81  Identities=16%  Similarity=0.096  Sum_probs=61.2

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC----cEE
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD----VGL  266 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vgl  266 (333)
                      .+..+++.|.-..-.+..|  -+....||.|||+++.+|+......|..|-+++++..||.+-++.+...|.-    ||.
T Consensus        73 lG~r~ydvQlig~l~L~~G--~IaEm~TGEGKTL~a~l~ayl~aL~G~~VhVvT~NdyLA~RD~e~m~pvy~~LGLsvg~  150 (870)
T CHL00122         73 LGLRHFDVQLIGGLVLNDG--KIAEMKTGEGKTLVATLPAYLNALTGKGVHIVTVNDYLAKRDQEWMGQIYRFLGLTVGL  150 (870)
T ss_pred             hCCCCCchHhhhhHhhcCC--ccccccCCCCchHHHHHHHHHHHhcCCceEEEeCCHHHHHHHHHHHHHHHHHcCCceee
Confidence            3445777777665555544  6789999999999999988755557889999999999999988777665542    677


Q ss_pred             EeCCCCC
Q psy2760         267 IDDLPPV  273 (333)
Q Consensus       267 ltGd~~~  273 (333)
                      +.++.+.
T Consensus       151 i~~~~~~  157 (870)
T CHL00122        151 IQEGMSS  157 (870)
T ss_pred             eCCCCCh
Confidence            7666554

>PRK11054 helD DNA helicase IV; Provisional

Probab=96.39  E-value=0.013  Score=62.69  Aligned_cols=68  Identities=15%  Similarity=0.160  Sum_probs=55.3

Q ss_pred             CCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc----CCCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         193 FELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN----HKTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       193 f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~----~g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      +.|++-|++|+..  ...+++|.|..|||||.+...-+.+.+.    .+.++++++.|+..|..+.+++.++++
T Consensus       195 ~~L~~~Q~~av~~--~~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~lg  266 (684)
T PRK11054        195 SPLNPSQARAVVN--GEDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRERLG  266 (684)
T ss_pred             CCCCHHHHHHHhC--CCCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHhcC
Confidence            4789999998863  3457899999999999998776654332    346899999999999999999988775

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=96.37  E-value=0.016  Score=63.20  Aligned_cols=81  Identities=17%  Similarity=0.088  Sum_probs=62.1

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC----CcEE
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ----DVGL  266 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~----~vgl  266 (333)
                      .+..++..|...--.+..|+  +....||.|||+++.+|+......|..|-+|++..-||..=.+.+...+.    .||.
T Consensus        82 lG~r~ydVQliGgl~Lh~G~--IAEM~TGEGKTL~atlpaylnAL~GkgVhVVTvNdYLA~RDae~m~~vy~~LGLtvg~  159 (939)
T PRK12902         82 LGMRHFDVQLIGGMVLHEGQ--IAEMKTGEGKTLVATLPSYLNALTGKGVHVVTVNDYLARRDAEWMGQVHRFLGLSVGL  159 (939)
T ss_pred             hCCCcchhHHHhhhhhcCCc--eeeecCCCChhHHHHHHHHHHhhcCCCeEEEeCCHHHHHhHHHHHHHHHHHhCCeEEE
Confidence            44567888877666666664  67999999999999999887777788899999999999887766655443    2777


Q ss_pred             EeCCCCC
Q psy2760         267 IDDLPPV  273 (333)
Q Consensus       267 ltGd~~~  273 (333)
                      +.++...
T Consensus       160 i~~~~~~  166 (939)
T PRK12902        160 IQQDMSP  166 (939)
T ss_pred             ECCCCCh
Confidence            7766554

>KOG0387|consensus

Probab=96.34  E-value=0.019  Score=61.50  Aligned_cols=129  Identities=12%  Similarity=0.034  Sum_probs=82.7

Q ss_pred             CCCHHHHHHHHHH----HcCCcEEEEcCCCCcHHHH--HHHHHHHHh-cCCCeEEEEcccHHHHHHHHHHHHHhcCC--c
Q psy2760         194 ELDVFQKQAIIKL----EEHNHVFVTAHTSAGKTVI--AEYAIALSQ-NHKTRTIYTSPIKALSNQKYRDFRETFQD--V  264 (333)
Q Consensus       194 ~l~~~Q~~ai~~l----~~g~~vlv~apTGSGKTl~--~~l~il~~l-~~g~ral~l~PtraLa~Q~~~~l~~~f~~--v  264 (333)
                      .|.++|++.+.=+    .++.--++.=.-|-|||.-  ++++.+.+. .--.++|+|+|. .+..|+..+|+.-++.  |
T Consensus       205 ~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQiisFLaaL~~S~k~~~paLIVCP~-Tii~qW~~E~~~w~p~~rv  283 (923)
T KOG0387|consen  205 KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIISFLAALHHSGKLTKPALIVCPA-TIIHQWMKEFQTWWPPFRV  283 (923)
T ss_pred             HhhHHHHHHHHHHHHHHhccCCCeecccccCccchhHHHHHHHHhhcccccCceEEEccH-HHHHHHHHHHHHhCcceEE
Confidence            6899999887664    4555667788889999953  334444333 333789999998 7889999999887776  6


Q ss_pred             EEEeCCCCC--------------------CCCcceEEecc-------------CcceEeccccccccccCcCcccccchh
Q psy2760         265 GLIDDLPPV--------------------FPDVEKLLEDL-------------NIGGLDELSIHDFNKHLKFWKPKVQLD  311 (333)
Q Consensus       265 glltGd~~~--------------------~~~a~ili~t~-------------~i~liViDe~H~~~~~~R~~~~~~~l~  311 (333)
                      .+++|..+.                    ..+..+++.|.             .-.++|.||-|++..+.-.....|--+
T Consensus       284 ~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~~~d~l~~~~W~y~ILDEGH~IrNpns~islackki  363 (923)
T KOG0387|consen  284 FILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRIQGDDLLGILWDYVILDEGHRIRNPNSKISLACKKI  363 (923)
T ss_pred             EEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhcccCcccccccccEEEecCcccccCCccHHHHHHHhc
Confidence            666654331                    11223555543             236789999999977653333333223


Q ss_pred             hhhhheeccCcc
Q psy2760         312 DLFDWTMASDAT  323 (333)
Q Consensus       312 ~l~~l~~~~d~~  323 (333)
                      +....++++.+|
T Consensus       364 ~T~~RiILSGTP  375 (923)
T KOG0387|consen  364 RTVHRIILSGTP  375 (923)
T ss_pred             cccceEEeeCcc
Confidence            344455555544

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=96.28  E-value=0.0078  Score=63.67  Aligned_cols=65  Identities=14%  Similarity=0.104  Sum_probs=48.5

Q ss_pred             CCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHH--HHHHHhc--CCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         195 LDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEY--AIALSQN--HKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       195 l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l--~il~~l~--~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      ..++|+.|+.....++..++.|++|+|||.+...  ..+....  ...++++++||.-=|..+.+.+..
T Consensus       153 ~~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~~  221 (615)
T PRK10875        153 EVDWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESLGK  221 (615)
T ss_pred             CCHHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHHh
Confidence            3589999999989999999999999999987543  2232222  235788889997777777766543

>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=96.26  E-value=0.017  Score=46.79  Aligned_cols=38  Identities=13%  Similarity=0.140  Sum_probs=27.8

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEccc
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPI  246 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Pt  246 (333)
                      ++.+++.||+|+|||..+...+......+..++++...
T Consensus        19 ~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~~   56 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNAS   56 (151)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEehh
Confidence            77899999999999987766554444445667766544

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.

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=96.17  E-value=0.026  Score=59.47  Aligned_cols=64  Identities=20%  Similarity=0.260  Sum_probs=47.3

Q ss_pred             CHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHH--HHHhcC---CCeEEEEcccHHHHHHHHHHHHH
Q psy2760         196 DVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAI--ALSQNH---KTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       196 ~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~i--l~~l~~---g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      ..+|+.|+..+..++.+++.|+.|+|||.+....+  +....+   +.++++++||--=|..+.+.+..
T Consensus       147 ~~~Qk~A~~~al~~~~~vitGgpGTGKTt~v~~ll~~l~~~~~~~~~~~I~l~APTGkAA~rL~e~~~~  215 (586)
T TIGR01447       147 QNWQKVAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPTGKAAARLAESLRK  215 (586)
T ss_pred             cHHHHHHHHHHhhCCeEEEEcCCCCCHHHHHHHHHHHHHHhccccCCCcEEEECCcHHHHHHHHHHHHh
Confidence            37999999999999999999999999998754332  322222   25799999997666666655543

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.

>PRK06526 transposase; Provisional

Probab=96.17  E-value=0.011  Score=55.91  Aligned_cols=47  Identities=13%  Similarity=0.076  Sum_probs=34.1

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKY  254 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~  254 (333)
                      ..+.+++++||+|+|||..+..........|.+++|+. ...|++++.
T Consensus        96 ~~~~nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f~t-~~~l~~~l~  142 (254)
T PRK06526         96 TGKENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFAT-AAQWVARLA  142 (254)
T ss_pred             hcCceEEEEeCCCCchHHHHHHHHHHHHHCCCchhhhh-HHHHHHHHH
Confidence            56789999999999999988765555556777777754 344555544

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=96.15  E-value=0.013  Score=62.72  Aligned_cols=67  Identities=18%  Similarity=0.102  Sum_probs=54.6

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc----CCCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN----HKTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~----~g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      .|++-|++|+..  ...+++|.|+.|||||.+...-+.+.+.    +..+++.++.|+.-|.++.+++.+.++
T Consensus         2 ~Ln~~Q~~av~~--~~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v~p~~IL~lTFT~kAA~em~~Rl~~~l~   72 (672)
T PRK10919          2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQTLG   72 (672)
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHHhC
Confidence            479999998864  3568899999999999998877765543    235799999999999999999987654

>KOG1802|consensus

Probab=96.15  E-value=0.015  Score=61.27  Aligned_cols=67  Identities=16%  Similarity=0.238  Sum_probs=57.5

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHH-HhcCCCeEEEEcccHHHHHHHHHHHHHh
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIAL-SQNHKTRTIYTSPIKALSNQKYRDFRET  260 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~-~l~~g~ral~l~PtraLa~Q~~~~l~~~  260 (333)
                      .++.-|..|...+++..--++.||.|.|||++..--+.+ ....+.++|+++|..--++|+.+.+.+.
T Consensus       410 kLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~~~~~VLvcApSNiAVDqLaeKIh~t  477 (935)
T KOG1802|consen  410 KLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQHAGPVLVCAPSNIAVDQLAEKIHKT  477 (935)
T ss_pred             hhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHhcCCceEEEcccchhHHHHHHHHHhc
Confidence            799999999999999999999999999999987654443 3356788999999999999999988763

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=96.11  E-value=0.024  Score=62.58  Aligned_cols=48  Identities=15%  Similarity=0.113  Sum_probs=38.5

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhc--CCCeEEEEcccHHHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQN--HKTRTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~--~g~ral~l~PtraLa~Q~~~~l  257 (333)
                      .++.+.++||+|||.+|+..|+....  .-.+.|++||+.|.-..+..-+
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~~~~~~~~fii~vp~~aI~egv~~~l  109 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELHQKYGLFKFIIVVPTPAIKEGTRNFI  109 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHHcCCcEEEEEeCCHHHHHHHHHHh
Confidence            48899999999999999998874432  3467999999999887776443

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=96.06  E-value=0.023  Score=60.59  Aligned_cols=70  Identities=27%  Similarity=0.316  Sum_probs=55.5

Q ss_pred             CCCCCCHHHHHHHHHHH----cC-CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC
Q psy2760         191 WPFELDVFQKQAIIKLE----EH-NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD  263 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~----~g-~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~  263 (333)
                      -+|.|+..|..++..+.    .+ ++.++.|.+|||||++... ++..  .+..+|+|+|+..+|.|+++.|+..++.
T Consensus         9 ~~~~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~lia~-l~~~--~~r~vLIVt~~~~~A~~l~~dL~~~~~~   83 (652)
T PRK05298          9 SPYKPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMAN-VIAR--LQRPTLVLAHNKTLAAQLYSEFKEFFPE   83 (652)
T ss_pred             cCCCCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHHHH-HHHH--hCCCEEEEECCHHHHHHHHHHHHHhcCC
Confidence            36799999999999862    33 2677999999999988543 2222  3567999999999999999999887765

>PHA02533 17 large terminase protein; Provisional

Probab=95.97  E-value=0.05  Score=56.71  Aligned_cols=72  Identities=10%  Similarity=0.119  Sum_probs=57.7

Q ss_pred             cCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHH-HH-hcCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy2760         190 TWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIA-LS-QNHKTRTIYTSPIKALSNQKYRDFRETF  261 (333)
Q Consensus       190 ~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il-~~-l~~g~ral~l~PtraLa~Q~~~~l~~~f  261 (333)
                      ..||.|+++|+..+..+..++..++..+=..|||.+....++ .+ ...+..+++++|++.-|..+++.++..+
T Consensus        55 ~~Pf~L~p~Q~~i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~~~~~~v~i~A~~~~QA~~vF~~ik~~i  128 (534)
T PHA02533         55 TIKVQMRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCFNKDKNVGILAHKASMAAEVLDRTKQAI  128 (534)
T ss_pred             ceecCCcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHhCCCCEEEEEeCCHHHHHHHHHHHHHHH
Confidence            468999999999998876677778888999999998765333 33 3567789999999999999998886543

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=95.76  E-value=0.03  Score=63.80  Aligned_cols=66  Identities=21%  Similarity=0.175  Sum_probs=54.5

Q ss_pred             CCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCC---CeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         195 LDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHK---TRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       195 l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g---~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      +++-|.+||.  ..+++++|.|..|||||.+..--++..+..+   .++++++=|++-|.++..++++.+.
T Consensus         2 ~t~~Q~~ai~--~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~~~~~il~~tFt~~aa~e~~~ri~~~l~   70 (1232)
T TIGR02785         2 WTDEQWQAIY--TRGQNILVSASAGSGKTAVLVERIIKKILRGVDIDRLLVVTFTNAAAREMKERIEEALQ   70 (1232)
T ss_pred             CCHHHHHHHh--CCCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCHhhEEEEeccHHHHHHHHHHHHHHHH
Confidence            6889999997  4688999999999999999877666554333   3599999999999999988877654

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.

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=95.72  E-value=0.029  Score=60.41  Aligned_cols=67  Identities=15%  Similarity=0.131  Sum_probs=54.8

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc----CCCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN----HKTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~----~g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      .|++-|++|+..  ...+++|.|..|||||.+...-+.+.+.    +..+++.++-|+.-|.++.+++.+..+
T Consensus         9 ~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~~~   79 (721)
T PRK11773          9 SLNDKQREAVAA--PLGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQLLG   79 (721)
T ss_pred             hcCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHHhc
Confidence            589999998864  3468999999999999998776665443    235799999999999999999988654

>KOG0926|consensus

Probab=95.59  E-value=0.048  Score=58.75  Aligned_cols=132  Identities=13%  Similarity=0.046  Sum_probs=74.5

Q ss_pred             HHHHHHHcCCcEEEEcCCCCcHHHH---HHHHHHHHh---cCCCeEEEEcccHHHHHHHHHHHHHhcC---C-cEEE-eC
Q psy2760         201 QAIIKLEEHNHVFVTAHTSAGKTVI---AEYAIALSQ---NHKTRTIYTSPIKALSNQKYRDFRETFQ---D-VGLI-DD  269 (333)
Q Consensus       201 ~ai~~l~~g~~vlv~apTGSGKTl~---~~l~il~~l---~~g~ral~l~PtraLa~Q~~~~l~~~f~---~-vgll-tG  269 (333)
                      +....+..+--++|||.||||||.-   |++-+=.+.   ..+.-+-+.-|.|--|-.+.++...-++   . |+-. .=
T Consensus       263 ~IMEaIn~n~vvIIcGeTGsGKTTQvPQFLYEAGf~s~~~~~~gmIGITqPRRVAaiamAkRVa~EL~~~~~eVsYqIRf  342 (1172)
T KOG0926|consen  263 RIMEAINENPVVIICGETGSGKTTQVPQFLYEAGFASEQSSSPGMIGITQPRRVAAIAMAKRVAFELGVLGSEVSYQIRF  342 (1172)
T ss_pred             HHHHHhhcCCeEEEecCCCCCccccchHHHHHcccCCccCCCCCeeeecCchHHHHHHHHHHHHHHhccCccceeEEEEe
Confidence            3445567888899999999999974   222111111   1133455567887666666655544333   2 4321 11


Q ss_pred             CCCCCCCcceEEecc--------------CcceEeccccccccccC--------cCcccccc------hhhhhhheeccC
Q psy2760         270 LPPVFPDVEKLLEDL--------------NIGGLDELSIHDFNKHL--------KFWKPKVQ------LDDLFDWTMASD  321 (333)
Q Consensus       270 d~~~~~~a~ili~t~--------------~i~liViDe~H~~~~~~--------R~~~~~~~------l~~l~~l~~~~d  321 (333)
                      +..+.+...+..+|-              ....|++||+|--+..+        |-.+...-      -+.-.+|+++|+
T Consensus       343 d~ti~e~T~IkFMTDGVLLrEi~~DflL~kYSvIIlDEAHERSvnTDILiGmLSRiV~LR~k~~ke~~~~kpLKLIIMSA  422 (1172)
T KOG0926|consen  343 DGTIGEDTSIKFMTDGVLLREIENDFLLTKYSVIILDEAHERSVNTDILIGMLSRIVPLRQKYYKEQCQIKPLKLIIMSA  422 (1172)
T ss_pred             ccccCCCceeEEecchHHHHHHHHhHhhhhceeEEechhhhccchHHHHHHHHHHHHHHHHHHhhhhcccCceeEEEEee
Confidence            333444455556653              45778999999654333        22111111      122467999998


Q ss_pred             cchhhhhhccc
Q psy2760         322 ATTLEIFTYNK  332 (333)
Q Consensus       322 ~~~~e~~~~~~  332 (333)
                      +=-.+=|+-+|
T Consensus       423 TLRVsDFtenk  433 (1172)
T KOG0926|consen  423 TLRVSDFTENK  433 (1172)
T ss_pred             eEEecccccCc
Confidence            87777776544

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=95.55  E-value=0.036  Score=58.80  Aligned_cols=66  Identities=17%  Similarity=0.120  Sum_probs=53.9

Q ss_pred             CCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc----CCCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         195 LDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN----HKTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       195 l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~----~g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      |++-|++++..  ...+++|.|+.|||||.+...-+...+.    ...++++|+.|+.-|.++.+++.+.++
T Consensus         2 Ln~~Q~~av~~--~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~~Aa~em~~Rl~~~l~   71 (664)
T TIGR01074         2 LNPQQQEAVEY--VTGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKTLG   71 (664)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHhC
Confidence            78899998764  3568999999999999998887765543    235789999999999999999987664

Designed to identify rep members of the uvrD/rep subfamily.

>TIGR01075 uvrD DNA helicase II

Probab=95.50  E-value=0.032  Score=59.96  Aligned_cols=67  Identities=15%  Similarity=0.130  Sum_probs=54.8

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc----CCCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN----HKTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~----~g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      .|++-|++|+..  ...+++|.|..|||||.+...-+...+.    +..+++.++.|+.-|.++.+++.+..+
T Consensus         4 ~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkAA~em~~Rl~~~~~   74 (715)
T TIGR01075         4 GLNDKQREAVAA--PPGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGALLG   74 (715)
T ss_pred             ccCHHHHHHHcC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHHHHHHHHHHHHHhc
Confidence            489999998864  3568999999999999998776665443    235799999999999999999988654

Designed to identify uvrD members of the uvrD/rep subfamily.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=95.48  E-value=0.029  Score=51.92  Aligned_cols=51  Identities=18%  Similarity=0.278  Sum_probs=40.3

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      .|..+++.||+|+|||..+..-+...+..|.+++|++ +-+-..|+.+++..
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs-~ee~~~~i~~~~~~   70 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVA-LEEHPVQVRRNMAQ   70 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEE-eeCCHHHHHHHHHH
Confidence            4789999999999999998877666667789999988 44566677666644

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.

>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=95.47  E-value=0.031  Score=48.76  Aligned_cols=48  Identities=10%  Similarity=0.138  Sum_probs=36.3

Q ss_pred             cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         211 HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      .+++.||+|+|||..+.--+......|.+++|++. .+...++.+++..
T Consensus         1 ~~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~s~-e~~~~~~~~~~~~   48 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTL-EESPEELIENAES   48 (187)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEEEC-CCCHHHHHHHHHH
Confidence            36899999999999887766666677889999864 3556666666544

A related protein is found in archaea.

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=95.47  E-value=0.038  Score=46.21  Aligned_cols=39  Identities=18%  Similarity=0.227  Sum_probs=29.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHH
Q psy2760         212 VFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALS  250 (333)
Q Consensus       212 vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa  250 (333)
                      ++++||+|+|||..+...+......+.+++|+.....+.
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~e~~~~   40 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIE   40 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCcchH
Confidence            689999999999988766555555678888887654443

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.

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=95.45  E-value=0.035  Score=54.17  Aligned_cols=54  Identities=26%  Similarity=0.409  Sum_probs=37.2

Q ss_pred             CCHHHHHHHHH-HHcCCcEEEEcCCCCcHHHHHHHHHHHH---hcCCCeEEEEcccHHH
Q psy2760         195 LDVFQKQAIIK-LEEHNHVFVTAHTSAGKTVIAEYAIALS---QNHKTRTIYTSPIKAL  249 (333)
Q Consensus       195 l~~~Q~~ai~~-l~~g~~vlv~apTGSGKTl~~~l~il~~---l~~g~ral~l~PtraL  249 (333)
                      +++.|.+.+.. +..+++++++|+||||||.... +++..   ..+..+++.+-.+.+|
T Consensus       133 ~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll~-aL~~~~~~~~~~~rivtIEd~~El  190 (319)
T PRK13894        133 MTAAQREAIIAAVRAHRNILVIGGTGSGKTTLVN-AIINEMVIQDPTERVFIIEDTGEI  190 (319)
T ss_pred             CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHHH-HHHHhhhhcCCCceEEEEcCCCcc
Confidence            56778888776 4788999999999999996543 33322   2344566666555554

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=95.43  E-value=0.023  Score=45.37  Aligned_cols=41  Identities=17%  Similarity=0.163  Sum_probs=29.6

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKAL  249 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraL  249 (333)
                      +.++++.||+|+|||..+...+......+..++++.+....
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~~~~~   42 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDIL   42 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEECCEEcc
Confidence            57899999999999998876554333333468888776543

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.

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=95.42  E-value=0.041  Score=53.90  Aligned_cols=54  Identities=17%  Similarity=0.249  Sum_probs=36.6

Q ss_pred             CCHHHHHHHHHH-HcCCcEEEEcCCCCcHHHHHHHHHHHHh---cCCCeEEEEcccHHH
Q psy2760         195 LDVFQKQAIIKL-EEHNHVFVTAHTSAGKTVIAEYAIALSQ---NHKTRTIYTSPIKAL  249 (333)
Q Consensus       195 l~~~Q~~ai~~l-~~g~~vlv~apTGSGKTl~~~l~il~~l---~~g~ral~l~PtraL  249 (333)
                      +++.|.+.+..+ ..+.+++++|+||||||...- +++...   ..+.|++.+=.+.+|
T Consensus       129 ~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTll~-aL~~~i~~~~~~~rivtiEd~~El  186 (323)
T PRK13833        129 MTEAQASVIRSAIDSRLNIVISGGTGSGKTTLAN-AVIAEIVASAPEDRLVILEDTAEI  186 (323)
T ss_pred             CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHHH-HHHHHHhcCCCCceEEEecCCccc
Confidence            567788777764 778899999999999998763 333332   234566655444444

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=95.36  E-value=0.065  Score=58.05  Aligned_cols=63  Identities=14%  Similarity=0.089  Sum_probs=48.3

Q ss_pred             CCCCCHHHHHHHHHHHc-CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHH
Q psy2760         192 PFELDVFQKQAIIKLEE-HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKY  254 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~-g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~  254 (333)
                      .+.+++-|++|+..+.. ++.+++.|+.|+|||.+.-..+......|.++++++||---+..+.
T Consensus       350 ~~~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll~~i~~~~~~~g~~V~~~ApTg~Aa~~L~  413 (744)
T TIGR02768       350 HYRLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTMLKAAREAWEAAGYRVIGAALSGKAAEGLQ  413 (744)
T ss_pred             cCCCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHHHHHHHHHHhCCCeEEEEeCcHHHHHHHH
Confidence            46789999999999865 4678999999999998765543333345889999999966554443

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.

>PRK10536 hypothetical protein; Provisional

Probab=95.35  E-value=0.047  Score=51.94  Aligned_cols=55  Identities=22%  Similarity=0.268  Sum_probs=41.5

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh-cCCCe-EEEEcccHH
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ-NHKTR-TIYTSPIKA  248 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l-~~g~r-al~l~Ptra  248 (333)
                      ..+..|..++..+..+..+++.||+|+|||+.+....+..+ ....+ +++.-|+..
T Consensus        59 p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI~RP~v~  115 (262)
T PRK10536         59 ARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRPVLQ  115 (262)
T ss_pred             CCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEEeCCCCC
Confidence            45888999999888888999999999999999988776544 33334 444445543

>KOG0349|consensus

Probab=95.25  E-value=0.0033  Score=63.32  Aligned_cols=39  Identities=26%  Similarity=0.132  Sum_probs=36.9

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHH
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIAL  232 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~  232 (333)
                      -|+.+|.++||.++.|.+++..|.||||||-+|-+||++
T Consensus        24 lptdvqaeaiplilgggdvlmaaetgsgktgaf~lpilq   62 (725)
T KOG0349|consen   24 LPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPILQ   62 (725)
T ss_pred             cccccccccccEEecCCcEEEEeccCCCCccceehhhHH
Confidence            589999999999999999999999999999999999984

>PRK08727 hypothetical protein; Validated

Probab=95.25  E-value=0.075  Score=49.20  Aligned_cols=45  Identities=16%  Similarity=0.262  Sum_probs=30.3

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYR  255 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~  255 (333)
                      ..++++||+|+|||.............+.+++|+. ..++.....+
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~-~~~~~~~~~~   86 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLP-LQAAAGRLRD   86 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEe-HHHhhhhHHH
Confidence            45899999999999776654444455677888865 4444443333

>PRK08181 transposase; Validated

Probab=95.24  E-value=0.079  Score=50.54  Aligned_cols=59  Identities=17%  Similarity=0.143  Sum_probs=40.5

Q ss_pred             CCHHHHHHHHH----HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHH
Q psy2760         195 LDVFQKQAIIK----LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKY  254 (333)
Q Consensus       195 l~~~Q~~ai~~----l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~  254 (333)
                      ++..|..++..    +..+++++++||+|+|||..+......+...|.+++|+ +..+|+.++.
T Consensus        88 ~~~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~-~~~~L~~~l~  150 (269)
T PRK08181         88 VSKAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFT-RTTDLVQKLQ  150 (269)
T ss_pred             CCHHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHHHHHHHHHHHcCCceeee-eHHHHHHHHH
Confidence            45566655533    35788999999999999987765444445567777765 4566766654

>KOG0922|consensus

Probab=95.23  E-value=0.08  Score=55.83  Aligned_cols=127  Identities=15%  Similarity=0.132  Sum_probs=74.4

Q ss_pred             CHHHHHHHHHHHcCCcEEEEcCCCCcHHHHH-HHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-----cEE--E
Q psy2760         196 DVFQKQAIIKLEEHNHVFVTAHTSAGKTVIA-EYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-----VGL--I  267 (333)
Q Consensus       196 ~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~-~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-----vgl--l  267 (333)
                      +..-.+.+..+..+..+++.|.||||||.=- .+.........+++.+.-|.|-=|--+.++..+-.+.     ||-  .
T Consensus        53 ~~~r~~il~~ve~nqvlIviGeTGsGKSTQipQyL~eaG~~~~g~I~~TQPRRVAavslA~RVAeE~~~~lG~~VGY~IR  132 (674)
T KOG0922|consen   53 YKYRDQILYAVEDNQVLIVIGETGSGKSTQIPQYLAEAGFASSGKIACTQPRRVAAVSLAKRVAEEMGCQLGEEVGYTIR  132 (674)
T ss_pred             HHHHHHHHHHHHHCCEEEEEcCCCCCccccHhHHHHhcccccCCcEEeecCchHHHHHHHHHHHHHhCCCcCceeeeEEE
Confidence            4455667777888999999999999999742 1111122334445777789887666666666554442     322  2


Q ss_pred             eCCCCCCCCcceEEecc--------------CcceEeccccccccccCcCcccccchhh----------hhhheeccCcc
Q psy2760         268 DDLPPVFPDVEKLLEDL--------------NIGGLDELSIHDFNKHLKFWKPKVQLDD----------LFDWTMASDAT  323 (333)
Q Consensus       268 tGd~~~~~~a~ili~t~--------------~i~liViDe~H~~~~~~R~~~~~~~l~~----------l~~l~~~~d~~  323 (333)
                      .-+.. ....++..+|-              ...++++||+|.-.-+     ..+ ++-          -++++++|++=
T Consensus       133 Fed~t-s~~TrikymTDG~LLRE~l~Dp~LskYsvIIlDEAHERsl~-----TDi-LlGlLKki~~~R~~LklIimSATl  205 (674)
T KOG0922|consen  133 FEDST-SKDTRIKYMTDGMLLREILKDPLLSKYSVIILDEAHERSLH-----TDI-LLGLLKKILKKRPDLKLIIMSATL  205 (674)
T ss_pred             ecccC-CCceeEEEecchHHHHHHhcCCccccccEEEEechhhhhhH-----HHH-HHHHHHHHHhcCCCceEEEEeeee
Confidence            22222 22333333332              5688999999964332     222 111          15678887765


Q ss_pred             hhhhhh
Q psy2760         324 TLEIFT  329 (333)
Q Consensus       324 ~~e~~~  329 (333)
                      ..|-|+
T Consensus       206 da~kfS  211 (674)
T KOG0922|consen  206 DAEKFS  211 (674)
T ss_pred             cHHHHH
Confidence            555543

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=95.23  E-value=0.039  Score=49.22  Aligned_cols=47  Identities=13%  Similarity=0.144  Sum_probs=32.3

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKY  254 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~  254 (333)
                      ..++++++.||+|+|||..+...+-.....|.+++|+ ++.+|..++.
T Consensus        45 ~~~~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~-~~~~L~~~l~   91 (178)
T PF01695_consen   45 ENGENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFI-TASDLLDELK   91 (178)
T ss_dssp             SC--EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEE-EHHHHHHHHH
T ss_pred             ccCeEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEe-ecCceecccc
Confidence            5678999999999999998776555566677778775 5556665543

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.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=95.14  E-value=0.07  Score=51.53  Aligned_cols=54  Identities=17%  Similarity=0.292  Sum_probs=36.5

Q ss_pred             CCHHHHHHHHHH-HcCCcEEEEcCCCCcHHHHHHHHHHHHh---cCCCeEEEEcccHHH
Q psy2760         195 LDVFQKQAIIKL-EEHNHVFVTAHTSAGKTVIAEYAIALSQ---NHKTRTIYTSPIKAL  249 (333)
Q Consensus       195 l~~~Q~~ai~~l-~~g~~vlv~apTGSGKTl~~~l~il~~l---~~g~ral~l~PtraL  249 (333)
                      +++.|.+.+..+ ..+++++++|+||||||...-. ++..+   ..+.|++.+=-+.+|
T Consensus       117 ~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll~a-l~~~i~~~~~~~ri~tiEd~~El  174 (299)
T TIGR02782       117 MTAAQRDVLREAVLARKNILVVGGTGSGKTTLANA-LLAEIAKNDPTDRVVIIEDTREL  174 (299)
T ss_pred             CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHHHH-HHHHhhccCCCceEEEECCchhh
Confidence            456666666664 6778999999999999987643 33332   124567666666555

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.

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=95.06  E-value=0.037  Score=50.39  Aligned_cols=51  Identities=14%  Similarity=0.265  Sum_probs=37.1

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcC-CCeEEEEcccHHHHHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNH-KTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~-g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      .|..+++.|++|+|||..+..-+...+.. |.+++|++ +.+-..++.+.+..
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs-~ee~~~~l~~~~~s   69 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVS-FEEPPEELIENMKS   69 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEE-SSS-HHHHHHHHHT
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEE-ecCCHHHHHHHHHH
Confidence            36789999999999999988777767777 88999987 33445666666653

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 ....

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=95.02  E-value=0.065  Score=57.66  Aligned_cols=67  Identities=13%  Similarity=0.119  Sum_probs=54.9

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC----CCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH----KTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~----g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      .|++-|++|+..  ...+++|.|..|||||.+...-+.+.+..    ..+++.++-|+.-|.++.+++.+.++
T Consensus         4 ~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i~P~~IL~lTFT~kAA~em~~Rl~~~~~   74 (726)
T TIGR01073         4 HLNPEQREAVKT--TEGPLLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTNKAAREMKERVEKLLG   74 (726)
T ss_pred             ccCHHHHHHHhC--CCCCEEEEeCCCCCHHHHHHHHHHHHHHcCCCCHHHeeeeeccHHHHHHHHHHHHHHhc
Confidence            489999999864  35689999999999999988877655432    25799999999999999999987654

Designed to identify pcrA members of the uvrD/rep subfamily.

>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=94.86  E-value=0.09  Score=49.11  Aligned_cols=71  Identities=17%  Similarity=0.143  Sum_probs=56.7

Q ss_pred             CCCCHHHHHHHHHHH---cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC
Q psy2760         193 FELDVFQKQAIIKLE---EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD  263 (333)
Q Consensus       193 f~l~~~Q~~ai~~l~---~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~  263 (333)
                      +-+++.|.+....+.   .|.|.+...-.|.|||.+-.-.+...+.+|.+.+.++=-++|..|.++.++.++++
T Consensus        22 iliR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsVI~Pmla~~LAdg~~LvrviVpk~Ll~q~~~~L~~~lg~   95 (229)
T PF12340_consen   22 ILIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSVIVPMLALALADGSRLVRVIVPKALLEQMRQMLRSRLGG   95 (229)
T ss_pred             ceeeHHHHHHHHHHhCCCCCCCeEeeecccCCccchHHHHHHHHHcCCCcEEEEEcCHHHHHHHHHHHHHHHHH
Confidence            358999999998873   56899999999999999865544566777777555544568999999999999875

There are two conserved sequence motifs: LLE and NMG.

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=94.85  E-value=0.063  Score=50.24  Aligned_cols=53  Identities=19%  Similarity=0.262  Sum_probs=42.9

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      .|+.+++.|++|||||..+...+......|.+++|++ +.+...++.+.+.. |+
T Consensus        22 ~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs-~~e~~~~l~~~~~~-~g   74 (260)
T COG0467          22 RGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVS-TEESPEELLENARS-FG   74 (260)
T ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHHHhcCCcEEEEE-ecCCHHHHHHHHHH-cC
Confidence            4789999999999999998888777777788999876 55667777777755 54

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=94.75  E-value=0.059  Score=53.19  Aligned_cols=44  Identities=16%  Similarity=0.171  Sum_probs=31.7

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHH
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALS  250 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa  250 (333)
                      +..+++++++||||||||... .+++.......+++.+=.+.+|.
T Consensus       159 v~~~~nilI~G~tGSGKTTll-~aLl~~i~~~~rivtiEd~~El~  202 (344)
T PRK13851        159 VVGRLTMLLCGPTGSGKTTMS-KTLISAIPPQERLITIEDTLELV  202 (344)
T ss_pred             HHcCCeEEEECCCCccHHHHH-HHHHcccCCCCCEEEECCCcccc
Confidence            478899999999999999875 34444455556666666666553

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=94.62  E-value=0.099  Score=46.50  Aligned_cols=48  Identities=17%  Similarity=0.242  Sum_probs=33.2

Q ss_pred             CCHHHHHHHHH-HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEE
Q psy2760         195 LDVFQKQAIIK-LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYT  243 (333)
Q Consensus       195 l~~~Q~~ai~~-l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l  243 (333)
                      +++.|.+.+.. +..|.+++++||||||||...-. ++.......+.+.+
T Consensus        10 ~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll~a-L~~~i~~~~~~i~i   58 (186)
T cd01130          10 FSPLQAAYLWLAVEARKNILISGGTGSGKTTLLNA-LLAFIPPDERIITI   58 (186)
T ss_pred             CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHHHH-HHhhcCCCCCEEEE
Confidence            57777777777 47899999999999999987643 33333333344443

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>KOG0390|consensus

Probab=94.61  E-value=0.16  Score=54.85  Aligned_cols=128  Identities=13%  Similarity=0.044  Sum_probs=77.3

Q ss_pred             CCCHHHHHHHHHH---HcCC-------cEEEEcCCCCcHHHHHHHHHHHHh--cCC-----CeEEEEcccHHHHHHHHHH
Q psy2760         194 ELDVFQKQAIIKL---EEHN-------HVFVTAHTSAGKTVIAEYAIALSQ--NHK-----TRTIYTSPIKALSNQKYRD  256 (333)
Q Consensus       194 ~l~~~Q~~ai~~l---~~g~-------~vlv~apTGSGKTl~~~l~il~~l--~~g-----~ral~l~PtraLa~Q~~~~  256 (333)
                      .++|||++.+.-+   ..|.       -++++=..|+|||+-.+.-+...+  .+.     .++|+|+|- .|+.-+.++
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~IsflwtlLrq~P~~~~~~~k~lVV~P~-sLv~nWkkE  316 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCISFIWTLLRQFPQAKPLINKPLVVAPS-SLVNNWKKE  316 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHHHHHHHHHHHhCcCccccccccEEEccH-HHHHHHHHH
Confidence            7999999999775   2222       245555679999998766655333  344     679999997 788888888


Q ss_pred             HHHhcCC--cEE--EeCCCCC---------CC---C--cceEEec-------------cCcceEecccccccc-ccCcCc
Q psy2760         257 FRETFQD--VGL--IDDLPPV---------FP---D--VEKLLED-------------LNIGGLDELSIHDFN-KHLKFW  304 (333)
Q Consensus       257 l~~~f~~--vgl--ltGd~~~---------~~---~--a~ili~t-------------~~i~liViDe~H~~~-~~~R~~  304 (333)
                      |.+-.+.  +..  +.|....         ..   +  ..+++..             ..++++|.||-|... ..++.|
T Consensus       317 F~KWl~~~~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~~il~~~~glLVcDEGHrlkN~~s~~~  396 (776)
T KOG0390|consen  317 FGKWLGNHRINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYCRKILLIRPGLLVCDEGHRLKNSDSLTL  396 (776)
T ss_pred             HHHhccccccceeeeecccchhhhhhHHHHHhhhhheeEEEEeccHHHHHHHHHHHhcCCCCeEEECCCCCccchhhHHH
Confidence            8876552  222  3333331         00   0  1122211             168999999999874 445555


Q ss_pred             ccccchhhhhhheeccCcc
Q psy2760         305 KPKVQLDDLFDWTMASDAT  323 (333)
Q Consensus       305 ~~~~~l~~l~~l~~~~d~~  323 (333)
                      ...- -++.-+.++.|.++
T Consensus       397 kaL~-~l~t~rRVLLSGTp  414 (776)
T KOG0390|consen  397 KALS-SLKTPRRVLLTGTP  414 (776)
T ss_pred             HHHH-hcCCCceEEeeCCc
Confidence            5433 22333445555443

>PRK09183 transposase/IS protein; Provisional

Probab=94.57  E-value=0.18  Score=47.66  Aligned_cols=47  Identities=17%  Similarity=0.143  Sum_probs=33.5

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHH
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQK  253 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~  253 (333)
                      +..+.++++.||+|+|||..+......+...|.+++|+. ..+|..++
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~~-~~~l~~~l  145 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTT-AADLLLQL  145 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEe-HHHHHHHH
Confidence            356889999999999999887654444445677787764 44555444

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

Probab=94.45  E-value=0.2  Score=54.36  Aligned_cols=51  Identities=16%  Similarity=0.166  Sum_probs=42.3

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHh-cCCCeEEEEcccHHHHHHHHHHHHHh
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQ-NHKTRTIYTSPIKALSNQKYRDFRET  260 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l-~~g~ral~l~PtraLa~Q~~~~l~~~  260 (333)
                      .-.+|.+|.|||||.+..-.+-..+ .++.++++++-.++|+.+...+|+..
T Consensus        50 ~V~vVRSpMGTGKTtaLi~wLk~~l~~~~~~VLvVShRrSL~~sL~~rf~~~  101 (824)
T PF02399_consen   50 GVLVVRSPMGTGKTTALIRWLKDALKNPDKSVLVVSHRRSLTKSLAERFKKA  101 (824)
T ss_pred             CeEEEECCCCCCcHHHHHHHHHHhccCCCCeEEEEEhHHHHHHHHHHHHhhc
Confidence            4558899999999988766555443 56889999999999999999999763

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

>PRK04328 hypothetical protein; Provisional

Probab=94.44  E-value=0.089  Score=49.24  Aligned_cols=51  Identities=18%  Similarity=0.307  Sum_probs=38.8

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      .|..+++.|++|+|||..+..-+...+..|.+++|++ +.+-..++.+.+..
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~~~~ge~~lyis-~ee~~~~i~~~~~~   72 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGVYVA-LEEHPVQVRRNMRQ   72 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEE-eeCCHHHHHHHHHH
Confidence            3788999999999999988877766777788999987 44455555555543

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=94.43  E-value=0.12  Score=56.62  Aligned_cols=81  Identities=15%  Similarity=0.060  Sum_probs=57.9

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHH---hcC-CcEE
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRE---TFQ-DVGL  266 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~---~f~-~vgl  266 (333)
                      ++..+++.|.-..-.+..|+  +....||-|||+++.+|+......|..|-+++..--||.-=.+.+..   .+| .||+
T Consensus        75 lG~r~ydVQliGglvLh~G~--IAEMkTGEGKTLvAtLpayLnAL~GkgVhVVTvNdYLA~RDae~mg~vy~fLGLsvG~  152 (925)
T PRK12903         75 LGKRPYDVQIIGGIILDLGS--VAEMKTGEGKTITSIAPVYLNALTGKGVIVSTVNEYLAERDAEEMGKVFNFLGLSVGI  152 (925)
T ss_pred             hCCCcCchHHHHHHHHhcCC--eeeecCCCCccHHHHHHHHHHHhcCCceEEEecchhhhhhhHHHHHHHHHHhCCceee
Confidence            34467888887777777775  68999999999999998876556677788887777787655544443   334 3777


Q ss_pred             EeCCCCC
Q psy2760         267 IDDLPPV  273 (333)
Q Consensus       267 ltGd~~~  273 (333)
                      .+.+...
T Consensus       153 i~~~~~~  159 (925)
T PRK12903        153 NKANMDP  159 (925)
T ss_pred             eCCCCCh
Confidence            7665543

>KOG1000|consensus

Probab=94.40  E-value=0.4  Score=49.49  Aligned_cols=135  Identities=16%  Similarity=0.149  Sum_probs=82.5

Q ss_pred             CCCHHHHHHHHH-HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC---cEEEeC
Q psy2760         194 ELDVFQKQAIIK-LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD---VGLIDD  269 (333)
Q Consensus       194 ~l~~~Q~~ai~~-l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~---vglltG  269 (333)
                      .+-|+|++-+.- +..|..+++.-.-|-|||+-++. |....+..-..++++|- .|--.+.+.+...++.   +.++.+
T Consensus       198 ~LlPFQreGv~faL~RgGR~llADeMGLGKTiQAla-IA~yyraEwplliVcPA-svrftWa~al~r~lps~~pi~vv~~  275 (689)
T KOG1000|consen  198 RLLPFQREGVIFALERGGRILLADEMGLGKTIQALA-IARYYRAEWPLLIVCPA-SVRFTWAKALNRFLPSIHPIFVVDK  275 (689)
T ss_pred             hhCchhhhhHHHHHhcCCeEEEecccccchHHHHHH-HHHHHhhcCcEEEEecH-HHhHHHHHHHHHhcccccceEEEec
Confidence            578889998776 58888999999999999987754 44344444557888886 3444555566554553   455554


Q ss_pred             CCCCCC---Cc-ceEEec-------------cCcceEecccccccccc-CcCcccccchhhhhh-heeccCcchh----h
Q psy2760         270 LPPVFP---DV-EKLLED-------------LNIGGLDELSIHDFNKH-LKFWKPKVQLDDLFD-WTMASDATTL----E  326 (333)
Q Consensus       270 d~~~~~---~a-~ili~t-------------~~i~liViDe~H~~~~~-~R~~~~~~~l~~l~~-l~~~~d~~~~----e  326 (333)
                      ....-+   .+ .+.|..             .....+++||.|++.+. +|+-+.-.-+++.++ .++.|.+|..    |
T Consensus       276 ~~D~~~~~~t~~~v~ivSye~ls~l~~~l~~~~~~vvI~DEsH~Lk~sktkr~Ka~~dllk~akhvILLSGTPavSRP~e  355 (689)
T KOG1000|consen  276 SSDPLPDVCTSNTVAIVSYEQLSLLHDILKKEKYRVVIFDESHMLKDSKTKRTKAATDLLKVAKHVILLSGTPAVSRPSE  355 (689)
T ss_pred             ccCCccccccCCeEEEEEHHHHHHHHHHHhcccceEEEEechhhhhccchhhhhhhhhHHHHhhheEEecCCcccCCchh
Confidence            433221   11 122221             14678999999999655 333332233344444 6677777753    5


Q ss_pred             hhhc
Q psy2760         327 IFTY  330 (333)
Q Consensus       327 ~~~~  330 (333)
                      .|+-
T Consensus       356 lytq  359 (689)
T KOG1000|consen  356 LYTQ  359 (689)
T ss_pred             hhhh
Confidence            5543

>PF12846 AAA_10: AAA-like domain

Probab=94.34  E-value=0.073  Score=49.42  Aligned_cols=43  Identities=19%  Similarity=0.278  Sum_probs=34.9

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSN  251 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~  251 (333)
                      +.|+++.|+||||||......+......|.+++++=|..+...
T Consensus         1 n~h~~i~G~tGsGKT~~~~~l~~~~~~~g~~~~i~D~~g~~~~   43 (304)
T PF12846_consen    1 NPHTLILGKTGSGKTTLLKNLLEQLIRRGPRVVIFDPKGDYSP   43 (304)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHcCCCEEEEcCCchHHH
Confidence            3689999999999998888666677788888888877755554

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

Probab=94.31  E-value=0.14  Score=56.91  Aligned_cols=53  Identities=17%  Similarity=0.273  Sum_probs=42.8

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHH--HHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIA--LSQNHKTRTIYTSPIKALSNQKYRDFRETFQD  263 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il--~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~  263 (333)
                      +..+|.=-||||||+......-  .......+++||+-.+.|-.|+.+.|.. |+.
T Consensus       274 ~~G~IWHtqGSGKTlTm~~~A~~l~~~~~~~~v~fvvDR~dLd~Q~~~~f~~-~~~  328 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFKLARLLLELPKNPKVLFVVDRKDLDDQTSDEFQS-FGK  328 (962)
T ss_pred             CceEEEeecCCchHHHHHHHHHHHHhccCCCeEEEEechHHHHHHHHHHHHH-HHH
Confidence            4689999999999998766543  3335668899999999999999999976 443

>PRK05973 replicative DNA helicase; Provisional

Probab=94.25  E-value=0.11  Score=48.68  Aligned_cols=53  Identities=13%  Similarity=0.147  Sum_probs=40.2

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      +..|.-++|.|++|+|||..++.-+......|.+++|++-.-. ..|+.+++..
T Consensus        61 l~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~Ge~vlyfSlEes-~~~i~~R~~s  113 (237)
T PRK05973         61 LKPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFTLEYT-EQDVRDRLRA  113 (237)
T ss_pred             CCCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEEEeCC-HHHHHHHHHH
Confidence            4567889999999999999988766666667888999864422 5666666654

>KOG1132|consensus

Probab=94.21  E-value=0.11  Score=56.53  Aligned_cols=71  Identities=17%  Similarity=0.230  Sum_probs=54.7

Q ss_pred             ccCCCCCCHHHHHHHHH----HHcCCcEEEEcCCCCcHHHHHHHHHH---HHh------------c--------------
Q psy2760         189 HTWPFELDVFQKQAIIK----LEEHNHVFVTAHTSAGKTVIAEYAIA---LSQ------------N--------------  235 (333)
Q Consensus       189 ~~~~f~l~~~Q~~ai~~----l~~g~~vlv~apTGSGKTl~~~l~il---~~l------------~--------------  235 (333)
                      -.|||.|++-|...+..    +....+.++..|||+|||+..+-..+   +..            .              
T Consensus        16 V~fP~qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~k~~~~~~~~s~~~~~~~p~~~s~~~g~   95 (945)
T KOG1132|consen   16 VEFPFQPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHLKSRKPKGKISERKAGFIPTQPSDSGGE   95 (945)
T ss_pred             eeccCCcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHhhccccccchhhhhccccCCCCccCCCC
Confidence            35899999999887665    46778999999999999998877555   111            0              


Q ss_pred             -------C------CCeEEEEcccHHHHHHHHHHHHH
Q psy2760         236 -------H------KTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       236 -------~------g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                             .      -.++.|-+-|..-..|+.+++++
T Consensus        96 ~s~e~~e~~~~~~~ipkIyyaSRTHsQltQvvrElrr  132 (945)
T KOG1132|consen   96 KSEEAGEPIACYTGIPKIYYASRTHSQLTQVVRELRR  132 (945)
T ss_pred             chhhhcCccccccCCceEEEecchHHHHHHHHHHHhh
Confidence                   0      24577778888889999999876

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=94.11  E-value=0.15  Score=48.20  Aligned_cols=51  Identities=14%  Similarity=0.094  Sum_probs=37.6

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFR  258 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~  258 (333)
                      .++.++++.||+|.|||..+..........|.+++| +++.+|+.++...+.
T Consensus       103 ~~~~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f-~~~~el~~~Lk~~~~  153 (254)
T COG1484         103 ERGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLF-ITAPDLLSKLKAAFD  153 (254)
T ss_pred             ccCCcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEE-EEHHHHHHHHHHHHh
Confidence            468899999999999998876544444455566665 678888888776654

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=94.03  E-value=0.14  Score=48.87  Aligned_cols=54  Identities=11%  Similarity=0.146  Sum_probs=34.2

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHH-hcCC-CeEEEEc--ccHHHHHHHHHHHHHhc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALS-QNHK-TRTIYTS--PIKALSNQKYRDFRETF  261 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~-l~~g-~ral~l~--PtraLa~Q~~~~l~~~f  261 (333)
                      .++.++++||||+|||......+... ...| .++.++.  |.|.-+.++...+.+..
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D~~r~~a~eql~~~~~~~  250 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDTYRIGAVEQLKTYAKIL  250 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECCccchhHHHHHHHHHHHh
Confidence            35678899999999998876544333 3323 5665553  44655666666665543

>KOG1133|consensus

Probab=94.02  E-value=0.074  Score=56.44  Aligned_cols=41  Identities=22%  Similarity=0.254  Sum_probs=36.0

Q ss_pred             CCCCCCHHHHHHHHH----HHcCCcEEEEcCCCCcHHHHHHHHHH
Q psy2760         191 WPFELDVFQKQAIIK----LEEHNHVFVTAHTSAGKTVIAEYAIA  231 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~----l~~g~~vlv~apTGSGKTl~~~l~il  231 (333)
                      |||.|+.+|.+....    +..|+--+..+|||.|||+..+-+.+
T Consensus        12 fPy~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaal   56 (821)
T KOG1133|consen   12 FPYTPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAAL   56 (821)
T ss_pred             CCCCchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHH
Confidence            788999999988776    47899889999999999999887766

>KOG4439|consensus

Probab=93.96  E-value=0.14  Score=54.52  Aligned_cols=107  Identities=17%  Similarity=0.103  Sum_probs=75.1

Q ss_pred             CCCCHHHHHHHHHHH-----cCCcEEEEcCCCCcHHHHHHHHHHH-----Hhc-----CCCeEEEEcccHHHHHHHHHHH
Q psy2760         193 FELDVFQKQAIIKLE-----EHNHVFVTAHTSAGKTVIAEYAIAL-----SQN-----HKTRTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       193 f~l~~~Q~~ai~~l~-----~g~~vlv~apTGSGKTl~~~l~il~-----~l~-----~g~ral~l~PtraLa~Q~~~~l  257 (333)
                      +.+-|||+.++.-+.     .+.--++.-.-|-|||+.-+..|+.     ..+     ...+.++|+|. .|.+|+..++
T Consensus       324 v~LmpHQkaal~Wl~wRE~q~~~GGILaddmGLGKTlsmislil~qK~~~~~~~~~~~~a~~TLII~Pa-Sli~qW~~Ev  402 (901)
T KOG4439|consen  324 VELMPHQKAALRWLLWRESQPPSGGILADDMGLGKTLSMISLILHQKAARKAREKKGESASKTLIICPA-SLIHQWEAEV  402 (901)
T ss_pred             eecchhhhhhhhhhcccccCCCCCcccccccccccchHHHHHHHHHHHHHHhhcccccccCCeEEeCcH-HHHHHHHHHH
Confidence            488999999987762     2334577788899999976666652     111     11258999998 7899999999


Q ss_pred             HHhcCC----cEEEeCCCCCCCC------cceEEeccC-----------------------cceEecccccccccc
Q psy2760         258 RETFQD----VGLIDDLPPVFPD------VEKLLEDLN-----------------------IGGLDELSIHDFNKH  300 (333)
Q Consensus       258 ~~~f~~----vglltGd~~~~~~------a~ili~t~~-----------------------i~liViDe~H~~~~~  300 (333)
                      ..+...    |.+++|.-..+..      ..+++.|.+                       -..||.||+|.+.++
T Consensus       403 ~~rl~~n~LsV~~~HG~n~r~i~~~~L~~YDvViTTY~lva~~~~~e~~~~~~~spL~~I~W~RVILDEAH~IrN~  478 (901)
T KOG4439|consen  403 ARRLEQNALSVYLYHGPNKREISAKELRKYDVVITTYNLVANKPDDELEEGKNSSPLARIAWSRVILDEAHNIRNS  478 (901)
T ss_pred             HHHHhhcceEEEEecCCccccCCHHHHhhcceEEEeeeccccCCchhhhcccCccHHHHhhHHHhhhhhhhhhccc
Confidence            888764    7888888754332      245666542                       134678999988655

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=93.93  E-value=0.16  Score=48.21  Aligned_cols=50  Identities=24%  Similarity=0.196  Sum_probs=31.8

Q ss_pred             CCCHHHHHHHHHHH--cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEE
Q psy2760         194 ELDVFQKQAIIKLE--EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYT  243 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~--~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l  243 (333)
                      .+.+.|.+.+..+.  .+..++++||||||||......+......+.+++.+
T Consensus        63 g~~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l~all~~i~~~~~~iiti  114 (264)
T cd01129          63 GLKPENLEIFRKLLEKPHGIILVTGPTGSGKTTTLYSALSELNTPEKNIITV  114 (264)
T ss_pred             CCCHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHHHHHHhhhCCCCCeEEEE
Confidence            35777888887653  345789999999999987643322222233444444

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=93.89  E-value=0.23  Score=46.04  Aligned_cols=68  Identities=15%  Similarity=0.163  Sum_probs=38.8

Q ss_pred             CCCHHHHHHHHHH----HcCC-cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy2760         194 ELDVFQKQAIIKL----EEHN-HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETF  261 (333)
Q Consensus       194 ~l~~~Q~~ai~~l----~~g~-~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f  261 (333)
                      .+++.+++++..+    ..+. .++++||+|+|||..+....-...........+.++..-..+....+...+
T Consensus        23 ~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~i~~~l   95 (269)
T TIGR03015        23 YPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIRNLLKRLDQERVVAAKLVNTRVDAEDLLRMVAADF   95 (269)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHHHHHHhcCCCCeEEeeeeCCCCCHHHHHHHHHHHc
Confidence            4677777777765    2333 688999999999988775432222222233333443333344444444433

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.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=93.85  E-value=0.14  Score=47.35  Aligned_cols=50  Identities=10%  Similarity=0.137  Sum_probs=36.8

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFR  258 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~  258 (333)
                      .|..+++.+++|+|||..+...+.....+|.+++|+... +-..+..+.+.
T Consensus        23 ~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~~e-~~~~~~~~~~~   72 (230)
T PRK08533         23 AGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVSTQ-LTTTEFIKQMM   72 (230)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEeCC-CCHHHHHHHHH
Confidence            478899999999999999766655555678899998843 33455555553

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=93.70  E-value=0.15  Score=45.78  Aligned_cols=39  Identities=13%  Similarity=0.141  Sum_probs=32.0

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEccc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPI  246 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Pt  246 (333)
                      .|.-+.++||+|||||..++..+......+.+++|+.-.
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~~e   49 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTE   49 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECC
Confidence            367889999999999999987666666678889998754

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=93.64  E-value=0.27  Score=54.89  Aligned_cols=62  Identities=11%  Similarity=-0.005  Sum_probs=46.1

Q ss_pred             CCCCCHHHHHHHHHHHcCC-cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHH
Q psy2760         192 PFELDVFQKQAIIKLEEHN-HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQK  253 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~g~-~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~  253 (333)
                      ++.|++-|++|+..+..++ .+++.|+.|+|||.+...........|.+++.++||---|..+
T Consensus       344 g~~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~l~~~~~~~e~~G~~V~~~ApTGkAA~~L  406 (988)
T PRK13889        344 GLVLSGEQADALAHVTDGRDLGVVVGYAGTGKSAMLGVAREAWEAAGYEVRGAALSGIAAENL  406 (988)
T ss_pred             CCCCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEecCcHHHHHHH
Confidence            4579999999999987654 5789999999999874332222334588999999996555444

>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=93.58  E-value=0.18  Score=45.64  Aligned_cols=51  Identities=16%  Similarity=0.190  Sum_probs=34.6

Q ss_pred             cEEEEcCCCCcHHHHHHH-HHHHHhcCCCeEEEEc--ccHHHHHHHHHHHHHhcC
Q psy2760         211 HVFVTAHTSAGKTVIAEY-AIALSQNHKTRTIYTS--PIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l-~il~~l~~g~ral~l~--PtraLa~Q~~~~l~~~f~  262 (333)
                      -+++.||||+|||....- +...... +.++.+++  ..|.=+.++.+.+.+.++
T Consensus         3 vi~lvGptGvGKTTt~aKLAa~~~~~-~~~v~lis~D~~R~ga~eQL~~~a~~l~   56 (196)
T PF00448_consen    3 VIALVGPTGVGKTTTIAKLAARLKLK-GKKVALISADTYRIGAVEQLKTYAEILG   56 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHT-T--EEEEEESTSSTHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCchHhHHHHHHHHHhhc-cccceeecCCCCCccHHHHHHHHHHHhc
Confidence            478899999999988654 4333334 66666654  458888888888877654

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 ....

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=93.55  E-value=0.16  Score=47.91  Aligned_cols=36  Identities=11%  Similarity=0.243  Sum_probs=30.9

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS  244 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~  244 (333)
                      |.-++++|++|+|||..+..-+......|.+++|++
T Consensus        36 gs~~lI~G~pGtGKT~l~~qf~~~~a~~Ge~vlyis   71 (259)
T TIGR03878        36 YSVINITGVSDTGKSLMVEQFAVTQASRGNPVLFVT   71 (259)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEE
Confidence            778999999999999998876666666788999987

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=93.53  E-value=0.18  Score=45.96  Aligned_cols=48  Identities=19%  Similarity=0.162  Sum_probs=34.3

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRD  256 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~  256 (333)
                      .|..+++.|++|+|||..+...+...+.++.+++|+.- -+...++.+.
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~~~~~g~~~~~is~-e~~~~~i~~~   66 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVTT-EESRESIIRQ   66 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEEc-cCCHHHHHHH
Confidence            47899999999999999877655555567888888864 2333444444

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.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=93.53  E-value=0.17  Score=49.69  Aligned_cols=43  Identities=19%  Similarity=0.233  Sum_probs=29.4

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHH
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKAL  249 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraL  249 (333)
                      +..+++++++|+||||||... .+++.......|++.+=-+.+|
T Consensus       157 v~~~~nili~G~tgSGKTTll-~aL~~~ip~~~ri~tiEd~~El  199 (332)
T PRK13900        157 VISKKNIIISGGTSTGKTTFT-NAALREIPAIERLITVEDAREI  199 (332)
T ss_pred             HHcCCcEEEECCCCCCHHHHH-HHHHhhCCCCCeEEEecCCCcc
Confidence            367899999999999999875 3445555555566555333443

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=93.47  E-value=0.2  Score=45.62  Aligned_cols=50  Identities=12%  Similarity=0.104  Sum_probs=38.3

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      |..+++.|++|+|||..+..-+...+..+.+++|+.-. +-.+|+.+++..
T Consensus        16 g~~~li~G~~G~GKt~~~~~~~~~~~~~g~~~~y~s~e-~~~~~l~~~~~~   65 (224)
T TIGR03880        16 GHVIVVIGEYGTGKTTFSLQFLYQGLKNGEKAMYISLE-EREERILGYAKS   65 (224)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECC-CCHHHHHHHHHH
Confidence            67889999999999998877666666678899998654 346666666644

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>PRK06835 DNA replication protein DnaC; Validated

Probab=93.42  E-value=0.2  Score=49.10  Aligned_cols=46  Identities=15%  Similarity=0.229  Sum_probs=33.0

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKY  254 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~  254 (333)
                      .+.+++++||||+|||..+...+-.....|.+|+|+. ...|..+..
T Consensus       182 ~~~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t-~~~l~~~l~  227 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRT-ADELIEILR  227 (329)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEE-HHHHHHHHH
Confidence            4689999999999999876654444556777787754 455655553

>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=93.34  E-value=0.16  Score=47.50  Aligned_cols=41  Identities=15%  Similarity=0.240  Sum_probs=28.2

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCC-CeEEEEcccHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQNHK-TRTIYTSPIKA  248 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l~~g-~ral~l~Ptra  248 (333)
                      ..+.+++++|+||||||.... +++...... .+++.+-.+.+
T Consensus       125 ~~~~~ili~G~tGSGKTT~l~-all~~i~~~~~~iv~iEd~~E  166 (270)
T PF00437_consen  125 RGRGNILISGPTGSGKTTLLN-ALLEEIPPEDERIVTIEDPPE  166 (270)
T ss_dssp             HTTEEEEEEESTTSSHHHHHH-HHHHHCHTTTSEEEEEESSS-
T ss_pred             ccceEEEEECCCccccchHHH-HHhhhccccccceEEeccccc
Confidence            568899999999999998763 444444444 66666654444

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 ....

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]

Probab=93.30  E-value=0.51  Score=49.14  Aligned_cols=112  Identities=16%  Similarity=0.168  Sum_probs=72.1

Q ss_pred             ccCCCCCCHHHHHHHHHHH------cC----CcEEEEcCCCCcHHHHHHHHHH----HHhcCCCeEEEEcccHHHHHHHH
Q psy2760         189 HTWPFELDVFQKQAIIKLE------EH----NHVFVTAHTSAGKTVIAEYAIA----LSQNHKTRTIYTSPIKALSNQKY  254 (333)
Q Consensus       189 ~~~~f~l~~~Q~~ai~~l~------~g----~~vlv~apTGSGKTl~~~l~il----~~l~~g~ral~l~PtraLa~Q~~  254 (333)
                      ..+|+.+-|||+-.+-.+.      .|    +-.++..|-+-|||..+..-++    .....+.+..+++|+.+-+.+.+
T Consensus        56 ~~~p~~l~PwQkFiia~l~G~~~k~T~~rrf~e~fI~v~RkngKt~l~A~i~~~~~l~~~~~~~~~~i~A~s~~qa~~~F  135 (546)
T COG4626          56 PGFPESLEPWQKFIVAALFGFYDKQTGIRRFKEAFIFIPRKNGKSTLAAGIMMTALLLNWRSGAGIYILAPSVEQAANSF  135 (546)
T ss_pred             CCCccccchHHHHHHHHHhceeecCCCceEEEEEEEEEecCCchHHHHHHHHHHHHHhhhhcCCcEEEEeccHHHHHHhh
Confidence            5678899999999998864      22    3578999999999987653222    22256788889999999998888


Q ss_pred             HHHHHhcCCc--------------EEEeCCCCCCCC----cceEEeccCcceEecccccccccc
Q psy2760         255 RDFRETFQDV--------------GLIDDLPPVFPD----VEKLLEDLNIGGLDELSIHDFNKH  300 (333)
Q Consensus       255 ~~l~~~f~~v--------------glltGd~~~~~~----a~ili~t~~i~liViDe~H~~~~~  300 (333)
                      ...+......              -+..+.+.....    ..-.....+..+.++||+|.|...
T Consensus       136 ~~ar~mv~~~~~l~~~~~~q~~s~~i~~~~~~s~ik~~aa~~~~~Dg~~~~~~I~DEih~f~~~  199 (546)
T COG4626         136 NPARDMVKRDDDLRDLCNVQTHSRTITHRKTDSTIKAVAADPNTVDGLNSVGAIIDELHLFGKQ  199 (546)
T ss_pred             HHHHHHHHhCcchhhhhccccceeEEEecccceeeeeeccCCCcccCCCcceEEEehhhhhcCH
Confidence            7665433211              112222111100    001111235678899999999886

>TIGR02012 tigrfam_recA protein RecA

Probab=93.26  E-value=0.18  Score=49.39  Aligned_cols=44  Identities=25%  Similarity=0.207  Sum_probs=36.9

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQ  252 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q  252 (333)
                      |+-+.+++|+|||||..++..+......+.+++|+....++..+
T Consensus        55 G~iteI~G~~GsGKTtLaL~~~~~~~~~g~~v~yId~E~~~~~~   98 (321)
T TIGR02012        55 GRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPV   98 (321)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEcccchhHHH
Confidence            77899999999999999998887777778899999776665554

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.

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=93.25  E-value=0.25  Score=43.40  Aligned_cols=54  Identities=22%  Similarity=0.258  Sum_probs=34.6

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhc----------CCCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQN----------HKTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~----------~g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      .|.-.++.||+|+|||.+..-.+.....          .+.+++|+..-.. ..++.+++.....
T Consensus        31 ~g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~~~   94 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRALLQ   94 (193)
T ss_dssp             TTSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHHHHT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHHhc
Confidence            4778999999999999998775553332          4678999876544 4566666655443

>PRK07952 DNA replication protein DnaC; Validated

Probab=93.25  E-value=0.38  Score=45.22  Aligned_cols=44  Identities=7%  Similarity=0.048  Sum_probs=29.8

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKY  254 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~  254 (333)
                      ..++++|++|+|||..+...+......+.+++|+ +...|...+.
T Consensus       100 ~~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~i-t~~~l~~~l~  143 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAAAICNELLLRGKSVLII-TVADIMSAMK  143 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEE-EHHHHHHHHH
Confidence            4789999999999987765444444557777766 4444444433

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=93.19  E-value=0.2  Score=55.82  Aligned_cols=74  Identities=18%  Similarity=0.165  Sum_probs=55.8

Q ss_pred             CHHHHHHHHHH--------HcCCcEEEEcCCCCcHHHHHHHHHHHHh---cCCCeEEEEcccHHHHHHHHHHHHHhcC--
Q psy2760         196 DVFQKQAIIKL--------EEHNHVFVTAHTSAGKTVIAEYAIALSQ---NHKTRTIYTSPIKALSNQKYRDFRETFQ--  262 (333)
Q Consensus       196 ~~~Q~~ai~~l--------~~g~~vlv~apTGSGKTl~~~l~il~~l---~~g~ral~l~PtraLa~Q~~~~l~~~f~--  262 (333)
                      ..||-.|+..+        ..|-.++-.|.||+|||++=.-.+ +++   ..|.|..+-.-.|.|.-|.-..++++++  
T Consensus       410 F~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aNARIm-yaLsd~~~g~RfsiALGLRTLTLQTGda~r~rL~L~  488 (1110)
T TIGR02562       410 FRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLANARAM-YALRDDKQGARFAIALGLRSLTLQTGHALKTRLNLS  488 (1110)
T ss_pred             cchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHHHHHH-HHhCCCCCCceEEEEccccceeccchHHHHHhcCCC
Confidence            56899998885        245577889999999999854433 333   3466888888999999999999999876  


Q ss_pred             --CcEEEeCC
Q psy2760         263 --DVGLIDDL  270 (333)
Q Consensus       263 --~vglltGd  270 (333)
                        ++.++.|+
T Consensus       489 ~ddLAVlIGs  498 (1110)
T TIGR02562       489 DDDLAVLIGG  498 (1110)
T ss_pred             ccceEEEECH
Confidence              25555553

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.

>KOG4150|consensus

Probab=93.17  E-value=0.011  Score=61.48  Aligned_cols=64  Identities=11%  Similarity=-0.047  Sum_probs=55.2

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHH--HHhcCCCeEEEEcccHHHHHHHHHHH
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIA--LSQNHKTRTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il--~~l~~g~ral~l~PtraLa~Q~~~~l  257 (333)
                      .+..+|.+++.-+.+|+++.+...|.|||.+++..+..  +.+.+....+|+.||+++++..-+.+
T Consensus       286 ~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~~s~~~~~~~~~~~~~~~~~~~  351 (1034)
T KOG4150|consen  286 SGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLCHATNSLLPSEMVEHLRNGSKGQ  351 (1034)
T ss_pred             chhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcCcccceecchhHHHHhhccCCce
Confidence            57899999999999999999999999999999988765  45567788999999999988766543

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=93.13  E-value=0.28  Score=46.76  Aligned_cols=60  Identities=12%  Similarity=0.223  Sum_probs=40.9

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc--ccHHHHHHHHHHHHHhcCCcEEEeC
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS--PIKALSNQKYRDFRETFQDVGLIDD  269 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~--PtraLa~Q~~~~l~~~f~~vglltG  269 (333)
                      .+-++++||+|+|||..+.-.+......|.+++++.  +.|.-+.++...+.++.+ +.++..
T Consensus        72 ~~vi~l~G~~G~GKTTt~akLA~~l~~~g~~V~li~~D~~r~~a~~ql~~~~~~~~-i~~~~~  133 (272)
T TIGR00064        72 PNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAAGDTFRAAAIEQLEEWAKRLG-VDVIKQ  133 (272)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEeCCCCCHHHHHHHHHHHHhCC-eEEEeC
Confidence            456788899999999876654444455677777765  567767777777766554 554443

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.

>KOG0389|consensus

Probab=93.10  E-value=0.25  Score=53.32  Aligned_cols=114  Identities=16%  Similarity=0.091  Sum_probs=79.0

Q ss_pred             CCCCHHHHHHHHHH----HcCCcEEEEcCCCCcHHHH--HHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC--c
Q psy2760         193 FELDVFQKQAIIKL----EEHNHVFVTAHTSAGKTVI--AEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD--V  264 (333)
Q Consensus       193 f~l~~~Q~~ai~~l----~~g~~vlv~apTGSGKTl~--~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~--v  264 (333)
                      +.|-++|.--+.=+    ..+-+.++.-.-|-|||.-  ++++.+......+.=|+|||.-.| .-+.++|.+.++.  |
T Consensus       398 i~LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKTiQvIaFlayLkq~g~~gpHLVVvPsSTl-eNWlrEf~kwCPsl~V  476 (941)
T KOG0389|consen  398 IQLKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQVIAFLAYLKQIGNPGPHLVVVPSSTL-ENWLREFAKWCPSLKV  476 (941)
T ss_pred             CcccchhhhhHHHHHHHHHccccceehhhccCcchhHHHHHHHHHHHcCCCCCcEEEecchhH-HHHHHHHHHhCCceEE
Confidence            56788887766553    5677889999999999954  455655555555677889998655 5577888886665  5


Q ss_pred             EEEeCCCCCC-----------CCcceEEecc----------------CcceEecccccccccc-CcCcccc
Q psy2760         265 GLIDDLPPVF-----------PDVEKLLEDL----------------NIGGLDELSIHDFNKH-LKFWKPK  307 (333)
Q Consensus       265 glltGd~~~~-----------~~a~ili~t~----------------~i~liViDe~H~~~~~-~R~~~~~  307 (333)
                      -.+.|.+..+           ..-.+++.|.                ...++|.||.|++... +-+|+..
T Consensus       477 e~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmLKN~~SeRy~~L  547 (941)
T KOG0389|consen  477 EPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLKNRTSERYKHL  547 (941)
T ss_pred             EeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHHHHHHHhccccEEEecchhhhhccchHHHHHh
Confidence            6677765422           1235777765                5778999999999654 4445543

>PRK04296 thymidine kinase; Provisional

Probab=93.09  E-value=0.14  Score=45.92  Aligned_cols=37  Identities=11%  Similarity=0.104  Sum_probs=30.3

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcc
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSP  245 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~P  245 (333)
                      |.-.+++||.|+|||..++-.+......+.+++++-|
T Consensus         2 g~i~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~k~   38 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTELLQRAYNYEERGMKVLVFKP   38 (190)
T ss_pred             cEEEEEECCCCCHHHHHHHHHHHHHHHcCCeEEEEec
Confidence            4567899999999998887777666677889998876

>KOG0924|consensus

Probab=92.96  E-value=0.62  Score=49.84  Aligned_cols=67  Identities=15%  Similarity=0.095  Sum_probs=44.8

Q ss_pred             CHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHH-HHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         196 DVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEY-AIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       196 ~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l-~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      ...+.+.+..+..++-+++.+.||||||.-.-- .........+-+-+.-|.|.-|-.+.+++.+-.+
T Consensus       358 f~~R~~ll~~ir~n~vvvivgETGSGKTTQl~QyL~edGY~~~GmIGcTQPRRvAAiSVAkrVa~EM~  425 (1042)
T KOG0924|consen  358 FACRDQLLSVIRENQVVVIVGETGSGKTTQLAQYLYEDGYADNGMIGCTQPRRVAAISVAKRVAEEMG  425 (1042)
T ss_pred             HHHHHHHHHHHhhCcEEEEEecCCCCchhhhHHHHHhcccccCCeeeecCchHHHHHHHHHHHHHHhC
Confidence            344556666677888999999999999975322 1112222333455567999888888888876553

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=92.95  E-value=0.21  Score=49.07  Aligned_cols=45  Identities=24%  Similarity=0.175  Sum_probs=37.7

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQK  253 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~  253 (333)
                      |+-+.+++|+|||||..++..+......+.+++|+.+..++-.+.
T Consensus        55 G~iteI~Gp~GsGKTtLal~~~~~~~~~g~~~vyId~E~~~~~~~   99 (325)
T cd00983          55 GRIIEIYGPESSGKTTLALHAIAEAQKLGGTVAFIDAEHALDPVY   99 (325)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEECccccHHHHH
Confidence            778899999999999999988877777788999998776665543

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK10436 hypothetical protein; Provisional

Probab=92.94  E-value=0.26  Score=50.53  Aligned_cols=40  Identities=20%  Similarity=0.176  Sum_probs=28.8

Q ss_pred             CCCHHHHHHHHHH--HcCCcEEEEcCCCCcHHHHHHHHHHHHh
Q psy2760         194 ELDVFQKQAIIKL--EEHNHVFVTAHTSAGKTVIAEYAIALSQ  234 (333)
Q Consensus       194 ~l~~~Q~~ai~~l--~~g~~vlv~apTGSGKTl~~~l~il~~l  234 (333)
                      .+.+.|.+.+..+  ..+.-++++||||||||.... +++..+
T Consensus       201 G~~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL~-a~l~~~  242 (462)
T PRK10436        201 GMTPAQLAQFRQALQQPQGLILVTGPTGSGKTVTLY-SALQTL  242 (462)
T ss_pred             CcCHHHHHHHHHHHHhcCCeEEEECCCCCChHHHHH-HHHHhh
Confidence            4577788878775  455679999999999998753 344333

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=92.85  E-value=0.15  Score=46.68  Aligned_cols=45  Identities=18%  Similarity=0.199  Sum_probs=33.5

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcC-CCeEEEEc---ccHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNH-KTRTIYTS---PIKALSNQ  252 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~-g~ral~l~---PtraLa~Q  252 (333)
                      .|.-++++|++|+|||..+.-.+...... +.+++|++   |..+++..
T Consensus        12 ~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s~E~~~~~~~~r   60 (242)
T cd00984          12 PGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSLEMSKEQLLQR   60 (242)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEeCCCCHHHHHHH
Confidence            47789999999999999887766655444 88999987   33444443

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.

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=92.67  E-value=0.12  Score=52.32  Aligned_cols=56  Identities=23%  Similarity=0.164  Sum_probs=42.3

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEE
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLI  267 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vgll  267 (333)
                      .++++.||||||||..+.+|-+..  .+..+|+.=|--+|.......++++..+|-++
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll~--~~~s~iV~D~KgEl~~~t~~~r~~~G~~V~vl  100 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLLN--YPGSMIVTDPKGELYEKTAGYRKKRGYKVYVL  100 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHHh--ccCCEEEEECCCcHHHHHHHHHHHCCCEEEEe
Confidence            589999999999999998887643  23367888899999888777666654445443

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

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=92.64  E-value=0.28  Score=48.42  Aligned_cols=55  Identities=13%  Similarity=0.135  Sum_probs=37.6

Q ss_pred             CCCHHHHHHHHHH-HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHH
Q psy2760         194 ELDVFQKQAIIKL-EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKAL  249 (333)
Q Consensus       194 ~l~~~Q~~ai~~l-~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraL  249 (333)
                      .+++.|...+..+ ....|++++|.||||||...-. +........|+|.+=-|.+|
T Consensus       157 t~~~~~a~~L~~av~~r~NILisGGTGSGKTTlLNa-l~~~i~~~eRvItiEDtaEL  212 (355)
T COG4962         157 TMIRRAAKFLRRAVGIRCNILISGGTGSGKTTLLNA-LSGFIDSDERVITIEDTAEL  212 (355)
T ss_pred             CcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHHHHH-HHhcCCCcccEEEEeehhhh
Confidence            5788888888886 4555999999999999986432 22222334466666555544

>PRK09354 recA recombinase A; Provisional

Probab=92.60  E-value=0.24  Score=49.11  Aligned_cols=44  Identities=27%  Similarity=0.209  Sum_probs=37.7

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQ  252 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q  252 (333)
                      |+-+.+++|+|||||..++..+......|.+++|+....++-.+
T Consensus        60 G~IteI~G~~GsGKTtLal~~~~~~~~~G~~~~yId~E~s~~~~  103 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPV  103 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCccchHHH
Confidence            77889999999999999999888777788999999877666653

>PRK08116 hypothetical protein; Validated

Probab=92.56  E-value=0.7  Score=43.87  Aligned_cols=47  Identities=15%  Similarity=0.164  Sum_probs=30.5

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l  257 (333)
                      ..+++.|++|+|||..+....-.....+.+++|+ +..+|..++...+
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~-~~~~ll~~i~~~~  161 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANELIEKGVPVIFV-NFPQLLNRIKSTY  161 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE-EHHHHHHHHHHHH
Confidence            3499999999999988764333333456666665 4555665554433

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=92.56  E-value=0.29  Score=51.41  Aligned_cols=40  Identities=28%  Similarity=0.287  Sum_probs=28.6

Q ss_pred             CCCHHHHHHHHHH--HcCCcEEEEcCCCCcHHHHHHHHHHHHh
Q psy2760         194 ELDVFQKQAIIKL--EEHNHVFVTAHTSAGKTVIAEYAIALSQ  234 (333)
Q Consensus       194 ~l~~~Q~~ai~~l--~~g~~vlv~apTGSGKTl~~~l~il~~l  234 (333)
                      .+.+.|.+.+..+  .....++++||||||||... .+++..+
T Consensus       299 g~~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~  340 (564)
T TIGR02538       299 GFEPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL-YTALNIL  340 (564)
T ss_pred             CCCHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHHhh
Confidence            4577777777775  34457899999999999875 4444444

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=92.50  E-value=0.21  Score=40.75  Aligned_cols=24  Identities=13%  Similarity=0.253  Sum_probs=16.4

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIA  231 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il  231 (333)
                      +++.+++.|++|+|||.+......
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~~   26 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLAR   26 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHHHHHH
Confidence            357899999999999998876554

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=92.47  E-value=0.3  Score=50.34  Aligned_cols=101  Identities=23%  Similarity=0.253  Sum_probs=54.1

Q ss_pred             CCCHHHHHHHHHHHcC--CcEEEEcCCCCcHHHHHHHHHHHHhcCCCe-EEE-------EcccHHHHHHH---------H
Q psy2760         194 ELDVFQKQAIIKLEEH--NHVFVTAHTSAGKTVIAEYAIALSQNHKTR-TIY-------TSPIKALSNQK---------Y  254 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g--~~vlv~apTGSGKTl~~~l~il~~l~~g~r-al~-------l~PtraLa~Q~---------~  254 (333)
                      .+.+.|.+.+..+...  -=+++.||||||||..- ++++..+....+ ++-       ..|-   ++|+         +
T Consensus       241 g~~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTTL-Y~~L~~ln~~~~nI~TiEDPVE~~~~g---I~Q~qVN~k~gltf  316 (500)
T COG2804         241 GMSPFQLARLLRLLNRPQGLILVTGPTGSGKTTTL-YAALSELNTPERNIITIEDPVEYQLPG---INQVQVNPKIGLTF  316 (500)
T ss_pred             CCCHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHHH-HHHHHHhcCCCceEEEeeCCeeeecCC---cceeecccccCCCH
Confidence            4578888888886433  35789999999999874 444444333222 221       1221   1111         1


Q ss_pred             -HHHHHhcC--CcEEEeCCCCCCCCcceEEeccCcceEecccccccc
Q psy2760         255 -RDFRETFQ--DVGLIDDLPPVFPDVEKLLEDLNIGGLDELSIHDFN  298 (333)
Q Consensus       255 -~~l~~~f~--~vglltGd~~~~~~a~ili~t~~i~liViDe~H~~~  298 (333)
                       +-++..+.  +--+..|......-+++.+.-.--+++|..+.|--+
T Consensus       317 a~~LRa~LRqDPDvImVGEIRD~ETAeiavqAalTGHLVlSTlHtnd  363 (500)
T COG2804         317 ARALRAILRQDPDVIMVGEIRDLETAEIAVQAALTGHLVLSTLHTND  363 (500)
T ss_pred             HHHHHHHhccCCCeEEEeccCCHHHHHHHHHHHhcCCeEeeecccCc
Confidence             12222222  134455666655555544444445666777777543

>cd01394 radB RadB

Probab=92.41  E-value=0.21  Score=45.10  Aligned_cols=37  Identities=19%  Similarity=0.144  Sum_probs=30.6

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS  244 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~  244 (333)
                      .|.-++++|++|+|||..+...+......+.+++|+.
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~~a~~~~~~g~~v~yi~   54 (218)
T cd01394          18 RGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYID   54 (218)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            3677899999999999999887766666788899983

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=92.39  E-value=0.23  Score=45.61  Aligned_cols=50  Identities=8%  Similarity=0.171  Sum_probs=37.1

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      |..+++.|++|+|||..+...+......|.+++|+.=- +-..++.+++.+
T Consensus        25 g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~~e-~~~~~~~~~~~~   74 (234)
T PRK06067         25 PSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITTE-NTSKSYLKQMES   74 (234)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHHHHhCCCEEEEEEcC-CCHHHHHHHHHH
Confidence            67899999999999999877666666678899998643 333455555543

>PRK12377 putative replication protein; Provisional

Probab=92.38  E-value=0.37  Score=45.46  Aligned_cols=48  Identities=8%  Similarity=0.090  Sum_probs=33.2

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l  257 (333)
                      ..++++.||+|+|||..+....-.....|..++|+ +..+|..++...+
T Consensus       101 ~~~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~i-~~~~l~~~l~~~~  148 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVV-TVPDVMSRLHESY  148 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEE-EHHHHHHHHHHHH
Confidence            46899999999999987765544445566667654 5556666655443

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=92.13  E-value=0.47  Score=48.11  Aligned_cols=53  Identities=13%  Similarity=0.146  Sum_probs=34.5

Q ss_pred             CCcEEEEcCCCCcHHHHHHH-HHHHH-hcCCCeEEEEc--ccHHHHHHHHHHHHHhc
Q psy2760         209 HNHVFVTAHTSAGKTVIAEY-AIALS-QNHKTRTIYTS--PIKALSNQKYRDFRETF  261 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l-~il~~-l~~g~ral~l~--PtraLa~Q~~~~l~~~f  261 (333)
                      ++.+++.||||+|||..... +.... ...+.++.++.  |.|.-+.++...+.+..
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~~r~~a~eqL~~~a~~~  277 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTYRIGAVEQLKTYAKIM  277 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCccHHHHHHHHHHHHHHh
Confidence            66889999999999987654 33333 34566776654  45655555555555533

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=92.07  E-value=0.25  Score=46.49  Aligned_cols=35  Identities=20%  Similarity=0.158  Sum_probs=26.2

Q ss_pred             CCHHHHHHHHH----HHcCCcEEEEcCCCCcHHHHHHHH
Q psy2760         195 LDVFQKQAIIK----LEEHNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       195 l~~~Q~~ai~~----l~~g~~vlv~apTGSGKTl~~~l~  229 (333)
                      .++..++....    +..|+++++.||+|+|||.++...
T Consensus         3 ~t~~~~~l~~~~l~~l~~g~~vLL~G~~GtGKT~lA~~l   41 (262)
T TIGR02640         3 ETDAVKRVTSRALRYLKSGYPVHLRGPAGTGKTTLAMHV   41 (262)
T ss_pred             CCHHHHHHHHHHHHHHhcCCeEEEEcCCCCCHHHHHHHH
Confidence            34444444443    578999999999999999998653

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=92.04  E-value=0.26  Score=44.46  Aligned_cols=42  Identities=19%  Similarity=0.407  Sum_probs=29.1

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALS  250 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa  250 (333)
                      .+.+++++||+|+|||..+....-.....+..++|+ +...+.
T Consensus        37 ~~~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i-~~~~~~   78 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYL-PLAELA   78 (226)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEE-eHHHHH
Confidence            457899999999999998876554444455566664 444443

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.

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=92.01  E-value=0.31  Score=50.26  Aligned_cols=34  Identities=21%  Similarity=0.146  Sum_probs=25.8

Q ss_pred             CCCHHHHHHHHHHHc-C-CcEEEEcCCCCcHHHHHH
Q psy2760         194 ELDVFQKQAIIKLEE-H-NHVFVTAHTSAGKTVIAE  227 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~-g-~~vlv~apTGSGKTl~~~  227 (333)
                      .+.+.|.+.+..+.. . .-++++||||||||....
T Consensus       225 g~~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL~  260 (486)
T TIGR02533       225 GMSPELLSRFERLIRRPHGIILVTGPTGSGKTTTLY  260 (486)
T ss_pred             CCCHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHH
Confidence            457788888877633 2 357899999999998764

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>PRK06921 hypothetical protein; Provisional

Probab=91.88  E-value=0.41  Score=45.42  Aligned_cols=47  Identities=13%  Similarity=0.079  Sum_probs=31.3

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcC-CCeEEEEcccHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNH-KTRTIYTSPIKALSNQKYR  255 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~-g~ral~l~PtraLa~Q~~~  255 (333)
                      .+.++++.|++|+|||..+...+-..... +..++|+. ..++..++..
T Consensus       116 ~~~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~-~~~l~~~l~~  163 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFP-FVEGFGDLKD  163 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEE-HHHHHHHHHH
Confidence            46789999999999998765333233444 67777765 4455555443

>KOG1131|consensus

Probab=91.84  E-value=0.63  Score=48.37  Aligned_cols=69  Identities=17%  Similarity=0.266  Sum_probs=48.9

Q ss_pred             CCC-CCCHHHHHHHHH----HHcCCcEEEEcCCCCcHHHHHHHHHHHH----hcCCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         191 WPF-ELDVFQKQAIIK----LEEHNHVFVTAHTSAGKTVIAEYAIALS----QNHKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       191 ~~f-~l~~~Q~~ai~~----l~~g~~vlv~apTGSGKTl~~~l~il~~----l~~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      ||| ..+|-|-+-...    +..+.++++-.|+|.|||++.+-.++..    .....+.+|.+-|..-+.....+++.
T Consensus        12 FPY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRTvpEieK~l~El~~   89 (755)
T KOG1131|consen   12 FPYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEELKR   89 (755)
T ss_pred             cCCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCcchHHHHHHHHHHH
Confidence            677 788988776655    4567799999999999998877665522    13457899998775555555544433

>KOG0923|consensus

Probab=91.82  E-value=0.36  Score=51.32  Aligned_cols=65  Identities=14%  Similarity=0.163  Sum_probs=46.1

Q ss_pred             CHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHH---HHhc-CCCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         196 DVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIA---LSQN-HKTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       196 ~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il---~~l~-~g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      +++-.+.+.++..+.-++|.|.||||||.-  +|-.   .... .|.++-+.-|.|--|-.+..+..+-.+
T Consensus       267 y~ykdell~av~e~QVLiI~GeTGSGKTTQ--iPQyL~EaGytk~gk~IgcTQPRRVAAmSVAaRVA~EMg  335 (902)
T KOG0923|consen  267 YPYKDELLKAVKEHQVLIIVGETGSGKTTQ--IPQYLYEAGYTKGGKKIGCTQPRRVAAMSVAARVAEEMG  335 (902)
T ss_pred             hhhHHHHHHHHHhCcEEEEEcCCCCCcccc--ccHHHHhcccccCCceEeecCcchHHHHHHHHHHHHHhC
Confidence            555567777788899999999999999974  2322   1223 344577778999888888877765443

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=91.81  E-value=0.12  Score=51.19  Aligned_cols=54  Identities=22%  Similarity=0.133  Sum_probs=40.2

Q ss_pred             cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC-CcEEE
Q psy2760         211 HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ-DVGLI  267 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~-~vgll  267 (333)
                      ++++.||||||||..+.+|-+..  .+..++++=|--++........++ .+ .|.++
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~--~~~s~vv~D~Kge~~~~t~~~r~~-~G~~V~v~   55 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLT--WPGSVVVLDPKGENFELTSEHRRA-LGRKVFVF   55 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhc--CCCCEEEEccchhHHHHHHHHHHH-cCCeEEEE
Confidence            57999999999999988776543  346788888999998777766654 44 35554

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.

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=91.79  E-value=0.28  Score=44.61  Aligned_cols=39  Identities=15%  Similarity=0.139  Sum_probs=31.2

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEccc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPI  246 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Pt  246 (333)
                      .|.-++++|++|+|||..+...+......+.+++|+.=.
T Consensus        22 ~g~i~~i~G~~GsGKT~l~~~la~~~~~~~~~v~yi~~e   60 (225)
T PRK09361         22 RGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE   60 (225)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            367889999999999999887666665667889988543

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=91.76  E-value=0.37  Score=47.44  Aligned_cols=54  Identities=11%  Similarity=0.121  Sum_probs=36.6

Q ss_pred             CCHHHHHHHHHH-HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHH
Q psy2760         195 LDVFQKQAIIKL-EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKAL  249 (333)
Q Consensus       195 l~~~Q~~ai~~l-~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraL  249 (333)
                      +++.+.+.+..+ ..+.+++++++||||||..... ++..+....+.+++--+.+|
T Consensus       163 ~~~~~~~~L~~~v~~~~~ili~G~tGsGKTTll~a-l~~~i~~~~riv~iEd~~El  217 (340)
T TIGR03819       163 FPPGVARLLRAIVAARLAFLISGGTGSGKTTLLSA-LLALVAPDERIVLVEDAAEL  217 (340)
T ss_pred             CCHHHHHHHHHHHhCCCeEEEECCCCCCHHHHHHH-HHccCCCCCcEEEECCccee
Confidence            456677777664 6778999999999999986543 33333444566666555555

Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer.

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=91.69  E-value=0.62  Score=49.70  Aligned_cols=52  Identities=23%  Similarity=0.271  Sum_probs=41.6

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHH--HHHHHHHHHHHh
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKA--LSNQKYRDFRET  260 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Ptra--La~Q~~~~l~~~  260 (333)
                      ..|++|.|+||+|||..+...+.+..+.|..++++=|-..  |...+....+..
T Consensus       176 ~~H~lv~G~TGsGKT~l~~~l~~q~i~~g~~viv~DpKgD~~l~~~~~~~~~~~  229 (634)
T TIGR03743       176 VGHTLVLGTTGVGKTRLAELLITQDIRRGDVVIVIDPKGDADLKRRMRAEAKRA  229 (634)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCCchHHHHHHHHHHHHh
Confidence            5799999999999999987777788888888888888744  777777666553

Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains.

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=91.69  E-value=0.82  Score=49.51  Aligned_cols=68  Identities=22%  Similarity=0.175  Sum_probs=50.6

Q ss_pred             CCCHHHHHHHHHH---H--cCCcEEEEcCCCCcHHHHHHHHHHHHhcCC--CeEEEEcccHHHHHHHHHHHHHhc
Q psy2760         194 ELDVFQKQAIIKL---E--EHNHVFVTAHTSAGKTVIAEYAIALSQNHK--TRTIYTSPIKALSNQKYRDFRETF  261 (333)
Q Consensus       194 ~l~~~Q~~ai~~l---~--~g~~vlv~apTGSGKTl~~~l~il~~l~~g--~ral~l~PtraLa~Q~~~~l~~~f  261 (333)
                      ..+.-|.+++..+   .  ..+-+++.|.-|-|||.+..+++......+  .++++.+|+.+=++.+++...+.+
T Consensus       211 ~~T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~~~~~~~~~~~iiVTAP~~~nv~~Lf~fa~~~l  285 (758)
T COG1444         211 CLTEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIALAAAARLAGSVRIIVTAPTPANVQTLFEFAGKGL  285 (758)
T ss_pred             hcChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHHHHHHhcCCceEEEeCCCHHHHHHHHHHHHHhH
Confidence            4677788776663   2  333688899999999999998775444333  589999999998888887665544

>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=91.67  E-value=0.45  Score=41.31  Aligned_cols=46  Identities=11%  Similarity=0.203  Sum_probs=29.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc--ccHHHHHHHHHHH
Q psy2760         212 VFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS--PIKALSNQKYRDF  257 (333)
Q Consensus       212 vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~--PtraLa~Q~~~~l  257 (333)
                      +++.|++|+|||..+...+......+.+++++.  +.|.-..++...+
T Consensus         3 ~~~~G~~G~GKTt~~~~la~~~~~~g~~v~~i~~D~~~~~~~~~l~~~   50 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADTYRPAAIEQLRVL   50 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEcCCCChHHHHHHHHh
Confidence            578999999999997665544444567777654  4444333434333

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.

>PRK08084 DNA replication initiation factor; Provisional

Probab=91.65  E-value=0.53  Score=43.58  Aligned_cols=38  Identities=13%  Similarity=0.157  Sum_probs=27.5

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSP  245 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~P  245 (333)
                      .+.+++++||+|+|||.............+.+++|+.-
T Consensus        44 ~~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~   81 (235)
T PRK08084         44 HSGYIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPL   81 (235)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEH
Confidence            34689999999999998776444334455777888654

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=91.65  E-value=0.48  Score=50.02  Aligned_cols=54  Identities=20%  Similarity=0.201  Sum_probs=43.0

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHh------cCCCeEEEEcccHHHHHHHHHHHHHh
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQ------NHKTRTIYTSPIKALSNQKYRDFRET  260 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l------~~g~ral~l~PtraLa~Q~~~~l~~~  260 (333)
                      ..++-++|.|..|||||.+++.-+.+.+      ..+..++++.|.+-+..-+.+.|-++
T Consensus       224 ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~vFleYis~VLPeL  283 (747)
T COG3973         224 EKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNRVFLEYISRVLPEL  283 (747)
T ss_pred             cCCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEcCcHHHHHHHHHhchhh
Confidence            4567789999999999999998665433      23445999999999999888888763

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=91.63  E-value=0.21  Score=48.67  Aligned_cols=18  Identities=28%  Similarity=0.416  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCCcHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAE  227 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~  227 (333)
                      -=++|.||||||||....
T Consensus       126 GLILVTGpTGSGKSTTlA  143 (353)
T COG2805         126 GLILVTGPTGSGKSTTLA  143 (353)
T ss_pred             ceEEEeCCCCCcHHHHHH
Confidence            368999999999987643

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=91.59  E-value=0.27  Score=45.83  Aligned_cols=39  Identities=21%  Similarity=0.066  Sum_probs=29.9

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHhcC-CCeEEEEcc
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQNH-KTRTIYTSP  245 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l~~-g~ral~l~P  245 (333)
                      ..|..+++.|++|+|||..+...+...... |.+++|++-
T Consensus        28 ~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~vl~iS~   67 (271)
T cd01122          28 RKGELIILTAGTGVGKTTFLREYALDLITQHGVRVGTISL   67 (271)
T ss_pred             cCCcEEEEEcCCCCCHHHHHHHHHHHHHHhcCceEEEEEc
Confidence            347889999999999998877655544444 888999863

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=91.59  E-value=0.33  Score=46.87  Aligned_cols=39  Identities=15%  Similarity=0.268  Sum_probs=26.1

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcc
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSP  245 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~P  245 (333)
                      +..+.+++++||||||||...-. ++.......+++++-.
T Consensus       141 v~~~~~ili~G~tGsGKTTll~a-l~~~~~~~~~iv~ied  179 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTFLKS-LVDEIPKDERIITIED  179 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHHHHH-HHccCCccccEEEEcC
Confidence            36789999999999999987643 3333333445555433

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>KOG1002|consensus

Probab=91.55  E-value=1.3  Score=45.82  Aligned_cols=77  Identities=18%  Similarity=0.189  Sum_probs=49.5

Q ss_pred             CCCCHHHHHHHHHHH-cCC----cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC---c
Q psy2760         193 FELDVFQKQAIIKLE-EHN----HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD---V  264 (333)
Q Consensus       193 f~l~~~Q~~ai~~l~-~g~----~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~---v  264 (333)
                      ..+-|+|++-+.=+. +..    --++.-.-|-|||.-.+..++. --.+...++++|+.||. |+..++...-.+   +
T Consensus       183 i~LL~fQkE~l~Wl~~QE~Ss~~GGiLADEMGMGKTIQtIaLlla-e~~ra~tLVvaP~VAlm-QW~nEI~~~T~gslkv  260 (791)
T KOG1002|consen  183 IPLLPFQKEGLAWLTSQEESSVAGGILADEMGMGKTIQTIALLLA-EVDRAPTLVVAPTVALM-QWKNEIERHTSGSLKV  260 (791)
T ss_pred             ecchhhhHHHHHHHHHhhhhhhccceehhhhccchHHHHHHHHHh-ccccCCeeEEccHHHHH-HHHHHHHHhccCceEE
Confidence            367899998776542 221    2355667899999876654443 33456699999999985 666666443222   5


Q ss_pred             EEEeCCC
Q psy2760         265 GLIDDLP  271 (333)
Q Consensus       265 glltGd~  271 (333)
                      -+++|..
T Consensus       261 ~~YhG~~  267 (791)
T KOG1002|consen  261 YIYHGAK  267 (791)
T ss_pred             EEEeccc
Confidence            5566643

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=91.54  E-value=0.37  Score=49.56  Aligned_cols=52  Identities=19%  Similarity=0.209  Sum_probs=41.5

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      ..|..+++.+|+|+|||..++.-+.....+|.+++|++ .-+-..|+.++...
T Consensus       261 ~~gs~~li~G~~G~GKt~l~~~f~~~~~~~ge~~~y~s-~eEs~~~i~~~~~~  312 (484)
T TIGR02655       261 FKDSIILATGATGTGKTLLVSKFLENACANKERAILFA-YEESRAQLLRNAYS  312 (484)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEE-eeCCHHHHHHHHHH
Confidence            35678999999999999988877766777888999987 55667777777644

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.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=91.52  E-value=0.51  Score=47.39  Aligned_cols=88  Identities=8%  Similarity=0.005  Sum_probs=48.8

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHH-HHh---cCCCeEEEEc--ccHHHHHHHHHHHHHhcCCcEEEeCCCCCCCCcceEEe
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIA-LSQ---NHKTRTIYTS--PIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLLE  282 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il-~~l---~~g~ral~l~--PtraLa~Q~~~~l~~~f~~vglltGd~~~~~~a~ili~  282 (333)
                      +..+++.||||+|||.+..-... ...   ..+.++.++.  +.|.-+.++.+.+.+..+ +.+..+....... ..+-.
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lg-vpv~~~~~~~~l~-~~L~~  251 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMG-IPVKAIESFKDLK-EEITQ  251 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCC-cceEeeCcHHHHH-HHHHH
Confidence            46789999999999988754332 222   2455665553  667777777777766543 2222211110000 00001


Q ss_pred             ccCcceEecccccccc
Q psy2760         283 DLNIGGLDELSIHDFN  298 (333)
Q Consensus       283 t~~i~liViDe~H~~~  298 (333)
                      ..+..++++|++.+..
T Consensus       252 ~~~~DlVLIDTaGr~~  267 (388)
T PRK12723        252 SKDFDLVLVDTIGKSP  267 (388)
T ss_pred             hCCCCEEEEcCCCCCc
Confidence            1255777888887543

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=91.48  E-value=0.31  Score=44.38  Aligned_cols=40  Identities=15%  Similarity=0.224  Sum_probs=32.4

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHh-cCCCeEEEEcccHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQ-NHKTRTIYTSPIKA  248 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l-~~g~ral~l~Ptra  248 (333)
                      ++++.|.|.||||||.....-+.... ..+.+++++=|.-+
T Consensus        23 ~~H~~I~G~TGsGKS~~~~~ll~~l~~~~~~~~ii~D~~GE   63 (229)
T PF01935_consen   23 NRHIAIFGTTGSGKSNTVKVLLEELLKKKGAKVIIFDPHGE   63 (229)
T ss_pred             cceEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEcCCCc
Confidence            58999999999999998877666666 77778888877644

It contains several conserved aspartates and histidines that could be metal ligands.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=91.44  E-value=0.56  Score=47.71  Aligned_cols=52  Identities=15%  Similarity=0.169  Sum_probs=37.2

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHH-HHhcCCCeEEEEc--ccHHHHHHHHHHHHHh
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIA-LSQNHKTRTIYTS--PIKALSNQKYRDFRET  260 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il-~~l~~g~ral~l~--PtraLa~Q~~~~l~~~  260 (333)
                      +..++++||||+|||..+...+. .....|.++.++.  +.|+.+..+.+++.+.
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~~~~~~G~~V~Lit~Dt~R~aA~eQLk~yAe~  277 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTTDNYRIAAIEQLKRYADT  277 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEecccchhhhHHHHHHHHHHh
Confidence            45688999999999998876544 3355666776654  5678777777776553

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=91.41  E-value=0.38  Score=49.48  Aligned_cols=51  Identities=12%  Similarity=0.137  Sum_probs=38.1

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcC-CCeEEEEcccHHHHHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNH-KTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~-g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      .|..++++|++|+|||..+..-+.....+ |.+++|++-. +-..++.+....
T Consensus        20 ~g~~~Li~G~pGsGKT~la~qfl~~g~~~~ge~~lyvs~e-E~~~~l~~~~~~   71 (484)
T TIGR02655        20 IGRSTLVSGTSGTGKTLFSIQFLYNGIIHFDEPGVFVTFE-ESPQDIIKNARS   71 (484)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEEe-cCHHHHHHHHHH
Confidence            47899999999999999988766655544 7899998743 555566655544

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.

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=91.33  E-value=0.83  Score=51.56  Aligned_cols=63  Identities=19%  Similarity=0.053  Sum_probs=49.2

Q ss_pred             CCCCCHHHHHHHHHHH-cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHH
Q psy2760         192 PFELDVFQKQAIIKLE-EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKY  254 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~-~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~  254 (333)
                      ++.|++-|++|+..+. .++-+++.|+.|+|||.+...........|.+++-++||-.=|..+.
T Consensus       379 ~~~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l~~~~~~~e~~G~~V~g~ApTgkAA~~L~  442 (1102)
T PRK13826        379 HARLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMMKAAREAWEAAGYRVVGGALAGKAAEGLE  442 (1102)
T ss_pred             CCCCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEcCcHHHHHHHH
Confidence            4679999999999874 46778999999999998876654444456889999999966554443

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=91.31  E-value=0.58  Score=45.70  Aligned_cols=60  Identities=13%  Similarity=0.175  Sum_probs=38.6

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc--ccHHHHHHHHHHHHHhcCCcEEEeC
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS--PIKALSNQKYRDFRETFQDVGLIDD  269 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~--PtraLa~Q~~~~l~~~f~~vglltG  269 (333)
                      +.-++++||+|+|||..+.-........+.+++++.  +.|+-+.++...+..+. ++.++..
T Consensus       114 ~~vi~lvGpnGsGKTTt~~kLA~~l~~~g~~V~Li~~D~~r~~a~eql~~~a~~~-~i~~~~~  175 (318)
T PRK10416        114 PFVILVVGVNGVGKTTTIGKLAHKYKAQGKKVLLAAGDTFRAAAIEQLQVWGERV-GVPVIAQ  175 (318)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHHhcCCeEEEEecCccchhhHHHHHHHHHHc-CceEEEe
Confidence            567889999999999887654443345566777664  34666656666665543 3555443

>PRK10867 signal recognition particle protein; Provisional

Probab=91.28  E-value=0.49  Score=48.23  Aligned_cols=51  Identities=14%  Similarity=0.223  Sum_probs=35.4

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcC-CCeEEEEc--ccHHHHHHHHHHHHHh
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNH-KTRTIYTS--PIKALSNQKYRDFRET  260 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~-g~ral~l~--PtraLa~Q~~~~l~~~  260 (333)
                      .-++++|++|+|||.++.-.+...... |.+++++.  +.|.-+.++.+.+.+.
T Consensus       101 ~vI~~vG~~GsGKTTtaakLA~~l~~~~G~kV~lV~~D~~R~aa~eQL~~~a~~  154 (433)
T PRK10867        101 TVIMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLVAADVYRPAAIEQLKTLGEQ  154 (433)
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHhcCCcEEEEEccccchHHHHHHHHHHhh
Confidence            467889999999998876544433344 77777664  5677777666666554

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=91.27  E-value=0.57  Score=47.80  Aligned_cols=53  Identities=9%  Similarity=0.161  Sum_probs=36.1

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc--ccHHHHHHHHHHHHHhc
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS--PIKALSNQKYRDFRETF  261 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~--PtraLa~Q~~~~l~~~f  261 (333)
                      ...++++|++|+|||.++..........|.+++++.  +.|.-+.++.+.+.+..
T Consensus        95 p~vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~~D~~R~aa~eQL~~la~~~  149 (437)
T PRK00771         95 PQTIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAADTYRPAAYDQLKQLAEKI  149 (437)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEecCCCCCHHHHHHHHHHHHHc
Confidence            357889999999999987665444445566777664  34665666666665544

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=91.11  E-value=0.4  Score=42.50  Aligned_cols=43  Identities=21%  Similarity=0.259  Sum_probs=33.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHH
Q psy2760         212 VFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       212 vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l  257 (333)
                      ++|.|++|||||..+..-+..   .+.+++|++-.+++-..+.+++
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~---~~~~~~y~at~~~~d~em~~rI   44 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAE---LGGPVTYIATAEAFDDEMAERI   44 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHh---cCCCeEEEEccCcCCHHHHHHH
Confidence            588999999999988765432   5678999988887766666554

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>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=91.10  E-value=0.35  Score=48.32  Aligned_cols=45  Identities=20%  Similarity=0.341  Sum_probs=31.1

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQ  252 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q  252 (333)
                      ..+++++.|.||||||.+....+-+....|.++|+.=|.-+....
T Consensus        14 e~~~~li~G~~GsGKT~~i~~ll~~~~~~g~~~iI~D~kg~~~~~   58 (386)
T PF10412_consen   14 ENRHILIIGATGSGKTQAIRHLLDQIRARGDRAIIYDPKGEFTER   58 (386)
T ss_dssp             GGG-EEEEE-TTSSHHHHHHHHHHHHHHTT-EEEEEEETTHHHHH
T ss_pred             hhCcEEEECCCCCCHHHHHHHHHHHHHHcCCEEEEEECCchHHHH
Confidence            468999999999999986544444556678888888888666443

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.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=91.08  E-value=0.5  Score=47.59  Aligned_cols=54  Identities=9%  Similarity=0.160  Sum_probs=36.3

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc--ccHHHHHHHHHHHHHhc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS--PIKALSNQKYRDFRETF  261 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~--PtraLa~Q~~~~l~~~f  261 (333)
                      .++.++++||||+|||....-........+.++.++.  |.|.=+..+.+.+.+..
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~l~~~g~~V~lItaDtyR~gAveQLk~yae~l  260 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFITTDTFRSGAVEQFQGYADKL  260 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCccCccHHHHHHHHhhcC
Confidence            4778999999999999887665444455566776654  55655555555555533

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=91.04  E-value=0.65  Score=47.11  Aligned_cols=53  Identities=15%  Similarity=0.132  Sum_probs=34.5

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc--ccHHHHHHHHHHHHHhc
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS--PIKALSNQKYRDFRETF  261 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~--PtraLa~Q~~~~l~~~f  261 (333)
                      .+.+++.||||+|||.............|.++.++.  |.|.-+.++...+.+..
T Consensus       241 ~~vI~LVGptGvGKTTTiaKLA~~L~~~GkkVglI~aDt~RiaAvEQLk~yae~l  295 (436)
T PRK11889        241 VQTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITTDHSRIGTVQQLQDYVKTI  295 (436)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEEecCCcchHHHHHHHHHhhhc
Confidence            367899999999999987664444445566666554  45654555555554533

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=90.98  E-value=0.81  Score=41.60  Aligned_cols=38  Identities=8%  Similarity=0.180  Sum_probs=27.2

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSP  245 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~P  245 (333)
                      .+..++++||+|+|||..+..........+..++|+..
T Consensus        41 ~~~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~~   78 (227)
T PRK08903         41 ADRFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDA   78 (227)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEeh
Confidence            35689999999999998776544444455666666653

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=90.83  E-value=0.3  Score=49.12  Aligned_cols=44  Identities=20%  Similarity=0.280  Sum_probs=33.3

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQ  252 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q  252 (333)
                      .+++++.|+||||||.+....+.+....+.+++++=|..++...
T Consensus        42 ~~h~~i~g~tGsGKt~~i~~l~~~~~~~~~~~vi~D~kg~~~~~   85 (410)
T cd01127          42 EAHTMIIGTTGTGKTTQIRELLASIRARGDRAIIYDPNGGFVSK   85 (410)
T ss_pred             hccEEEEcCCCCCHHHHHHHHHHHHHhcCCCEEEEeCCcchhHh
Confidence            57999999999999987433333555667889998898776543

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.

>KOG0385|consensus

Probab=90.71  E-value=1  Score=48.80  Aligned_cols=107  Identities=14%  Similarity=0.067  Sum_probs=73.8

Q ss_pred             CCCCHHHHHHHHHH----HcCCcEEEEcCCCCcHHHHHH--HHHHHH-hcCCCeEEEEcccHHHHHHHHHHHHHhcCC--
Q psy2760         193 FELDVFQKQAIIKL----EEHNHVFVTAHTSAGKTVIAE--YAIALS-QNHKTRTIYTSPIKALSNQKYRDFRETFQD--  263 (333)
Q Consensus       193 f~l~~~Q~~ai~~l----~~g~~vlv~apTGSGKTl~~~--l~il~~-l~~g~ral~l~PtraLa~Q~~~~l~~~f~~--  263 (333)
                      ..++++|.+-+.=+    ..|-|+++.-.-|-|||+-.+  ++.+.. ....+.-++++|.-.|. .+.++|++..++  
T Consensus       166 g~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQtIs~l~yl~~~~~~~GPfLVi~P~StL~-NW~~Ef~rf~P~l~  244 (971)
T KOG0385|consen  166 GELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQTISLLGYLKGRKGIPGPFLVIAPKSTLD-NWMNEFKRFTPSLN  244 (971)
T ss_pred             CccchhhhccHHHHHHHHhcCcccEeehhcccchHHHHHHHHHHHHHhcCCCCCeEEEeeHhhHH-HHHHHHHHhCCCcc
Confidence            36899998876553    688899999999999998643  344433 23345678899986664 567788764454  


Q ss_pred             cEEEeCCCCCC----------CCcceEEecc-------------CcceEecccccccccc
Q psy2760         264 VGLIDDLPPVF----------PDVEKLLEDL-------------NIGGLDELSIHDFNKH  300 (333)
Q Consensus       264 vglltGd~~~~----------~~a~ili~t~-------------~i~liViDe~H~~~~~  300 (333)
                      +.++.|+...+          ..-.+++.+.             +-.++|+||.|.+...
T Consensus       245 ~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~dk~~lk~~~W~ylvIDEaHRiKN~  304 (971)
T KOG0385|consen  245 VVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKDKSFLKKFNWRYLVIDEAHRIKNE  304 (971)
T ss_pred             eEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhhHHHHhcCCceEEEechhhhhcch
Confidence            67788875421          1234555554             4467999999998655

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=90.59  E-value=0.16  Score=49.96  Aligned_cols=22  Identities=23%  Similarity=0.439  Sum_probs=18.6

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l  228 (333)
                      ++.-|+++.||||||||+.+.-
T Consensus        95 L~KSNILLiGPTGsGKTlLAqT  116 (408)
T COG1219          95 LSKSNILLIGPTGSGKTLLAQT  116 (408)
T ss_pred             eeeccEEEECCCCCcHHHHHHH
Confidence            3456999999999999998854

>PRK05642 DNA replication initiation factor; Validated

Probab=90.46  E-value=0.42  Score=44.28  Aligned_cols=42  Identities=10%  Similarity=0.212  Sum_probs=28.3

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQ  252 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q  252 (333)
                      ..++++||+|+|||.............+.+++|+.. ..+...
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~~-~~~~~~   87 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPL-AELLDR   87 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEeeH-HHHHhh
Confidence            568899999999998744332233445778888654 555543

>TIGR00959 ffh signal recognition particle protein

Probab=90.35  E-value=0.75  Score=46.81  Aligned_cols=52  Identities=6%  Similarity=0.132  Sum_probs=35.4

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHh-cCCCeEEEEc--ccHHHHHHHHHHHHHhc
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQ-NHKTRTIYTS--PIKALSNQKYRDFRETF  261 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l-~~g~ral~l~--PtraLa~Q~~~~l~~~f  261 (333)
                      ..++++|++|+|||.++.-.+.... ..|.+++++.  +.|.-+.++.+.+.+..
T Consensus       100 ~vi~~vG~~GsGKTTtaakLA~~l~~~~g~kV~lV~~D~~R~~a~~QL~~~a~~~  154 (428)
T TIGR00959       100 TVILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLVACDLYRPAAIEQLKVLGQQV  154 (428)
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHhCCCeEEEEeccccchHHHHHHHHHHHhc
Confidence            3678899999999998766444432 4567777664  45666666666665543

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.

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=90.30  E-value=0.6  Score=46.72  Aligned_cols=56  Identities=14%  Similarity=0.133  Sum_probs=36.4

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHH-HhcCC-CeEEEEc--ccHHHHHHHHHHHHHhcC
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIAL-SQNHK-TRTIYTS--PIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~-~l~~g-~ral~l~--PtraLa~Q~~~~l~~~f~  262 (333)
                      ..|..+++.||||+|||......... ....| .++.++.  +.|.=+.++.+.+.+.++
T Consensus       135 ~~g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~g  194 (374)
T PRK14722        135 ERGGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILG  194 (374)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcC
Confidence            34789999999999999987654433 23434 3554443  235456677777766554

>PRK08939 primosomal protein DnaI; Reviewed

Probab=90.21  E-value=0.75  Score=44.62  Aligned_cols=46  Identities=4%  Similarity=0.039  Sum_probs=31.2

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKY  254 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~  254 (333)
                      .++.+++.||+|+|||..+....-.....|.++.|+. .-+|+.++.
T Consensus       155 ~~~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~-~~~l~~~lk  200 (306)
T PRK08939        155 KVKGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLH-FPEFIRELK  200 (306)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEE-HHHHHHHHH
Confidence            3568999999999999887654444456677777663 224444443

>KOG0925|consensus

Probab=90.18  E-value=0.72  Score=47.64  Aligned_cols=66  Identities=14%  Similarity=0.180  Sum_probs=45.3

Q ss_pred             CHHHHHHHHHHHcCCcEEEEcCCCCcHHHHH-HHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy2760         196 DVFQKQAIIKLEEHNHVFVTAHTSAGKTVIA-EYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETF  261 (333)
Q Consensus       196 ~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~-~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f  261 (333)
                      +..+.+-+..+..+..+++.|.||||||.-. ...+...+.....+...-|.|--|.++..+..+-.
T Consensus        49 w~~k~~F~~~l~~nQ~~v~vGetgsGKttQiPq~~~~~~~~~~~~v~CTQprrvaamsva~RVadEM  115 (699)
T KOG0925|consen   49 WEQKEEFLKLLLNNQIIVLVGETGSGKTTQIPQFVLEYELSHLTGVACTQPRRVAAMSVAQRVADEM  115 (699)
T ss_pred             HHhHHHHHHHHhcCceEEEEecCCCCccccCcHHHHHHHHhhccceeecCchHHHHHHHHHHHHHHh
Confidence            4444444455688889999999999999642 22333334444667778899988888888776543

>cd01131 PilT Pilus retraction ATPase PilT

Probab=90.16  E-value=0.44  Score=42.90  Aligned_cols=18  Identities=33%  Similarity=0.374  Sum_probs=15.1

Q ss_pred             cEEEEcCCCCcHHHHHHH
Q psy2760         211 HVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l  228 (333)
                      -++++||||||||.....
T Consensus         3 lilI~GptGSGKTTll~~   20 (198)
T cd01131           3 LVLVTGPTGSGKSTTLAA   20 (198)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            478999999999998643

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.

>PRK06893 DNA replication initiation factor; Validated

Probab=89.96  E-value=0.47  Score=43.69  Aligned_cols=36  Identities=14%  Similarity=0.169  Sum_probs=26.4

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcc
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSP  245 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~P  245 (333)
                      ..++++||+|+|||.......-....++.+++|+.-
T Consensus        40 ~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~   75 (229)
T PRK06893         40 PFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPL   75 (229)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeH
Confidence            357899999999998766554444556777887654

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=89.94  E-value=0.7  Score=46.66  Aligned_cols=89  Identities=22%  Similarity=0.179  Sum_probs=54.9

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-cEEEeCCCCCCCCcceEEeccC
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-VGLIDDLPPVFPDVEKLLEDLN  285 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-vglltGd~~~~~~a~ili~t~~  285 (333)
                      -.|.+|++.|+||.||++++...-....+......+-+..-++.+....-  +.||- -|.+||-......   ++...+
T Consensus        99 p~~~~vLi~GetGtGKel~A~~iH~~s~r~~~~PFI~~NCa~~~en~~~~--eLFG~~kGaftGa~~~k~G---lfe~A~  173 (403)
T COG1221          99 PSGLPVLIIGETGTGKELFARLIHALSARRAEAPFIAFNCAAYSENLQEA--ELFGHEKGAFTGAQGGKAG---LFEQAN  173 (403)
T ss_pred             CCCCcEEEecCCCccHHHHHHHHHHhhhcccCCCEEEEEHHHhCcCHHHH--HHhccccceeecccCCcCc---hheecC
Confidence            46899999999999999998764432222122233334554544443322  26875 5889984333221   344556


Q ss_pred             cceEecccccccccc
Q psy2760         286 IGGLDELSIHDFNKH  300 (333)
Q Consensus       286 i~liViDe~H~~~~~  300 (333)
                      =+.+..||+|.+...
T Consensus       174 GGtLfLDEI~~LP~~  188 (403)
T COG1221         174 GGTLFLDEIHRLPPE  188 (403)
T ss_pred             CCEEehhhhhhCCHh
Confidence            677788999987544

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=89.93  E-value=0.64  Score=42.00  Aligned_cols=40  Identities=13%  Similarity=0.052  Sum_probs=31.0

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCC------CeEEEEcccH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHK------TRTIYTSPIK  247 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g------~ral~l~Ptr  247 (333)
                      .|.-+.+.||+|+|||..+...+......+      .+++|+....
T Consensus        18 ~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~   63 (226)
T cd01393          18 TGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEG   63 (226)
T ss_pred             CCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCC
Confidence            367889999999999999887665555555      7889987543

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=89.93  E-value=0.76  Score=46.79  Aligned_cols=51  Identities=12%  Similarity=0.099  Sum_probs=35.5

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc--ccHHHHHHHHHHHHHh
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS--PIKALSNQKYRDFRET  260 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~--PtraLa~Q~~~~l~~~  260 (333)
                      .-++++|++|+|||..+.-........|.+++++.  |.|.-+.++.+.+.+.
T Consensus       101 ~vi~lvG~~GvGKTTtaaKLA~~l~~~G~kV~lV~~D~~R~aA~eQLk~~a~~  153 (429)
T TIGR01425       101 NVIMFVGLQGSGKTTTCTKLAYYYQRKGFKPCLVCADTFRAGAFDQLKQNATK  153 (429)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEcCcccchhHHHHHHHHhhc
Confidence            46789999999998776543333445577777665  5677777777766654

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.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=89.77  E-value=1.1  Score=43.74  Aligned_cols=97  Identities=18%  Similarity=0.093  Sum_probs=53.4

Q ss_pred             HHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-cEEEeCCCCCCCC
Q psy2760         198 FQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-VGLIDDLPPVFPD  276 (333)
Q Consensus       198 ~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-vglltGd~~~~~~  276 (333)
                      ...++-.....+.+|++.|++|+||+.++-..-....+ ..+..+.+...++.....+.  ..|+. -|.++|.......
T Consensus        11 ~~~~~~~~a~~~~pVLI~GE~GtGK~~lAr~iH~~s~r-~~~pfv~vnc~~~~~~~l~~--~lfG~~~g~~~ga~~~~~G   87 (329)
T TIGR02974        11 VLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYLSKR-WQGPLVKLNCAALSENLLDS--ELFGHEAGAFTGAQKRHQG   87 (329)
T ss_pred             HHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHhcCc-cCCCeEEEeCCCCChHHHHH--HHhccccccccCcccccCC
Confidence            33444444567889999999999999987643322222 23345555554444433322  24654 4556665432211


Q ss_pred             cceEEeccCcceEecccccccccc
Q psy2760         277 VEKLLEDLNIGGLDELSIHDFNKH  300 (333)
Q Consensus       277 a~ili~t~~i~liViDe~H~~~~~  300 (333)
                         .+...+-+.+.+||++.+...
T Consensus        88 ---~~~~a~gGtL~Ldei~~L~~~  108 (329)
T TIGR02974        88 ---RFERADGGTLFLDELATASLL  108 (329)
T ss_pred             ---chhhCCCCEEEeCChHhCCHH
Confidence               122234466778888876543

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=89.32  E-value=0.84  Score=47.05  Aligned_cols=53  Identities=19%  Similarity=0.198  Sum_probs=40.7

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      .|..+++.+++|+|||..+...+......|.+++|++-. +-..|+.+.+.. |+
T Consensus       272 ~g~~~li~G~~G~GKT~l~~~~~~~~~~~g~~~~yis~e-~~~~~i~~~~~~-~g  324 (509)
T PRK09302        272 RGSIILVSGATGTGKTLLASKFAEAACRRGERCLLFAFE-ESRAQLIRNARS-WG  324 (509)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEEec-CCHHHHHHHHHH-cC
Confidence            467889999999999999887776677788999998644 446677666643 44

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]

Probab=89.32  E-value=0.93  Score=48.04  Aligned_cols=67  Identities=15%  Similarity=0.153  Sum_probs=54.1

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCC----CeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHK----TRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g----~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      .+++-|++|+...  ...++|.|..|||||.+...-+.+....+    .+++.++=|+.-|.++.+++.+.++
T Consensus         2 ~Ln~~Q~~av~~~--~gp~lV~AGaGsGKT~vlt~Ria~li~~~~v~p~~Il~vTFTnkAA~em~~Rl~~~~~   72 (655)
T COG0210           2 KLNPEQREAVLHP--DGPLLVLAGAGSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKAAAEMRERLLKLLG   72 (655)
T ss_pred             CCCHHHHHHHhcC--CCCeEEEECCCCCchhhHHHHHHHHHHcCCcChHHeeeeechHHHHHHHHHHHHHHhC
Confidence            4789999998764  56889999999999999888776554332    3588888999999999999988765

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=89.28  E-value=0.77  Score=51.02  Aligned_cols=80  Identities=18%  Similarity=0.101  Sum_probs=51.7

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHH---HHhcC-CcEE
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDF---RETFQ-DVGL  266 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l---~~~f~-~vgl  266 (333)
                      |...++..|.-.--.+.+|+  +.-..||-|||+++.+|+......|..|-+|+..-=||.-=.+.+   .+.+| .||+
T Consensus       135 wdm~~ydVQLiGgivLh~G~--IAEM~TGEGKTLvatlp~yLnAL~G~gVHvVTvNDYLA~RDaewm~p~y~flGLtVg~  212 (1025)
T PRK12900        135 WDMVPYDVQLIGGIVLHSGK--ISEMATGEGKTLVSTLPTFLNALTGRGVHVVTVNDYLAQRDKEWMNPVFEFHGLSVGV  212 (1025)
T ss_pred             cCccccchHHhhhHHhhcCC--ccccCCCCCcchHhHHHHHHHHHcCCCcEEEeechHhhhhhHHHHHHHHHHhCCeeee
Confidence            34466666666555566665  568999999999999998765556666766666656665433333   33333 2676


Q ss_pred             EeCCCC
Q psy2760         267 IDDLPP  272 (333)
Q Consensus       267 ltGd~~  272 (333)
                      +..+..
T Consensus       213 i~~~~~  218 (1025)
T PRK12900        213 ILNTMR  218 (1025)
T ss_pred             eCCCCC
Confidence            655443

>COG0630 VirB11 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=89.20  E-value=0.97  Score=43.98  Aligned_cols=33  Identities=18%  Similarity=0.298  Sum_probs=25.0

Q ss_pred             CCHHHHHHHHH-HHcCCcEEEEcCCCCcHHHHHH
Q psy2760         195 LDVFQKQAIIK-LEEHNHVFVTAHTSAGKTVIAE  227 (333)
Q Consensus       195 l~~~Q~~ai~~-l~~g~~vlv~apTGSGKTl~~~  227 (333)
                      +.+.|..-+.. +..++++++||+||||||..-.
T Consensus       128 ~~~~~~ayL~~~ie~~~siii~G~t~sGKTt~ln  161 (312)
T COG0630         128 ISPEQAAYLWLAIEARKSIIICGGTASGKTTLLN  161 (312)
T ss_pred             CCHHHHHHHHHHHHcCCcEEEECCCCCCHHHHHH
Confidence            45555555444 5889999999999999997643

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=89.14  E-value=0.84  Score=50.98  Aligned_cols=77  Identities=18%  Similarity=0.157  Sum_probs=49.6

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHH---HhcC-CcEE
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFR---ETFQ-DVGL  266 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~---~~f~-~vgl  266 (333)
                      |...++..|.-.--.+.+|+  +.-..||-|||+++.+|+......|..|-+|+..-=||.-=.+.+.   +.+| .||+
T Consensus       166 W~m~~yDVQliGgivLh~G~--IAEM~TGEGKTLvAtlp~yLnAL~GkgVHvVTVNDYLA~RDaewmgply~fLGLsvg~  243 (1112)
T PRK12901        166 WDMVHYDVQLIGGVVLHQGK--IAEMATGEGKTLVATLPVYLNALTGNGVHVVTVNDYLAKRDSEWMGPLYEFHGLSVDC  243 (1112)
T ss_pred             CCCcccchHHhhhhhhcCCc--eeeecCCCCchhHHHHHHHHHHHcCCCcEEEEechhhhhccHHHHHHHHHHhCCceee
Confidence            44456666655544456664  6799999999999999887665566677777766667754443333   3333 2665


Q ss_pred             EeC
Q psy2760         267 IDD  269 (333)
Q Consensus       267 ltG  269 (333)
                      +..
T Consensus       244 i~~  246 (1112)
T PRK12901        244 IDK  246 (1112)
T ss_pred             cCC
Confidence            544

>PRK14974 cell division protein FtsY; Provisional

Probab=89.06  E-value=1.2  Score=43.91  Aligned_cols=53  Identities=9%  Similarity=0.091  Sum_probs=34.1

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcc--cHHHHHHHHHHHHHhcC
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSP--IKALSNQKYRDFRETFQ  262 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~P--traLa~Q~~~~l~~~f~  262 (333)
                      .-++++|++|+|||....-.+......|.+++++..  .|+=+.++.+.+.+.++
T Consensus       141 ~vi~~~G~~GvGKTTtiakLA~~l~~~g~~V~li~~Dt~R~~a~eqL~~~a~~lg  195 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTIAKLAYYLKKNGFSVVIAAGDTFRAGAIEQLEEHAERLG  195 (336)
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEecCCcCcHHHHHHHHHHHHHcC
Confidence            467889999999998765544444455677776653  35555555555555443

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=89.06  E-value=1.1  Score=47.98  Aligned_cols=51  Identities=25%  Similarity=0.310  Sum_probs=41.1

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccH--HHHHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIK--ALSNQKYRDFRE  259 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Ptr--aLa~Q~~~~l~~  259 (333)
                      ..+.+|.|+||+|||......+.+..+.|.+++++=|-.  +|..-++...+.
T Consensus       180 ~gHtlV~GtTGsGKT~l~~~li~q~i~~g~~vi~fDpkgD~el~~~~~~~~~~  232 (643)
T TIGR03754       180 VGHTLVLGTTRVGKTRLAELLITQDIRRGDVVIVFDPKGDADLLKRMYAEAKR  232 (643)
T ss_pred             cCceEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCCCHHHHHHHHHHHHH
Confidence            568999999999999999988888888888899988875  456566555544

Members of this protein are assigned by homology to the TraD family of conjugative coupling factor. This particular clade serves as a marker for an extended gene region that occurs occasionally on plasmids, including the toluene catabolism TOL plasmid. More commonly, the gene region is chromosomal, flanked by various markers of conjugative transfer and insertion.

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=88.94  E-value=3.1  Score=40.48  Aligned_cols=69  Identities=22%  Similarity=0.178  Sum_probs=51.6

Q ss_pred             CCCHHHHHHHHHHH----------cCCcEEEEcCCCCcHHHHHHHHHHHHhcCC-CeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         194 ELDVFQKQAIIKLE----------EHNHVFVTAHTSAGKTVIAEYAIALSQNHK-TRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~----------~g~~vlv~apTGSGKTl~~~l~il~~l~~g-~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      .+...|.+++--+.          .+.-.++.=.||.||--...-.|+.....| .|+|+++....|-....++|+..-.
T Consensus        37 ~LS~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~iAgiI~~n~l~Gr~r~vwvS~s~dL~~Da~RDl~DIG~  116 (303)
T PF13872_consen   37 LLSALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQIAGIILENWLRGRKRAVWVSVSNDLKYDAERDLRDIGA  116 (303)
T ss_pred             cccHHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccchhHHHHHHHHHcCCCceEEEECChhhhhHHHHHHHHhCC
Confidence            47888888876542          234567788899999877666666554444 5699999999999999999987543

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=88.79  E-value=1.1  Score=45.32  Aligned_cols=55  Identities=20%  Similarity=0.352  Sum_probs=38.2

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHh--cCCCeEEEEcccH-------HHHHHHHHHHHHhcCCc
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQ--NHKTRTIYTSPIK-------ALSNQKYRDFRETFQDV  264 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l--~~g~ral~l~Ptr-------aLa~Q~~~~l~~~f~~v  264 (333)
                      ...++++||+|+|||...-.......  .+..+++|+....       ++-+.-...|++.+ .+
T Consensus       113 ~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~se~f~~~~v~a~~~~~~~~Fk~~y-~~  176 (408)
T COG0593         113 YNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTNDFVKALRDNEMEKFKEKY-SL  176 (408)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEeccHHHHHHHHHHHHHhhhHHHHHHhh-cc
Confidence            45789999999999987655444444  3455888887654       55555666787777 53

>TIGR02746 TraC-F-type type-IV secretion system protein TraC

Probab=88.71  E-value=0.61  Score=50.54  Aligned_cols=41  Identities=12%  Similarity=0.115  Sum_probs=32.4

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKA  248 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Ptra  248 (333)
                      .+.|++|.|+||||||......+...+..|.+++++=|-.+
T Consensus       429 ~n~n~~I~G~tGsGKS~~~~~l~~~~~~~g~~v~iiD~~~s  469 (797)
T TIGR02746       429 TNYNIAVVGGSGAGKSFFMQELIVDNLSRGGKVWVIDVGRS  469 (797)
T ss_pred             CccceEEEcCCCCCHHHHHHHHHHHHHhCCCEEEEEeCCCC
Confidence            35689999999999999987766666667788888777654

The protein family described here is common among the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The protein conyains the Walker A and B motifs and so is a putative nucleotide triphosphatase.

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=88.40  E-value=0.67  Score=48.78  Aligned_cols=41  Identities=17%  Similarity=0.262  Sum_probs=29.5

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKAL  249 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraL  249 (333)
                      .+++++.|+||||||.+.-..+.+....+.+++++=|.-+.
T Consensus       176 ~~h~li~G~tGsGKs~~i~~ll~~~~~~g~~~ii~D~~g~~  216 (566)
T TIGR02759       176 TQHILIHGTTGSGKSVAIRKLLRWIRQRGDRAIIYDKGCTF  216 (566)
T ss_pred             ccceEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEEECCCCe
Confidence            57999999999999975433333445567788887776444

The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM).

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=88.35  E-value=1.8  Score=51.88  Aligned_cols=65  Identities=15%  Similarity=0.186  Sum_probs=50.0

Q ss_pred             CCCCCHHHHHHHHHHHcC--CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHH
Q psy2760         192 PFELDVFQKQAIIKLEEH--NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRD  256 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~g--~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~  256 (333)
                      .|.+++-|++|+..++..  +-.++.|+.|+|||.+....+......|.+++.++||-.-+.++.+.
T Consensus       427 ~~~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~l~~l~~~~~~~G~~V~~lAPTgrAA~~L~e~  493 (1960)
T TIGR02760       427 EFALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEIAQLLLHLASEQGYEIQIITAGSLSAQELRQK  493 (1960)
T ss_pred             cCCCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHHHHHHHHHHHhcCCeEEEEeCCHHHHHHHHHH
Confidence            467899999999997553  67899999999999886554444445688999999997655555443

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.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=88.33  E-value=0.7  Score=45.34  Aligned_cols=41  Identities=17%  Similarity=0.105  Sum_probs=26.3

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHhc--CCCeEEEEcccHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQN--HKTRTIYTSPIKA  248 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l~--~g~ral~l~Ptra  248 (333)
                      ..+..++++||||||||..... ++..+.  .+.+++.+--..+
T Consensus       120 ~~~g~ili~G~tGSGKTT~l~a-l~~~i~~~~~~~i~tiEdp~E  162 (343)
T TIGR01420       120 RPRGLILVTGPTGSGKSTTLAS-MIDYINKNAAGHIITIEDPIE  162 (343)
T ss_pred             hcCcEEEEECCCCCCHHHHHHH-HHHhhCcCCCCEEEEEcCChh
Confidence            3467899999999999988643 333332  2455665543333

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.

>PRK13764 ATPase; Provisional

Probab=88.24  E-value=0.72  Score=48.88  Aligned_cols=22  Identities=23%  Similarity=0.430  Sum_probs=18.3

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l  228 (333)
                      ..+++++++||||||||.....
T Consensus       255 ~~~~~ILIsG~TGSGKTTll~A  276 (602)
T PRK13764        255 ERAEGILIAGAPGAGKSTFAQA  276 (602)
T ss_pred             hcCCEEEEECCCCCCHHHHHHH
Confidence            4578999999999999987633

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=88.18  E-value=0.64  Score=47.89  Aligned_cols=51  Identities=12%  Similarity=0.214  Sum_probs=37.5

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcC-CCeEEEEcccHHHHHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNH-KTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~-g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      .|..+++.|++|+|||..+..-+...+.+ |.+++|++ +-+-..|+.+.+..
T Consensus        30 ~Gs~~li~G~pGsGKT~l~~qf~~~~~~~~ge~~lyis-~ee~~~~i~~~~~~   81 (509)
T PRK09302         30 KGRPTLVSGTAGTGKTLFALQFLVNGIKRFDEPGVFVT-FEESPEDIIRNVAS   81 (509)
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCEEEEE-ccCCHHHHHHHHHH
Confidence            37889999999999999987766555555 88899885 33455566666544

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=88.11  E-value=0.83  Score=51.82  Aligned_cols=55  Identities=13%  Similarity=0.154  Sum_probs=44.4

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcC---CCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNH---KTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~---g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      ..++++|.|+.|||||.+-..-++..+..   ..++++|+-|+.=|.++..++.+.+.
T Consensus         9 p~~~~~~~a~agsgkt~~l~~~~~~~~~~~~~~~~i~~~t~t~~aa~em~~Ri~~~L~   66 (1141)
T TIGR02784         9 PKTSAWVSANAGSGKTHVLTQRVIRLLLNGVPPSKILCLTYTKAAAAEMQNRVFDRLG   66 (1141)
T ss_pred             CCCCEEEEEECCCCHHHHHHHHHHHHHHcCCCCCeEEEEecCHHHHHHHHHHHHHHHH
Confidence            36799999999999999887766644432   36799999999999999988877664

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 alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species.

>PF02374 ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_A 3IBG_B 3SJA_A 3H84_B 3SJD_A 3ZS9_A 3A37_A 2WOJ_A 3SJC_B 3A36_B

Probab=88.03  E-value=0.93  Score=43.90  Aligned_cols=42  Identities=26%  Similarity=0.353  Sum_probs=32.8

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc--ccHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS--PIKALSN  251 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~--PtraLa~  251 (333)
                      +-+++.|.-|.|||.++....+...+.|.|+++++  |...|.+
T Consensus         2 r~~~~~GKGGVGKTT~aaA~A~~~A~~G~rtLlvS~Dpa~~L~d   45 (305)
T PF02374_consen    2 RILFFGGKGGVGKTTVAAALALALARRGKRTLLVSTDPAHSLSD   45 (305)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEESSTTTHHHH
T ss_pred             eEEEEecCCCCCcHHHHHHHHHHHhhCCCCeeEeecCCCccHHH
Confidence            45788999999999999887776667889998885  7766654

...

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=88.02  E-value=2.8  Score=42.95  Aligned_cols=66  Identities=9%  Similarity=0.161  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHH-----cC----CcEEEEcCCCCcHHHHHHHHHHHHh----cCCCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         197 VFQKQAIIKLE-----EH----NHVFVTAHTSAGKTVIAEYAIALSQ----NHKTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       197 ~~Q~~ai~~l~-----~g----~~vlv~apTGSGKTl~~~l~il~~l----~~g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      |||+-.+..+.     .|    +.+++.-|=+.|||.......+..+    ..+..++++++++.-|..++..++....
T Consensus         1 PwQ~fi~~~i~G~~~~~g~rrf~~~~l~v~RkNGKS~l~a~i~ly~l~~~g~~~~~i~~~A~~~~QA~~~f~~~~~~i~   79 (477)
T PF03354_consen    1 PWQKFILRSIFGWRKDDGRRRFREVYLEVPRKNGKSTLAAAIALYMLFLDGEPGAEIYCAANTRDQAKIVFDEAKKMIE   79 (477)
T ss_pred             CcHHHHHHHHhceEcCCCCEEEEEEEEEEcCccCccHHHHHHHHHHHhcCCccCceEEEEeCCHHHHHHHHHHHHHHHH
Confidence            46666665543     12    4678889999999988765444332    2467899999999999999988877554

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>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=87.82  E-value=1.4  Score=41.35  Aligned_cols=20  Identities=25%  Similarity=0.419  Sum_probs=16.7

Q ss_pred             CcEEEEcCCCCcHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~  229 (333)
                      .+++.+||.|.|||..+.+-
T Consensus        51 ~h~lf~GPPG~GKTTLA~II   70 (233)
T PF05496_consen   51 DHMLFYGPPGLGKTTLARII   70 (233)
T ss_dssp             -EEEEESSTTSSHHHHHHHH
T ss_pred             ceEEEECCCccchhHHHHHH
Confidence            37999999999999887653

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.

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=87.81  E-value=0.39  Score=38.72  Aligned_cols=19  Identities=26%  Similarity=0.310  Sum_probs=16.1

Q ss_pred             EEEEcCCCCcHHHHHHHHH
Q psy2760         212 VFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       212 vlv~apTGSGKTl~~~l~i  230 (333)
                      |+++|++|||||.++....
T Consensus         1 I~i~G~~GsGKtTia~~L~   19 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELA   19 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHH
Confidence            6899999999999986643

...

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=87.74  E-value=0.52  Score=38.09  Aligned_cols=20  Identities=15%  Similarity=0.380  Sum_probs=16.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHH
Q psy2760         212 VFVTAHTSAGKTVIAEYAIA  231 (333)
Q Consensus       212 vlv~apTGSGKTl~~~l~il  231 (333)
                      ++++|++|||||.++-...-
T Consensus         2 I~I~G~~gsGKST~a~~La~   21 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAE   21 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999876543

...

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=87.72  E-value=0.99  Score=39.94  Aligned_cols=45  Identities=18%  Similarity=0.259  Sum_probs=30.9

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l  257 (333)
                      +.+++.|++|||||..+...+..   .+.+++|++.....-.++.+++
T Consensus         2 ~~ili~G~~~sGKS~~a~~l~~~---~~~~~~~iat~~~~~~e~~~ri   46 (170)
T PRK05800          2 MLILVTGGARSGKSRFAERLAAQ---SGLQVLYIATAQPFDDEMAARI   46 (170)
T ss_pred             CEEEEECCCCccHHHHHHHHHHH---cCCCcEeCcCCCCChHHHHHHH
Confidence            46899999999999988765432   2446788876555555554444

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=87.71  E-value=1.6  Score=48.09  Aligned_cols=23  Identities=26%  Similarity=0.300  Sum_probs=18.7

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      ...|+++.||+|.|||.++...+
T Consensus       193 ~~~n~lL~G~pGvGKT~l~~~la  215 (852)
T TIGR03346       193 TKNNPVLIGEPGVGKTAIVEGLA  215 (852)
T ss_pred             CCCceEEEcCCCCCHHHHHHHHH
Confidence            34589999999999999886543

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.

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=87.55  E-value=1  Score=40.93  Aligned_cols=38  Identities=13%  Similarity=0.142  Sum_probs=29.0

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcC------CCeEEEEcc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNH------KTRTIYTSP  245 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~------g~ral~l~P  245 (333)
                      .|.-+.++||+|+|||..+...+.....+      +.+++|+.-
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~   61 (235)
T cd01123          18 TGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDT   61 (235)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeC
Confidence            47788999999999999988766543332      367888863

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=87.55  E-value=0.68  Score=49.16  Aligned_cols=57  Identities=14%  Similarity=-0.053  Sum_probs=42.7

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-cEEEe
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-VGLID  268 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-vgllt  268 (333)
                      ..++++.||||||||..+.+|-+...  +..+|++=|--++........++ +|. |-++.
T Consensus       158 ~~hvLviapTgSGKg~g~VIPnLL~~--~~S~VV~DpKGEl~~~Ta~~R~~-~G~~V~vfd  215 (606)
T PRK13897        158 FQHALLFAPTGSGKGVGFVIPNLLFW--EDSVVVHDIKLENYELTSGWREK-QGQKVFVWE  215 (606)
T ss_pred             CceEEEEcCCCCCcceEEehhhHHhC--CCCEEEEeCcHHHHHHHHHHHHH-CCCeEEEEe
Confidence            46899999999999999999877543  45677778888888777755544 664 65543

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=87.42  E-value=0.51  Score=44.94  Aligned_cols=25  Identities=20%  Similarity=0.349  Sum_probs=21.0

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHHHHH
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      +..+++++++||+|+|||......+
T Consensus        30 ~~~~~pvLl~G~~GtGKT~li~~~l   54 (272)
T PF12775_consen   30 LSNGRPVLLVGPSGTGKTSLIQNFL   54 (272)
T ss_dssp             HHCTEEEEEESSTTSSHHHHHHHHH
T ss_pred             HHcCCcEEEECCCCCchhHHHHhhh
Confidence            3788999999999999998766543

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=87.41  E-value=1.5  Score=44.58  Aligned_cols=47  Identities=15%  Similarity=0.237  Sum_probs=30.1

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhc--CCCeEEEEcccHHHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQN--HKTRTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~--~g~ral~l~PtraLa~Q~~~~l  257 (333)
                      ..++++||+|+|||.......-....  .+.+++|+. ...+.++....+
T Consensus       149 ~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~-~~~~~~~~~~~~  197 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVT-SEKFTNDFVNAL  197 (450)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEE-HHHHHHHHHHHH
Confidence            46899999999999876543333332  366788774 445555544443

>PRK11823 DNA repair protein RadA; Provisional

Probab=87.38  E-value=1.2  Score=45.40  Aligned_cols=87  Identities=13%  Similarity=0.024  Sum_probs=51.7

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC----cEEEeCCCCCCCCcceEEec
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD----VGLIDDLPPVFPDVEKLLED  283 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~~~~~a~ili~t  283 (333)
                      .|.-+++.|++|+|||...+..+......+.+++|+.-. +-..|+..+..+ ++-    +.+. .......-.. .+..
T Consensus        79 ~Gs~~lI~G~pG~GKTtL~lq~a~~~a~~g~~vlYvs~E-es~~qi~~ra~r-lg~~~~~l~~~-~e~~l~~i~~-~i~~  154 (446)
T PRK11823         79 PGSVVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVSGE-ESASQIKLRAER-LGLPSDNLYLL-AETNLEAILA-TIEE  154 (446)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEcc-ccHHHHHHHHHH-cCCChhcEEEe-CCCCHHHHHH-HHHh
Confidence            367889999999999998877655544567899998743 445666665543 331    2211 1111100000 0111


Q ss_pred             cCcceEecccccccc
Q psy2760         284 LNIGGLDELSIHDFN  298 (333)
Q Consensus       284 ~~i~liViDe~H~~~  298 (333)
                      .+..++|+|+++.+.
T Consensus       155 ~~~~lVVIDSIq~l~  169 (446)
T PRK11823        155 EKPDLVVIDSIQTMY  169 (446)
T ss_pred             hCCCEEEEechhhhc
Confidence            256778999998654

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=87.16  E-value=2.1  Score=51.37  Aligned_cols=63  Identities=22%  Similarity=0.145  Sum_probs=46.7

Q ss_pred             CCCCCHHHHHHHHHHHc--CCcEEEEcCCCCcHHHHHH---HHHHHHh-cCCCeEEEEcccHHHHHHHH
Q psy2760         192 PFELDVFQKQAIIKLEE--HNHVFVTAHTSAGKTVIAE---YAIALSQ-NHKTRTIYTSPIKALSNQKY  254 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~--g~~vlv~apTGSGKTl~~~---l~il~~l-~~g~ral~l~PtraLa~Q~~  254 (333)
                      .+.+++.|++|+..++.  ++.+++.|+.|+|||.+..   -++.... ..+.+++.++||..=+.++.
T Consensus      1017 ~~~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~~g~~v~glApT~~Aa~~L~ 1085 (1960)
T TIGR02760      1017 LERLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFESEQLQVIGLAPTHEAVGELK 1085 (1960)
T ss_pred             cCCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHhcCCeEEEEeChHHHHHHHH
Confidence            35789999999999754  4677889999999998873   2333333 35778999999966665553

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.

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=87.08  E-value=1.1  Score=37.18  Aligned_cols=20  Identities=25%  Similarity=0.331  Sum_probs=17.1

Q ss_pred             cEEEEcCCCCcHHHHHHHHH
Q psy2760         211 HVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~i  230 (333)
                      +|++.||+|+|||..+....
T Consensus         1 ~vlL~G~~G~GKt~l~~~la   20 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELA   20 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHH
Confidence            58999999999999887644

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=87.07  E-value=1.3  Score=45.13  Aligned_cols=45  Identities=13%  Similarity=0.296  Sum_probs=30.4

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYR  255 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~  255 (333)
                      ..++++||+|+|||..+....-.....+.+++|+.. ..+.++...
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~-~~f~~~~~~  186 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRS-ELFTEHLVS  186 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeH-HHHHHHHHH
Confidence            468999999999998766433333445788888764 344444433

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=86.96  E-value=1.5  Score=43.68  Aligned_cols=46  Identities=20%  Similarity=0.250  Sum_probs=29.0

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHh--cCCCeEEEEcccHHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQ--NHKTRTIYTSPIKALSNQKYRD  256 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l--~~g~ral~l~PtraLa~Q~~~~  256 (333)
                      ..++++||+|+|||.......-...  ..+.+++|+.. ..+..+....
T Consensus       137 n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~-~~~~~~~~~~  184 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSS-EKFTNDFVNA  184 (405)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEH-HHHHHHHHHH
Confidence            4678999999999988744332222  23677888753 3444444433

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).

>PRK04195 replication factor C large subunit; Provisional

Probab=86.80  E-value=2.5  Score=43.33  Aligned_cols=33  Identities=15%  Similarity=0.125  Sum_probs=22.5

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS  244 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~  244 (333)
                      .+.++++||+|+|||.++...+- .+  +..++.+-
T Consensus        39 ~~~lLL~GppG~GKTtla~ala~-el--~~~~ieln   71 (482)
T PRK04195         39 KKALLLYGPPGVGKTSLAHALAN-DY--GWEVIELN   71 (482)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH-Hc--CCCEEEEc
Confidence            46899999999999988754332 22  34455553

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=86.64  E-value=1.9  Score=44.58  Aligned_cols=55  Identities=11%  Similarity=0.120  Sum_probs=36.1

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHH-HHHhcCCC-eEEEEc--ccHHHHHHHHHHHHHhcC
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAI-ALSQNHKT-RTIYTS--PIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~i-l~~l~~g~-ral~l~--PtraLa~Q~~~~l~~~f~  262 (333)
                      .|.-+++.||||+|||....... ......|. ++.++.  +.|.=+.++.+.|.+.++
T Consensus       255 ~g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI~~Dt~RigA~EQLr~~AeilG  313 (484)
T PRK06995        255 RGGVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIGGHEQLRIYGKILG  313 (484)
T ss_pred             CCcEEEEECCCCccHHHHHHHHHHHHHHhcCCCeEEEEeCCccchhHHHHHHHHHHHhC
Confidence            35668899999999999875533 33344443 554442  456667777777766554

>PRK10865 protein disaggregation chaperone; Provisional

Probab=86.47  E-value=1.4  Score=48.60  Aligned_cols=24  Identities=25%  Similarity=0.285  Sum_probs=19.1

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIA  231 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il  231 (333)
                      ...|+++.||+|+|||.++.....
T Consensus       198 ~~~n~lL~G~pGvGKT~l~~~la~  221 (857)
T PRK10865        198 TKNNPVLIGEPGVGKTAIVEGLAQ  221 (857)
T ss_pred             CcCceEEECCCCCCHHHHHHHHHH
Confidence            344899999999999999865443

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=86.39  E-value=1.2  Score=50.64  Aligned_cols=56  Identities=16%  Similarity=0.186  Sum_probs=45.7

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCC-----CeEEEEcccHHHHHHHHHHHHHhcCC
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHK-----TRTIYTSPIKALSNQKYRDFRETFQD  263 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g-----~ral~l~PtraLa~Q~~~~l~~~f~~  263 (333)
                      .+.+++|.|..|||||.+-..-++..+..+     .++++++.|++=+.++..++.+++..
T Consensus        15 ~~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~~v~~ILvvTFT~aAa~Emk~RI~~~L~~   75 (1139)
T COG1074          15 PGQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRDRLKE   75 (1139)
T ss_pred             CCCcEEEEEcCCCCchhHHHHHHHHHHhhcCCCChhHeeeeeccHHHHHHHHHHHHHHHHH
Confidence            477999999999999999777666544332     46899999999999999988887764

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=86.21  E-value=7  Score=37.04  Aligned_cols=129  Identities=18%  Similarity=0.133  Sum_probs=72.5

Q ss_pred             CHHHHHHHHH----HHc---CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccH-HHHHHHHHHHHHhcCCc---
Q psy2760         196 DVFQKQAIIK----LEE---HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIK-ALSNQKYRDFRETFQDV---  264 (333)
Q Consensus       196 ~~~Q~~ai~~----l~~---g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Ptr-aLa~Q~~~~l~~~f~~v---  264 (333)
                      ...|++.+..    ...   ..|+|+.|+-|+|||-..-..+......|-|.|-|.... .-...+++.++.+-...   
T Consensus        32 ie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~~GLRlIev~k~~L~~l~~l~~~l~~~~~kFIlf  111 (249)
T PF05673_consen   32 IERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYADQGLRLIEVSKEDLGDLPELLDLLRDRPYKFILF  111 (249)
T ss_pred             HHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhhcCceEEEECHHHhccHHHHHHHHhcCCCCEEEE
Confidence            3456655544    233   369999999999998765543334445677776654331 12234445554321122   


Q ss_pred             -----------------EEEeCCCCCCCCcceEEeccCcceEec-----------cccccccccCcCcccccchhhhhhh
Q psy2760         265 -----------------GLIDDLPPVFPDVEKLLEDLNIGGLDE-----------LSIHDFNKHLKFWKPKVQLDDLFDW  316 (333)
Q Consensus       265 -----------------glltGd~~~~~~a~ili~t~~i~liVi-----------De~H~~~~~~R~~~~~~~l~~l~~l  316 (333)
                                       .++.|+....+..-++.+|.+.-.++.           +|+|..+..    ....+|.+.|.+
T Consensus       112 ~DDLsFe~~d~~yk~LKs~LeGgle~~P~NvliyATSNRRHLv~E~~~d~~~~~~~eih~~d~~----eEklSLsDRFGL  187 (249)
T PF05673_consen  112 CDDLSFEEGDTEYKALKSVLEGGLEARPDNVLIYATSNRRHLVPESFSDREDIQDDEIHPSDTI----EEKLSLSDRFGL  187 (249)
T ss_pred             ecCCCCCCCcHHHHHHHHHhcCccccCCCcEEEEEecchhhccchhhhhccCCCccccCcchHH----HHHHhHHHhCCc
Confidence                             234555555555556666765443333           234433322    123567888888


Q ss_pred             eeccCcchhhhh
Q psy2760         317 TMASDATTLEIF  328 (333)
Q Consensus       317 ~~~~d~~~~e~~  328 (333)
                      .+..-+++-|.|
T Consensus       188 ~l~F~~~~q~~Y  199 (249)
T PF05673_consen  188 WLSFYPPDQEEY  199 (249)
T ss_pred             EEEecCCCHHHH
Confidence            888877777766

>TIGR01817 nifA Nif-specific regulatory protein

Probab=86.17  E-value=3.3  Score=42.97  Aligned_cols=88  Identities=20%  Similarity=0.170  Sum_probs=48.0

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-cEEEeCCCCCCCCcceEEecc
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-VGLIDDLPPVFPDVEKLLEDL  284 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-vglltGd~~~~~~a~ili~t~  284 (333)
                      ...+.+|++.|++|+||+.++-..-....+. .+.++.+...++.....+.  ..|+. -|.++|.......   .+...
T Consensus       216 a~~~~pvli~Ge~GtGK~~lA~~ih~~s~r~-~~pfv~i~c~~~~~~~~~~--~lfg~~~~~~~~~~~~~~g---~~~~a  289 (534)
T TIGR01817       216 ARSNSTVLLRGESGTGKELIAKAIHYLSPRA-KRPFVKVNCAALSETLLES--ELFGHEKGAFTGAIAQRKG---RFELA  289 (534)
T ss_pred             hCcCCCEEEECCCCccHHHHHHHHHHhCCCC-CCCeEEeecCCCCHHHHHH--HHcCCCCCccCCCCcCCCC---ccccc
Confidence            3567899999999999999886543332222 3344444444443333322  34654 3445554322111   11222


Q ss_pred             CcceEeccccccccc
Q psy2760         285 NIGGLDELSIHDFNK  299 (333)
Q Consensus       285 ~i~liViDe~H~~~~  299 (333)
                      +-+.+.+||++.+..
T Consensus       290 ~~GtL~ldei~~L~~  304 (534)
T TIGR01817       290 DGGTLFLDEIGEISP  304 (534)
T ss_pred             CCCeEEEechhhCCH
Confidence            345677888887653

This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.

>TIGR03744 traC_PFL_4706 conjugative transfer ATPase, PFL_4706 family

Probab=86.07  E-value=0.97  Score=50.05  Aligned_cols=40  Identities=18%  Similarity=0.274  Sum_probs=32.6

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhc-CCCeEEEEcccHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQN-HKTRTIYTSPIKA  248 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~-~g~ral~l~Ptra  248 (333)
                      ..|.+|.|+||||||+.....+.+.+. .+.+++++=|-++
T Consensus       475 n~n~~I~G~TGSGKS~l~~~li~q~~~~~~~~v~IiD~g~s  515 (893)
T TIGR03744       475 NAHLLILGPTGAGKSATLTNLLMQVMAVHRPRLFIVEAGNS  515 (893)
T ss_pred             cccEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEcCCCC
Confidence            569999999999999988777766654 4788888877765

Members of this protein family are predicted ATP-binding proteins apparently associated with DNA conjugal transfer. Members are found both in plasmids and in bacterial chromosomal regions that appear to derive from integrative elements such as conjugative transposons. More distant homologs, outside the scope of this family, include type IV secretion/conjugal transfer proteins such as TraC, VirB4 and TrsE. The granularity of this protein family definition is chosen so as to represent one distinctive clade and act as a marker through which to define and recognize the class of mobile element it serves.

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=86.05  E-value=1.5  Score=38.89  Aligned_cols=41  Identities=15%  Similarity=0.183  Sum_probs=26.1

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhc-CCCeEEEEcccHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQN-HKTRTIYTSPIKALSN  251 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~-~g~ral~l~PtraLa~  251 (333)
                      .+++++||||+|||..+....- .+. .+.+.++.+-+-.+..
T Consensus         4 ~~~ll~GpsGvGKT~la~~la~-~l~~~~~~~~~~~d~s~~~~   45 (171)
T PF07724_consen    4 SNFLLAGPSGVGKTELAKALAE-LLFVGSERPLIRIDMSEYSE   45 (171)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHH-HHT-SSCCEEEEEEGGGHCS
T ss_pred             EEEEEECCCCCCHHHHHHHHHH-HhccCCccchHHHhhhcccc
Confidence            3789999999999987655332 233 4455565555544433

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>KOG2028|consensus

Probab=85.98  E-value=0.83  Score=45.85  Aligned_cols=54  Identities=22%  Similarity=0.297  Sum_probs=39.6

Q ss_pred             HHcCC--cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         206 LEEHN--HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       206 l~~g~--~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      +.+++  ++++.||.|.|||..+-+.+-.......+-+=++-|.+-++++..-|.+
T Consensus       157 ieq~~ipSmIlWGppG~GKTtlArlia~tsk~~SyrfvelSAt~a~t~dvR~ife~  212 (554)
T KOG2028|consen  157 IEQNRIPSMILWGPPGTGKTTLARLIASTSKKHSYRFVELSATNAKTNDVRDIFEQ  212 (554)
T ss_pred             HHcCCCCceEEecCCCCchHHHHHHHHhhcCCCceEEEEEeccccchHHHHHHHHH
Confidence            35554  7899999999999988776554445556677778888877777666643

>PF01580 FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR002543 The FtsK/SpoIIIE domain is found extensively in a wide variety of proteins from prokaryotes and plasmids [] some of which contain up to three copies

Probab=85.97  E-value=1.1  Score=39.97  Aligned_cols=23  Identities=17%  Similarity=0.426  Sum_probs=16.3

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIA  231 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il  231 (333)
                      ..|+++.|.||||||.+....+.
T Consensus        38 ~~h~li~G~tgsGKS~~l~~ll~   60 (205)
T PF01580_consen   38 NPHLLIAGATGSGKSTLLRTLLL   60 (205)
T ss_dssp             S-SEEEE--TTSSHHHHHHHHHH
T ss_pred             CceEEEEcCCCCCccHHHHHHHH
Confidence            45999999999999988765444

The domain contains a putative ATP binding P-loop motif. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification []. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer []. ; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0005524 ATP binding, 0007049 cell cycle, 0007059 chromosome segregation, 0051301 cell division, 0016021 integral to membrane; PDB: 2IUS_E 2IUU_A 2IUT_A.

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=85.95  E-value=2.8  Score=40.88  Aligned_cols=96  Identities=18%  Similarity=0.115  Sum_probs=50.0

Q ss_pred             HHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-cEEEeCCCCCCC
Q psy2760         197 VFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-VGLIDDLPPVFP  275 (333)
Q Consensus       197 ~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-vglltGd~~~~~  275 (333)
                      ....++-.....+.+|++.|.+|+||+.++-..-....+ ..+.++.+...++.......  ..|+. -+.++|......
T Consensus        17 ~~~~~i~~~a~~~~pVlI~GE~GtGK~~lA~~iH~~s~r-~~~pfv~v~c~~~~~~~~~~--~lfg~~~~~~~g~~~~~~   93 (326)
T PRK11608         17 EVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHYLSSR-WQGPFISLNCAALNENLLDS--ELFGHEAGAFTGAQKRHP   93 (326)
T ss_pred             HHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhCCc-cCCCeEEEeCCCCCHHHHHH--HHccccccccCCcccccC
Confidence            334444444567889999999999999988643322221 23345555554443322221  23553 344444432211


Q ss_pred             CcceEEeccCcceEecccccccc
Q psy2760         276 DVEKLLEDLNIGGLDELSIHDFN  298 (333)
Q Consensus       276 ~a~ili~t~~i~liViDe~H~~~  298 (333)
                      .   .+...+-+.+.+|+++.+.
T Consensus        94 g---~l~~a~gGtL~l~~i~~L~  113 (326)
T PRK11608         94 G---RFERADGGTLFLDELATAP  113 (326)
T ss_pred             C---chhccCCCeEEeCChhhCC
Confidence            0   1122234556677777655

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=85.74  E-value=1.2  Score=44.10  Aligned_cols=21  Identities=29%  Similarity=0.515  Sum_probs=17.8

Q ss_pred             HcCCcEEEEcCCCCcHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAE  227 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~  227 (333)
                      ..+..++++||||||||...-
T Consensus       132 ~~~glilI~GpTGSGKTTtL~  152 (358)
T TIGR02524       132 PQEGIVFITGATGSGKSTLLA  152 (358)
T ss_pred             ccCCEEEEECCCCCCHHHHHH
Confidence            357799999999999998763

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.

>PRK05541 adenylylsulfate kinase; Provisional

Probab=85.56  E-value=1.5  Score=38.17  Aligned_cols=36  Identities=22%  Similarity=0.278  Sum_probs=23.8

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEE
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYT  243 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l  243 (333)
                      .+..++++|+.|||||.++..........+..++++
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~~l~~~~~~~~~~   41 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYERLKLKYSNVIYL   41 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEE
Confidence            467899999999999999865433222233334444

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=85.48  E-value=0.77  Score=34.24  Aligned_cols=20  Identities=15%  Similarity=0.355  Sum_probs=17.0

Q ss_pred             CCcEEEEcCCCCcHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l  228 (333)
                      |...++.+++|||||.+...
T Consensus        23 g~~tli~G~nGsGKSTllDA   42 (62)
T PF13555_consen   23 GDVTLITGPNGSGKSTLLDA   42 (62)
T ss_pred             CcEEEEECCCCCCHHHHHHH
Confidence            56799999999999988654

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=85.45  E-value=0.81  Score=48.82  Aligned_cols=57  Identities=21%  Similarity=0.061  Sum_probs=40.3

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-cEEE
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-VGLI  267 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-vgll  267 (333)
                      ..++++.||||||||..+.+|-+..  -+..+|++=|--++......-.++..+. |-++
T Consensus       175 ~~HvlviapTgSGKgvg~ViPnLL~--~~~S~VV~D~KGE~~~~Tag~R~~~~G~~V~~f  232 (636)
T PRK13880        175 PEHVLTYAPTRSGKGVGLVVPTLLS--WGHSSVITDLKGELWALTAGWRQKHAKNKVLRF  232 (636)
T ss_pred             CceEEEEecCCCCCceEEEccchhh--CCCCEEEEeCcHHHHHHHHHHHHHhCCCeEEEE
Confidence            4689999999999999998877643  3556888888888875554433333443 5444

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=85.32  E-value=0.62  Score=38.62  Aligned_cols=18  Identities=17%  Similarity=0.392  Sum_probs=15.4

Q ss_pred             EEEEcCCCCcHHHHHHHH
Q psy2760         212 VFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       212 vlv~apTGSGKTl~~~l~  229 (333)
                      ++++||+|||||..+..-
T Consensus         2 ii~~G~pgsGKSt~a~~l   19 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRL   19 (143)
T ss_dssp             EEEEESTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            689999999999987653

...

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=85.31  E-value=1.2  Score=44.91  Aligned_cols=45  Identities=11%  Similarity=0.066  Sum_probs=29.2

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l  257 (333)
                      .+.++.||.|+|||.++.+..-   ..+.....+..+.+=+.++...+
T Consensus        49 ~SmIl~GPPG~GKTTlA~liA~---~~~~~f~~~sAv~~gvkdlr~i~   93 (436)
T COG2256          49 HSMILWGPPGTGKTTLARLIAG---TTNAAFEALSAVTSGVKDLREII   93 (436)
T ss_pred             ceeEEECCCCCCHHHHHHHHHH---hhCCceEEeccccccHHHHHHHH
Confidence            3889999999999998875332   22344555666655555554444

>TIGR00416 sms DNA repair protein RadA

Probab=85.31  E-value=1.8  Score=44.28  Aligned_cols=51  Identities=10%  Similarity=0.080  Sum_probs=37.4

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      .|.-+++.|++|+|||..++..+......+.+++|+... +-..|+..+..+
T Consensus        93 ~GsvilI~G~pGsGKTTL~lq~a~~~a~~g~kvlYvs~E-Es~~qi~~ra~r  143 (454)
T TIGR00416        93 PGSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGE-ESLQQIKMRAIR  143 (454)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEECc-CCHHHHHHHHHH
Confidence            467889999999999999887655555566789999765 335566655533

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=85.30  E-value=1.5  Score=38.09  Aligned_cols=35  Identities=14%  Similarity=0.131  Sum_probs=24.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEccc
Q psy2760         212 VFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPI  246 (333)
Q Consensus       212 vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Pt  246 (333)
                      +.++|++|||||......+-.....|.++.++-+.
T Consensus         2 i~i~G~~gsGKTtl~~~l~~~l~~~G~~V~viK~~   36 (155)
T TIGR00176         2 LQIVGPKNSGKTTLIERLVKALKARGYRVATIKHD   36 (155)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEecc
Confidence            46789999999998766554444456677777543

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>TIGR03783 Bac_Flav_CT_G Bacteroides conjugation system ATPase, TraG family

Probab=85.25  E-value=0.57  Score=51.49  Aligned_cols=38  Identities=11%  Similarity=0.237  Sum_probs=31.8

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSP  245 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~P  245 (333)
                      ...|.+|.|+||+|||......+.+....|.+++++=|
T Consensus       437 ~n~N~~I~G~sGsGKS~l~~~l~~~~~~~g~~vviiD~  474 (829)
T TIGR03783       437 TNRNKFILGPSGSGKSFFTNHLVRQYYEQGTHILLVDT  474 (829)
T ss_pred             ccCceEEECCCCCCHHHHHHHHHHHHHhcCCEEEEECC
Confidence            46789999999999999988777777777888877755

Members of this family include the predicted ATPase, TraG, encoded by transfer region genes of conjugative transposons of Bacteroides, such as CTnDOT, found on the main chromosome. Members also include TraG homologs borne on plasmids in Bacteroides. The protein family is related to the conjugative transfer system ATPase VirB4.

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=85.24  E-value=2.5  Score=42.69  Aligned_cols=55  Identities=16%  Similarity=0.262  Sum_probs=36.5

Q ss_pred             cCCcEEEEcCCCCcHHHH-HHHHHHHH-hcCCCeE-EEEc-ccHHHHHHHHHHHHHhcC
Q psy2760         208 EHNHVFVTAHTSAGKTVI-AEYAIALS-QNHKTRT-IYTS-PIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~-~~l~il~~-l~~g~ra-l~l~-PtraLa~Q~~~~l~~~f~  262 (333)
                      +++.+.+.||||.|||.. +-+|.... +....++ ++.. -+|-=|.++.+.+.+..+
T Consensus       202 ~~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA~EQLk~Ya~im~  260 (407)
T COG1419         202 QKRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQLKTYADIMG  260 (407)
T ss_pred             cCcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhHHHHHHHHHHHhC
Confidence            378899999999999987 44444444 3344444 3333 347777777777766654

>COG3451 VirB4 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]

Probab=85.22  E-value=1  Score=49.34  Aligned_cols=39  Identities=21%  Similarity=0.298  Sum_probs=29.7

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcCC-CeEEEEcccHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNHK-TRTIYTSPIKA  248 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~g-~ral~l~Ptra  248 (333)
                      .|.+|+||||+|||+...+.+.++.+.+ .+++++=+-+.
T Consensus       437 ghT~I~G~tGaGKTvLl~~llaq~~k~~~~~iv~fDk~~g  476 (796)
T COG3451         437 GHTLIIGPTGAGKTVLLSFLLAQALKYGNPQIVAFDKDNG  476 (796)
T ss_pred             CCeEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEcCCCc
Confidence            4899999999999998877777666555 66676655544

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain

Probab=85.22  E-value=1.9  Score=32.36  Aligned_cols=33  Identities=24%  Similarity=0.309  Sum_probs=24.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc
Q psy2760         212 VFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS  244 (333)
Q Consensus       212 vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~  244 (333)
                      +++++..|+|||..+...+......|.+++++-
T Consensus         2 ~~~~g~~G~Gktt~~~~l~~~l~~~g~~v~~~~   34 (99)
T cd01983           2 IVVTGKGGVGKTTLAANLAAALAKRGKRVLLID   34 (99)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEC
Confidence            467788899999998775554445677887766

Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=85.16  E-value=1.7  Score=45.55  Aligned_cols=53  Identities=13%  Similarity=0.189  Sum_probs=32.2

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHH-HHHhcC-CCeEEEEc--ccHHHHHHHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAI-ALSQNH-KTRTIYTS--PIKALSNQKYRDFRE  259 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~i-l~~l~~-g~ral~l~--PtraLa~Q~~~~l~~  259 (333)
                      ..|+.+.++||||+|||..+...+ ...... +.++.++.  +.|.-+.++...+.+
T Consensus       348 ~~G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtDtyRigA~EQLk~ya~  404 (559)
T PRK12727        348 ERGGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHSYGR  404 (559)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEecccccccHHHHHHHhhc
Confidence            357889999999999998875433 223332 34555543  456555555544433

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=85.11  E-value=0.95  Score=41.67  Aligned_cols=30  Identities=23%  Similarity=0.356  Sum_probs=20.7

Q ss_pred             HHHHHHH-HHcCCcEEEEcCCCCcHHHHHHH
Q psy2760         199 QKQAIIK-LEEHNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       199 Q~~ai~~-l~~g~~vlv~apTGSGKTl~~~l  228 (333)
                      .++|+.. +..++++++.||.|+|||..+..
T Consensus        11 aKrAL~iAAaG~h~lLl~GppGtGKTmlA~~   41 (206)
T PF01078_consen   11 AKRALEIAAAGGHHLLLIGPPGTGKTMLARR   41 (206)
T ss_dssp             HHHHHHHHHHCC--EEEES-CCCTHHHHHHH
T ss_pred             HHHHHHHHHcCCCCeEEECCCCCCHHHHHHH
Confidence            3455554 36788999999999999998755

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>PF05729 NACHT: NACHT domain

Probab=85.00  E-value=1.6  Score=36.48  Aligned_cols=22  Identities=9%  Similarity=0.302  Sum_probs=17.4

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIA  231 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il  231 (333)
                      +-+++.|+.|+|||......+.
T Consensus         1 r~l~I~G~~G~GKStll~~~~~   22 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQ   22 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHH
Confidence            3478999999999998765443

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=84.98  E-value=1.8  Score=42.60  Aligned_cols=87  Identities=10%  Similarity=0.098  Sum_probs=55.8

Q ss_pred             cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc-cc-HHHHHHHHHHHHHhcCCcEEEeCCCCCCCCcceEEe------
Q psy2760         211 HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS-PI-KALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLLE------  282 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~-Pt-raLa~Q~~~~l~~~f~~vglltGd~~~~~~a~ili~------  282 (333)
                      -+++.|..|+|||....-...+....|.++++.+ -| ||=|-++.+.|-++. ++.++.+....++-+ +...      
T Consensus       141 Vil~vGVNG~GKTTTIaKLA~~l~~~g~~VllaA~DTFRAaAiEQL~~w~er~-gv~vI~~~~G~DpAa-VafDAi~~Ak  218 (340)
T COG0552         141 VILFVGVNGVGKTTTIAKLAKYLKQQGKSVLLAAGDTFRAAAIEQLEVWGERL-GVPVISGKEGADPAA-VAFDAIQAAK  218 (340)
T ss_pred             EEEEEecCCCchHhHHHHHHHHHHHCCCeEEEEecchHHHHHHHHHHHHHHHh-CCeEEccCCCCCcHH-HHHHHHHHHH
Confidence            5788999999999986655556667788888765 33 999999999998875 355555432222211 1110      


Q ss_pred             ccCcceEeccccccccc
Q psy2760         283 DLNIGGLDELSIHDFNK  299 (333)
Q Consensus       283 t~~i~liViDe~H~~~~  299 (333)
                      .-++.++++|++-+.-+
T Consensus       219 ar~~DvvliDTAGRLhn  235 (340)
T COG0552         219 ARGIDVVLIDTAGRLHN  235 (340)
T ss_pred             HcCCCEEEEeCcccccC
Confidence            01566666776655433

>PRK13700 conjugal transfer protein TraD; Provisional

Probab=84.93  E-value=1.2  Score=48.19  Aligned_cols=44  Identities=7%  Similarity=0.092  Sum_probs=35.0

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQ  252 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q  252 (333)
                      .+++++.|.||||||.+..-.+-+...+|.|+|+.=|.-+.+..
T Consensus       185 ~~H~li~GttGSGKS~~i~~LL~~ir~RGdrAIIyD~~GeFv~~  228 (732)
T PRK13700        185 IQNFCLHGTVGAGKSEVIRRLANYARQRGDMVVIYDRSGEFVKS  228 (732)
T ss_pred             hcceEEeCCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCCchHHH
Confidence            57999999999999997765555666778889888888666543

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=84.80  E-value=1.5  Score=38.86  Aligned_cols=19  Identities=26%  Similarity=0.284  Sum_probs=15.7

Q ss_pred             EEEEcCCCCcHHHHHHHHH
Q psy2760         212 VFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       212 vlv~apTGSGKTl~~~l~i  230 (333)
                      +.++|++|||||..+..-.
T Consensus         2 i~i~G~sgsGKttla~~l~   20 (179)
T cd02028           2 VGIAGPSGSGKTTFAKKLS   20 (179)
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            5789999999999886543

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PLN02165 adenylate isopentenyltransferase

Probab=84.78  E-value=0.4  Score=47.21  Aligned_cols=22  Identities=18%  Similarity=0.238  Sum_probs=18.7

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l  228 (333)
                      ..|..+++.||||||||..+..
T Consensus        41 ~~g~iivIiGPTGSGKStLA~~   62 (334)
T PLN02165         41 CKDKVVVIMGATGSGKSRLSVD   62 (334)
T ss_pred             CCCCEEEEECCCCCcHHHHHHH
Confidence            4467899999999999998865

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=84.67  E-value=1.6  Score=37.33  Aligned_cols=36  Identities=19%  Similarity=0.131  Sum_probs=26.4

Q ss_pred             cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEccc
Q psy2760         211 HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPI  246 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Pt  246 (333)
                      -+.++|+.+||||......+-...+.|.++.++..+
T Consensus         2 vv~VvG~~~sGKTTl~~~Li~~l~~~g~~v~~ik~~   37 (140)
T PF03205_consen    2 VVQVVGPKNSGKTTLIRKLINELKRRGYRVAVIKHT   37 (140)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEE-
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhHcCCceEEEEEc
Confidence            368999999999999887776667778887766533

>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=84.50  E-value=0.97  Score=36.52  Aligned_cols=32  Identities=16%  Similarity=0.110  Sum_probs=21.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEccc
Q psy2760         212 VFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPI  246 (333)
Q Consensus       212 vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Pt  246 (333)
                      +++.||.|+|||..+...+-. +  +...+.+...
T Consensus         1 ill~G~~G~GKT~l~~~la~~-l--~~~~~~i~~~   32 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQY-L--GFPFIEIDGS   32 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHH-T--TSEEEEEETT
T ss_pred             CEEECcCCCCeeHHHHHHHhh-c--cccccccccc
Confidence            689999999999988765432 2  3445555443

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 ....

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=84.44  E-value=1.6  Score=43.57  Aligned_cols=20  Identities=20%  Similarity=0.341  Sum_probs=16.8

Q ss_pred             cCCcEEEEcCCCCcHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAE  227 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~  227 (333)
                      .+..++++||||||||....
T Consensus       148 ~~GlilI~G~TGSGKTT~l~  167 (372)
T TIGR02525       148 AAGLGLICGETGSGKSTLAA  167 (372)
T ss_pred             cCCEEEEECCCCCCHHHHHH
Confidence            45579999999999998763

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).

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=84.26  E-value=1.4  Score=47.40  Aligned_cols=56  Identities=25%  Similarity=0.159  Sum_probs=42.1

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEE
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLI  267 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vgll  267 (333)
                      ..++++.||||||||..+.+|-+...  ...+|++=|--++..... .+++.++.|-++
T Consensus       144 ~~hvLviApTrSGKgvg~VIPnLL~~--~~S~VV~D~KGEl~~~Ta-~~R~~~G~V~~F  199 (663)
T PRK13876        144 PEHVLCFAPTRSGKGVGLVVPTLLTW--PGSAIVHDIKGENWQLTA-GFRARFGRVLLF  199 (663)
T ss_pred             CceEEEEecCCCCcceeEehhhHHhC--CCCEEEEeCcchHHHHHH-HHHHhCCeEEEE
Confidence            47999999999999999999876543  356777788888876554 456667765444

>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional

Probab=84.25  E-value=0.76  Score=44.63  Aligned_cols=22  Identities=27%  Similarity=0.230  Sum_probs=17.7

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      ++-+++.||||||||..++-..
T Consensus         4 ~~ii~I~GpTasGKS~LAl~LA   25 (300)
T PRK14729          4 NKIVFIFGPTAVGKSNILFHFP   25 (300)
T ss_pred             CcEEEEECCCccCHHHHHHHHH
Confidence            3458999999999999876543

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=84.22  E-value=1.9  Score=42.77  Aligned_cols=52  Identities=8%  Similarity=0.238  Sum_probs=39.0

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHH-HHhc--CCCeEEEEcccHH-HHHHHHHHHHHhc
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIA-LSQN--HKTRTIYTSPIKA-LSNQKYRDFRETF  261 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il-~~l~--~g~ral~l~Ptra-La~Q~~~~l~~~f  261 (333)
                      +..+++|+.|||||.++...++ ....  ++.+++++-|+.. |..-++..+...+
T Consensus         2 ~~~i~~GgrgSGKS~~~~~~~~~~~~~~~~~~~~~~~r~~~~sl~~sv~~~l~~~i   57 (396)
T TIGR01547         2 EEIIAKGGRRSGKTFAIALKLVEKLAINKKQQNILAARKVQNSIRDSVFKDIENLL   57 (396)
T ss_pred             ceEEEeCCCCcccHHHHHHHHHHHHHhcCCCcEEEEEehhhhHHHHHHHHHHHHHH
Confidence            3567899999999999887655 4444  6788999989855 6666777776543

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.

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=84.17  E-value=3.7  Score=48.19  Aligned_cols=62  Identities=15%  Similarity=0.074  Sum_probs=46.1

Q ss_pred             CCCCHHHHHHHHHHH--cCCcEEEEcCCCCcHHHHHHH--HHHHHh--cCCCeEEEEcccHHHHHHHH
Q psy2760         193 FELDVFQKQAIIKLE--EHNHVFVTAHTSAGKTVIAEY--AIALSQ--NHKTRTIYTSPIKALSNQKY  254 (333)
Q Consensus       193 f~l~~~Q~~ai~~l~--~g~~vlv~apTGSGKTl~~~l--~il~~l--~~g~ral~l~PtraLa~Q~~  254 (333)
                      ..|++-|++|+..++  .++.+++.|..|+|||.+...  .++..+  ..+.+++.++||-.-+..+.
T Consensus       834 ~~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e~~g~~V~glAPTgkAa~~L~  901 (1623)
T PRK14712        834 EKLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMR  901 (1623)
T ss_pred             cccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhhccCceEEEEechHHHHHHHH
Confidence            368999999999976  447899999999999988533  222222  34677888999966665553

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=83.98  E-value=2.1  Score=41.00  Aligned_cols=36  Identities=19%  Similarity=0.132  Sum_probs=27.5

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhc------CCCeEEEEc
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQN------HKTRTIYTS  244 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~------~g~ral~l~  244 (333)
                      |.-+.++|++|+|||..++..+.....      .+.+++|+.
T Consensus        95 g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~  136 (310)
T TIGR02236        95 QAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYID  136 (310)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEE
Confidence            677899999999999998876654331      234899986

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>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=83.98  E-value=1.8  Score=40.32  Aligned_cols=38  Identities=18%  Similarity=0.121  Sum_probs=30.2

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcC-CCeEEEEcc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNH-KTRTIYTSP  245 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~-g~ral~l~P  245 (333)
                      .|.-+++.|.||.|||..++-.+...... +..++|++.
T Consensus        18 ~g~L~vi~a~pg~GKT~~~l~ia~~~a~~~~~~vly~Sl   56 (259)
T PF03796_consen   18 PGELTVIAARPGVGKTAFALQIALNAALNGGYPVLYFSL   56 (259)
T ss_dssp             TT-EEEEEESTTSSHHHHHHHHHHHHHHTTSSEEEEEES
T ss_pred             cCcEEEEEecccCCchHHHHHHHHHHHHhcCCeEEEEcC
Confidence            45678999999999999998877765554 689999875

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 ....

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=83.87  E-value=1.2  Score=47.74  Aligned_cols=56  Identities=27%  Similarity=0.126  Sum_probs=40.8

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-cEEE
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-VGLI  267 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-vgll  267 (333)
                      ..++++.||||||||..+.+|-+...  ...+|++=|--++........ +..+. |-++
T Consensus       139 ~~hvlviApTgSGKgvg~VIPnLL~~--~gS~VV~DpKGE~~~~Ta~~R-~~~G~~V~~F  195 (670)
T PRK13850        139 QPHSLVVAPTRAGKGVGVVIPTLLTF--KGSVIALDVKGELFELTSRAR-KASGDAVFKF  195 (670)
T ss_pred             CceEEEEecCCCCceeeehHhHHhcC--CCCEEEEeCCchHHHHHHHHH-HhCCCEEEEe
Confidence            45999999999999999998876443  346777788888887765444 44665 4433

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=83.83  E-value=2.3  Score=42.48  Aligned_cols=87  Identities=13%  Similarity=0.060  Sum_probs=50.9

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC----CcEEEeCCCCCCCCcceEEec
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ----DVGLIDDLPPVFPDVEKLLED  283 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~----~vglltGd~~~~~~a~ili~t  283 (333)
                      .|.-+++.|++|+|||...+..+......+.+++|+.-. +-..|+..+..+ ++    ++.++ .......-.. .+..
T Consensus        81 ~GslvLI~G~pG~GKStLllq~a~~~a~~g~~VlYvs~E-Es~~qi~~Ra~r-lg~~~~~l~l~-~e~~le~I~~-~i~~  156 (372)
T cd01121          81 PGSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSGE-ESPEQIKLRADR-LGISTENLYLL-AETNLEDILA-SIEE  156 (372)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEECC-cCHHHHHHHHHH-cCCCcccEEEE-ccCcHHHHHH-HHHh
Confidence            367889999999999998876555445566789998754 334565555433 32    12211 1111100000 0112


Q ss_pred             cCcceEecccccccc
Q psy2760         284 LNIGGLDELSIHDFN  298 (333)
Q Consensus       284 ~~i~liViDe~H~~~  298 (333)
                      ....++|+|+++.+.
T Consensus       157 ~~~~lVVIDSIq~l~  171 (372)
T cd01121         157 LKPDLVIIDSIQTVY  171 (372)
T ss_pred             cCCcEEEEcchHHhh
Confidence            356788999998763

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.

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=83.82  E-value=1.9  Score=47.11  Aligned_cols=44  Identities=23%  Similarity=0.199  Sum_probs=36.9

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQ  252 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q  252 (333)
                      |.-+.+++|+|+|||..++..+......|.+++|+.....+...
T Consensus        60 GsiteI~G~~GsGKTtLal~~~~~a~~~G~~v~yId~E~t~~~~  103 (790)
T PRK09519         60 GRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPD  103 (790)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCccchhHH
Confidence            67889999999999999988777777778899999877666644

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=83.80  E-value=2.5  Score=41.58  Aligned_cols=38  Identities=21%  Similarity=0.248  Sum_probs=28.5

Q ss_pred             CCCCHHHHHHHHH-HHcCCcEEEEcCCCCcHHHHHHHHH
Q psy2760         193 FELDVFQKQAIIK-LEEHNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       193 f~l~~~Q~~ai~~-l~~g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      |.+++--.+++.. +..++++++.||+|+|||..+....
T Consensus        47 y~f~~~~~~~vl~~l~~~~~ilL~G~pGtGKTtla~~lA   85 (327)
T TIGR01650        47 YLFDKATTKAICAGFAYDRRVMVQGYHGTGKSTHIEQIA   85 (327)
T ss_pred             ccCCHHHHHHHHHHHhcCCcEEEEeCCCChHHHHHHHHH
Confidence            4566655554444 5778999999999999999887543

This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=83.76  E-value=2  Score=39.03  Aligned_cols=40  Identities=20%  Similarity=0.120  Sum_probs=34.5

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIK  247 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Ptr  247 (333)
                      ...++.+.+++|-|||.+++--.+.+...|.+++++-=.+
T Consensus        21 ~~g~v~v~~g~GkGKtt~a~g~a~ra~g~G~~V~ivQFlK   60 (191)
T PRK05986         21 EKGLLIVHTGNGKGKSTAAFGMALRAVGHGKKVGVVQFIK   60 (191)
T ss_pred             cCCeEEEECCCCCChHHHHHHHHHHHHHCCCeEEEEEEec
Confidence            4569999999999999999998889999999999875443

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=83.75  E-value=2.2  Score=41.93  Aligned_cols=46  Identities=26%  Similarity=0.183  Sum_probs=32.0

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKY  254 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~  254 (333)
                      |+-+-+.+|+|||||..++..+......+..++|+-|..+|-....
T Consensus        53 G~ivEi~G~~ssGKttLaL~~ia~~q~~g~~~a~ID~e~~ld~~~a   98 (322)
T PF00154_consen   53 GRIVEIYGPESSGKTTLALHAIAEAQKQGGICAFIDAEHALDPEYA   98 (322)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHTT-EEEEEESSS---HHHH
T ss_pred             CceEEEeCCCCCchhhhHHHHHHhhhcccceeEEecCcccchhhHH
Confidence            7788899999999999999888766555666666666555544433

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>PRK00131 aroK shikimate kinase; Reviewed

Probab=83.52  E-value=0.73  Score=39.35  Aligned_cols=22  Identities=18%  Similarity=0.336  Sum_probs=19.0

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~  229 (333)
                      .+..++++|++|||||.++...
T Consensus         3 ~~~~i~l~G~~GsGKstla~~L   24 (175)
T PRK00131          3 KGPNIVLIGFMGAGKSTIGRLL   24 (175)
T ss_pred             CCCeEEEEcCCCCCHHHHHHHH
Confidence            4678999999999999998654

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=83.44  E-value=0.62  Score=45.28  Aligned_cols=104  Identities=20%  Similarity=0.220  Sum_probs=54.1

Q ss_pred             CCHHHHHHHHHHH---------cCCcEEEEcCCCCcHHHHHHHHHHHHh---cCC---CeEEE-EcccHHHHHHHHHHHH
Q psy2760         195 LDVFQKQAIIKLE---------EHNHVFVTAHTSAGKTVIAEYAIALSQ---NHK---TRTIY-TSPIKALSNQKYRDFR  258 (333)
Q Consensus       195 l~~~Q~~ai~~l~---------~g~~vlv~apTGSGKTl~~~l~il~~l---~~g---~ral~-l~PtraLa~Q~~~~l~  258 (333)
                      -++.-.+++..+.         .-.+++++|+|+.|||.+..--.-.+.   ..+   ..+++ -+|...-....+..+-
T Consensus        38 gY~~A~~~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL  117 (302)
T PF05621_consen   38 GYPRAKEALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAIL  117 (302)
T ss_pred             cCHHHHHHHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHH
Confidence            4565666666641         224899999999999987643222111   111   12444 4676666666665554


Q ss_pred             HhcCC-cEEEeCCCCCCCCcceEEeccCcceEecccccccc
Q psy2760         259 ETFQD-VGLIDDLPPVFPDVEKLLEDLNIGGLDELSIHDFN  298 (333)
Q Consensus       259 ~~f~~-vglltGd~~~~~~a~ili~t~~i~liViDe~H~~~  298 (333)
                      ..++- +.--........+..-++...++-++|+||+|.+-
T Consensus       118 ~~lgaP~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lL  158 (302)
T PF05621_consen  118 EALGAPYRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLL  158 (302)
T ss_pred             HHhCcccCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHHh
Confidence            43321 11100000000011112334578889999999864

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=83.33  E-value=7.6  Score=42.46  Aligned_cols=35  Identities=29%  Similarity=0.221  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHH--cCCcEEEEcCCCCcHHHHHHHHHH
Q psy2760         197 VFQKQAIIKLE--EHNHVFVTAHTSAGKTVIAEYAIA  231 (333)
Q Consensus       197 ~~Q~~ai~~l~--~g~~vlv~apTGSGKTl~~~l~il  231 (333)
                      +.=.+++..+.  ...|+++.||+|+|||.++.....
T Consensus       193 ~ei~~~i~iL~r~~~~n~LLvGppGvGKT~lae~la~  229 (758)
T PRK11034        193 KELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAW  229 (758)
T ss_pred             HHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHH
Confidence            33344444443  356999999999999999866443

>TIGR00929 VirB4_CagE type IV secretion/conjugal transfer ATPase, VirB4 family

Probab=83.29  E-value=2.1  Score=46.25  Aligned_cols=50  Identities=18%  Similarity=0.228  Sum_probs=37.8

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCC-eEEEEcccHHHHHHHHHHHHHhcCC
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKT-RTIYTSPIKALSNQKYRDFRETFQD  263 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~-ral~l~PtraLa~Q~~~~l~~~f~~  263 (333)
                      ..|.+|.|+||||||......+......+. +++++=|-++     +..+.+.+++
T Consensus       434 ~~n~~I~G~tGsGKS~~~~~l~~~~~~~~~~~v~iiD~~~~-----~~~~~~~~gG  484 (785)
T TIGR00929       434 LGHTLIFGPTGSGKTTLLNFLLAQMQKYGGMTIFAFDKDRG-----MEIFIRAFGG  484 (785)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhhccCCCeEEEEeCCCC-----hHHhhhccCC
Confidence            568999999999999988776666666666 8999888876     3445555554

Type IV secretion systems are found in Gram-negative pathogens. They export proteins, DNA, or complexes in different systems and are related to plasmid conjugation systems. This model represents related ATPases that include VirB4 in Agrobacterium tumefaciens (DNA export) CagE in Helicobacter pylori (protein export) and plasmid TraB (conjugation).

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=83.25  E-value=3.1  Score=39.66  Aligned_cols=33  Identities=18%  Similarity=0.310  Sum_probs=23.0

Q ss_pred             HHHHHHH-HHcCC--cEEEEcCCCCcHHHHHHHHHH
Q psy2760         199 QKQAIIK-LEEHN--HVFVTAHTSAGKTVIAEYAIA  231 (333)
Q Consensus       199 Q~~ai~~-l~~g~--~vlv~apTGSGKTl~~~l~il  231 (333)
                      ..+.+.. +..++  +++++||+|+|||..+....-
T Consensus        23 ~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~~~   58 (337)
T PRK12402         23 VVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALAR   58 (337)
T ss_pred             HHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            3333444 34555  799999999999998866443

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=83.24  E-value=4.7  Score=41.73  Aligned_cols=89  Identities=18%  Similarity=0.101  Sum_probs=48.3

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-cEEEeCCCCCCCCcceEEecc
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-VGLIDDLPPVFPDVEKLLEDL  284 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-vglltGd~~~~~~a~ili~t~  284 (333)
                      ...+.+|++.|++|+||+.++...-....+.+. .++.+...++.....+  ...|+. -|.++|.......   .+...
T Consensus       207 a~~~~pVlI~Ge~GtGK~~~A~~ih~~s~r~~~-p~v~v~c~~~~~~~~e--~~lfG~~~g~~~ga~~~~~g---~~~~a  280 (509)
T PRK05022        207 AASDLNVLILGETGVGKELVARAIHAASPRADK-PLVYLNCAALPESLAE--SELFGHVKGAFTGAISNRSG---KFELA  280 (509)
T ss_pred             hCCCCcEEEECCCCccHHHHHHHHHHhCCcCCC-CeEEEEcccCChHHHH--HHhcCccccccCCCcccCCc---chhhc
Confidence            467789999999999999988764433333333 3344433333332222  134664 3455554322111   11223


Q ss_pred             CcceEecccccccccc
Q psy2760         285 NIGGLDELSIHDFNKH  300 (333)
Q Consensus       285 ~i~liViDe~H~~~~~  300 (333)
                      +-+.+.+|+++.+...
T Consensus       281 ~gGtL~ldeI~~L~~~  296 (509)
T PRK05022        281 DGGTLFLDEIGELPLA  296 (509)
T ss_pred             CCCEEEecChhhCCHH
Confidence            4455678888877643

>PRK13721 conjugal transfer ATP-binding protein TraC; Provisional

Probab=83.21  E-value=2.8  Score=46.14  Aligned_cols=50  Identities=16%  Similarity=0.149  Sum_probs=36.9

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD  263 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~  263 (333)
                      +.|.+|.|+||||||+..-..+...+..+.+++++=|-++     +..+.+.+++
T Consensus       449 N~N~~I~G~sGsGKS~l~k~l~~~~~~~g~~viiiD~~~s-----y~~l~~~lGG  498 (844)
T PRK13721        449 NYNMAVCGTSGAGKTGLIQPLIRSVLDSGGFAVVFDMGDG-----YKSLCENMGG  498 (844)
T ss_pred             cccEEEEcCCCCCHHHHHHHHHHhhhccCCEEEEEeCCCC-----HHHHHHHcCC
Confidence            4589999999999999887655556667888888877765     3344455554

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=83.07  E-value=2  Score=46.49  Aligned_cols=24  Identities=29%  Similarity=0.356  Sum_probs=19.5

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIA  231 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il  231 (333)
                      ...|+++.||+|+|||.++.....
T Consensus       202 ~~~n~lL~G~pG~GKT~l~~~la~  225 (731)
T TIGR02639       202 KKNNPLLVGEPGVGKTAIAEGLAL  225 (731)
T ss_pred             CCCceEEECCCCCCHHHHHHHHHH
Confidence            345999999999999999866443

>PRK13873 conjugal transfer ATPase TrbE; Provisional

Probab=83.06  E-value=1.6  Score=47.84  Aligned_cols=39  Identities=18%  Similarity=0.141  Sum_probs=28.6

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhc-CCCeEEEEcccHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQN-HKTRTIYTSPIKA  248 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~-~g~ral~l~Ptra  248 (333)
                      .|.+|.|+||||||+.....+.+... .|.+++++=|-++
T Consensus       442 gn~~I~G~tGsGKS~l~~~l~~~~~~~~g~~v~i~D~~~s  481 (811)
T PRK13873        442 GHTLVVGPTGAGKSVLLALMALQFRRYPGAQVFAFDFGGS  481 (811)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhhhcCCCeEEEEeCCCC
Confidence            38999999999999987775544444 4677777766543

>KOG1805|consensus

Probab=83.02  E-value=3.5  Score=45.75  Aligned_cols=66  Identities=17%  Similarity=0.208  Sum_probs=54.4

Q ss_pred             CCCHHHHHHHHHH-HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         194 ELDVFQKQAIIKL-EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       194 ~l~~~Q~~ai~~l-~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      .++..|++|+..+ ......+|.|=+|+|||..-...|-.....|.+++..+=|..=++-+.-+++.
T Consensus       669 ~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~~LIkiL~~~gkkVLLtsyThsAVDNILiKL~~  735 (1100)
T KOG1805|consen  669 RLNNDQRQALLKALAAEDYALILGMPGTGKTTTISLLIKILVALGKKVLLTSYTHSAVDNILIKLKG  735 (1100)
T ss_pred             hcCHHHHHHHHHHHhccchheeecCCCCCchhhHHHHHHHHHHcCCeEEEEehhhHHHHHHHHHHhc
Confidence            6899999999886 55567789999999999987766665666788999999998888888877765

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=82.83  E-value=2.3  Score=37.56  Aligned_cols=34  Identities=21%  Similarity=0.039  Sum_probs=29.1

Q ss_pred             cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc
Q psy2760         211 HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS  244 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~  244 (333)
                      -+.|..++|.|||.+++--.+.+...|.+++++-
T Consensus         4 ~i~vy~g~G~Gkt~~a~g~~~ra~~~g~~v~~vQ   37 (159)
T cd00561           4 LIQVYTGNGKGKTTAALGLALRALGHGYRVGVVQ   37 (159)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            4677888899999999988888888899999953

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.

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=82.74  E-value=1.5  Score=47.95  Aligned_cols=46  Identities=15%  Similarity=0.110  Sum_probs=34.7

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHH-HhcC-CCeEEEEcccHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIAL-SQNH-KTRTIYTSPIKALSNQKY  254 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~-~l~~-g~ral~l~PtraLa~Q~~  254 (333)
                      .-|+=|.+.||.|||.+|+-.|.. +..- -.+-|+|||+.|.-.-++
T Consensus        74 ~lNiDI~METGTGKTy~YlrtmfeLhk~YG~~KFIivVPs~AIkeGv~  121 (985)
T COG3587          74 KLNIDILMETGTGKTYTYLRTMFELHKKYGLFKFIIVVPSLAIKEGVF  121 (985)
T ss_pred             cceeeEEEecCCCceeeHHHHHHHHHHHhCceeEEEEeccHHHHhhhH
Confidence            358889999999999999998862 2222 357899999988655533

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=82.58  E-value=1.6  Score=44.74  Aligned_cols=34  Identities=15%  Similarity=0.259  Sum_probs=27.1

Q ss_pred             CCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHH
Q psy2760         195 LDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       195 l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l  228 (333)
                      +.......+..+..+++++++||+|+|||..+..
T Consensus       180 ~e~~le~l~~~L~~~~~iil~GppGtGKT~lA~~  213 (459)
T PRK11331        180 PETTIETILKRLTIKKNIILQGPPGVGKTFVARR  213 (459)
T ss_pred             CHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHH
Confidence            3445555666678899999999999999988864

>PRK00889 adenylylsulfate kinase; Provisional

Probab=82.58  E-value=2.3  Score=36.93  Aligned_cols=36  Identities=22%  Similarity=0.116  Sum_probs=24.7

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEE
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYT  243 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l  243 (333)
                      .|..+++.|+.|||||.++....-.....+..++++
T Consensus         3 ~g~~i~~~G~~GsGKST~a~~la~~l~~~g~~v~~i   38 (175)
T PRK00889          3 RGVTVWFTGLSGAGKTTIARALAEKLREAGYPVEVL   38 (175)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            467889999999999999876443332344445544

>TIGR02767 TraG-Ti Ti-type conjugative transfer system protien TraG

Probab=82.53  E-value=2.1  Score=45.68  Aligned_cols=57  Identities=18%  Similarity=0.140  Sum_probs=42.2

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC--CcEEEe
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ--DVGLID  268 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~--~vgllt  268 (333)
                      ..++++.||||||||..+.+|-+.  .-+..++++=|--++...... +++.++  +|-++.
T Consensus       211 ~~H~lv~ApTgsGKgvg~VIPnLL--~~~gS~VV~DpKgE~~~~Ta~-~R~~~Gg~~V~vfd  269 (623)
T TIGR02767       211 STHMIFFAGSGGFKTTSVVVPTAL--KYGGPLVCLDPSTEVAPMVCE-HRRQAGNRKVIVLD  269 (623)
T ss_pred             CceEEEEeCCCCCccceeehhhhh--cCCCCEEEEEChHHHHHHHHH-HHHHcCCCcEEEEe
Confidence            369999999999999999998643  335568888898888766664 555565  365553

This protein is found in the Agrobacterium tumefaciens Ti plasmid tra region responsible for conjugative transfer of the entire plasmid among Agrobacterium strains. The protein is distantly related to the F-type conjugation system TraG protein. Both of these systems are examples of type IV secretion systems.

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=82.50  E-value=2.9  Score=42.03  Aligned_cols=39  Identities=21%  Similarity=0.214  Sum_probs=30.9

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHHHHHHHH-hcCCCeEEEEc
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAEYAIALS-QNHKTRTIYTS  244 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~l~il~~-l~~g~ral~l~  244 (333)
                      +..|.-+++.|++|+|||..++-.+... ...+.+++|++
T Consensus       191 ~~~g~liviag~pg~GKT~~al~ia~~~a~~~g~~v~~fS  230 (421)
T TIGR03600       191 LVKGDLIVIGARPSMGKTTLALNIAENVALREGKPVLFFS  230 (421)
T ss_pred             CCCCceEEEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEE
Confidence            4567888999999999999888766543 35678888886

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.

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=82.26  E-value=2.1  Score=40.29  Aligned_cols=35  Identities=17%  Similarity=0.320  Sum_probs=22.1

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcCCCe-EEEEcc
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTR-TIYTSP  245 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~g~r-al~l~P  245 (333)
                      -++++.|++|||||......+ ..+....+ +++++|
T Consensus        14 fr~viIG~sGSGKT~li~~lL-~~~~~~f~~I~l~t~   49 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTTLIKSLL-YYLRHKFDHIFLITP   49 (241)
T ss_pred             ceEEEECCCCCCHHHHHHHHH-HhhcccCCEEEEEec
Confidence            378999999999998655443 33333333 333444

This is thought to be an ATPase involved in viral DNA packaging [].

>KOG1806|consensus

Probab=82.10  E-value=2.2  Score=47.60  Aligned_cols=66  Identities=18%  Similarity=0.191  Sum_probs=54.6

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHH--HHHhcCCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAI--ALSQNHKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~i--l~~l~~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      .+++-|.+|+..-.+.....+.+|+|.|||-++.--+  +++-.+..|+++++....--+|.++.+.+
T Consensus       738 ~ft~~qveai~sg~qpgltmvvgppgtgktd~avqil~~lyhn~p~qrTlivthsnqaln~lfeKi~~  805 (1320)
T KOG1806|consen  738 KFTPTQVEAILSGMQPGLTMVVGPPGTGKTDVAVQILSVLYHNSPNQRTLIVTHSNQALNQLFEKIMA  805 (1320)
T ss_pred             ccCHHHHHHHHhcCCCCceeeecCCCCCCcchhhhhhhhhhhcCCCcceEEEEecccchhHHHHHHHh
Confidence            5688999999887778899999999999998875543  46667889999999988888888876654

>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=81.96  E-value=3.9  Score=37.49  Aligned_cols=34  Identities=32%  Similarity=0.401  Sum_probs=23.7

Q ss_pred             cEEEEcCCCCcHHHHHHHHHHH---HhcCCCeEEEEcc
Q psy2760         211 HVFVTAHTSAGKTVIAEYAIAL---SQNHKTRTIYTSP  245 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~il~---~l~~g~ral~l~P  245 (333)
                      .++++||+|+|||.. +.++..   ...++.+++|+..
T Consensus        36 ~l~l~G~~G~GKTHL-L~Ai~~~~~~~~~~~~v~y~~~   72 (219)
T PF00308_consen   36 PLFLYGPSGLGKTHL-LQAIANEAQKQHPGKRVVYLSA   72 (219)
T ss_dssp             EEEEEESTTSSHHHH-HHHHHHHHHHHCTTS-EEEEEH
T ss_pred             ceEEECCCCCCHHHH-HHHHHHHHHhccccccceeecH
Confidence            589999999999985 334432   2346788998764

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.

>PRK00300 gmk guanylate kinase; Provisional

Probab=81.96  E-value=1.4  Score=39.20  Aligned_cols=22  Identities=14%  Similarity=0.249  Sum_probs=18.3

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~  229 (333)
                      .|+-+++.||+|||||..+...
T Consensus         4 ~g~~i~i~G~sGsGKstl~~~l   25 (205)
T PRK00300          4 RGLLIVLSGPSGAGKSTLVKAL   25 (205)
T ss_pred             CCCEEEEECCCCCCHHHHHHHH
Confidence            4788999999999999876543

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=81.83  E-value=2.8  Score=40.05  Aligned_cols=20  Identities=30%  Similarity=0.336  Sum_probs=17.4

Q ss_pred             CCcEEEEcCCCCcHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l  228 (333)
                      +.++++.||+|+|||.++..
T Consensus        58 ~~~vll~G~pGTGKT~lA~~   77 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVALR   77 (284)
T ss_pred             CceEEEEcCCCCCHHHHHHH
Confidence            45899999999999998854

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.

>PRK13891 conjugal transfer protein TrbE; Provisional

Probab=81.81  E-value=1.9  Score=47.59  Aligned_cols=39  Identities=18%  Similarity=0.083  Sum_probs=28.9

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhc-CCCeEEEEcccHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQN-HKTRTIYTSPIKA  248 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~-~g~ral~l~Ptra  248 (333)
                      .|.+|.||||||||+.....+.+..+ .+.+++++=|-++
T Consensus       489 gh~~I~G~tGsGKS~l~~~L~~~~~k~~~~~v~i~D~~~s  528 (852)
T PRK13891        489 GHTFMFGPTGAGKSTHLGIIAAQLRRYAGMSIYAFDKGMS  528 (852)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhcCCCEEEEEcCCcc
Confidence            47899999999999988766555443 5667777766544

>TIGR00767 rho transcription termination factor Rho

Probab=81.79  E-value=0.82  Score=46.28  Aligned_cols=22  Identities=27%  Similarity=0.348  Sum_probs=19.2

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l  228 (333)
                      -.|..+++.||+|+|||..+..
T Consensus       166 g~Gq~~~IvG~~g~GKTtL~~~  187 (415)
T TIGR00767       166 GKGQRGLIVAPPKAGKTVLLQK  187 (415)
T ss_pred             CCCCEEEEECCCCCChhHHHHH
Confidence            5789999999999999987655

Members of this family differ in the specificity of RNA binding.

>PHA02244 ATPase-like protein

Probab=81.76  E-value=2  Score=43.13  Aligned_cols=24  Identities=29%  Similarity=0.408  Sum_probs=20.7

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHHHH
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~l~  229 (333)
                      +..+.++++.||||+|||.++...
T Consensus       116 l~~~~PVLL~GppGtGKTtLA~aL  139 (383)
T PHA02244        116 VNANIPVFLKGGAGSGKNHIAEQI  139 (383)
T ss_pred             HhcCCCEEEECCCCCCHHHHHHHH
Confidence            578899999999999999877553

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=81.74  E-value=0.87  Score=38.50  Aligned_cols=43  Identities=23%  Similarity=0.278  Sum_probs=26.1

Q ss_pred             HHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHH
Q psy2760         205 KLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALS  250 (333)
Q Consensus       205 ~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa  250 (333)
                      .+..|.-+++.|+-|||||...- +++..+  |...-+.+||=.|+
T Consensus        11 ~l~~g~vi~L~GdLGaGKTtf~r-~l~~~l--g~~~~V~SPTF~l~   53 (123)
T PF02367_consen   11 ILKPGDVILLSGDLGAGKTTFVR-GLARAL--GIDEEVTSPTFSLV   53 (123)
T ss_dssp             HHSS-EEEEEEESTTSSHHHHHH-HHHHHT--T--S----TTTTSE
T ss_pred             hCCCCCEEEEECCCCCCHHHHHH-HHHHHc--CCCCCcCCCCeEEE
Confidence            35667778899999999998765 444555  33347789996665

They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=81.66  E-value=1.3  Score=45.45  Aligned_cols=28  Identities=21%  Similarity=0.353  Sum_probs=22.3

Q ss_pred             HHHHHH-HHcCCcEEEEcCCCCcHHHHHH
Q psy2760         200 KQAIIK-LEEHNHVFVTAHTSAGKTVIAE  227 (333)
Q Consensus       200 ~~ai~~-l~~g~~vlv~apTGSGKTl~~~  227 (333)
                      ++|+.. +..|+|+++.||.|||||+.+-
T Consensus       188 KrAleiAAAGgHnLl~~GpPGtGKTmla~  216 (490)
T COG0606         188 KRALEIAAAGGHNLLLVGPPGTGKTMLAS  216 (490)
T ss_pred             HHHHHHHHhcCCcEEEecCCCCchHHhhh
Confidence            444444 3788999999999999998864

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=81.65  E-value=2  Score=45.94  Aligned_cols=57  Identities=19%  Similarity=0.128  Sum_probs=41.7

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-cEEEe
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-VGLID  268 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-vgllt  268 (333)
                      ..++++.||||||||..+.+|-+.  .-+..++++=|-.++...+.. +++.++. |-++.
T Consensus       224 ~~H~Lv~ApTgsGKt~g~VIPnLL--~~~gS~VV~DpKgEl~~~Ta~-~R~~~G~~V~vfd  281 (641)
T PRK13822        224 STHGLVFAGSGGFKTTSVVVPTAL--KWGGPLVVLDPSTEVAPMVSE-HRRDAGREVIVLD  281 (641)
T ss_pred             CceEEEEeCCCCCccceEehhhhh--cCCCCEEEEeCcHHHHHHHHH-HHHHCCCeEEEEe
Confidence            469999999999999999998653  334567777798888776655 4455664 55543

>PRK13768 GTPase; Provisional

Probab=81.62  E-value=2.2  Score=40.07  Aligned_cols=33  Identities=15%  Similarity=0.173  Sum_probs=23.4

Q ss_pred             cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEE
Q psy2760         211 HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYT  243 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l  243 (333)
                      -+++.++.|+|||..+..........|.+++++
T Consensus         4 ~i~v~G~~G~GKTt~~~~~~~~l~~~g~~v~~i   36 (253)
T PRK13768          4 IVFFLGTAGSGKTTLTKALSDWLEEQGYDVAIV   36 (253)
T ss_pred             EEEEECCCCccHHHHHHHHHHHHHhcCCceEEE
Confidence            578899999999997755443334456666665

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=81.59  E-value=3  Score=40.34  Aligned_cols=37  Identities=16%  Similarity=0.134  Sum_probs=28.2

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhc------CCCeEEEEcc
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQN------HKTRTIYTSP  245 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~------~g~ral~l~P  245 (333)
                      |.-+.++||+|+|||..++..+.....      .+.+++|+.-
T Consensus       102 g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~t  144 (317)
T PRK04301        102 QSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDT  144 (317)
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeC
Confidence            678899999999999998876664432      2358888863

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=81.57  E-value=4.6  Score=41.96  Aligned_cols=88  Identities=15%  Similarity=0.150  Sum_probs=47.8

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-cEEEeCCCCCCCCcceEEecc
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-VGLIDDLPPVFPDVEKLLEDL  284 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-vglltGd~~~~~~a~ili~t~  284 (333)
                      +..+..+++.|.||+||+.++-..- .....+.+..+.+...++..+..+.  ..|+. -|-++|.......   ++...
T Consensus       224 A~~~~pvlI~GE~GtGK~~lA~aiH-~~s~r~~~pfv~inca~~~~~~~e~--elFG~~~~~~~~~~~~~~g---~~e~a  297 (520)
T PRK10820        224 AMLDAPLLITGDTGTGKDLLAYACH-LRSPRGKKPFLALNCASIPDDVVES--ELFGHAPGAYPNALEGKKG---FFEQA  297 (520)
T ss_pred             hCCCCCEEEECCCCccHHHHHHHHH-HhCCCCCCCeEEeccccCCHHHHHH--HhcCCCCCCcCCcccCCCC---hhhhc
Confidence            4678899999999999999886632 2222233455555655554444332  34654 2333332211100   11122


Q ss_pred             CcceEeccccccccc
Q psy2760         285 NIGGLDELSIHDFNK  299 (333)
Q Consensus       285 ~i~liViDe~H~~~~  299 (333)
                      +-+.+.+|+++.+..
T Consensus       298 ~~GtL~LdeI~~L~~  312 (520)
T PRK10820        298 NGGSVLLDEIGEMSP  312 (520)
T ss_pred             CCCEEEEeChhhCCH
Confidence            345566788877654

>TIGR03263 guanyl_kin guanylate kinase

Probab=81.49  E-value=1.5  Score=38.14  Aligned_cols=22  Identities=9%  Similarity=0.270  Sum_probs=17.6

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      |+-+++.||+|||||..+...+
T Consensus         1 g~ii~l~G~~GsGKsTl~~~L~   22 (180)
T TIGR03263         1 GLLIVISGPSGVGKSTLVKALL   22 (180)
T ss_pred             CcEEEEECCCCCCHHHHHHHHH
Confidence            4678999999999999765543

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>PRK08506 replicative DNA helicase; Provisional

Probab=81.41  E-value=3.7  Score=42.20  Aligned_cols=40  Identities=18%  Similarity=0.236  Sum_probs=32.1

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcc
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSP  245 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~P  245 (333)
                      +..|.-+++.|.||.|||..++-.+......|.+++|++.
T Consensus       189 ~~~G~LivIaarpg~GKT~fal~ia~~~~~~g~~V~~fSl  228 (472)
T PRK08506        189 FNKGDLIIIAARPSMGKTTLCLNMALKALNQDKGVAFFSL  228 (472)
T ss_pred             CCCCceEEEEcCCCCChHHHHHHHHHHHHhcCCcEEEEeC
Confidence            3557788999999999999988776666667788888864

>PHA00350 putative assembly protein

Probab=81.40  E-value=3.5  Score=41.69  Aligned_cols=29  Identities=10%  Similarity=0.013  Sum_probs=22.9

Q ss_pred             EEEEcCCCCcHHHHHHH-HHHHHhcCCCeE
Q psy2760         212 VFVTAHTSAGKTVIAEY-AIALSQNHKTRT  240 (333)
Q Consensus       212 vlv~apTGSGKTl~~~l-~il~~l~~g~ra  240 (333)
                      .++.|..|||||+.+.. -|+.++..|+++
T Consensus         4 ~l~tG~pGSGKT~~aV~~~i~palk~GR~V   33 (399)
T PHA00350          4 YAIVGRPGSYKSYEAVVYHIIPALKDGRKV   33 (399)
T ss_pred             EEEecCCCCchhHHHHHHHHHHHHHCCCEE
Confidence            57899999999999887 466677777544

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=81.36  E-value=2.7  Score=40.98  Aligned_cols=39  Identities=15%  Similarity=0.103  Sum_probs=28.9

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHh------cCCCeEEEEcccH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQ------NHKTRTIYTSPIK  247 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l------~~g~ral~l~Ptr  247 (333)
                      |.-..++|+.|+|||..++..+....      ..+.+++|+.-.-
T Consensus        96 G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~  140 (313)
T TIGR02238        96 MSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEG  140 (313)
T ss_pred             CeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCC
Confidence            67788999999999999876554322      2357899987443

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=81.32  E-value=4.5  Score=41.33  Aligned_cols=46  Identities=17%  Similarity=0.186  Sum_probs=30.4

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHh---cCCCeEEEEcccHHHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQ---NHKTRTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l---~~g~ral~l~PtraLa~Q~~~~l  257 (333)
                      ..++++|++|+|||... .++...+   .++.+++|+.+ ..+.++....+
T Consensus       142 npl~i~G~~G~GKTHLl-~Ai~~~l~~~~~~~~v~yv~~-~~f~~~~~~~l  190 (450)
T PRK14087        142 NPLFIYGESGMGKTHLL-KAAKNYIESNFSDLKVSYMSG-DEFARKAVDIL  190 (450)
T ss_pred             CceEEECCCCCcHHHHH-HHHHHHHHHhCCCCeEEEEEH-HHHHHHHHHHH
Confidence            46899999999999665 4444322   45678888765 45555554444

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=81.31  E-value=4  Score=43.40  Aligned_cols=38  Identities=11%  Similarity=0.185  Sum_probs=25.9

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCC--CeEEEEc
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHK--TRTIYTS  244 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g--~ral~l~  244 (333)
                      +..+++++++||+|+|||.++.... ..+...  ..++|+.
T Consensus        34 ~~~~~~~ll~G~pG~GKT~la~~la-~~l~~~~~~~~~~~~   73 (608)
T TIGR00764        34 AKQKRNVLLIGEPGVGKSMLAKAMA-ELLPDEELEDILVYP   73 (608)
T ss_pred             HHcCCCEEEECCCCCCHHHHHHHHH-HHcCchhheeEEEEe
Confidence            3677899999999999998876533 333332  3445443

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=81.23  E-value=6  Score=46.99  Aligned_cols=63  Identities=16%  Similarity=0.095  Sum_probs=46.1

Q ss_pred             CCCCCHHHHHHHHHHHc--CCcEEEEcCCCCcHHHHHHHHH--HHHh--cCCCeEEEEcccHHHHHHHH
Q psy2760         192 PFELDVFQKQAIIKLEE--HNHVFVTAHTSAGKTVIAEYAI--ALSQ--NHKTRTIYTSPIKALSNQKY  254 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~--g~~vlv~apTGSGKTl~~~l~i--l~~l--~~g~ral~l~PtraLa~Q~~  254 (333)
                      .+.|++.|++|+..++.  ++.+++.|..|+|||.+.-..+  +..+  ..+.+++.++||-.=|.++.
T Consensus       965 ~~~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l~~v~~~~~~l~~~~~~~V~glAPTgrAAk~L~ 1033 (1747)
T PRK13709        965 MEGLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQFRAVMSAVNTLPESERPRVVGLGPTHRAVGEMR 1033 (1747)
T ss_pred             cCCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhhcccCceEEEECCcHHHHHHHH
Confidence            34689999999999865  4688999999999998864322  2222  24567888999966565443

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=81.11  E-value=1.2  Score=46.18  Aligned_cols=66  Identities=20%  Similarity=0.128  Sum_probs=46.7

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHH--HHHhcCCCeEEEEcccHHHHHHHHHHHHHh
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAI--ALSQNHKTRTIYTSPIKALSNQKYRDFRET  260 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~i--l~~l~~g~ral~l~PtraLa~Q~~~~l~~~  260 (333)
                      .+...|++|.-..-.|.- .+.|-.|||||.+..+-.  +...++.-++++..-|+.|+.++.+...+.
T Consensus       162 nfD~~Q~kaa~~~~~G~q-rIrGLAGSGKT~~La~Kaa~lh~knPd~~I~~Tfftk~L~s~~r~lv~~F  229 (660)
T COG3972         162 NFDTDQTKAAFQSGFGKQ-RIRGLAGSGKTELLAHKAAELHSKNPDSRIAFTFFTKILASTMRTLVPEF  229 (660)
T ss_pred             cccchhheeeeecCCchh-hhhcccCCCchhHHHHHHHHHhcCCCCceEEEEeehHHHHHHHHHHHHHH
Confidence            356677766544434444 678889999999877633  345567789999988999888887665553

>PHA00729 NTP-binding motif containing protein

Probab=81.07  E-value=3.6  Score=38.42  Aligned_cols=47  Identities=9%  Similarity=-0.058  Sum_probs=29.9

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHH-------------hcCCCeEEEEcccHHHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALS-------------QNHKTRTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~-------------l~~g~ral~l~PtraLa~Q~~~~l  257 (333)
                      .++++.|++|+|||..+.......             ...+.+++ ++...+|...+...+
T Consensus        18 ~nIlItG~pGvGKT~LA~aLa~~l~~~l~~l~~~~~~~d~~~~~~-fid~~~Ll~~L~~a~   77 (226)
T PHA00729         18 VSAVIFGKQGSGKTTYALKVARDVFWKLNNLSTKDDAWQYVQNSY-FFELPDALEKIQDAI   77 (226)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHhhcccccchhhHHhcCCcEE-EEEHHHHHHHHHHHH
Confidence            489999999999998876533221             12334444 456667776665443

>CHL00095 clpC Clp protease ATP binding subunit

Probab=81.02  E-value=5.3  Score=43.89  Aligned_cols=24  Identities=29%  Similarity=0.329  Sum_probs=19.7

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIA  231 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il  231 (333)
                      ...|+++.||+|.|||.++.....
T Consensus       199 ~~~n~lL~G~pGvGKTal~~~la~  222 (821)
T CHL00095        199 TKNNPILIGEPGVGKTAIAEGLAQ  222 (821)
T ss_pred             ccCCeEEECCCCCCHHHHHHHHHH
Confidence            445999999999999999866443

>KOG0060|consensus

Probab=81.00  E-value=1.4  Score=46.30  Aligned_cols=21  Identities=19%  Similarity=0.384  Sum_probs=18.2

Q ss_pred             cCCcEEEEcCCCCcHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l  228 (333)
                      +|++++||||+|+|||-.+-.
T Consensus       460 ~g~~LLItG~sG~GKtSLlRv  480 (659)
T KOG0060|consen  460 SGQNLLITGPSGCGKTSLLRV  480 (659)
T ss_pred             CCCeEEEECCCCCchhHHHHH
Confidence            499999999999999977644

>PF09439 SRPRB: Signal recognition particle receptor beta subunit; InterPro: IPR019009 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=80.97  E-value=1.5  Score=39.61  Aligned_cols=23  Identities=17%  Similarity=0.320  Sum_probs=17.1

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIA  231 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il  231 (333)
                      ...++++||.|||||..|.....
T Consensus         3 ~~~vlL~Gps~SGKTaLf~~L~~   25 (181)
T PF09439_consen    3 RPTVLLVGPSGSGKTALFSQLVN   25 (181)
T ss_dssp             --EEEEE-STTSSHHHHHHHHHH
T ss_pred             CceEEEEcCCCCCHHHHHHHHhc
Confidence            46799999999999998876554

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 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase, which anchors the alpha subunit to the endoplasmic reticulum membrane []. ; PDB: 2GED_B 1NRJ_B 2GO5_2 2FH5_B.

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=80.95  E-value=4.2  Score=35.74  Aligned_cols=35  Identities=23%  Similarity=0.263  Sum_probs=24.0

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEE
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYT  243 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l  243 (333)
                      |+.+++.|+.|||||..+-...-.....|.+++++
T Consensus         3 g~~IvieG~~GsGKsT~~~~L~~~l~~~g~~v~~~   37 (195)
T TIGR00041         3 GMFIVIEGIDGAGKTTQANLLKKLLQENGYDVLFT   37 (195)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            67899999999999988766433222345555544

Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=80.86  E-value=1.3  Score=39.24  Aligned_cols=21  Identities=10%  Similarity=0.237  Sum_probs=18.2

Q ss_pred             CCcEEEEcCCCCcHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~  229 (333)
                      |..+++.||.|||||.++-..
T Consensus         2 g~~i~l~G~sGsGKsTl~~~l   22 (186)
T PRK10078          2 GKLIWLMGPSGSGKDSLLAAL   22 (186)
T ss_pred             CcEEEEECCCCCCHHHHHHHH
Confidence            678999999999999987654

>KOG0745|consensus

Probab=80.56  E-value=1  Score=46.02  Aligned_cols=21  Identities=33%  Similarity=0.552  Sum_probs=17.9

Q ss_pred             cCCcEEEEcCCCCcHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l  228 (333)
                      ..-|+++.+|||||||+.+.-
T Consensus       225 eKSNvLllGPtGsGKTllaqT  245 (564)
T KOG0745|consen  225 EKSNVLLLGPTGSGKTLLAQT  245 (564)
T ss_pred             ecccEEEECCCCCchhHHHHH
Confidence            456999999999999998754

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=80.54  E-value=2.3  Score=37.99  Aligned_cols=31  Identities=16%  Similarity=0.132  Sum_probs=19.6

Q ss_pred             EEEEcCCCCcHHHHHHHH-HHHHhcCCCeEEE
Q psy2760         212 VFVTAHTSAGKTVIAEYA-IALSQNHKTRTIY  242 (333)
Q Consensus       212 vlv~apTGSGKTl~~~l~-il~~l~~g~ral~  242 (333)
                      .+++|..|||||..+..- +..++..|.+++.
T Consensus         3 ~~~~G~pGsGKS~~av~~~i~~~l~~gr~V~t   34 (193)
T PF05707_consen    3 YLITGKPGSGKSYYAVSYVIIPALKKGRPVYT   34 (193)
T ss_dssp             EEEE--TTSSHHHHHHHHHHH-GGGS---EEE
T ss_pred             EEEEcCCCCcHhHHHHHHHHHHHHhCCCEEEE
Confidence            578999999999988776 6666766655554

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>cd03114 ArgK-like The function of this protein family is unkown

Probab=80.50  E-value=3.1  Score=35.78  Aligned_cols=32  Identities=19%  Similarity=0.222  Sum_probs=23.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEE
Q psy2760         212 VFVTAHTSAGKTVIAEYAIALSQNHKTRTIYT  243 (333)
Q Consensus       212 vlv~apTGSGKTl~~~l~il~~l~~g~ral~l  243 (333)
                      +.+.|+.|+|||.............+.+++++
T Consensus         2 i~~~G~~GsGKTt~~~~l~~~~~~~g~~v~ii   33 (148)
T cd03114           2 IGITGVPGAGKSTLIDALITALRARGKRVAVL   33 (148)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHCCCEEEEE
Confidence            57889999999998766554444556666664

The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.

>TIGR00368 Mg chelatase-related protein

Probab=80.40  E-value=1.6  Score=45.27  Aligned_cols=22  Identities=18%  Similarity=0.336  Sum_probs=19.3

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l  228 (333)
                      ..++++++.+|+|+|||..+..
T Consensus       209 ~~g~~vlliG~pGsGKTtlar~  230 (499)
T TIGR00368       209 AGGHNLLLFGPPGSGKTMLASR  230 (499)
T ss_pred             cCCCEEEEEecCCCCHHHHHHH
Confidence            5678999999999999998754

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed

Probab=80.39  E-value=1.2  Score=43.35  Aligned_cols=20  Identities=25%  Similarity=0.338  Sum_probs=17.0

Q ss_pred             CcEEEEcCCCCcHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~  229 (333)
                      +-++++||||||||.++...
T Consensus         5 ~~i~i~GptgsGKt~la~~l   24 (307)
T PRK00091          5 KVIVIVGPTASGKTALAIEL   24 (307)
T ss_pred             eEEEEECCCCcCHHHHHHHH
Confidence            45789999999999988754

>PF02456 Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR003389 Va2 protein can interact with the adenoviral packaging signal and this interaction involves DNA sequences that have previously been demonstrated to be required for packaging []

Probab=80.37  E-value=1.9  Score=42.37  Aligned_cols=41  Identities=17%  Similarity=0.186  Sum_probs=26.3

Q ss_pred             cEEEEcCCCCcHHHHHHHHHH-HHhcC-CCeEEEEcccHHHHH
Q psy2760         211 HVFVTAHTSAGKTVIAEYAIA-LSQNH-KTRTIYTSPIKALSN  251 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~il-~~l~~-g~ral~l~PtraLa~  251 (333)
                      -.+|.|||||||+-...-.+- +.+.+ .-.++||+|++..+-
T Consensus        89 I~~VYGPTG~GKSqLlRNLis~~lI~P~PETVfFItP~~~mIp  131 (369)
T PF02456_consen   89 IGVVYGPTGSGKSQLLRNLISCQLIQPPPETVFFITPQKDMIP  131 (369)
T ss_pred             EEEEECCCCCCHHHHHHHhhhcCcccCCCCceEEECCCCCCCC
Confidence            458899999999964332221 12222 357899999876543

During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter [].; GO: 0019083 viral transcription

>PRK07261 topology modulation protein; Provisional

Probab=80.36  E-value=1.3  Score=38.98  Aligned_cols=18  Identities=17%  Similarity=0.372  Sum_probs=16.1

Q ss_pred             cEEEEcCCCCcHHHHHHH
Q psy2760         211 HVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l  228 (333)
                      .++++|++|||||..+..
T Consensus         2 ri~i~G~~GsGKSTla~~   19 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARK   19 (171)
T ss_pred             EEEEEcCCCCCHHHHHHH
Confidence            588999999999999865

>PRK08118 topology modulation protein; Reviewed

Probab=80.35  E-value=1.3  Score=38.93  Aligned_cols=20  Identities=15%  Similarity=0.358  Sum_probs=16.5

Q ss_pred             CcEEEEcCCCCcHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~  229 (333)
                      +.++|+||.|||||..+-..
T Consensus         2 ~rI~I~G~~GsGKSTlak~L   21 (167)
T PRK08118          2 KKIILIGSGGSGKSTLARQL   21 (167)
T ss_pred             cEEEEECCCCCCHHHHHHHH
Confidence            36899999999999877543

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=80.34  E-value=2.5  Score=35.51  Aligned_cols=28  Identities=21%  Similarity=0.283  Sum_probs=20.7

Q ss_pred             HHHHHHHcCCcEEEEcCCCCcHHHHHHH
Q psy2760         201 QAIIKLEEHNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       201 ~ai~~l~~g~~vlv~apTGSGKTl~~~l  228 (333)
                      ++-.....+.+|++.|+.|+||+.++..
T Consensus        13 ~l~~~a~~~~pvli~GE~GtGK~~~A~~   40 (138)
T PF14532_consen   13 QLERLAKSSSPVLITGEPGTGKSLLARA   40 (138)
T ss_dssp             HHHHHHCSSS-EEEECCTTSSHHHHHHC
T ss_pred             HHHHHhCCCCcEEEEcCCCCCHHHHHHH
Confidence            3333346778999999999999998754

>CHL00181 cbbX CbbX; Provisional

Probab=80.21  E-value=3.6  Score=39.47  Aligned_cols=23  Identities=26%  Similarity=0.226  Sum_probs=19.3

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIA  231 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il  231 (333)
                      +.++++.||+|+|||.++....-
T Consensus        59 ~~~ill~G~pGtGKT~lAr~la~   81 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVALKMAD   81 (287)
T ss_pred             CceEEEECCCCCCHHHHHHHHHH
Confidence            56799999999999999876543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	333
4a4z_A	997	Crystal Structure Of The S. Cerevisiae Dexh Helicas		4e-33
2xgj_A	1010	Structure Of Mtr4, A Dexh Helicase Involved In Nucl		2e-22
3l9o_A	1108	Crystal Structure Of Mtr4, A Co-Factor Of The Nucle		2e-22
4f92_B	1724	Brr2 Helicase Region S1087l Length = 1724		2e-07
4f91_B	1724	Brr2 Helicase Region Length = 1724		2e-07
2va8_A	715	Dna Repair Helicase Hel308 Length = 715		3e-05
2p6r_A	702	Crystal Structure Of Superfamily 2 Helicase Hel308		2e-04

>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2 Bound To Amppnp Length = 997

Iteration: 1
 Score =  138 bits (348), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 67/120 (55%), Positives = 89/120 (74%), Gaps = 2/120 (1%)
Query: 164 QTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKT 223
           + EWA ++D++  + +FD  +P  A +WPFELD FQK+A+  LE+ + VFV AHTSAGKT
Sbjct: 9   KKEWAHVVDLNHKIENFDELIPNPARSWPFELDTFQKEAVYHLEQGDSVFVAAHTSAGKT 68
Query: 224 VIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDV--GLIDDLPPVFPDVEKLL 281
           V+AEYAIA++  + T+TIYTSPIKALSNQK+RDF+ETF DV  GLI     + PD   L+
Sbjct: 69  VVAEYAIAMAHRNMTKTIYTSPIKALSNQKFRDFKETFDDVNIGLITGDVQINPDANCLI 128

>pdb|2XGJ|A Chain A, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna Processing And Surveillance Length = 1010

Iteration: 1
 Score =  102 bits (255), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 53/94 (56%), Positives = 63/94 (67%)
Query: 188 AHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIK 247
           A T+PF LD FQ  AI  ++    V V+AHTSAGKTV+AEYAIA S  +K R IYTSPIK
Sbjct: 80  ARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIK 139
Query: 248 ALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLL 281
           ALSNQKYR+    F DVGL+     + PD   L+
Sbjct: 140 ALSNQKYRELLAEFGDVGLMTGDITINPDAGCLV 173

>pdb|3L9O|A Chain A, Crystal Structure Of Mtr4, A Co-Factor Of The Nuclear Exosome Length = 1108

Iteration: 1
 Score =  102 bits (255), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 53/94 (56%), Positives = 63/94 (67%)
Query: 188 AHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIK 247
           A T+PF LD FQ  AI  ++    V V+AHTSAGKTV+AEYAIA S  +K R IYTSPIK
Sbjct: 178 ARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIK 237
Query: 248 ALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLL 281
           ALSNQKYR+    F DVGL+     + PD   L+
Sbjct: 238 ALSNQKYRELLAEFGDVGLMTGDITINPDAGCLV 271

>pdb|4F92|B Chain B, Brr2 Helicase Region S1087l Length = 1724

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/56 (46%), Positives = 39/56 (69%), Gaps = 2/56 (3%)
Query: 210 NHVFVTAHTSAGKTVIAEYAI--ALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD 263
           ++VFV A T +GKT+ AE+AI   L Q+ + R +Y +P++AL+ Q Y D+ E FQD
Sbjct: 943 DNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQD 998

>pdb|4F91|B Chain B, Brr2 Helicase Region Length = 1724

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/56 (46%), Positives = 39/56 (69%), Gaps = 2/56 (3%)
Query: 210 NHVFVTAHTSAGKTVIAEYAI--ALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD 263
           ++VFV A T +GKT+ AE+AI   L Q+ + R +Y +P++AL+ Q Y D+ E FQD
Sbjct: 943 DNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQD 998

>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308 Length = 715

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/63 (38%), Positives = 41/63 (65%), Gaps = 2/63 (3%)
Query: 199 QKQAIIK-LEEHNHVFVTAHTSAGKTVIAEYAI-ALSQNHKTRTIYTSPIKALSNQKYRD 256
           Q +A+ K L E N + +T+ T +GKT+IAE  I +    +  + IY +P++AL+N+KY  
Sbjct: 35  QTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVTPLRALTNEKYLT 94
Query: 257 FRE 259
           F++
Sbjct: 95  FKD 97

>pdb|2P6R|A Chain A, Crystal Structure Of Superfamily 2 Helicase Hel308 In Complex With Unwound Dna Length = 702

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/68 (29%), Positives = 42/68 (61%), Gaps = 1/68 (1%)
Query: 199 QKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFR 258
           Q +A+ K+    ++ +   T+AGKT++AE A+        +++Y  P++AL+ +KY  F+
Sbjct: 30  QAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGEKYESFK 89
Query: 259 ETFQDVGL 266
           + ++ +GL
Sbjct: 90  K-WEKIGL 96

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	333
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	1e-43
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	8e-43
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	1e-42
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	9e-19
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	3e-12
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	5e-11
3b6e_A	216	Interferon-induced helicase C domain-containing P;	6e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-06
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	4e-04
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	5e-04

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A Length = 997

 Score =  159 bits (403), Expect = 1e-43
 Identities = 62/106 (58%), Positives = 84/106 (79%), Gaps = 2/106 (1%)

Query: 164 QTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKT 223
           + EWA ++D++  + +FD  +P  A +WPFELD FQK+A+  LE+ + VFV AHTSAGKT
Sbjct: 9   KKEWAHVVDLNHKIENFDELIPNPARSWPFELDTFQKEAVYHLEQGDSVFVAAHTSAGKT 68

Query: 224 VIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETF--QDVGLI 267
           V+AEYAIA++  + T+TIYTSPIKALSNQK+RDF+ETF   ++GLI
Sbjct: 69  VVAEYAIAMAHRNMTKTIYTSPIKALSNQKFRDFKETFDDVNIGLI 114

>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} Length = 1108

 Score =  157 bits (397), Expect = 8e-43
 Identities = 56/172 (32%), Positives = 78/172 (45%), Gaps = 7/172 (4%)

Query: 103 ENASKFEQGLWESHEVISGDAKEEQEKATVFPSNEEENNVIPQEVDIPILKISNTLPKHV 162
           E+     +           + K ++    V   + E+      +    +        +  
Sbjct: 86  EHEENNSENKKIKSNKSKTEDKNKKVVVPVLADSFEQEASREVDASKGLTNSETLQVEQD 145

Query: 163 TQTEWAEMLDVSKPVLDFDAKVPI-------MAHTWPFELDVFQKQAIIKLEEHNHVFVT 215
            +   +  +     +       PI        A T+PF LD FQ  AI  ++    V V+
Sbjct: 146 GKVRLSHQVRHQVALPPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVS 205

Query: 216 AHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLI 267
           AHTSAGKTV+AEYAIA S  +K R IYTSPIKALSNQKYR+    F DVGL+
Sbjct: 206 AHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLM 257

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae} Length = 1010

 Score =  156 bits (395), Expect = 1e-42
 Identities = 57/159 (35%), Positives = 78/159 (49%), Gaps = 8/159 (5%)

Query: 116 HEVISGDAKEEQEKATVFPSNEEEN-------NVIPQEVDIPILKISNTLPKHVTQTEWA 168
           H     +   +   + +  S E+E          +     + + +       H  + + A
Sbjct: 2   HHHHHENLYFQGAASMLADSFEQEASREVDASKGLTNSETLQVEQDGKVRLSHQVRHQVA 61

Query: 169 EMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEY 228
              +        + K    A T+PF LD FQ  AI  ++    V V+AHTSAGKTV+AEY
Sbjct: 62  LPPNY-DYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEY 120

Query: 229 AIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLI 267
           AIA S  +K R IYTSPIKALSNQKYR+    F DVGL+
Sbjct: 121 AIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLM 159

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 86.3 bits (214), Expect = 9e-19
 Identities = 27/85 (31%), Positives = 51/85 (60%), Gaps = 3/85 (3%)

Query: 184 VPIMAHTWPFELDVFQKQAIIK-LEEHNHVFVTAHTSAGKTVIAEYAI-ALSQNHKTRTI 241
           + I+      +L+  Q +A+ K L E N + +T+ T +GKT+IAE  I +    +  + I
Sbjct: 20  IEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAI 79

Query: 242 YTSPIKALSNQKYRDFRETFQDVGL 266
           Y +P++AL+N+KY  F++ ++ +G 
Sbjct: 80  YVTPLRALTNEKYLTFKD-WELIGF 103

>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 = 66.4 bits (162), Expect = 3e-12
 Identities = 22/73 (30%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQK 253
           EL   Q +A+ K+    ++ +   T+AGKT++AE A+        +++Y  P++AL+ +K
Sbjct: 25  ELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGEK 84

Query: 254 YRDFRETFQDVGL 266
           Y  F++ ++ +GL
Sbjct: 85  YESFKK-WEKIGL 96

>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 = 62.6 bits (152), Expect = 5e-11
 Identities = 23/92 (25%), Positives = 48/92 (52%), Gaps = 4/92 (4%)

Query: 178 LDFDAKVPIMAHTWPFE-LDVFQKQAI-IKLEEHNHVFVTAHTSAGKTVIAEYAIA-LSQ 234
           L  D ++         E     Q +A+   + E  +  ++  T++GKT+IAE A+     
Sbjct: 6   LRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRIL 65

Query: 235 NHKTRTIYTSPIKALSNQKYRDFRETFQDVGL 266
               + +Y  P+KAL+ +K+++F++ ++ +GL
Sbjct: 66  TQGGKAVYIVPLKALAEEKFQEFQD-WEKIGL 96

>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 = 51.7 bits (124), Expect = 6e-08
 Identities = 16/98 (16%), Positives = 31/98 (31%), Gaps = 10/98 (10%)

Query: 174 SKPVLDFDAKVPIMAHTW----PFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYA 229
               +  D+    +A         +L  +Q +      E  ++ +   T +GKT +A Y 
Sbjct: 9   DSGTMGSDSDEENVAARASPEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYI 68

Query: 230 IA------LSQNHKTRTIYTSPIKALSNQKYRDFRETF 261
                      +   + I       L  Q +R   + F
Sbjct: 69  AKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPF 106

>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 = 48.7 bits (115), Expect = 2e-06
 Identities = 50/321 (15%), Positives = 93/321 (28%), Gaps = 73/321 (22%)

Query: 6   VTESSIKIYVDHRALIIPRGGLFWDTLYEYDVITILDPGPRIDDLPPVFPDVEKLLEDLN 65
           VT+        H +L      L   T  E   + +     R  DLP            + 
Sbjct: 277 VTDFLSAATTTHISLDHHSMTL---TPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSI- 332

Query: 66  IGGLDELSIHDFNKHLKFWKPKVQLVAGIINLIQLGGENASKFEQGLWESHEVIS-GDAK 124
           I      SI D       WK    +             N  K    +  S  V+   + +
Sbjct: 333 IA----ESIRDGLATWDNWK---HV-------------NCDKLTTIIESSLNVLEPAEYR 372

Query: 125 EEQEKATVFPSNEEENNVIPQEVDIPILKISNTLPKHVTQTEWAEML-DVSKPVLDFDAK 183
           +  ++ +VFP +            IP           +    W +++      V++   K
Sbjct: 373 KMFDRLSVFPPS----------AHIPT---------ILLSLIWFDVIKSDVMVVVNKLHK 413

Query: 184 VPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAI--ALSQNHKTRT- 240
              +    P E  +      ++L+         H    ++++  Y I      +      
Sbjct: 414 YS-LVEKQPKESTISIPSIYLELKVKLENEYALH----RSIVDHYNIPKTFDSDDLIPPY 468

Query: 241 ----IYTSPI-----KALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLLEDLNIGGLDE 291
                Y S I          ++   FR  F D   ++         +K+  D        
Sbjct: 469 LDQYFY-SHIGHHLKNIEHPERMTLFRMVFLDFRFLE---------QKIRHDSTAWNASG 518

Query: 292 LSIHDFNKHLKFWKPKVQLDD 312
             ++   + LKF+KP +  +D
Sbjct: 519 SILNTLQQ-LKFYKPYICDND 538

>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 = 9e-06
 Identities = 40/296 (13%), Positives = 101/296 (34%), Gaps = 69/296 (23%)

Query: 49  DLPPVFPDVEKLLEDLNIGGLDE-----LSIHDFNKHLKFWKPKVQLVAGIINLIQLGGE 103
           D+  VF   +  +++ +   + +     LS  +   H+   K  V     +   +    E
Sbjct: 20  DILSVF--EDAFVDNFDCKDVQDMPKSILSKEEI-DHIIMSKDAVSGTLRLFWTLLSKQE 76

Query: 104 NASK--FEQGLWESHE-VISGDAKEEQEKATVFPSNEEENNVIPQEVDIPILKISNTLPK 160
              +   E+ L  +++ ++S    E+++ + +     E+ + +    D  +         
Sbjct: 77  EMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYN--DNQVFA-----KY 129

Query: 161 HVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSA 220
           +V++ +         P L               +L    +QA+++L    +V +     +
Sbjct: 130 NVSRLQ---------PYL---------------KL----RQALLELRPAKNVLIDGVLGS 161

Query: 221 GKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKL 280
           GKT +   A+ +  ++K +      I  L+       +       +++ L  +   ++  
Sbjct: 162 GKTWV---ALDVCLSYKVQCKMDFKIFWLN------LKNCNSPETVLEMLQKLLYQIDPN 212

Query: 281 LEDLNIGGLD-ELSIHDFNKHLK---FWKPKVQ----LDDLFDWTMASDATTLEIF 328
               +    + +L IH     L+     KP       L ++       +A     F
Sbjct: 213 WTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNV--Q----NAKAWNAF 262

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 41.1 bits (95), Expect = 4e-04
 Identities = 14/83 (16%), Positives = 31/83 (37%), Gaps = 8/83 (9%)

Query: 187 MAHTW---PFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIA-----LSQNHKT 238
           ++ T    PF+   +Q +  +   +  +  + A T  GKT ++            Q  K 
Sbjct: 3   VSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKG 62

Query: 239 RTIYTSPIKALSNQKYRDFRETF 261
           + ++ +    +  Q    F + F
Sbjct: 63  KVVFFANQIPVYEQNKSVFSKYF 85

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A Length = 677

 Score = 40.7 bits (94), Expect = 5e-04
 Identities = 11/58 (18%), Positives = 24/58 (41%), Gaps = 4/58 (6%)

Query: 210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLI 267
             +F +  T++GKT  A      ++      +Y  P+K L+++ +           L+
Sbjct: 156 KIIFHSGPTNSGKTYHAIQKYFSAK----SGVYCGPLKLLAHEIFEKSNAAGVPCDLV 209

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	333
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.82
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.81
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.81
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.8
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.78
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.78
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.78
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.77
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.77
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.77
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.76
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.76
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.76
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.76
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.76
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.75
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.75
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.74
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.72
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.72
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.71
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.71
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.71
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.71
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.71
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.71
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.7
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.7
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.7
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.7
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.69
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.69
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.68
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.68
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.68
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.67
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.66
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.66
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.66
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.66
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.66
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.66
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.61
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.6
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.6
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.6
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.59
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.59
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.59
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.58
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.58
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.55
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.54
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.53
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.53
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.52
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.44
3h1t_A	590	Type I site-specific restriction-modification syst	99.37
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.34
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.31
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.26
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.25
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.2
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.2
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.2
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.2
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.19
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.18
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.16
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.15
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.15
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.12
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.12
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.1
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.09
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	98.91
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	98.82
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.81
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	98.81
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	98.68
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.1
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.76
3jux_A	822	Protein translocase subunit SECA; protein transloc	97.65
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	97.64
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	97.49
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	97.34
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	97.32
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.22
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	97.21
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	97.14
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	96.94
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	96.7
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	96.67
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	96.63
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	96.51
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	96.04
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	95.37
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	94.82
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	94.47
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	93.96
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	93.44
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	92.89
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	92.81
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	92.73
3bos_A	242	Putative DNA replication factor; P-loop containing	92.46
2qgz_A	308	Helicase loader, putative primosome component; str	92.13
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	92.09
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	91.98
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	91.58
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	91.2
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	91.05
3co5_A	143	Putative two-component system transcriptional RES	91.01
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	90.92
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	90.79
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	90.35
2z43_A	324	DNA repair and recombination protein RADA; archaea	90.23
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	90.22
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	90.12
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	89.84
2cvh_A	220	DNA repair and recombination protein RADB; filamen	89.7
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	89.62
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	89.61
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	89.6
1p9r_A	418	General secretion pathway protein E; bacterial typ	89.36
1u94_A	356	RECA protein, recombinase A; homologous recombinat	89.34
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	89.27
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	89.25
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	89.13
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	89.1
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	88.77
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	88.7
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	88.67
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	88.35
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	88.17
1xp8_A	366	RECA protein, recombinase A; recombination, radior	87.64
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	87.49
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	87.38
3io5_A	333	Recombination and repair protein; storage dimer, i	87.27
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	87.11
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	86.82
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	86.76
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	86.61
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	86.59
2eyu_A	261	Twitching motility protein PILT; pilus retraction	86.55
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	86.48
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	86.31
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	85.9
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	85.86
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	85.78
4a74_A	231	DNA repair and recombination protein RADA; hydrola	85.61
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	84.95
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	84.92
3pvs_A	447	Replication-associated recombination protein A; ma	84.88
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	84.72
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	84.69
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	84.45
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	84.37
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	84.35
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	84.33
2ewv_A	372	Twitching motility protein PILT; pilus retraction	84.16
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	84.07
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	83.8
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	83.62
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	83.59
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	83.58
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	83.58
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	83.47
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	83.47
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	83.47
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	83.43
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	83.4
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	83.35
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	83.18
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	83.15
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	83.12
2r44_A	331	Uncharacterized protein; putative ATPase, structur	83.07
2r6a_A	454	DNAB helicase, replicative helicase; replication,	82.9
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	82.67
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	82.65
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	82.6
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	82.59
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	82.53
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	82.34
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	82.19
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	82.14
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	82.05
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	82.05
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	82.01
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	81.97
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	81.96
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	81.75
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	81.72
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	81.72
2chg_A	226	Replication factor C small subunit; DNA-binding pr	81.63
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	81.61
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	81.6
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	81.52
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	81.38
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	81.29
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	81.03
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	80.9
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	80.74
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	80.7
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	80.63
2xxa_A	433	Signal recognition particle protein; protein trans	80.58
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	80.54
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	80.51
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	80.48
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	80.31
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	80.17
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	80.13

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=99.82  E-value=1.9e-20  Score=205.03  Aligned_cols=135  Identities=41%  Similarity=0.529  Sum_probs=120.3

Q ss_pred             cccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEE
Q psy2760         188 AHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLI  267 (333)
Q Consensus       188 ~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vgll  267 (333)
                      ...++|.|+++|.+|++.+..|++++++||||||||++|.+|++..+..+.+++|++||++|++|++++|++.|+.+|++
T Consensus       178 ~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~g~rvlvl~PtraLa~Q~~~~l~~~~~~Vgll  257 (1108)
T 3l9o_A          178 ARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLM  257 (1108)
T ss_dssp             SSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHHHHTSSEEEE
T ss_pred             HHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEcCcHHHHHHHHHHHHHHhCCccEE
Confidence            45678899999999999999999999999999999999999999988899999999999999999999999999999999


Q ss_pred             eCCCCCCCCcceEEecc---------------CcceEeccccccccccCcCcccccchh---hhhhheeccCc
Q psy2760         268 DDLPPVFPDVEKLLEDL---------------NIGGLDELSIHDFNKHLKFWKPKVQLD---DLFDWTMASDA  322 (333)
Q Consensus       268 tGd~~~~~~a~ili~t~---------------~i~liViDe~H~~~~~~R~~~~~~~l~---~l~~l~~~~d~  322 (333)
                      +|+.+.+.+..++|+|+               ++.++|+||+|++.+.+|+..|...+.   ..++++++|++
T Consensus       258 tGd~~~~~~~~IlV~Tpe~L~~~L~~~~~~l~~l~lVVIDEaH~l~d~~rg~~~e~ii~~l~~~~qvl~lSAT  330 (1108)
T 3l9o_A          258 TGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSAT  330 (1108)
T ss_dssp             CSSCBCCCSCSEEEEEHHHHHHHHHHCSSHHHHEEEEEEETGGGTTSHHHHHHHHHHHHHSCTTSEEEEEECS
T ss_pred             eCccccCCCCCEEEeChHHHHHHHHcCccccccCCEEEEhhhhhccccchHHHHHHHHHhcCCCceEEEEcCC
Confidence            99999999999999985               578999999999998888866654222   23567777776

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.81  E-value=5.4e-20  Score=199.69  Aligned_cols=162  Identities=42%  Similarity=0.641  Sum_probs=141.1

Q ss_pred             CcccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEE
Q psy2760         163 TQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIY  242 (333)
Q Consensus       163 ~~~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~  242 (333)
                      ...+|+...++..++.+|....+.....+||.|+++|.++++.+..|++++++||||||||++|.+++......+.+++|
T Consensus         8 ~~~~wa~~~~~~~~~~~f~~l~~~~~~~~~f~l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~~g~~vlv   87 (997)
T 4a4z_A            8 VKKEWAHVVDLNHKIENFDELIPNPARSWPFELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRNMTKTIY   87 (997)
T ss_dssp             -CCCSEEECCTTCCCTTHHHHCSSCSCCCSSCCCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHHTTCEEEE
T ss_pred             ccccccchhcccccccchhhhhHhHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHhcCCeEEE
Confidence            45688887788888888888888888899999999999999999999999999999999999999999988888999999


Q ss_pred             EcccHHHHHHHHHHHHHhcC--CcEEEeCCCCCCCCcceEEecc---------------CcceEeccccccccccCcCcc
Q psy2760         243 TSPIKALSNQKYRDFRETFQ--DVGLIDDLPPVFPDVEKLLEDL---------------NIGGLDELSIHDFNKHLKFWK  305 (333)
Q Consensus       243 l~PtraLa~Q~~~~l~~~f~--~vglltGd~~~~~~a~ili~t~---------------~i~liViDe~H~~~~~~R~~~  305 (333)
                      ++|+++|+.|++++|++.|+  .++.++|+...+.+..++++|+               ++.++|+||+|++.+..|+..
T Consensus        88 l~PtraLa~Q~~~~l~~~~~~~~v~~l~G~~~~~~~~~IlV~Tpe~L~~~l~~~~~~l~~l~lvViDEaH~l~d~~~g~~  167 (997)
T 4a4z_A           88 TSPIKALSNQKFRDFKETFDDVNIGLITGDVQINPDANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQDRGVV  167 (997)
T ss_dssp             EESCGGGHHHHHHHHHTTC--CCEEEECSSCEECTTSSEEEEEHHHHHHHHHHTCSGGGGEEEEEECCTTCCCTTCTTCC
T ss_pred             EeCCHHHHHHHHHHHHHHcCCCeEEEEeCCCccCCCCCEEEECHHHHHHHHHhCchhhcCCCEEEEECcccccccchHHH
Confidence            99999999999999999886  4899999999988899999986               578899999999999888888


Q ss_pred             cccchhh---hhhheeccCcch
Q psy2760         306 PKVQLDD---LFDWTMASDATT  324 (333)
Q Consensus       306 ~~~~l~~---l~~l~~~~d~~~  324 (333)
                      |...+..   .++++++|++.+
T Consensus       168 ~e~ii~~l~~~v~iIlLSAT~~  189 (997)
T 4a4z_A          168 WEEVIIMLPQHVKFILLSATVP  189 (997)
T ss_dssp             HHHHHHHSCTTCEEEEEECCCT
T ss_pred             HHHHHHhcccCCCEEEEcCCCC
Confidence            7753332   366788888753

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=99.81  E-value=2.5e-19  Score=160.80  Aligned_cols=157  Identities=13%  Similarity=-0.029  Sum_probs=114.0

Q ss_pred             CcccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc-------
Q psy2760         163 TQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN-------  235 (333)
Q Consensus       163 ~~~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~-------  235 (333)
                      +...|.+..++++.+...+...++.      .|+++|.++++.+.+|++++++||||||||++|++|++..+.       
T Consensus        17 p~~~f~~~~~l~~~l~~~l~~~g~~------~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~   90 (228)
T 3iuy_A           17 PTCRFKDAFQQYPDLLKSIIRVGIL------KPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISRE   90 (228)
T ss_dssp             CCCSHHHHHTTCHHHHHHHHHHTCC------SCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC-------
T ss_pred             ChhhHhhhhccCHHHHHHHHHCCCC------CCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhh
Confidence            3445666567888888877766665      799999999999999999999999999999999999886442       


Q ss_pred             --CCCeEEEEcccHHHHHHHHHHHHHhcC---CcEEEeCCCCCCCC-------cceEEecc---------------Ccce
Q psy2760         236 --HKTRTIYTSPIKALSNQKYRDFRETFQ---DVGLIDDLPPVFPD-------VEKLLEDL---------------NIGG  288 (333)
Q Consensus       236 --~g~ral~l~PtraLa~Q~~~~l~~~f~---~vglltGd~~~~~~-------a~ili~t~---------------~i~l  288 (333)
                        .+.+++|++||++|+.|+++++++...   .++.++|+.....+       ..++++|+               ++.+
T Consensus        91 ~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~~~  170 (228)
T 3iuy_A           91 QRNGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITY  170 (228)
T ss_dssp             --CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC------CHHHHHSCCSEEEECHHHHHHHHHTTCCCCTTCCE
T ss_pred             ccCCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCcCcccceE
Confidence              678899999999999999999988532   26777777665433       37888875               4788


Q ss_pred             EeccccccccccCcCcccccchhhh----hhheeccCcchhh
Q psy2760         289 LDELSIHDFNKHLKFWKPKVQLDDL----FDWTMASDATTLE  326 (333)
Q Consensus       289 iViDe~H~~~~~~R~~~~~~~l~~l----~~l~~~~d~~~~e  326 (333)
                      +|+||+|.+...+++..... ++..    .+.+++|++-.-+
T Consensus       171 lViDEah~~~~~~~~~~~~~-i~~~~~~~~~~l~~SAT~~~~  211 (228)
T 3iuy_A          171 LVIDEADKMLDMEFEPQIRK-ILLDVRPDRQTVMTSATWPDT  211 (228)
T ss_dssp             EEECCHHHHHHTTCHHHHHH-HHHHSCSSCEEEEEESCCCHH
T ss_pred             EEEECHHHHhccchHHHHHH-HHHhCCcCCeEEEEEeeCCHH
Confidence            99999998876543222221 2222    3456777764433

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.80  E-value=8.9e-20  Score=198.20  Aligned_cols=136  Identities=41%  Similarity=0.524  Sum_probs=121.1

Q ss_pred             cccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEE
Q psy2760         188 AHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLI  267 (333)
Q Consensus       188 ~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vgll  267 (333)
                      ...+||.|+++|.+|++.+..|++++++||||||||++|.++++..+..+.+++|++||++|++|++++|++.|+.+|++
T Consensus        80 ~~~~~f~L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~g~rvL~l~PtkaLa~Q~~~~l~~~~~~vgll  159 (1010)
T 2xgj_A           80 ARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLM  159 (1010)
T ss_dssp             SCCCSSCCCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHHHHHSCEEEE
T ss_pred             HHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhccCCeEEEECChHHHHHHHHHHHHHHhCCEEEE
Confidence            56789999999999999999999999999999999999999999888889999999999999999999999999999999


Q ss_pred             eCCCCCCCCcceEEecc---------------CcceEeccccccccccCcCcccccchh---hhhhheeccCcc
Q psy2760         268 DDLPPVFPDVEKLLEDL---------------NIGGLDELSIHDFNKHLKFWKPKVQLD---DLFDWTMASDAT  323 (333)
Q Consensus       268 tGd~~~~~~a~ili~t~---------------~i~liViDe~H~~~~~~R~~~~~~~l~---~l~~l~~~~d~~  323 (333)
                      +|+.+.+.++.++|+|+               ++.++|+||+|++.+..|+..|...+.   ..++++++|++-
T Consensus       160 tGd~~~~~~~~IvV~Tpe~L~~~L~~~~~~l~~l~lVViDEaH~l~d~~rg~~~e~il~~l~~~~~il~LSATi  233 (1010)
T 2xgj_A          160 TGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATI  233 (1010)
T ss_dssp             CSSCEECTTCSEEEEEHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHHHHHHHHHSCTTCEEEEEECCC
T ss_pred             eCCCccCCCCCEEEEcHHHHHHHHHcCcchhhcCCEEEEechhhhcccchhHHHHHHHHhcCCCCeEEEEcCCC
Confidence            99999998899999986               578999999999999999987765222   235567777753

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=99.78  E-value=1.4e-18  Score=164.40  Aligned_cols=154  Identities=9%  Similarity=0.034  Sum_probs=114.6

Q ss_pred             ccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcC--CcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcc
Q psy2760         171 LDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEH--NHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSP  245 (333)
Q Consensus       171 ~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g--~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~P  245 (333)
                      .+|++.+...+...++.      .|+++|.++++.++.|  ++++++||||||||++|++|++..+.   .+.++||++|
T Consensus        97 l~l~~~l~~~l~~~g~~------~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~lil~P  170 (300)
T 3fmo_B           97 LRLKPQLLQGVYAMGFN------RPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSP  170 (300)
T ss_dssp             GTCCHHHHHHHHHTTCC------SCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECS
T ss_pred             cCCCHHHHHHHHHcCCC------CCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccCCCceEEEEcC
Confidence            35788888777666655      8999999999999887  99999999999999999999997653   3458999999


Q ss_pred             cHHHHHHHHHHHHHhcC---C--cEEEeCCCCCCC----CcceEEecc----------------CcceEecccccccccc
Q psy2760         246 IKALSNQKYRDFRETFQ---D--VGLIDDLPPVFP----DVEKLLEDL----------------NIGGLDELSIHDFNKH  300 (333)
Q Consensus       246 traLa~Q~~~~l~~~f~---~--vglltGd~~~~~----~a~ili~t~----------------~i~liViDe~H~~~~~  300 (333)
                      ||+||.|+++.+++...   .  ++...|+.....    ...++|+|+                ++.++|+||+|.+.+.
T Consensus       171 treLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~l~~l~~lVlDEad~l~~~  250 (300)
T 3fmo_B          171 TYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIAT  250 (300)
T ss_dssp             SHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTCCCCCSEEEECHHHHHHHHTTTCCCCGGGCSEEEETTHHHHHHS
T ss_pred             cHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhhcCCCCEEEECHHHHHHHHHhcCCCChhhceEEEEeCHHHHhhc
Confidence            99999999999877543   2  566777665433    236888875                4678999999987753


Q ss_pred             CcCcccccchhh----hhhheeccCcchhhhhhc
Q psy2760         301 LKFWKPKVQLDD----LFDWTMASDATTLEIFTY  330 (333)
Q Consensus       301 ~R~~~~~~~l~~----l~~l~~~~d~~~~e~~~~  330 (333)
                      .++......+..    ..+.+++|++-.-++...
T Consensus       251 ~~~~~~~~~i~~~~~~~~q~i~~SAT~~~~v~~~  284 (300)
T 3fmo_B          251 QGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKF  284 (300)
T ss_dssp             TTHHHHHHHHHTTSCTTCEEEEEESCCCHHHHHH
T ss_pred             cCcHHHHHHHHHhCCCCCEEEEEeccCCHHHHHH
Confidence            322222221222    245778888777666543

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=99.78  E-value=5e-19  Score=160.52  Aligned_cols=160  Identities=14%  Similarity=0.119  Sum_probs=116.8

Q ss_pred             CcccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc----CCC
Q psy2760         163 TQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN----HKT  238 (333)
Q Consensus       163 ~~~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~----~g~  238 (333)
                      ++.++....++++.+...+...|+.      .|+++|.++++.+..|++++++||||||||++|.+|++..+.    .+.
T Consensus        26 ~f~~l~~~~~l~~~l~~~l~~~g~~------~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~   99 (245)
T 3dkp_A           26 TFQQLDQEYKINSRLLQNILDAGFQ------MPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGF   99 (245)
T ss_dssp             SHHHHHHHHCCCHHHHHHHHHTTCC------SCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHCSCCSSSC
T ss_pred             CHHHhhhccCCCHHHHHHHHHCCCC------CCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHhhcccCCc
Confidence            5666655568888888877666655      799999999999999999999999999999999999986653    567


Q ss_pred             eEEEEcccHHHHHHHHHHHHHhcCC----cEEEeCCCC--------CCCCcceEEecc-----------------CcceE
Q psy2760         239 RTIYTSPIKALSNQKYRDFRETFQD----VGLIDDLPP--------VFPDVEKLLEDL-----------------NIGGL  289 (333)
Q Consensus       239 ral~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~--------~~~~a~ili~t~-----------------~i~li  289 (333)
                      +++|++||++|+.|+++++++.+..    ++.++|+..        ......++++|+                 ++.++
T Consensus       100 ~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~~~l  179 (245)
T 3dkp_A          100 RALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWL  179 (245)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTSCCCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSCSCCCTTCCEE
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCCCcccccCcEE
Confidence            8999999999999999999887654    333443321        122346888874                 46779


Q ss_pred             eccccccccccC-cCcccccc-hh-----hhhhheeccCcchhhhh
Q psy2760         290 DELSIHDFNKHL-KFWKPKVQ-LD-----DLFDWTMASDATTLEIF  328 (333)
Q Consensus       290 ViDe~H~~~~~~-R~~~~~~~-l~-----~l~~l~~~~d~~~~e~~  328 (333)
                      |+||+|.+.+.+ +++..... ++     ...+.+++|++-.-++.
T Consensus       180 ViDEah~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~SAT~~~~v~  225 (245)
T 3dkp_A          180 VVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVE  225 (245)
T ss_dssp             EESSHHHHHHHC--CHHHHHHHHHHHCCCTTCEEEEEESSCCHHHH
T ss_pred             EEeChHHhcccccccHHHHHHHHHHhcCCCCcEEEEEeccCCHHHH
Confidence            999999987654 34433221 11     12456777777554443

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=99.78  E-value=3.2e-19  Score=164.99  Aligned_cols=157  Identities=16%  Similarity=0.078  Sum_probs=114.9

Q ss_pred             CcccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh-------c
Q psy2760         163 TQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ-------N  235 (333)
Q Consensus       163 ~~~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l-------~  235 (333)
                      .|..|..  .+++.+...++..|+.      .|+++|.++++.+..|++++++||||||||++|.+|++..+       .
T Consensus        53 ~f~~l~~--~l~~~l~~~l~~~g~~------~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~  124 (262)
T 3ly5_A           53 SFASLCN--LVNENTLKAIKEMGFT------NMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPR  124 (262)
T ss_dssp             CC-------CCCHHHHHHHHHTTCC------BCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGG
T ss_pred             ChhHhcc--ccCHHHHHHHHHCCCC------CCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhcccccc
Confidence            4555543  4677777777665554      79999999999999999999999999999999999998544       2


Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHhcCC----cEEEeCCCCCCC-------CcceEEecc----------------Ccce
Q psy2760         236 HKTRTIYTSPIKALSNQKYRDFRETFQD----VGLIDDLPPVFP-------DVEKLLEDL----------------NIGG  288 (333)
Q Consensus       236 ~g~ral~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~~~~-------~a~ili~t~----------------~i~l  288 (333)
                      .+.+++|++|||+|+.|+++.+++.+..    ++.++|+.....       ...++|+|+                ++.+
T Consensus       125 ~~~~~lil~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~  204 (262)
T 3ly5_A          125 NGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQC  204 (262)
T ss_dssp             GCCCEEEECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHCTTCCCTTCCE
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHccCCcccccCCE
Confidence            5788999999999999999999887653    678888876432       246888874                4788


Q ss_pred             EeccccccccccCcCcccccchhh----hhhheeccCcchhhhh
Q psy2760         289 LDELSIHDFNKHLKFWKPKVQLDD----LFDWTMASDATTLEIF  328 (333)
Q Consensus       289 iViDe~H~~~~~~R~~~~~~~l~~----l~~l~~~~d~~~~e~~  328 (333)
                      +|+||+|.+.+.+++-.... +..    ..+.+++|++..-++.
T Consensus       205 lViDEah~l~~~~~~~~l~~-i~~~~~~~~q~l~~SAT~~~~v~  247 (262)
T 3ly5_A          205 LVIDEADRILDVGFEEELKQ-IIKLLPTRRQTMLFSATQTRKVE  247 (262)
T ss_dssp             EEECSHHHHHHTTCHHHHHH-HHHHSCSSSEEEEECSSCCHHHH
T ss_pred             EEEcChHHHhhhhHHHHHHH-HHHhCCCCCeEEEEEecCCHHHH
Confidence            99999998876542222111 222    2346777877665543

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=99.77  E-value=1.7e-18  Score=152.37  Aligned_cols=151  Identities=9%  Similarity=-0.055  Sum_probs=113.4

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~Ptra  248 (333)
                      ++++.+...+...|+.      .|+++|.++++.+..|+++++++|||||||++|.++++..+.   .+.+++|++||++
T Consensus         9 ~l~~~l~~~l~~~g~~------~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~   82 (206)
T 1vec_A            9 CLKRELLMGIFEMGWE------KPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRE   82 (206)
T ss_dssp             CCCHHHHHHHHTTTCC------SCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHH
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhcccCCCeeEEEEeCcHH
Confidence            4677777777655554      799999999999999999999999999999999999986653   4568999999999


Q ss_pred             HHHHHHHHHHHhcC---C--cEEEeCCCCCC-------CCcceEEecc---------------CcceEeccccccccccC
Q psy2760         249 LSNQKYRDFRETFQ---D--VGLIDDLPPVF-------PDVEKLLEDL---------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       249 La~Q~~~~l~~~f~---~--vglltGd~~~~-------~~a~ili~t~---------------~i~liViDe~H~~~~~~  301 (333)
                      |+.|+++.+++.+.   +  ++.++|+....       ....++++|+               ++.++|+||+|.+.+.+
T Consensus        83 L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~  162 (206)
T 1vec_A           83 LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQD  162 (206)
T ss_dssp             HHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTT
T ss_pred             HHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcCCCCCEEEeCHHHHHHHHHcCCcCcccCCEEEEEChHHhHhhC
Confidence            99999999987653   2  67788876532       3456888876               56889999999876643


Q ss_pred             cCcccccchhh----hhhheeccCcchhhhhh
Q psy2760         302 KFWKPKVQLDD----LFDWTMASDATTLEIFT  329 (333)
Q Consensus       302 R~~~~~~~l~~----l~~l~~~~d~~~~e~~~  329 (333)
                      .+..... +..    ..+.+++|++..-++..
T Consensus       163 ~~~~l~~-i~~~~~~~~~~l~~SAT~~~~~~~  193 (206)
T 1vec_A          163 FVQIMED-IILTLPKNRQILLYSATFPLSVQK  193 (206)
T ss_dssp             THHHHHH-HHHHSCTTCEEEEEESCCCHHHHH
T ss_pred             cHHHHHH-HHHhCCccceEEEEEeeCCHHHHH
Confidence            2211111 222    24567778777655543

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=99.77  E-value=2.7e-18  Score=156.61  Aligned_cols=150  Identities=13%  Similarity=-0.013  Sum_probs=109.9

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc------------CCCe
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN------------HKTR  239 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~------------~g~r  239 (333)
                      ++++.+.+.+...++.      .|+++|.++++.+..|+++++++|||||||++|+++++..+.            .+.+
T Consensus        29 ~l~~~l~~~l~~~g~~------~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~~~  102 (253)
T 1wrb_A           29 KLDPTIRNNILLASYQ------RPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPK  102 (253)
T ss_dssp             SCCCSTTTTTTTTTCC------SCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCS
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCCce
Confidence            4566666655544444      799999999999999999999999999999999999986542            2468


Q ss_pred             EEEEcccHHHHHHHHHHHHHhcCC----cEEEeCCCCCC-------CCcceEEecc---------------CcceEeccc
Q psy2760         240 TIYTSPIKALSNQKYRDFRETFQD----VGLIDDLPPVF-------PDVEKLLEDL---------------NIGGLDELS  293 (333)
Q Consensus       240 al~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~~~-------~~a~ili~t~---------------~i~liViDe  293 (333)
                      +||++|||+|+.|+++++++....    ++.+.|+....       ....++++|+               ++.++|+||
T Consensus       103 ~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~lViDE  182 (253)
T 1wrb_A          103 CLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDE  182 (253)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEEEEET
T ss_pred             EEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhCCCCCEEEECHHHHHHHHHcCCCChhhCCEEEEeC
Confidence            999999999999999999875542    57778876543       2346888876               356899999


Q ss_pred             cccccccCcCcccccchhh--------hhhheeccCcchhhhh
Q psy2760         294 IHDFNKHLKFWKPKVQLDD--------LFDWTMASDATTLEIF  328 (333)
Q Consensus       294 ~H~~~~~~R~~~~~~~l~~--------l~~l~~~~d~~~~e~~  328 (333)
                      +|.+.+.+++-.... ++.        ..+.+++|++..-++.
T Consensus       183 ah~~~~~~~~~~~~~-i~~~~~~~~~~~~q~l~~SAT~~~~~~  224 (253)
T 1wrb_A          183 ADRMLDMGFEPQIRK-IIEESNMPSGINRQTLMFSATFPKEIQ  224 (253)
T ss_dssp             HHHHHHTTCHHHHHH-HHHSSCCCCGGGCEEEEEESSCCHHHH
T ss_pred             HHHHHhCchHHHHHH-HHhhccCCCCCCcEEEEEEEeCCHHHH
Confidence            998765543222111 222        2346777777665543

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=99.77  E-value=5.2e-19  Score=160.79  Aligned_cols=149  Identities=17%  Similarity=0.016  Sum_probs=110.7

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc--------CCCeEEEE
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN--------HKTRTIYT  243 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~--------~g~ral~l  243 (333)
                      ++++.+.+.+...++.      .|+++|.++++.+..|++++++||||||||++|++|++..+.        .+.+++|+
T Consensus        35 ~l~~~l~~~l~~~g~~------~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~~~~lil  108 (242)
T 3fe2_A           35 NFPANVMDVIARQNFT------EPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVL  108 (242)
T ss_dssp             TCCHHHHHHHHTTTCC------SCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCCCSEEEE
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhccccccCCCCEEEEE
Confidence            5677777776665544      699999999999999999999999999999999999986543        46789999


Q ss_pred             cccHHHHHHHHHHHHHhcC----CcEEEeCCCCCCC-------CcceEEecc---------------CcceEeccccccc
Q psy2760         244 SPIKALSNQKYRDFRETFQ----DVGLIDDLPPVFP-------DVEKLLEDL---------------NIGGLDELSIHDF  297 (333)
Q Consensus       244 ~PtraLa~Q~~~~l~~~f~----~vglltGd~~~~~-------~a~ili~t~---------------~i~liViDe~H~~  297 (333)
                      +|||+|+.|+++.+++...    .++.++|+.....       ...++++|+               ++.++|+||+|.+
T Consensus       109 ~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~lViDEah~l  188 (242)
T 3fe2_A          109 APTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRM  188 (242)
T ss_dssp             CSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHHTSCCCTTCCEEEETTHHHH
T ss_pred             eCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCCcccccEEEEeCHHHH
Confidence            9999999999998877543    2677888866432       246888876               5678999999988


Q ss_pred             cccCcCcccccchhh----hhhheeccCcchhhh
Q psy2760         298 NKHLKFWKPKVQLDD----LFDWTMASDATTLEI  327 (333)
Q Consensus       298 ~~~~R~~~~~~~l~~----l~~l~~~~d~~~~e~  327 (333)
                      .+.+++-.... +++    ..+.+++|++-.-++
T Consensus       189 ~~~~~~~~~~~-i~~~~~~~~q~~~~SAT~~~~~  221 (242)
T 3fe2_A          189 LDMGFEPQIRK-IVDQIRPDRQTLMWSATWPKEV  221 (242)
T ss_dssp             HHTTCHHHHHH-HHTTSCSSCEEEEEESCCCHHH
T ss_pred             hhhCcHHHHHH-HHHhCCccceEEEEEeecCHHH
Confidence            76542221111 121    234677777654443

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.76  E-value=2.4e-18  Score=155.13  Aligned_cols=149  Identities=17%  Similarity=0.057  Sum_probs=110.3

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh-------cCCCeEEEEc
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ-------NHKTRTIYTS  244 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l-------~~g~ral~l~  244 (333)
                      ++++.+...++..++.      .|+++|.++++.+..|+++++++|||||||++|.++++..+       ..+.+++|++
T Consensus        31 ~l~~~l~~~l~~~~~~------~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~lil~  104 (236)
T 2pl3_A           31 PLSKKTLKGLQEAQYR------LVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIIS  104 (236)
T ss_dssp             CCCHHHHHHHHHTTCC------BCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEEC
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceEEEEe
Confidence            4777777777665555      79999999999999999999999999999999999988553       3578999999


Q ss_pred             ccHHHHHHHHHHHHHhcCC----cEEEeCCCCCC------CCcceEEecc----------------CcceEecccccccc
Q psy2760         245 PIKALSNQKYRDFRETFQD----VGLIDDLPPVF------PDVEKLLEDL----------------NIGGLDELSIHDFN  298 (333)
Q Consensus       245 PtraLa~Q~~~~l~~~f~~----vglltGd~~~~------~~a~ili~t~----------------~i~liViDe~H~~~  298 (333)
                      ||++|+.|+++.+++.+..    ++.++|+....      ....++++|+                ++.++|+||+|.+.
T Consensus       105 Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~~~  184 (236)
T 2pl3_A          105 PTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERINNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRIL  184 (236)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHHTTCSEEEECHHHHHHHHHHCSSCCCTTCCEEEETTHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhCCCCCEEEECHHHHHHHHHhcCCcccccccEEEEeChHHHh
Confidence            9999999999999886542    67788876543      2346888875                45689999999876


Q ss_pred             ccCcCcccccchhh----hhhheeccCcchhhh
Q psy2760         299 KHLKFWKPKVQLDD----LFDWTMASDATTLEI  327 (333)
Q Consensus       299 ~~~R~~~~~~~l~~----l~~l~~~~d~~~~e~  327 (333)
                      +.+.+..... ++.    ..+.+++|++.+-++
T Consensus       185 ~~~~~~~~~~-i~~~~~~~~~~l~~SAT~~~~~  216 (236)
T 2pl3_A          185 DMGFADTMNA-VIENLPKKRQTLLFSATQTKSV  216 (236)
T ss_dssp             HTTTHHHHHH-HHHTSCTTSEEEEEESSCCHHH
T ss_pred             cCCcHHHHHH-HHHhCCCCCeEEEEEeeCCHHH
Confidence            5542222111 222    233677777654443

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=99.76  E-value=2.6e-18  Score=153.32  Aligned_cols=150  Identities=13%  Similarity=0.018  Sum_probs=108.8

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh---cCCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ---NHKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l---~~g~ral~l~Ptra  248 (333)
                      ++++.+...+...++.      .|+++|.++++.+..|+++++++|||||||++|.++++..+   ..+.+++|++||++
T Consensus        20 ~l~~~l~~~l~~~g~~------~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   93 (224)
T 1qde_A           20 ELDENLLRGVFGYGFE------EPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRE   93 (224)
T ss_dssp             TCCHHHHHHHHHHTCC------SCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHH
T ss_pred             CCCHHHHHHHHHCCCC------CCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEEEECCHH
Confidence            4777777776665554      79999999999999999999999999999999999998765   34678999999999


Q ss_pred             HHHHHHHHHHHhcCC----cEEEeCCCCCCC------CcceEEecc---------------CcceEeccccccccccCcC
Q psy2760         249 LSNQKYRDFRETFQD----VGLIDDLPPVFP------DVEKLLEDL---------------NIGGLDELSIHDFNKHLKF  303 (333)
Q Consensus       249 La~Q~~~~l~~~f~~----vglltGd~~~~~------~a~ili~t~---------------~i~liViDe~H~~~~~~R~  303 (333)
                      |+.|+++.+++.+..    ++.++|+.....      ...++++|+               ++.++|+||+|.+.+.+.+
T Consensus        94 L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~  173 (224)
T 1qde_A           94 LALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFK  173 (224)
T ss_dssp             HHHHHHHHHHHHTTTSCCCEEEECC----------CTTCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhcCCCCCEEEECHHHHHHHHHhCCcchhhCcEEEEcChhHHhhhhhH
Confidence            999999999886542    677777765432      246888875               3688999999987654322


Q ss_pred             cccccchhh----hhhheeccCcchhhhh
Q psy2760         304 WKPKVQLDD----LFDWTMASDATTLEIF  328 (333)
Q Consensus       304 ~~~~~~l~~----l~~l~~~~d~~~~e~~  328 (333)
                      -.... +..    ..+.+++|++..-++.
T Consensus       174 ~~l~~-i~~~~~~~~~~i~lSAT~~~~~~  201 (224)
T 1qde_A          174 EQIYQ-IFTLLPPTTQVVLLSATMPNDVL  201 (224)
T ss_dssp             HHHHH-HHHHSCTTCEEEEEESSCCHHHH
T ss_pred             HHHHH-HHHhCCccCeEEEEEeecCHHHH
Confidence            11111 222    2336777777665543

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=99.76  E-value=3.5e-18  Score=154.15  Aligned_cols=150  Identities=13%  Similarity=-0.011  Sum_probs=112.0

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh---cCCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ---NHKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l---~~g~ral~l~Ptra  248 (333)
                      ++++.+.+.++..++.      .|+++|.++++.+..|+++++++|||||||++|.++++..+   ..+.+++|++||++
T Consensus        30 ~l~~~l~~~l~~~g~~------~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~  103 (230)
T 2oxc_A           30 LLSRPVLEGLRAAGFE------RPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTRE  103 (230)
T ss_dssp             TCCHHHHHHHHHTTCC------SCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEeCCHH
Confidence            5777788777665544      69999999999999999999999999999999999998665   34579999999999


Q ss_pred             HHHHHHHHHHHhcC---C--cEEEeCCCCCC------CCcceEEecc---------------CcceEeccccccccccCc
Q psy2760         249 LSNQKYRDFRETFQ---D--VGLIDDLPPVF------PDVEKLLEDL---------------NIGGLDELSIHDFNKHLK  302 (333)
Q Consensus       249 La~Q~~~~l~~~f~---~--vglltGd~~~~------~~a~ili~t~---------------~i~liViDe~H~~~~~~R  302 (333)
                      |+.|+++++++...   +  ++.++|+....      ....++++|+               ++.++|+||+|.+...+.
T Consensus       104 L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~~~lViDEah~~~~~~~  183 (230)
T 2oxc_A          104 IAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKKCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGS  183 (230)
T ss_dssp             HHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHTTSCSEEEECHHHHHHHHHTTSSCGGGCCEEEESSHHHHHSTTS
T ss_pred             HHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhccCCCEEEECHHHHHHHHhcCCcccccCCEEEeCCchHhhcCcc
Confidence            99999999987543   2  67888886532      2356888876               356899999999865531


Q ss_pred             Ccccc-cchhh----hhhheeccCcchhhhh
Q psy2760         303 FWKPK-VQLDD----LFDWTMASDATTLEIF  328 (333)
Q Consensus       303 ~~~~~-~~l~~----l~~l~~~~d~~~~e~~  328 (333)
                       +... ..+..    ..+.+++|++..-++.
T Consensus       184 -~~~~~~~i~~~~~~~~~~l~lSAT~~~~~~  213 (230)
T 2oxc_A          184 -FQEQINWIYSSLPASKQMLAVSATYPEFLA  213 (230)
T ss_dssp             -SHHHHHHHHHHSCSSCEEEEEESCCCHHHH
T ss_pred             -hHHHHHHHHHhCCCCCeEEEEEeccCHHHH
Confidence             2211 11222    2346777777655543

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=99.76  E-value=3.2e-18  Score=150.46  Aligned_cols=149  Identities=13%  Similarity=-0.018  Sum_probs=112.7

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc------CCCeEEEEcc
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN------HKTRTIYTSP  245 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~------~g~ral~l~P  245 (333)
                      ++++.+...++..++.      .|+++|.++++.+.+|+++++++|||||||++|.++++..+.      .+.+++|++|
T Consensus         7 ~l~~~l~~~l~~~~~~------~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P   80 (207)
T 2gxq_A            7 PLKPEILEALHGRGLT------TPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTP   80 (207)
T ss_dssp             CCCHHHHHHHHHTTCC------SCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECS
T ss_pred             CCCHHHHHHHHHcCCC------CCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEEC
Confidence            5777777777665555      799999999999999999999999999999999999987653      5678999999


Q ss_pred             cHHHHHHHHHHHHHhcCC--cEEEeCCCCCC-------CCcceEEecc---------------CcceEeccccccccccC
Q psy2760         246 IKALSNQKYRDFRETFQD--VGLIDDLPPVF-------PDVEKLLEDL---------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       246 traLa~Q~~~~l~~~f~~--vglltGd~~~~-------~~a~ili~t~---------------~i~liViDe~H~~~~~~  301 (333)
                      |++|+.|+++.+++.++.  ++.++|+....       ....++++|+               ++.++|+||+|.+.+.+
T Consensus        81 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~  160 (207)
T 2gxq_A           81 TRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMG  160 (207)
T ss_dssp             SHHHHHHHHHHHHHHCTTSCEEEECSSSCSHHHHHHHHHCCSEEEECHHHHHHHHHHTSSCCTTCSEEEEESHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHHhhcceEEEEECCCChHHHHHHhhCCCCEEEECHHHHHHHHHcCCcchhhceEEEEEChhHhhccc
Confidence            999999999999887654  67788876542       2346888875               46889999999876543


Q ss_pred             cCcccccchhh----hhhheeccCcchhhh
Q psy2760         302 KFWKPKVQLDD----LFDWTMASDATTLEI  327 (333)
Q Consensus       302 R~~~~~~~l~~----l~~l~~~~d~~~~e~  327 (333)
                      .+..... +..    ..+.+++|++..-++
T Consensus       161 ~~~~~~~-i~~~~~~~~~~i~~SAT~~~~~  189 (207)
T 2gxq_A          161 FEEEVEA-LLSATPPSRQTLLFSATLPSWA  189 (207)
T ss_dssp             CHHHHHH-HHHTSCTTSEEEEECSSCCHHH
T ss_pred             hHHHHHH-HHHhCCccCeEEEEEEecCHHH
Confidence            2211111 111    234677777765443

>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=99.76  E-value=2.8e-18  Score=194.58  Aligned_cols=116  Identities=16%  Similarity=0.157  Sum_probs=100.3

Q ss_pred             CCCHHHHHHHHHH-HcCCcEEEEcCCCCcHHHHHHHHHHHHhc-----------CCCeEEEEcccHHHHHHHHHHHHHhc
Q psy2760         194 ELDVFQKQAIIKL-EEHNHVFVTAHTSAGKTVIAEYAIALSQN-----------HKTRTIYTSPIKALSNQKYRDFRETF  261 (333)
Q Consensus       194 ~l~~~Q~~ai~~l-~~g~~vlv~apTGSGKTl~~~l~il~~l~-----------~g~ral~l~PtraLa~Q~~~~l~~~f  261 (333)
                      .|+++|.++++.+ .+++|++++||||||||++|+++|+..+.           .+.++||++|+||||+|+++.|+++|
T Consensus        79 ~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~kALa~e~~~~l~~~~  158 (1724)
T 4f92_B           79 TLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFGKRL  158 (1724)
T ss_dssp             BCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSSHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCHHHHHHHHHHHHHHHH
Confidence            7999999999986 67899999999999999999999996652           36789999999999999999999988


Q ss_pred             CC----cEEEeCCCCCCCC----cceEEecc-----------------CcceEeccccccccccCcCcccccch
Q psy2760         262 QD----VGLIDDLPPVFPD----VEKLLEDL-----------------NIGGLDELSIHDFNKHLKFWKPKVQL  310 (333)
Q Consensus       262 ~~----vglltGd~~~~~~----a~ili~t~-----------------~i~liViDe~H~~~~~~R~~~~~~~l  310 (333)
                      +.    |+.+|||.+...+    .+++|+|+                 ++.++|+||+|++++ .||..++..+
T Consensus       159 ~~~gi~V~~~tGd~~~~~~~~~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l~d-~RG~~lE~~l  231 (1724)
T 4f92_B          159 ATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHD-DRGPVLEALV  231 (1724)
T ss_dssp             TTTTCCEEECCSSCSSCCTTGGGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGGGS-TTHHHHHHHH
T ss_pred             hhCCCEEEEEECCCCCCccccCCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchhcCC-ccHHHHHHHH
Confidence            74    7889999887643    57899885                 478999999999987 6998776533

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.75  E-value=2.6e-18  Score=153.45  Aligned_cols=150  Identities=9%  Similarity=-0.026  Sum_probs=111.7

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~Ptra  248 (333)
                      ++++.+.+.++..++.      .|+++|.++++.+..|+++++++|||||||++|.++++..+.   .+.+++|++||++
T Consensus        10 ~l~~~l~~~l~~~g~~------~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~   83 (219)
T 1q0u_A           10 PFQPFIIEAIKTLRFY------KPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRE   83 (219)
T ss_dssp             CCCHHHHHHHHHTTCC------SCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcCcHH
Confidence            5777788777665555      799999999999999999999999999999999999987654   4678999999999


Q ss_pred             HHHHHHHHHHHhcC--------CcEEEeCCCCCC-------CCcceEEecc---------------CcceEecccccccc
Q psy2760         249 LSNQKYRDFRETFQ--------DVGLIDDLPPVF-------PDVEKLLEDL---------------NIGGLDELSIHDFN  298 (333)
Q Consensus       249 La~Q~~~~l~~~f~--------~vglltGd~~~~-------~~a~ili~t~---------------~i~liViDe~H~~~  298 (333)
                      |+.|+++.+++...        .++.+.|+....       ....++++|+               ++.++|+||+|.+.
T Consensus        84 L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~  163 (219)
T 1q0u_A           84 LATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLML  163 (219)
T ss_dssp             HHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHHH
T ss_pred             HHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHHHHHcCCCCcCcceEEEEcCchHHh
Confidence            99999999887643        256677775422       2346888875               46789999999987


Q ss_pred             ccCcCcccccchhh----hhhheeccCcchhhhh
Q psy2760         299 KHLKFWKPKVQLDD----LFDWTMASDATTLEIF  328 (333)
Q Consensus       299 ~~~R~~~~~~~l~~----l~~l~~~~d~~~~e~~  328 (333)
                      +.+....... +..    ..+.+++|++..-++.
T Consensus       164 ~~~~~~~l~~-i~~~~~~~~~~l~~SAT~~~~~~  196 (219)
T 1q0u_A          164 DMGFITDVDQ-IAARMPKDLQMLVFSATIPEKLK  196 (219)
T ss_dssp             HTTCHHHHHH-HHHTSCTTCEEEEEESCCCGGGH
T ss_pred             hhChHHHHHH-HHHhCCcccEEEEEecCCCHHHH
Confidence            6542211111 221    2346777777655543

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=99.75  E-value=2.5e-18  Score=156.05  Aligned_cols=150  Identities=12%  Similarity=0.016  Sum_probs=107.6

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~Ptra  248 (333)
                      ++++.+...+...++.      .|+++|.++++.+..|+++++++|||||||++|.++++..+.   .+.+++|++||++
T Consensus        36 ~l~~~l~~~l~~~g~~------~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~  109 (237)
T 3bor_A           36 NLKESLLRGIYAYGFE------KPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRE  109 (237)
T ss_dssp             CCCHHHHHHHHHHTCC------SCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEECcHH
Confidence            4677777766555544      699999999999999999999999999999999999987654   4679999999999


Q ss_pred             HHHHHHHHHHHhcCC----cEEEeCCCCCCCC--------cceEEecc---------------CcceEeccccccccccC
Q psy2760         249 LSNQKYRDFRETFQD----VGLIDDLPPVFPD--------VEKLLEDL---------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       249 La~Q~~~~l~~~f~~----vglltGd~~~~~~--------a~ili~t~---------------~i~liViDe~H~~~~~~  301 (333)
                      |+.|+++.+++....    ++.+.|+.....+        ..++++|+               .+.++|+||+|.+.+.+
T Consensus       110 L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~lViDEah~~~~~~  189 (237)
T 3bor_A          110 LAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRG  189 (237)
T ss_dssp             HHHHHHHHHHHHTTTTTCCEEEECC-------------CCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHHTT
T ss_pred             HHHHHHHHHHHHhhhcCceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHhCCcCcccCcEEEECCchHhhccC
Confidence            999999999886542    5667776554321        46888874               46889999999876543


Q ss_pred             cCcccccchhh----hhhheeccCcchhhhh
Q psy2760         302 KFWKPKVQLDD----LFDWTMASDATTLEIF  328 (333)
Q Consensus       302 R~~~~~~~l~~----l~~l~~~~d~~~~e~~  328 (333)
                      .+-.. ..+.+    ..+.+++|++..-++.
T Consensus       190 ~~~~l-~~i~~~~~~~~~~i~~SAT~~~~~~  219 (237)
T 3bor_A          190 FKDQI-YEIFQKLNTSIQVVLLSATMPTDVL  219 (237)
T ss_dssp             CHHHH-HHHHHHSCTTCEEEEECSSCCHHHH
T ss_pred             cHHHH-HHHHHhCCCCCeEEEEEEecCHHHH
Confidence            21111 11221    2346777777655443

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=99.74  E-value=8.7e-18  Score=149.73  Aligned_cols=150  Identities=12%  Similarity=0.022  Sum_probs=109.8

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC---CCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH---KTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~---g~ral~l~Ptra  248 (333)
                      ++++.+...+...++.      .|+++|.++++.+.+|+++++++|||+|||++|.++++..+..   +.+++|++||++
T Consensus        20 ~l~~~l~~~l~~~g~~------~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~   93 (220)
T 1t6n_A           20 LLKPELLRAIVDCGFE------HPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE   93 (220)
T ss_dssp             CCCHHHHHHHHHTTCC------CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHH
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeCCHH
Confidence            5677777766654444      6999999999999999999999999999999999999876543   458999999999


Q ss_pred             HHHHHHHHHHHhcC-----CcEEEeCCCCCC--------CCcceEEecc---------------CcceEecccccccccc
Q psy2760         249 LSNQKYRDFRETFQ-----DVGLIDDLPPVF--------PDVEKLLEDL---------------NIGGLDELSIHDFNKH  300 (333)
Q Consensus       249 La~Q~~~~l~~~f~-----~vglltGd~~~~--------~~a~ili~t~---------------~i~liViDe~H~~~~~  300 (333)
                      |+.|+++.+++...     .++.++|+....        ....++++|+               ++.++|+||+|.+...
T Consensus        94 L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~~~~~  173 (220)
T 1t6n_A           94 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQ  173 (220)
T ss_dssp             HHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHSS
T ss_pred             HHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHhCCCCcccCCEEEEcCHHHHhcc
Confidence            99999999987542     278888886532        1236888875               4678999999988542


Q ss_pred             CcCcccccchhh----hhhheeccCcchhhh
Q psy2760         301 LKFWKPKVQLDD----LFDWTMASDATTLEI  327 (333)
Q Consensus       301 ~R~~~~~~~l~~----l~~l~~~~d~~~~e~  327 (333)
                      ...+.....+.+    ..+.+++|++..-++
T Consensus       174 ~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~  204 (220)
T 1t6n_A          174 LDMRRDVQEIFRMTPHEKQVMMFSATLSKEI  204 (220)
T ss_dssp             HHHHHHHHHHHHTSCSSSEEEEEESCCCTTT
T ss_pred             cCcHHHHHHHHHhCCCcCeEEEEEeecCHHH
Confidence            111111111211    234677777765544

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=99.72  E-value=1.4e-17  Score=152.85  Aligned_cols=150  Identities=12%  Similarity=-0.032  Sum_probs=110.8

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh---cCCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ---NHKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l---~~g~ral~l~Ptra  248 (333)
                      ++++.+...++..++.      .|+++|.++++.+..|+++++++|||||||++|.++++..+   ..+.+++|++|||+
T Consensus        49 ~l~~~l~~~l~~~g~~------~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~~~~~~lil~Ptr~  122 (249)
T 3ber_A           49 GVTDVLCEACDQLGWT------KPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTPTRE  122 (249)
T ss_dssp             TCCHHHHHHHHHTTCC------SCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCCSSCEEEECSSHH
T ss_pred             CCCHHHHHHHHHcCCC------CCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCCCCceEEEEeCCHH
Confidence            5677777777665554      79999999999999999999999999999999999998554   23567999999999


Q ss_pred             HHHHHHHHHHHhcC----CcEEEeCCCCCC-------CCcceEEecc----------------CcceEeccccccccccC
Q psy2760         249 LSNQKYRDFRETFQ----DVGLIDDLPPVF-------PDVEKLLEDL----------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       249 La~Q~~~~l~~~f~----~vglltGd~~~~-------~~a~ili~t~----------------~i~liViDe~H~~~~~~  301 (333)
                      |+.|+++++++...    .++.+.|+....       ....++++|+                ++.++|+||+|.+.+.+
T Consensus       123 L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lViDEah~l~~~~  202 (249)
T 3ber_A          123 LAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMD  202 (249)
T ss_dssp             HHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHHHTCCSEEEECHHHHHHHHHHSTTCCCTTCCEEEECSHHHHHHTT
T ss_pred             HHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCcCccccCEEEEcChhhhhccC
Confidence            99999999977543    267788876532       2346888875                36789999999876553


Q ss_pred             cCcccccchh----hhhhheeccCcchhhhh
Q psy2760         302 KFWKPKVQLD----DLFDWTMASDATTLEIF  328 (333)
Q Consensus       302 R~~~~~~~l~----~l~~l~~~~d~~~~e~~  328 (333)
                      .+-.... ++    ...+.+++|++-.-++.
T Consensus       203 ~~~~l~~-i~~~~~~~~~~l~~SAT~~~~v~  232 (249)
T 3ber_A          203 FETEVDK-ILKVIPRDRKTFLFSATMTKKVQ  232 (249)
T ss_dssp             CHHHHHH-HHHSSCSSSEEEEEESSCCHHHH
T ss_pred             hHHHHHH-HHHhCCCCCeEEEEeccCCHHHH
Confidence            2211111 11    12446777777655543

>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=99.72  E-value=1.8e-17  Score=163.50  Aligned_cols=154  Identities=14%  Similarity=0.061  Sum_probs=114.6

Q ss_pred             cchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc--------CC
Q psy2760         166 EWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN--------HK  237 (333)
Q Consensus       166 ~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~--------~g  237 (333)
                      .|.. .+|++.+...++..++.      .|+++|+++++.+.+|++++++||||||||++|++|++..+.        .+
T Consensus        57 ~f~~-~~l~~~l~~~l~~~g~~------~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~  129 (434)
T 2db3_A           57 HFTS-ADLRDIIIDNVNKSGYK------IPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGR  129 (434)
T ss_dssp             CGGG-SCCCHHHHHHHHHTTCC------SCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTC
T ss_pred             Chhh-cCCCHHHHHHHHHcCCC------CCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccccccCC
Confidence            3443 36788888877666655      799999999999999999999999999999999999985542        25


Q ss_pred             CeEEEEcccHHHHHHHHHHHHHhcCC----cEEEeCCCCCC-------CCcceEEecc---------------CcceEec
Q psy2760         238 TRTIYTSPIKALSNQKYRDFRETFQD----VGLIDDLPPVF-------PDVEKLLEDL---------------NIGGLDE  291 (333)
Q Consensus       238 ~ral~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~~~-------~~a~ili~t~---------------~i~liVi  291 (333)
                      .++||++|||+|+.|+++++++....    ++.++|+....       ....++++|+               ++.++|+
T Consensus       130 ~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~~~~~l~~~~~lVl  209 (434)
T 2db3_A          130 PQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVL  209 (434)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSCCCTTCCEEEE
T ss_pred             ccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHHHHHhCCcccccCCeEEE
Confidence            68999999999999999999875532    67888887642       2357888876               4678999


Q ss_pred             cccccccccCcCcccccchh------hhhhheeccCcchhhh
Q psy2760         292 LSIHDFNKHLKFWKPKVQLD------DLFDWTMASDATTLEI  327 (333)
Q Consensus       292 De~H~~~~~~R~~~~~~~l~------~l~~l~~~~d~~~~e~  327 (333)
                      ||+|.+.+.+..-.... ++      ...+.+++|++..-++
T Consensus       210 DEah~~~~~gf~~~~~~-i~~~~~~~~~~q~l~~SAT~~~~~  250 (434)
T 2db3_A          210 DEADRMLDMGFSEDMRR-IMTHVTMRPEHQTLMFSATFPEEI  250 (434)
T ss_dssp             ETHHHHTSTTTHHHHHH-HHHCTTSCSSCEEEEEESCCCHHH
T ss_pred             ccHhhhhccCcHHHHHH-HHHhcCCCCCceEEEEeccCCHHH
Confidence            99998876542111111 11      1234677777755443

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=99.71  E-value=6.2e-18  Score=176.31  Aligned_cols=145  Identities=19%  Similarity=0.244  Sum_probs=116.1

Q ss_pred             CChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHH
Q psy2760         173 VSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQ  252 (333)
Q Consensus       173 L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q  252 (333)
                      |++.+.++++..|+.      .|+++|.++++.+.++++++++||||||||+++.++++..+..+.+++|++|+|+|+.|
T Consensus        10 l~~~~~~~l~~~g~~------~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~l~i~P~r~La~q   83 (702)
T 2p6r_A           10 ISSYAVGILKEEGIE------ELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGE   83 (702)
T ss_dssp             HHHHHHHHHHCC---------CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEESSHHHHHH
T ss_pred             cCHHHHHHHHhCCCC------CCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHhCCcEEEEeCcHHHHHH
Confidence            567777777665544      79999999999999999999999999999999999999777778999999999999999


Q ss_pred             HHHHHHHhcC----CcEEEeCCCCCCC----CcceEEecc---------------CcceEeccccccccccCcCcccccc
Q psy2760         253 KYRDFRETFQ----DVGLIDDLPPVFP----DVEKLLEDL---------------NIGGLDELSIHDFNKHLKFWKPKVQ  309 (333)
Q Consensus       253 ~~~~l~~~f~----~vglltGd~~~~~----~a~ili~t~---------------~i~liViDe~H~~~~~~R~~~~~~~  309 (333)
                      ++++++ .+.    .++.++|+.....    ...++++|+               ++.++|+||+|.+.+..|+..+...
T Consensus        84 ~~~~~~-~~~~~g~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~~l~~~~~~l~~~~~vIiDE~H~l~~~~r~~~~~~l  162 (702)
T 2p6r_A           84 KYESFK-KWEKIGLRIGISTGDYESRDEHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEIL  162 (702)
T ss_dssp             HHHHHT-TTTTTTCCEEEECSSCBCCSSCSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTTTHHHHHHH
T ss_pred             HHHHHH-HHHhcCCEEEEEeCCCCcchhhccCCCEEEECHHHHHHHHHcChhHHhhcCEEEEeeeeecCCCCcccHHHHH
Confidence            999994 443    3788999876654    467888885               5689999999999988888766542


Q ss_pred             hhh------hhhheeccCcch
Q psy2760         310 LDD------LFDWTMASDATT  324 (333)
Q Consensus       310 l~~------l~~l~~~~d~~~  324 (333)
                      +..      .++++++|++..
T Consensus       163 l~~l~~~~~~~~ii~lSATl~  183 (702)
T 2p6r_A          163 VTKMRRMNKALRVIGLSATAP  183 (702)
T ss_dssp             HHHHHHHCTTCEEEEEECCCT
T ss_pred             HHHHHhcCcCceEEEECCCcC
Confidence            222      255777777643

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=99.71  E-value=4.1e-17  Score=161.84  Aligned_cols=154  Identities=9%  Similarity=0.030  Sum_probs=113.5

Q ss_pred             ccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcC--CcEEEEcCCCCcHHHHHHHHHHHHhcC---CCeEEEEcc
Q psy2760         171 LDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEH--NHVFVTAHTSAGKTVIAEYAIALSQNH---KTRTIYTSP  245 (333)
Q Consensus       171 ~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g--~~vlv~apTGSGKTl~~~l~il~~l~~---g~ral~l~P  245 (333)
                      .+|++.+...+...++.      .|+++|.++++.+..+  ++++++||||||||++|++|++..+..   +.++||++|
T Consensus        97 ~~l~~~l~~~l~~~g~~------~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~P  170 (479)
T 3fmp_B           97 LRLKPQLLQGVYAMGFN------RPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSP  170 (479)
T ss_dssp             GTCCHHHHHHHHHTTCC------SCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTTSCSCCEEEECS
T ss_pred             cCCCHHHHHHHHHcCCC------CCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhcCCCCcEEEEeC
Confidence            35777777766665555      7999999999999876  999999999999999999999866543   348999999


Q ss_pred             cHHHHHHHHHHHHHhcC---C--cEEEeCCCCCCC----CcceEEecc----------------CcceEecccccccccc
Q psy2760         246 IKALSNQKYRDFRETFQ---D--VGLIDDLPPVFP----DVEKLLEDL----------------NIGGLDELSIHDFNKH  300 (333)
Q Consensus       246 traLa~Q~~~~l~~~f~---~--vglltGd~~~~~----~a~ili~t~----------------~i~liViDe~H~~~~~  300 (333)
                      |++|+.|+++.+++...   .  ++...|+.....    ...++|+|+                ++.++|+||+|.+...
T Consensus       171 t~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEah~~~~~  250 (479)
T 3fmp_B          171 TYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIAT  250 (479)
T ss_dssp             SHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTTCCCCCSEEEECHHHHHHHHTTSCCCCGGGCCEEEECCHHHHHTS
T ss_pred             hHHHHHHHHHHHHHHHhhCCCceEEEEeCCccccccccCCCCEEEECchHHHHHHHhcCCcCcccCCEEEEECHHHHhhc
Confidence            99999999888766432   2  566666554332    236888875                5678999999987654


Q ss_pred             CcCcccccchh----hhhhheeccCcchhhhhhc
Q psy2760         301 LKFWKPKVQLD----DLFDWTMASDATTLEIFTY  330 (333)
Q Consensus       301 ~R~~~~~~~l~----~l~~l~~~~d~~~~e~~~~  330 (333)
                      .+.......+.    ...+.+++|++.+-+++..
T Consensus       251 ~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~  284 (479)
T 3fmp_B          251 QGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKF  284 (479)
T ss_dssp             TTHHHHHHHHHTTSCTTSEEEEEESCCCHHHHHH
T ss_pred             CCcHHHHHHHHhhCCccceEEEEeCCCCHHHHHH
Confidence            33322222222    2356888999888877653

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.71  E-value=2e-17  Score=172.57  Aligned_cols=145  Identities=22%  Similarity=0.246  Sum_probs=117.1

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHH-HHcCCcEEEEcCCCCcHHHHHHHHHHHHhc-CCCeEEEEcccHHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIK-LEEHNHVFVTAHTSAGKTVIAEYAIALSQN-HKTRTIYTSPIKAL  249 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~-l~~g~~vlv~apTGSGKTl~~~l~il~~l~-~g~ral~l~PtraL  249 (333)
                      +|++.+.++++..|+.      .|+++|.++++. +..+++++++||||||||+++.++++..+. .+.+++|++|+|+|
T Consensus        14 ~l~~~~~~~l~~~g~~------~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~il~i~P~r~L   87 (715)
T 2va8_A           14 KLPSNVIEIIKKRGIK------KLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVTPLRAL   87 (715)
T ss_dssp             SSCHHHHHHHHTTSCC------BCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCSEEEEECSCHHH
T ss_pred             CCCHHHHHHHHhCCCC------CCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHCCCeEEEEeCcHHH
Confidence            4778888877665554      799999999999 788999999999999999999999986654 78899999999999


Q ss_pred             HHHHHHHHHHhcC----CcEEEeCCCCCCC----CcceEEecc---------------CcceEeccccccccccCcCccc
Q psy2760         250 SNQKYRDFRETFQ----DVGLIDDLPPVFP----DVEKLLEDL---------------NIGGLDELSIHDFNKHLKFWKP  306 (333)
Q Consensus       250 a~Q~~~~l~~~f~----~vglltGd~~~~~----~a~ili~t~---------------~i~liViDe~H~~~~~~R~~~~  306 (333)
                      +.|++++++ .+.    .++.++|+.....    ...++++|+               ++.++|+||+|.+.+..|+..+
T Consensus        88 a~q~~~~~~-~~~~~g~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~~~~~l  166 (715)
T 2va8_A           88 TNEKYLTFK-DWELIGFKVAMTSGDYDTDDAWLKNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDPERGPVV  166 (715)
T ss_dssp             HHHHHHHHG-GGGGGTCCEEECCSCSSSCCGGGGGCSEEEECHHHHHHHHHHCCGGGGGEEEEEECSGGGGGCTTTHHHH
T ss_pred             HHHHHHHHH-HhhcCCCEEEEEeCCCCCchhhcCCCCEEEEcHHHHHHHHhCChhHhhccCEEEEechhhcCCcccchHH
Confidence            999999994 343    3788999876654    457888876               5689999999999887887655


Q ss_pred             ccchhh--hhhheeccCcc
Q psy2760         307 KVQLDD--LFDWTMASDAT  323 (333)
Q Consensus       307 ~~~l~~--l~~l~~~~d~~  323 (333)
                      ...+.+  ..+++.+|++.
T Consensus       167 ~~i~~~~~~~~ii~lSATl  185 (715)
T 2va8_A          167 ESVTIRAKRRNLLALSATI  185 (715)
T ss_dssp             HHHHHHHHTSEEEEEESCC
T ss_pred             HHHHHhcccCcEEEEcCCC
Confidence            542222  36678888775

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=99.71  E-value=1.9e-17  Score=167.20  Aligned_cols=160  Identities=12%  Similarity=-0.003  Sum_probs=118.7

Q ss_pred             CCCcccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHH--cCCcEEEEcCCCCcHHHHHHHHHHHHhcC--
Q psy2760         161 HVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLE--EHNHVFVTAHTSAGKTVIAEYAIALSQNH--  236 (333)
Q Consensus       161 ~~~~~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~--~g~~vlv~apTGSGKTl~~~l~il~~l~~--  236 (333)
                      ..++..|.....|++.+...+...++.      .|+++|.++++.++  .+++++++||||||||++|++|++..+..  
T Consensus        67 ~~~~~~l~~~~~l~~~l~~~l~~~g~~------~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~  140 (563)
T 3i5x_A           67 EVTLDSLLEEGVLDKEIHKAITRMEFP------GLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTK  140 (563)
T ss_dssp             CCCHHHHHHTTSSCHHHHHHHHTTCCS------SCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTT
T ss_pred             CcCHHHHhhcCCCCHHHHHHHHHCCCC------CCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhcc
Confidence            346777777767889988877666655      79999999999987  67899999999999999999999865532  


Q ss_pred             -----CCeEEEEcccHHHHHHHHHHHHHhcC--------CcEEEeCCCCCC--------CCcceEEecc-----------
Q psy2760         237 -----KTRTIYTSPIKALSNQKYRDFRETFQ--------DVGLIDDLPPVF--------PDVEKLLEDL-----------  284 (333)
Q Consensus       237 -----g~ral~l~PtraLa~Q~~~~l~~~f~--------~vglltGd~~~~--------~~a~ili~t~-----------  284 (333)
                           +.++||++||++|+.|+++++++.+.        .+..+.|+....        ....++|+|+           
T Consensus       141 ~~~~~~~~~lil~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~  220 (563)
T 3i5x_A          141 FDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYS  220 (563)
T ss_dssp             TSSTTSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHH
T ss_pred             ccccCCeeEEEEcCcHHHHHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhcc
Confidence                 35899999999999999999987432        156677775532        2357888876           


Q ss_pred             -----CcceEeccccccccccCcCcccccchhh-----------hhhheeccCcchhhh
Q psy2760         285 -----NIGGLDELSIHDFNKHLKFWKPKVQLDD-----------LFDWTMASDATTLEI  327 (333)
Q Consensus       285 -----~i~liViDe~H~~~~~~R~~~~~~~l~~-----------l~~l~~~~d~~~~e~  327 (333)
                           .+.++|+||+|.+...+++-.... +..           .++.+++|++..-++
T Consensus       221 ~~~~~~~~~lViDEah~l~~~~f~~~~~~-i~~~l~~~~~~~~~~~~~l~~SAT~~~~v  278 (563)
T 3i5x_A          221 NKFFRFVDYKVLDEADRLLEIGFRDDLET-ISGILNEKNSKSADNIKTLLFSATLDDKV  278 (563)
T ss_dssp             HHHCTTCCEEEEETHHHHTSTTTHHHHHH-HHHHHHHHCSSCTTCCEEEEEESSCCTHH
T ss_pred             ccccccceEEEEeCHHHHhccchHHHHHH-HHHhhhhccccCccCceEEEEEccCCHHH
Confidence                 478899999999876653322221 111           124677777766443

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=99.71  E-value=1.1e-17  Score=174.85  Aligned_cols=146  Identities=18%  Similarity=0.192  Sum_probs=117.3

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHH-HHcCCcEEEEcCCCCcHHHHHHHHHHHHhc-CCCeEEEEcccHHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIK-LEEHNHVFVTAHTSAGKTVIAEYAIALSQN-HKTRTIYTSPIKAL  249 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~-l~~g~~vlv~apTGSGKTl~~~l~il~~l~-~g~ral~l~PtraL  249 (333)
                      +|++.+.++++..|+.      .|+++|.++++. +..+++++++||||||||++|.++++..+. .+.+++|++|+|+|
T Consensus         7 ~l~~~~~~~l~~~g~~------~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~~l~i~P~raL   80 (720)
T 2zj8_A            7 RVDERIKSTLKERGIE------SFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPLKAL   80 (720)
T ss_dssp             CSCHHHHHHHHHTTCC------BCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHHCSEEEEECSSGGG
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhCCCEEEEEcCcHHH
Confidence            4777888877665554      799999999998 789999999999999999999999986553 68899999999999


Q ss_pred             HHHHHHHHHHh--cC-CcEEEeCCCCCCC----CcceEEecc---------------CcceEeccccccccccCcCcccc
Q psy2760         250 SNQKYRDFRET--FQ-DVGLIDDLPPVFP----DVEKLLEDL---------------NIGGLDELSIHDFNKHLKFWKPK  307 (333)
Q Consensus       250 a~Q~~~~l~~~--f~-~vglltGd~~~~~----~a~ili~t~---------------~i~liViDe~H~~~~~~R~~~~~  307 (333)
                      +.|++++|++.  ++ .++.++|+.....    ...++++|+               ++.++|+||+|.+.+..|+..+.
T Consensus        81 a~q~~~~~~~l~~~g~~v~~~~G~~~~~~~~~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~l~~~~r~~~~~  160 (720)
T 2zj8_A           81 AEEKFQEFQDWEKIGLRVAMATGDYDSKDEWLGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRDRGATLE  160 (720)
T ss_dssp             HHHHHHHTGGGGGGTCCEEEECSCSSCCCGGGGGCSEEEECHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHHHH
T ss_pred             HHHHHHHHHHHHhcCCEEEEecCCCCccccccCCCCEEEECHHHHHHHHHcChhhhhcCCEEEEECCcccCCCcccHHHH
Confidence            99999999532  22 3899999877654    457888876               46899999999999888887766


Q ss_pred             cchhhh---hhheeccCcc
Q psy2760         308 VQLDDL---FDWTMASDAT  323 (333)
Q Consensus       308 ~~l~~l---~~l~~~~d~~  323 (333)
                      ..+..+   .+++++|++-
T Consensus       161 ~ll~~l~~~~~ii~lSATl  179 (720)
T 2zj8_A          161 VILAHMLGKAQIIGLSATI  179 (720)
T ss_dssp             HHHHHHBTTBEEEEEECCC
T ss_pred             HHHHHhhcCCeEEEEcCCc
Confidence            523222   5677777763

>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=99.71  E-value=1.1e-17  Score=189.65  Aligned_cols=114  Identities=28%  Similarity=0.325  Sum_probs=98.0

Q ss_pred             CCCHHHHHHHHHH-HcCCcEEEEcCCCCcHHHHHHHHHHHHh--cCCCeEEEEcccHHHHHHHHHHHHHhcCC-----cE
Q psy2760         194 ELDVFQKQAIIKL-EEHNHVFVTAHTSAGKTVIAEYAIALSQ--NHKTRTIYTSPIKALSNQKYRDFRETFQD-----VG  265 (333)
Q Consensus       194 ~l~~~Q~~ai~~l-~~g~~vlv~apTGSGKTl~~~l~il~~l--~~g~ral~l~PtraLa~Q~~~~l~~~f~~-----vg  265 (333)
                      .|+|+|.++|+.+ ..++|++++||||||||++|.+||+..+  .++.+++|++||||||+|++++|+++|+.     |+
T Consensus       926 ~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~~~~kavyi~P~raLa~q~~~~~~~~f~~~~g~~V~ 1005 (1724)
T 4f92_B          926 FFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLNKKVV 1005 (1724)
T ss_dssp             BCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHHHTTTSCCCEE
T ss_pred             CCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhCCCCEEEEEcChHHHHHHHHHHHHHHhchhcCCEEE
Confidence            4999999999997 5678999999999999999999999766  35779999999999999999999988864     78


Q ss_pred             EEeCCCCCC----CCcceEEecc-----------------CcceEeccccccccccCcCccccc
Q psy2760         266 LIDDLPPVF----PDVEKLLEDL-----------------NIGGLDELSIHDFNKHLKFWKPKV  308 (333)
Q Consensus       266 lltGd~~~~----~~a~ili~t~-----------------~i~liViDe~H~~~~~~R~~~~~~  308 (333)
                      .++|+...+    ..+.++|+|+                 ++.++|+||+|++++ .||..+..
T Consensus      1006 ~ltGd~~~~~~~~~~~~IiV~TPEkld~llr~~~~~~~l~~v~lvViDE~H~l~d-~rg~~le~ 1068 (1724)
T 4f92_B         1006 LLTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGG-ENGPVLEV 1068 (1724)
T ss_dssp             ECCSCHHHHHHHHHHCSEEEECHHHHHHHHTTTTTCHHHHSCSEEEECCGGGGGS-TTHHHHHH
T ss_pred             EEECCCCcchhhcCCCCEEEECHHHHHHHHhCcccccccceeeEEEeechhhcCC-CCCccHHH
Confidence            899987654    3467999986                 589999999999987 47766654

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=99.70  E-value=8.8e-17  Score=154.20  Aligned_cols=152  Identities=9%  Similarity=0.023  Sum_probs=112.2

Q ss_pred             ccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcC--CcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcc
Q psy2760         171 LDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEH--NHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSP  245 (333)
Q Consensus       171 ~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g--~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~P  245 (333)
                      .++++.+.+.+...++.      .|+++|.++++.+..+  +++++++|||||||++|+++++..+.   .+.+++|++|
T Consensus        30 ~~l~~~l~~~l~~~g~~------~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~P  103 (412)
T 3fht_A           30 LRLKPQLLQGVYAMGFN------RPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSP  103 (412)
T ss_dssp             GTCCHHHHHHHHHTTCC------SCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECS
T ss_pred             CCCCHHHHHHHHHcCCC------CCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcCCCCCEEEECC
Confidence            35777888777666655      7999999999999876  99999999999999999999987654   3458999999


Q ss_pred             cHHHHHHHHHHHHHhcC---C--cEEEeCCCCCCC----CcceEEecc----------------CcceEecccccccccc
Q psy2760         246 IKALSNQKYRDFRETFQ---D--VGLIDDLPPVFP----DVEKLLEDL----------------NIGGLDELSIHDFNKH  300 (333)
Q Consensus       246 traLa~Q~~~~l~~~f~---~--vglltGd~~~~~----~a~ili~t~----------------~i~liViDe~H~~~~~  300 (333)
                      |++|+.|+++.+++...   .  ++...|+.....    ...++++|+                ++.++|+||+|.+...
T Consensus       104 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~~iViDEah~~~~~  183 (412)
T 3fht_A          104 TYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIAT  183 (412)
T ss_dssp             SHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTTCCCCCSEEEECHHHHHHHHTTSCSSCGGGCCEEEEETHHHHHST
T ss_pred             CHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhhhcCCCCEEEECchHHHHHHHhcCCcChhhCcEEEEeCHHHHhhc
Confidence            99999999988877543   2  566776655433    246888875                4778999999988654


Q ss_pred             CcCcccccchhh----hhhheeccCcchhhhh
Q psy2760         301 LKFWKPKVQLDD----LFDWTMASDATTLEIF  328 (333)
Q Consensus       301 ~R~~~~~~~l~~----l~~l~~~~d~~~~e~~  328 (333)
                      .+.......+..    ..+.+++|++..-+++
T Consensus       184 ~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~  215 (412)
T 3fht_A          184 QGHQDQSIRIQRMLPRNCQMLLFSATFEDSVW  215 (412)
T ss_dssp             TTTHHHHHHHHHTSCTTCEEEEEESCCCHHHH
T ss_pred             CCcHHHHHHHHhhCCCCceEEEEEeecCHHHH
Confidence            333332222222    2457778887665544

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.70  E-value=3.1e-17  Score=158.16  Aligned_cols=124  Identities=15%  Similarity=0.051  Sum_probs=100.4

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc----------------
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN----------------  235 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~----------------  235 (333)
                      ++++.+.+.+...++.      .|+++|.++++.+..|++++++||||||||++|.+|++..+.                
T Consensus        21 ~l~~~l~~~l~~~~~~------~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~~~~   94 (417)
T 2i4i_A           21 EMGEIIMGNIELTRYT------RPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGR   94 (417)
T ss_dssp             CCCHHHHHHHHHHTCC------SCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHHCBT
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhccccccc
Confidence            5778888877666655      799999999999999999999999999999999999885431                


Q ss_pred             -----CCCeEEEEcccHHHHHHHHHHHHHhcCC----cEEEeCCCCCC-------CCcceEEecc---------------
Q psy2760         236 -----HKTRTIYTSPIKALSNQKYRDFRETFQD----VGLIDDLPPVF-------PDVEKLLEDL---------------  284 (333)
Q Consensus       236 -----~g~ral~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~~~-------~~a~ili~t~---------------  284 (333)
                           .+.+++|++||++|+.|+++.+++....    ++.++|+....       ....++++|+               
T Consensus        95 ~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~  174 (417)
T 2i4i_A           95 YGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLD  174 (417)
T ss_dssp             TBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSBCCT
T ss_pred             cccccCCccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHHHhhCCCCEEEEChHHHHHHHHcCCcChh
Confidence                 1267999999999999999999876542    67788876532       3357888876               


Q ss_pred             CcceEeccccccccccC
Q psy2760         285 NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       285 ~i~liViDe~H~~~~~~  301 (333)
                      .+.++|+||+|.+...+
T Consensus       175 ~~~~iViDEah~~~~~~  191 (417)
T 2i4i_A          175 FCKYLVLDEADRMLDMG  191 (417)
T ss_dssp             TCCEEEESSHHHHHHTT
T ss_pred             hCcEEEEEChhHhhccC
Confidence            35779999999877654

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.70  E-value=1.9e-17  Score=160.97  Aligned_cols=111  Identities=12%  Similarity=0.027  Sum_probs=95.7

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC---CcEEE
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ---DVGLI  267 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~---~vgll  267 (333)
                      ++|.|+++|.++++.+..|++++++||||||||++|+++++.....+.+++|++||++|+.|+++++++...   .++.+
T Consensus        18 ~~~~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~   97 (414)
T 3oiy_A           18 FGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGF   97 (414)
T ss_dssp             HSSCCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEEC
T ss_pred             cCCCCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhcCCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEE
Confidence            466899999999999999999999999999999999999888778889999999999999999999988544   37888


Q ss_pred             eCCCCC-----------CCCcceEEecc-------------CcceEeccccccccccC
Q psy2760         268 DDLPPV-----------FPDVEKLLEDL-------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       268 tGd~~~-----------~~~a~ili~t~-------------~i~liViDe~H~~~~~~  301 (333)
                      +|+...           .....++++|+             ++.++|+||+|.+...+
T Consensus        98 ~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~iViDEaH~~~~~~  155 (414)
T 3oiy_A           98 YSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDFVFVDDVDAVLKAS  155 (414)
T ss_dssp             CTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHHHTTCCCSEEEESCHHHHHHCH
T ss_pred             ECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHHhccccccEEEEeChHhhhhcc
Confidence            998765           12357888876             57889999999876543

>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=99.70  E-value=2.9e-18  Score=188.54  Aligned_cols=219  Identities=17%  Similarity=0.175  Sum_probs=145.5

Q ss_pred             chhhhhhhhhcccccccccccchhHHHhh-cc-----CcccccccccccccccCCchhhhhhhcCCCCCCcccCCCCC-C
Q psy2760          73 SIHDFNKHLKFWKPKVQLVAGIINLIQLG-GE-----NASKFEQGLWESHEVISGDAKEEQEKATVFPSNEEENNVIP-Q  145 (333)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~i-~~-----~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~-~  145 (333)
                      ..+++.+..|++.+++++|++.+++++.+ +.     ..++++...|++....-.+..                .+++ +
T Consensus       507 ~~~~~~~~~y~~~~~l~vp~~~l~~~~~y~g~~~~~~~l~~l~~~~w~~~k~~~~~~~----------------~~~a~~  570 (1151)
T 2eyq_A          507 ITGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRARQKAAEKV----------------RDVAAE  570 (1151)
T ss_dssp             CEEEEEEEECGGGCEEEEEGGGGGGEEECCCSCSSSCCCCCTTCSHHHHHHHHHHHHH----------------HHHHHH
T ss_pred             CCcceEEEEecCCCceeeeHHHhhhHhcccCCCCCCCchhhcCchhHHHHHHHHHHHH----------------HHHHHH
Confidence            45688999999999999999999999988 32     345566777765511100000                0000 0


Q ss_pred             ccCCcccccCCCCCCCCCcccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHc----CC--cEEEEcCCC
Q psy2760         146 EVDIPILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEE----HN--HVFVTAHTS  219 (333)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~----g~--~vlv~apTG  219 (333)
                      ++.....+.............|..         .       ....|||.++++|.+|++.+..    |+  ++++++|||
T Consensus       571 l~~~~a~r~~~~g~~~~~~~~~~~---------~-------~~~~f~~~~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TG  634 (1151)
T 2eyq_A          571 LLDIYAQRAAKEGFAFKHDREQYQ---------L-------FCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVG  634 (1151)
T ss_dssp             HHHHHHHHHTSCCCCCCCCHHHHH---------H-------HHHTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCC
T ss_pred             HHHHHHHHhhCCCCCCCCCHHHHH---------H-------HHHhCCCCCCHHHHHHHHHHHHHHhcCCcCcEEEECCCC
Confidence            000000000000000001112221         1       2345788899999999999754    65  999999999


Q ss_pred             CcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC----cEEEeCCCCCC-----------CCcceEEecc
Q psy2760         220 AGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD----VGLIDDLPPVF-----------PDVEKLLEDL  284 (333)
Q Consensus       220 SGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~~~-----------~~a~ili~t~  284 (333)
                      +|||++|+.+++.....+.+++|++||++|+.|+++.|++.|+.    ++.++|.....           ....++|+|+
T Consensus       635 sGKT~val~aa~~~~~~g~~vlvlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~  714 (1151)
T 2eyq_A          635 FGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTH  714 (1151)
T ss_dssp             TTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECT
T ss_pred             CCHHHHHHHHHHHHHHhCCeEEEEechHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            99999999999888888899999999999999999999988864    67777754421           2357888885


Q ss_pred             ----------CcceEeccccccccccCcCcccccchhhhhhheeccCcchh
Q psy2760         285 ----------NIGGLDELSIHDFNKHLKFWKPKVQLDDLFDWTMASDATTL  325 (333)
Q Consensus       285 ----------~i~liViDe~H~~~~~~R~~~~~~~l~~l~~l~~~~d~~~~  325 (333)
                                ++.++|+||+|.++...+..  ...+....+.+++|+++.-
T Consensus       715 ~ll~~~~~~~~l~lvIiDEaH~~g~~~~~~--l~~l~~~~~vl~lSATp~p  763 (1151)
T 2eyq_A          715 KLLQSDVKFKDLGLLIVDEEHRFGVRHKER--IKAMRANVDILTLTATPIP  763 (1151)
T ss_dssp             HHHHSCCCCSSEEEEEEESGGGSCHHHHHH--HHHHHTTSEEEEEESSCCC
T ss_pred             HHHhCCccccccceEEEechHhcChHHHHH--HHHhcCCCCEEEEcCCCCh
Confidence                      67899999999986543221  1222233567888888653

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=99.69  E-value=1.2e-16  Score=151.96  Aligned_cols=151  Identities=12%  Similarity=0.058  Sum_probs=109.6

Q ss_pred             ccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcC--CcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcc
Q psy2760         171 LDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEH--NHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSP  245 (333)
Q Consensus       171 ~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g--~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~P  245 (333)
                      .+|++.+...+...++.      .|+++|.++++.+..+  +++++++|||||||++|.++++..+.   .+.+++|++|
T Consensus        10 ~~l~~~l~~~l~~~~~~------~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P   83 (395)
T 3pey_A           10 LGLAPELLKGIYAMKFQ------KPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAP   83 (395)
T ss_dssp             SCCCHHHHHHHHHTTCC------SCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEECS
T ss_pred             CCCCHHHHHHHHHCCCC------CCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEECC
Confidence            35677777777665555      7999999999999887  99999999999999999999987653   5678999999


Q ss_pred             cHHHHHHHHHHHHHhcCC----cEEEeCCCCCC---CCcceEEecc---------------CcceEeccccccccccCcC
Q psy2760         246 IKALSNQKYRDFRETFQD----VGLIDDLPPVF---PDVEKLLEDL---------------NIGGLDELSIHDFNKHLKF  303 (333)
Q Consensus       246 traLa~Q~~~~l~~~f~~----vglltGd~~~~---~~a~ili~t~---------------~i~liViDe~H~~~~~~R~  303 (333)
                      |++|+.|+++.+++....    ++...|+....   ....++++|+               ++.++|+||+|.+......
T Consensus        84 ~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~  163 (395)
T 3pey_A           84 SRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNKQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGL  163 (395)
T ss_dssp             SHHHHHHHHHHHHHHTTTSCCCEEEESTTSSCTTSCBCCSEEEECHHHHHHHHHTTCBCCTTCCEEEEETHHHHHHSTTH
T ss_pred             CHHHHHHHHHHHHHHhcccCeeEEEEecCchhhhccCCCCEEEEcHHHHHHHHHcCCcccccCCEEEEEChhhhcCcccc
Confidence            999999999999885432    55566654332   2456888875               4678999999988653321


Q ss_pred             cccccchh----hhhhheeccCcchhhh
Q psy2760         304 WKPKVQLD----DLFDWTMASDATTLEI  327 (333)
Q Consensus       304 ~~~~~~l~----~l~~l~~~~d~~~~e~  327 (333)
                      ......+.    ...+.+++|++..-.+
T Consensus       164 ~~~~~~~~~~~~~~~~~i~~SAT~~~~~  191 (395)
T 3pey_A          164 GDQCIRVKRFLPKDTQLVLFSATFADAV  191 (395)
T ss_dssp             HHHHHHHHHTSCTTCEEEEEESCCCHHH
T ss_pred             HHHHHHHHHhCCCCcEEEEEEecCCHHH
Confidence            11111111    1245677777655433

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.69  E-value=8.9e-17  Score=163.89  Aligned_cols=135  Identities=13%  Similarity=0.029  Sum_probs=107.5

Q ss_pred             CCCcccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHH--cCCcEEEEcCCCCcHHHHHHHHHHHHhcC--
Q psy2760         161 HVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLE--EHNHVFVTAHTSAGKTVIAEYAIALSQNH--  236 (333)
Q Consensus       161 ~~~~~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~--~g~~vlv~apTGSGKTl~~~l~il~~l~~--  236 (333)
                      ..++..|.....|++.+...++..|+.      .|+++|.++++.++  .|++++++||||||||++|++|++..+..  
T Consensus        16 ~~~~~~l~~~~~l~~~l~~~l~~~g~~------~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~   89 (579)
T 3sqw_A           16 EVTLDSLLEEGVLDKEIHKAITRMEFP------GLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTK   89 (579)
T ss_dssp             CCCHHHHHHTTSSCHHHHHHHHTTTCS------SCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTT
T ss_pred             CcCHHHHhhcCCCCHHHHHHHHHCCCC------CCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhcc
Confidence            346777777777899998887766655      79999999999988  78999999999999999999999865422  


Q ss_pred             -----CCeEEEEcccHHHHHHHHHHHHHhcC--------CcEEEeCCCCCC--------CCcceEEecc-----------
Q psy2760         237 -----KTRTIYTSPIKALSNQKYRDFRETFQ--------DVGLIDDLPPVF--------PDVEKLLEDL-----------  284 (333)
Q Consensus       237 -----g~ral~l~PtraLa~Q~~~~l~~~f~--------~vglltGd~~~~--------~~a~ili~t~-----------  284 (333)
                           +.++||++||++|+.|+.+++++.+.        .+..+.|+....        ....++|+|+           
T Consensus        90 ~~~~~~~~~lvl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~  169 (579)
T 3sqw_A           90 FDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYS  169 (579)
T ss_dssp             TSSTTSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHH
T ss_pred             ccccCCCeEEEEcchHHHHHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhcc
Confidence                 45899999999999999999987541        155666765432        1356888875           


Q ss_pred             -----CcceEeccccccccccC
Q psy2760         285 -----NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       285 -----~i~liViDe~H~~~~~~  301 (333)
                           .+.++|+||+|.+...+
T Consensus       170 ~~~~~~~~~lViDEah~l~~~g  191 (579)
T 3sqw_A          170 NKFFRFVDYKVLDEADRLLEIG  191 (579)
T ss_dssp             HHHCTTCCEEEEETHHHHTSTT
T ss_pred             ccccccCCEEEEEChHHhhcCC
Confidence                 46788999999987655

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=99.68  E-value=7.8e-17  Score=154.90  Aligned_cols=151  Identities=13%  Similarity=0.011  Sum_probs=111.1

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~Ptra  248 (333)
                      ++++.+...+...+..      .|+++|.++++.+..|+++++++|||||||++|.++++..+.   .+.+++|++||++
T Consensus        46 ~l~~~~~~~l~~~~~~------~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  119 (414)
T 3eiq_A           46 NLSESLLRGIYAYGFE------KPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRE  119 (414)
T ss_dssp             CCCHHHHHHHHHTTCC------SCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CCCHHHHHHHHHcCCC------CCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcCCceeEEEEeChHH
Confidence            4666676666554444      799999999999999999999999999999999999987654   5678999999999


Q ss_pred             HHHHHHHHHHHhcCC----cEEEeCCCCCC--------CCcceEEecc---------------CcceEeccccccccccC
Q psy2760         249 LSNQKYRDFRETFQD----VGLIDDLPPVF--------PDVEKLLEDL---------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       249 La~Q~~~~l~~~f~~----vglltGd~~~~--------~~a~ili~t~---------------~i~liViDe~H~~~~~~  301 (333)
                      |+.|+.+.+++.+..    ++...|+....        ....++++|+               .+.++|+||+|.+...+
T Consensus       120 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~~vViDEah~~~~~~  199 (414)
T 3eiq_A          120 LAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRG  199 (414)
T ss_dssp             HHHHHHHHHHHHGGGSCCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTSSCSTTCCEEEECSHHHHHHTT
T ss_pred             HHHHHHHHHHHHhcccCceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccCcEEEEECHHHhhccC
Confidence            999999999885532    56666765532        3457888875               36889999999876544


Q ss_pred             cCccccc---chhhhhhheeccCcchhhhh
Q psy2760         302 KFWKPKV---QLDDLFDWTMASDATTLEIF  328 (333)
Q Consensus       302 R~~~~~~---~l~~l~~l~~~~d~~~~e~~  328 (333)
                      .......   .+-...+.+++|++..-++.
T Consensus       200 ~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~  229 (414)
T 3eiq_A          200 FKDQIYDIFQKLNSNTQVVLLSATMPSDVL  229 (414)
T ss_dssp             THHHHHHHHTTSCTTCEEEEECSCCCHHHH
T ss_pred             cHHHHHHHHHhCCCCCeEEEEEEecCHHHH
Confidence            2211111   11123456788887654443

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.68  E-value=1.4e-16  Score=158.40  Aligned_cols=110  Identities=13%  Similarity=0.144  Sum_probs=94.6

Q ss_pred             CCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC-----CCeEEEEcccHHHHHHHHHHHHHhcC----
Q psy2760         192 PFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH-----KTRTIYTSPIKALSNQKYRDFRETFQ----  262 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~-----g~ral~l~PtraLa~Q~~~~l~~~f~----  262 (333)
                      ||.|+++|.++++.+..|+++++++|||||||++|.++++..+..     +.++||++||++|+.|+++.+++.+.    
T Consensus         2 ~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~   81 (555)
T 3tbk_A            2 PLKPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERLGY   81 (555)
T ss_dssp             CCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhccCCc
Confidence            568999999999999999999999999999999999999866543     78999999999999999999988764    


Q ss_pred             CcEEEeCCCCCCCC-------cceEEecc----------------CcceEeccccccccccC
Q psy2760         263 DVGLIDDLPPVFPD-------VEKLLEDL----------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       263 ~vglltGd~~~~~~-------a~ili~t~----------------~i~liViDe~H~~~~~~  301 (333)
                      .++.++|+.....+       ..++++|+                ++.++|+||+|.+...+
T Consensus        82 ~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~  143 (555)
T 3tbk_A           82 NIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVFTLMIFDECHNTSKNH  143 (555)
T ss_dssp             CEEEECTTTGGGSCHHHHHHHCSEEEECHHHHHHHHHTSSSCCGGGCSEEEETTGGGCSTTC
T ss_pred             EEEEEcCCCcchhhHHHHhcCCCEEEECHHHHHHHHhcCcccccccCCEEEEECccccCCcc
Confidence            27889999866544       46888875                35789999999987654

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=99.68  E-value=1.4e-16  Score=153.79  Aligned_cols=151  Identities=12%  Similarity=0.009  Sum_probs=111.5

Q ss_pred             ccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcccH
Q psy2760         171 LDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSPIK  247 (333)
Q Consensus       171 ~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~Ptr  247 (333)
                      .++++.+...+...++.      .|+++|+++++.+..|+++++++|||||||++|.++++..+.   .+.+++|++||+
T Consensus        42 ~~l~~~l~~~l~~~g~~------~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~Pt~  115 (410)
T 2j0s_A           42 MGLREDLLRGIYAYGFE------KPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTR  115 (410)
T ss_dssp             GCCCHHHHHHHHHHTCC------SCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSH
T ss_pred             cCCCHHHHHHHHHcCCC------CCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhccCCceEEEEcCcH
Confidence            35777777766655554      699999999999999999999999999999999999987653   568999999999


Q ss_pred             HHHHHHHHHHHHhcCC----cEEEeCCCCCC-------CCcceEEecc---------------CcceEeccccccccccC
Q psy2760         248 ALSNQKYRDFRETFQD----VGLIDDLPPVF-------PDVEKLLEDL---------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       248 aLa~Q~~~~l~~~f~~----vglltGd~~~~-------~~a~ili~t~---------------~i~liViDe~H~~~~~~  301 (333)
                      +|+.|+++.+++....    ++.++|+....       ....++++|+               .+.++|+||+|.+...+
T Consensus       116 ~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~~~~~~~~~~~vViDEah~~~~~~  195 (410)
T 2j0s_A          116 ELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKG  195 (410)
T ss_dssp             HHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTSTT
T ss_pred             HHHHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHhCCccHhheeEEEEccHHHHHhhh
Confidence            9999999999875432    67777876542       2246788775               36789999999876543


Q ss_pred             cCcccccchh----hhhhheeccCcchhhhh
Q psy2760         302 KFWKPKVQLD----DLFDWTMASDATTLEIF  328 (333)
Q Consensus       302 R~~~~~~~l~----~l~~l~~~~d~~~~e~~  328 (333)
                      ..-.. ..+.    ...+.+++|++..-++.
T Consensus       196 ~~~~~-~~i~~~~~~~~~~i~~SAT~~~~~~  225 (410)
T 2j0s_A          196 FKEQI-YDVYRYLPPATQVVLISATLPHEIL  225 (410)
T ss_dssp             THHHH-HHHHTTSCTTCEEEEEESCCCHHHH
T ss_pred             hHHHH-HHHHHhCccCceEEEEEcCCCHHHH
Confidence            11110 0011    22456777777655543

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=99.67  E-value=1.4e-16  Score=149.83  Aligned_cols=150  Identities=14%  Similarity=0.089  Sum_probs=112.3

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcC-CcEEEEcCCCCcHHHHHHHHHHHHhc--CCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEH-NHVFVTAHTSAGKTVIAEYAIALSQN--HKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g-~~vlv~apTGSGKTl~~~l~il~~l~--~g~ral~l~Ptra  248 (333)
                      ++++.+...++..++.      .|+++|+++++.+..+ +++++++|||||||+++..+++..+.  .+.+++|++|+++
T Consensus        12 ~l~~~~~~~l~~~g~~------~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~~~~~~lil~P~~~   85 (367)
T 1hv8_A           12 NLSDNILNAIRNKGFE------KPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRE   85 (367)
T ss_dssp             SCCHHHHHHHHHHTCC------SCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHH
T ss_pred             CCCHHHHHHHHHcCCC------CCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhcccCCCcEEEEcCCHH
Confidence            4777788777766655      7999999999998777 79999999999999999999887654  4789999999999


Q ss_pred             HHHHHHHHHHHhcCC----cEEEeCCCCCCC------CcceEEecc---------------CcceEeccccccccccCcC
Q psy2760         249 LSNQKYRDFRETFQD----VGLIDDLPPVFP------DVEKLLEDL---------------NIGGLDELSIHDFNKHLKF  303 (333)
Q Consensus       249 La~Q~~~~l~~~f~~----vglltGd~~~~~------~a~ili~t~---------------~i~liViDe~H~~~~~~R~  303 (333)
                      |+.|+.+++++.++.    ++.++|+.....      ...++++|+               ++.++|+||+|.+...+..
T Consensus        86 L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~  165 (367)
T 1hv8_A           86 LAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFI  165 (367)
T ss_dssp             HHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHHTCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTTTH
T ss_pred             HHHHHHHHHHHHhCCCCceEEEEECCcchHHHHhhcCCCCEEEecHHHHHHHHHcCCcccccCCEEEEeCchHhhhhchH
Confidence            999999999987653    677777765321      356788775               4678999999998654311


Q ss_pred             cccccchh----hhhhheeccCcchhhhh
Q psy2760         304 WKPKVQLD----DLFDWTMASDATTLEIF  328 (333)
Q Consensus       304 ~~~~~~l~----~l~~l~~~~d~~~~e~~  328 (333)
                       .....+.    ...+.+++|++..-++.
T Consensus       166 -~~~~~~~~~~~~~~~~i~~SAT~~~~~~  193 (367)
T 1hv8_A          166 -KDVEKILNACNKDKRILLFSATMPREIL  193 (367)
T ss_dssp             -HHHHHHHHTSCSSCEEEEECSSCCHHHH
T ss_pred             -HHHHHHHHhCCCCceEEEEeeccCHHHH
Confidence             1111111    22456777887765544

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=99.66  E-value=1.2e-16  Score=152.35  Aligned_cols=122  Identities=11%  Similarity=0.010  Sum_probs=99.2

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~Ptra  248 (333)
                      ++++.+...+...++.      .|+++|.++++.+..|+++++++|||+|||++|+++++..+.   .+.+++|++||++
T Consensus        14 ~l~~~l~~~l~~~g~~------~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~   87 (391)
T 1xti_A           14 LLKPELLRAIVDCGFE------HPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE   87 (391)
T ss_dssp             CCCHHHHHHHHHHSCC------SCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSCHH
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCCHH
Confidence            5677777776665544      699999999999999999999999999999999999987653   3568999999999


Q ss_pred             HHHHHHHHHHHhcC-----CcEEEeCCCCCC--------CCcceEEecc---------------CcceEeccccccccc
Q psy2760         249 LSNQKYRDFRETFQ-----DVGLIDDLPPVF--------PDVEKLLEDL---------------NIGGLDELSIHDFNK  299 (333)
Q Consensus       249 La~Q~~~~l~~~f~-----~vglltGd~~~~--------~~a~ili~t~---------------~i~liViDe~H~~~~  299 (333)
                      |+.|+.+.+++...     .++.++|+....        ....++++|+               ++.++|+||+|.+..
T Consensus        88 L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~vViDEaH~~~~  166 (391)
T 1xti_A           88 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLE  166 (391)
T ss_dssp             HHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCSEEEECSHHHHTS
T ss_pred             HHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHcCCccccccCEEEEeCHHHHhh
Confidence            99999999977542     278888886532        2246888875               467899999998865

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=99.66  E-value=4.5e-16  Score=149.38  Aligned_cols=124  Identities=12%  Similarity=0.009  Sum_probs=100.5

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~Ptra  248 (333)
                      ++++.+.+.+...++.      .|+++|.++++.+..|+++++++|||||||++|.++++..+.   .+.+++|++||++
T Consensus        27 ~l~~~l~~~l~~~g~~------~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~  100 (400)
T 1s2m_A           27 YLKRELLMGIFEAGFE------KPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRE  100 (400)
T ss_dssp             CCCHHHHHHHHHTTCC------SCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcCCHH
Confidence            4677777766555544      699999999999999999999999999999999999987654   4668999999999


Q ss_pred             HHHHHHHHHHHhcCC----cEEEeCCCCC-------CCCcceEEecc---------------CcceEeccccccccccC
Q psy2760         249 LSNQKYRDFRETFQD----VGLIDDLPPV-------FPDVEKLLEDL---------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       249 La~Q~~~~l~~~f~~----vglltGd~~~-------~~~a~ili~t~---------------~i~liViDe~H~~~~~~  301 (333)
                      |+.|+++.+++.+..    ++.++|+...       .....++++|+               ++.++|+||+|.+....
T Consensus       101 L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~  179 (400)
T 1s2m_A          101 LALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRD  179 (400)
T ss_dssp             HHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHH
T ss_pred             HHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHhCCcccccCCEEEEeCchHhhhhc
Confidence            999999999886653    6777887653       23457888875               46889999999876543

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=99.66  E-value=4.7e-16  Score=144.93  Aligned_cols=120  Identities=13%  Similarity=0.086  Sum_probs=96.3

Q ss_pred             CChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHH
Q psy2760         173 VSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQ  252 (333)
Q Consensus       173 L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q  252 (333)
                      |++.+.+.++..|+.      .|+++|+++++.+.+++++++++|||+|||++|..+++..   +.+++|++|+++|+.|
T Consensus         1 l~~~i~~~l~~~g~~------~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~---~~~~liv~P~~~L~~q   71 (337)
T 2z0m_A            1 MNEKIEQAIREMGFK------NFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL---GMKSLVVTPTRELTRQ   71 (337)
T ss_dssp             CCHHHHHHHHHTTCC------SCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH---TCCEEEECSSHHHHHH
T ss_pred             CCHHHHHHHHHcCCC------CCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh---cCCEEEEeCCHHHHHH
Confidence            345566666655554      7999999999999999999999999999999999988653   7789999999999999


Q ss_pred             HHHHHHHhcC----CcEEEeCCCCCC------CCcceEEecc---------------CcceEeccccccccccC
Q psy2760         253 KYRDFRETFQ----DVGLIDDLPPVF------PDVEKLLEDL---------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       253 ~~~~l~~~f~----~vglltGd~~~~------~~a~ili~t~---------------~i~liViDe~H~~~~~~  301 (333)
                      +++++++...    .++.+.|+....      ....++++|+               ++.++|+||+|.+...+
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~  145 (337)
T 2z0m_A           72 VASHIRDIGRYMDTKVAEVYGGMPYKAQINRVRNADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMG  145 (337)
T ss_dssp             HHHHHHHHTTTSCCCEEEECTTSCHHHHHHHHTTCSEEEECHHHHHHHHHTTSCCGGGCSEEEEESHHHHHHTT
T ss_pred             HHHHHHHHhhhcCCcEEEEECCcchHHHHhhcCCCCEEEECHHHHHHHHHcCCcchhhCcEEEEEChHHhhccc
Confidence            9999987543    267788876532      2356888875               45789999999886554

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=99.66  E-value=1.7e-16  Score=151.33  Aligned_cols=147  Identities=13%  Similarity=0.009  Sum_probs=110.1

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~Ptra  248 (333)
                      ++++.+...+...++.      .|+++|+++++.+..|+++++++|||+|||++|.++++..+.   .+.+++|++|+++
T Consensus        27 ~l~~~l~~~l~~~g~~------~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~  100 (394)
T 1fuu_A           27 ELDENLLRGVFGYGFE------EPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRE  100 (394)
T ss_dssp             CCCHHHHHHHHHHTCC------SCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEECSSHH
T ss_pred             CCCHHHHHHHHHcCCC------CCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEcCCHH
Confidence            5777777766655554      799999999999999999999999999999999999986653   4679999999999


Q ss_pred             HHHHHHHHHHHhcCC----cEEEeCCCCCCC------CcceEEecc---------------CcceEeccccccccccCcC
Q psy2760         249 LSNQKYRDFRETFQD----VGLIDDLPPVFP------DVEKLLEDL---------------NIGGLDELSIHDFNKHLKF  303 (333)
Q Consensus       249 La~Q~~~~l~~~f~~----vglltGd~~~~~------~a~ili~t~---------------~i~liViDe~H~~~~~~R~  303 (333)
                      |+.|+.+.+++.+..    ++.++|+.....      ...++++|+               ++.++|+||+|.+...+..
T Consensus       101 L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~vIiDEah~~~~~~~~  180 (394)
T 1fuu_A          101 LALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFK  180 (394)
T ss_dssp             HHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHHHCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcCCCCEEEECHHHHHHHHHhCCcchhhCcEEEEEChHHhhCCCcH
Confidence            999999999886543    677888765422      246788875               4678999999987654322


Q ss_pred             cccccchh----hhhhheeccCcchh
Q psy2760         304 WKPKVQLD----DLFDWTMASDATTL  325 (333)
Q Consensus       304 ~~~~~~l~----~l~~l~~~~d~~~~  325 (333)
                      -.... +.    ...+.+++|++..-
T Consensus       181 ~~~~~-~~~~~~~~~~~i~~SAT~~~  205 (394)
T 1fuu_A          181 EQIYQ-IFTLLPPTTQVVLLSATMPN  205 (394)
T ss_dssp             HHHHH-HHHHSCTTCEEEEECSSCCH
T ss_pred             HHHHH-HHHhCCCCceEEEEEEecCH
Confidence            11111 11    12346777776653

>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=99.66  E-value=1.5e-16  Score=168.69  Aligned_cols=136  Identities=21%  Similarity=0.242  Sum_probs=107.2

Q ss_pred             cCCCCCCHHHHHHHHHHHcC------CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC
Q psy2760         190 TWPFELDVFQKQAIIKLEEH------NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD  263 (333)
Q Consensus       190 ~~~f~l~~~Q~~ai~~l~~g------~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~  263 (333)
                      .+||.|+++|++|++.+..+      ++++++||||||||++|.++++..+..|.+++|++||++||.|+++.+++.++.
T Consensus       364 ~lpf~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~g~qvlvlaPtr~La~Q~~~~l~~~~~~  443 (780)
T 1gm5_A          364 SLPFKLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTVESFSK  443 (780)
T ss_dssp             HSSSCCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHHHHHHHHHTC
T ss_pred             hCCCCCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhhh
Confidence            46889999999999997544      699999999999999999999988888899999999999999999999998753


Q ss_pred             ----cEEEeCCCCCC-----------CCcceEEecc----------CcceEeccccccccccCcCcccccchhhhhhhee
Q psy2760         264 ----VGLIDDLPPVF-----------PDVEKLLEDL----------NIGGLDELSIHDFNKHLKFWKPKVQLDDLFDWTM  318 (333)
Q Consensus       264 ----vglltGd~~~~-----------~~a~ili~t~----------~i~liViDe~H~~~~~~R~~~~~~~l~~l~~l~~  318 (333)
                          ++.++|+....           ....++|+|+          ++.++|+||+|.++...|..-...  ....+.++
T Consensus       444 ~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~~~~~~l~lVVIDEaHr~g~~qr~~l~~~--~~~~~vL~  521 (780)
T 1gm5_A          444 FNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVIIDEQHRFGVKQREALMNK--GKMVDTLV  521 (780)
T ss_dssp             SSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEEEESCCCC-----CCCCSS--SSCCCEEE
T ss_pred             cCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhhhhhccCCceEEecccchhhHHHHHHHHHh--CCCCCEEE
Confidence                78899987643           2467888886          578999999999987766432222  23466888


Q ss_pred             ccCcchhhh
Q psy2760         319 ASDATTLEI  327 (333)
Q Consensus       319 ~~d~~~~e~  327 (333)
                      +|++++-+.
T Consensus       522 mSATp~p~t  530 (780)
T 1gm5_A          522 MSATPIPRS  530 (780)
T ss_dssp             EESSCCCHH
T ss_pred             EeCCCCHHH
Confidence            888875544

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=99.66  E-value=2.5e-16  Score=157.01  Aligned_cols=110  Identities=12%  Similarity=0.072  Sum_probs=88.7

Q ss_pred             CCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC-----CCeEEEEcccHHHHHHHHHHHHHhcC----
Q psy2760         192 PFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH-----KTRTIYTSPIKALSNQKYRDFRETFQ----  262 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~-----g~ral~l~PtraLa~Q~~~~l~~~f~----  262 (333)
                      ++.|+++|.++++.+..|+++++++|||||||++|.++++..+..     +.++||++||++|+.|+.+.+++.+.    
T Consensus         5 ~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~   84 (556)
T 4a2p_A            5 TKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGY   84 (556)
T ss_dssp             ---CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGGTC
T ss_pred             CCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhcccCc
Confidence            468999999999999999999999999999999999999866543     78999999999999999999988765    


Q ss_pred             CcEEEeCCCCCCCC-------cceEEecc----------------CcceEeccccccccccC
Q psy2760         263 DVGLIDDLPPVFPD-------VEKLLEDL----------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       263 ~vglltGd~~~~~~-------a~ili~t~----------------~i~liViDe~H~~~~~~  301 (333)
                      .++.++|+.....+       ..++++|+                ++.++|+||+|.+...+
T Consensus        85 ~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~  146 (556)
T 4a2p_A           85 SVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNH  146 (556)
T ss_dssp             CEEECCCC-----CHHHHHHHCSEEEECHHHHHHHHHSSSCCCSTTCSEEEEETGGGCSTTS
T ss_pred             eEEEEeCCCCcchhHHHhhCCCCEEEECHHHHHHHHHhCcccccccCCEEEEECCcccCCcc
Confidence            27888898865543       46888875                35789999999987654

>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=99.61  E-value=1.4e-15  Score=141.18  Aligned_cols=130  Identities=16%  Similarity=0.106  Sum_probs=97.0

Q ss_pred             CCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC-CCeEEEEcccHHHHHHHHHHHHHhcCC----cEEE
Q psy2760         193 FELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH-KTRTIYTSPIKALSNQKYRDFRETFQD----VGLI  267 (333)
Q Consensus       193 f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~-g~ral~l~PtraLa~Q~~~~l~~~f~~----vgll  267 (333)
                      +.|+++|.++++.+..+++.++++|||+|||+++..++...... +.+++|++||++|++|+.+++++.+..    ++.+
T Consensus       112 ~~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~l~~~~~~~~~~~~~~  191 (282)
T 1rif_A          112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKI  191 (282)
T ss_dssp             CCCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEEC
T ss_pred             cCccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHHHHHhcccccceEEEE
Confidence            47999999999998777889999999999999998877755543 349999999999999999999875432    4666


Q ss_pred             eCCCCCC----CCcceEEecc------------CcceEeccccccccccCcCcccccc-hhhhhhheeccCcch
Q psy2760         268 DDLPPVF----PDVEKLLEDL------------NIGGLDELSIHDFNKHLKFWKPKVQ-LDDLFDWTMASDATT  324 (333)
Q Consensus       268 tGd~~~~----~~a~ili~t~------------~i~liViDe~H~~~~~~R~~~~~~~-l~~l~~l~~~~d~~~  324 (333)
                      .|+....    ....++++|+            ++.++|+||+|.+...  .+...+. +......++.|+++.
T Consensus       192 ~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~vIiDEaH~~~~~--~~~~il~~~~~~~~~l~lSATp~  263 (282)
T 1rif_A          192 GGGASKDDKYKNDAPVVVGTWQTVVKQPKEWFSQFGMMMNDECHLATGK--SISSIISGLNNCMFKFGLSGSLR  263 (282)
T ss_dssp             STTCSSTTCCCTTCSEEEECHHHHTTSCGGGGGGEEEEEEETGGGCCHH--HHHHHTTTCTTCCEEEEECSSCC
T ss_pred             eCCCcchhhhccCCcEEEEchHHHHhhHHHHHhhCCEEEEECCccCCcc--cHHHHHHHhhcCCeEEEEeCCCC
Confidence            6665543    4567888875            5688999999998754  2221111 112345667777663

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.60  E-value=9.6e-16  Score=152.96  Aligned_cols=132  Identities=17%  Similarity=0.117  Sum_probs=101.5

Q ss_pred             CCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCC-CeEEEEcccHHHHHHHHHHHHHh--cC--CcEE
Q psy2760         192 PFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHK-TRTIYTSPIKALSNQKYRDFRET--FQ--DVGL  266 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g-~ral~l~PtraLa~Q~~~~l~~~--f~--~vgl  266 (333)
                      ++.|+++|.+|++.+..++++++++|||+|||++++.++...+..+ .+++|++||++|+.|++++|++.  +.  .++.
T Consensus       111 ~~~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~~~~~~~~~~~v~~  190 (510)
T 2oca_A          111 RIEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKK  190 (510)
T ss_dssp             EECCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHCSSEEEEEESSHHHHHHHHHHHHHTTSSCGGGEEE
T ss_pred             CCCCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCCCCeEEEEECcHHHHHHHHHHHHHhhcCCccceEE
Confidence            4489999999999998889999999999999999998888665444 49999999999999999999765  33  2677


Q ss_pred             EeCCCCCC----CCcceEEecc------------CcceEeccccccccccCcCcccccc-hhhhhhheeccCcchh
Q psy2760         267 IDDLPPVF----PDVEKLLEDL------------NIGGLDELSIHDFNKHLKFWKPKVQ-LDDLFDWTMASDATTL  325 (333)
Q Consensus       267 ltGd~~~~----~~a~ili~t~------------~i~liViDe~H~~~~~~R~~~~~~~-l~~l~~l~~~~d~~~~  325 (333)
                      ++|+....    ....++++|+            ++.++|+||+|.+...  .+..... +......+.+|+++.-
T Consensus       191 ~~~~~~~~~~~~~~~~I~i~T~~~l~~~~~~~~~~~~liIiDE~H~~~~~--~~~~il~~~~~~~~~l~lSATp~~  264 (510)
T 2oca_A          191 IGGGASKDDKYKNDAPVVVGTWQTVVKQPKEWFSQFGMMMNDECHLATGK--SISSIISGLNNCMFKFGLSGSLRD  264 (510)
T ss_dssp             CGGGCCTTGGGCTTCSEEEEEHHHHTTSCGGGGGGEEEEEEETGGGCCHH--HHHHHGGGCTTCCEEEEEESCGGG
T ss_pred             EecCCccccccccCCcEEEEeHHHHhhchhhhhhcCCEEEEECCcCCCcc--cHHHHHHhcccCcEEEEEEeCCCC
Confidence            88887665    5567888875            5789999999998763  2322211 1122346666777743

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.60  E-value=2.5e-15  Score=164.67  Aligned_cols=113  Identities=12%  Similarity=0.050  Sum_probs=98.0

Q ss_pred             ccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC----Cc
Q psy2760         189 HTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ----DV  264 (333)
Q Consensus       189 ~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~----~v  264 (333)
                      ..++|.|+++|.+|++.+..|++++++||||||||++|+.+++..+..+.+++|++|||+||.|+++++++ |+    .+
T Consensus        73 ~~~gf~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~~~~~~Lil~PtreLa~Q~~~~l~~-l~~~~i~v  151 (1104)
T 4ddu_A           73 KKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQK-LADEKVKI  151 (1104)
T ss_dssp             HHSSSCCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHT-TSCTTSCE
T ss_pred             HhcCCCCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHhcCCeEEEEechHHHHHHHHHHHHH-hhCCCCeE
Confidence            34677899999999999999999999999999999999889888888899999999999999999999988 43    37


Q ss_pred             EEEeCCCCCC-----------CCcceEEecc-------------CcceEeccccccccccCc
Q psy2760         265 GLIDDLPPVF-----------PDVEKLLEDL-------------NIGGLDELSIHDFNKHLK  302 (333)
Q Consensus       265 glltGd~~~~-----------~~a~ili~t~-------------~i~liViDe~H~~~~~~R  302 (333)
                      +.++|+.+..           ....++|+|+             ++.++|+||+|.+...+|
T Consensus       152 ~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~l~~~~l~~lViDEaH~l~~~~r  213 (1104)
T 4ddu_A          152 FGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDFVFVDDVDAVLKASR  213 (1104)
T ss_dssp             EEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHHHHTSCCSEEEESCHHHHTTSSH
T ss_pred             EEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHhhcccCcCEEEEeCCCccccccc
Confidence            8899998762           2367889886             578999999998876553

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.60  E-value=3.1e-15  Score=154.51  Aligned_cols=110  Identities=13%  Similarity=0.100  Sum_probs=91.5

Q ss_pred             CCC-CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC-----CCeEEEEcccHHHHHHHHHHHHHhcC--
Q psy2760         191 WPF-ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH-----KTRTIYTSPIKALSNQKYRDFRETFQ--  262 (333)
Q Consensus       191 ~~f-~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~-----g~ral~l~PtraLa~Q~~~~l~~~f~--  262 (333)
                      ++| .|+++|.++++.++.|+++++++|||+|||++|.++++..+..     +.+++|++||++|+.|+.+.+++.+.  
T Consensus         9 ~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~~~~~~~~~   88 (696)
T 2ykg_A            9 YSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFSKYFERH   88 (696)
T ss_dssp             TC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHHHHHHTTTT
T ss_pred             cCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHHHHHHhccC
Confidence            444 8999999999999999999999999999999999999865432     27899999999999999999988774  


Q ss_pred             --CcEEEeCCCCCCC-------CcceEEecc----------------CcceEecccccccccc
Q psy2760         263 --DVGLIDDLPPVFP-------DVEKLLEDL----------------NIGGLDELSIHDFNKH  300 (333)
Q Consensus       263 --~vglltGd~~~~~-------~a~ili~t~----------------~i~liViDe~H~~~~~  300 (333)
                        .++.++|+.....       ...++++|+                ++.++|+||+|.+...
T Consensus        89 ~~~v~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~L~~~l~~~~~~~l~~~~~vViDEaH~~~~~  151 (696)
T 2ykg_A           89 GYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQ  151 (696)
T ss_dssp             TCCEEEECSSSCSSSCHHHHHHTCSEEEECHHHHHHHHHTTSSCCGGGCSEEEEETGGGCSTT
T ss_pred             CceEEEEeCCccccccHHHhccCCCEEEECHHHHHHHHhcCcccccccccEEEEeCCCcccCc
Confidence              2788999876543       346888875                3578999999998644

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=99.59  E-value=6.4e-15  Score=151.78  Aligned_cols=156  Identities=11%  Similarity=0.133  Sum_probs=113.7

Q ss_pred             cccchh-hccCChhhhhhhhccccccccCCC-CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEE
Q psy2760         164 QTEWAE-MLDVSKPVLDFDAKVPIMAHTWPF-ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTI  241 (333)
Q Consensus       164 ~~~w~~-~~~L~~~l~~~~~~~~~~~~~~~f-~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral  241 (333)
                      ...|.. ..++++.+...++.      .|+| .|+++|.++++.++.|+++++.+|||+|||++|.+|++.   .+.++|
T Consensus        18 ~~~w~~~~~~l~~~l~~~L~~------~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~---~~g~~l   88 (591)
T 2v1x_A           18 PAAWNKEDFPWSGKVKDILQN------VFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALC---SDGFTL   88 (591)
T ss_dssp             GGGGCCSCSTTHHHHHHHHHH------TSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHT---SSSEEE
T ss_pred             hhccccccCCCCHHHHHHHHH------HhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHH---cCCcEE
Confidence            345544 23455566665543      2344 799999999999999999999999999999999999864   356899


Q ss_pred             EEcccHHHHHHHHHHHHHhcCCcEEEeCCCCC-------------CCCcceEEecc--------------------Ccce
Q psy2760         242 YTSPIKALSNQKYRDFRETFQDVGLIDDLPPV-------------FPDVEKLLEDL--------------------NIGG  288 (333)
Q Consensus       242 ~l~PtraLa~Q~~~~l~~~f~~vglltGd~~~-------------~~~a~ili~t~--------------------~i~l  288 (333)
                      |++|+++|+.|+.+.+++..-.++.++|+...             .....+++.|+                    .+.+
T Consensus        89 VisP~~~L~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~~~~~~~i~~  168 (591)
T 2v1x_A           89 VICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTR  168 (591)
T ss_dssp             EECSCHHHHHHHHHHHHHHTCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHHHHHTTCEEE
T ss_pred             EEeCHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHhhhhccCCcE
Confidence            99999999999999998853347788887653             23456888776                    4678


Q ss_pred             EeccccccccccCcCcccccch----hh---hhhheeccCcchhhhh
Q psy2760         289 LDELSIHDFNKHLKFWKPKVQL----DD---LFDWTMASDATTLEIF  328 (333)
Q Consensus       289 iViDe~H~~~~~~R~~~~~~~l----~~---l~~l~~~~d~~~~e~~  328 (333)
                      +|+||+|.+...+..++.....    .+   .+..+++|++..-+++
T Consensus       169 iViDEAH~is~~g~dfr~~~~~l~~l~~~~~~~~ii~lSAT~~~~v~  215 (591)
T 2v1x_A          169 IAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHVL  215 (591)
T ss_dssp             EEEETGGGGSTTCTTCCGGGGGGGHHHHHCTTSEEEEEESSCCHHHH
T ss_pred             EEEECcccccccccccHHHHHHHHHHHHhCCCCcEEEEecCCCHHHH
Confidence            9999999987765444443211    11   2346777777665543

>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=99.59  E-value=3.6e-15  Score=130.99  Aligned_cols=108  Identities=16%  Similarity=0.138  Sum_probs=80.0

Q ss_pred             CCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc------CCCeEEEEcccHHHHHH-HHHHHHHhcC--
Q psy2760         192 PFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN------HKTRTIYTSPIKALSNQ-KYRDFRETFQ--  262 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~------~g~ral~l~PtraLa~Q-~~~~l~~~f~--  262 (333)
                      .+.|+++|.++++.+..++++++++|||+|||+++..++...+.      .+.+++|++|+++|+.| +.+.+.+...  
T Consensus        31 ~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~~~~~~~~  110 (216)
T 3b6e_A           31 ELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKW  110 (216)
T ss_dssp             CCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTHHHHHTTT
T ss_pred             CCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHHHHHhccC
Confidence            45899999999999999999999999999999999998875432      36799999999999999 6666666443  


Q ss_pred             -CcEEEeCCCCCCCC-------cceEEecc---------------------CcceEeccccccccc
Q psy2760         263 -DVGLIDDLPPVFPD-------VEKLLEDL---------------------NIGGLDELSIHDFNK  299 (333)
Q Consensus       263 -~vglltGd~~~~~~-------a~ili~t~---------------------~i~liViDe~H~~~~  299 (333)
                       .++.++|+......       ..++++|+                     ++.++|+||+|.+..
T Consensus       111 ~~v~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~~~  176 (216)
T 3b6e_A          111 YRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNK  176 (216)
T ss_dssp             SCEEECCC---CCCCHHHHHHHCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC-----
T ss_pred             ceEEEEeCCcccchhHHhhccCCCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchhhcc
Confidence             37778887665432       45677654                     346899999999864

>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=99.58  E-value=4e-15  Score=157.42  Aligned_cols=108  Identities=13%  Similarity=0.096  Sum_probs=90.3

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC-----CCeEEEEcccHHHHHHHHHHHHHhcC----Cc
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH-----KTRTIYTSPIKALSNQKYRDFRETFQ----DV  264 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~-----g~ral~l~PtraLa~Q~~~~l~~~f~----~v  264 (333)
                      .|+++|.++++.+..|+++++++|||||||++|.++++..+..     +.++||++||++|+.|+++.|++.++    .+
T Consensus       248 ~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~~~~~~~v  327 (797)
T 4a2q_A          248 KARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSV  327 (797)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGGTCCE
T ss_pred             CCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHhcccCCceE
Confidence            8999999999999999999999999999999999999876544     78999999999999999999998765    27


Q ss_pred             EEEeCCCCCCC-------CcceEEecc----------------CcceEeccccccccccC
Q psy2760         265 GLIDDLPPVFP-------DVEKLLEDL----------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       265 glltGd~~~~~-------~a~ili~t~----------------~i~liViDe~H~~~~~~  301 (333)
                      +.++|+.....       ...++|+|+                ++.++|+||+|.+....
T Consensus       328 ~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEaH~~~~~~  387 (797)
T 4a2q_A          328 QGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNH  387 (797)
T ss_dssp             EEECCC-----CHHHHHHTCSEEEECHHHHHHHHHSSSCCCGGGCSEEEETTGGGCSTTS
T ss_pred             EEEeCCcchhhhHHHhhCCCCEEEEchHHHHHHHHhccccccccCCEEEEECccccCCCc
Confidence            88999886554       346888875                35889999999987654

>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=99.58  E-value=4.2e-15  Score=146.94  Aligned_cols=126  Identities=17%  Similarity=0.054  Sum_probs=100.3

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC-C-cEEEe
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ-D-VGLID  268 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~-~-vgllt  268 (333)
                      +++.|+++|.+++..+..++++++++|||+|||++++.++...   +.+++|++|+++|+.|+.++|++ |+ . +++++
T Consensus        90 ~~~~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~---~~~~Lvl~P~~~L~~Q~~~~~~~-~~~~~v~~~~  165 (472)
T 2fwr_A           90 AEISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL---STPTLIVVPTLALAEQWKERLGI-FGEEYVGEFS  165 (472)
T ss_dssp             CCCCBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH---CSCEEEEESSHHHHHHHHHHGGG-GCGGGEEEBS
T ss_pred             CCCCcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc---CCCEEEEECCHHHHHHHHHHHHh-CCCcceEEEC
Confidence            3568999999999999888899999999999999999988754   67899999999999999999988 76 4 88888


Q ss_pred             CCCCCCCCcceEEecc------------CcceEeccccccccccCcCcccccchhhhhhheeccCcch
Q psy2760         269 DLPPVFPDVEKLLEDL------------NIGGLDELSIHDFNKHLKFWKPKVQLDDLFDWTMASDATT  324 (333)
Q Consensus       269 Gd~~~~~~a~ili~t~------------~i~liViDe~H~~~~~~R~~~~~~~l~~l~~l~~~~d~~~  324 (333)
                      |+...  ...++++|+            ++.++|+||+|.+....  ++...........+++|+++.
T Consensus       166 g~~~~--~~~Ivv~T~~~l~~~~~~~~~~~~liIvDEaH~~~~~~--~~~~~~~~~~~~~l~lSATp~  229 (472)
T 2fwr_A          166 GRIKE--LKPLTVSTYDSAYVNAEKLGNRFMLLIFDEVHHLPAES--YVQIAQMSIAPFRLGLTATFE  229 (472)
T ss_dssp             SSCBC--CCSEEEEEHHHHHHTHHHHTTTCSEEEEETGGGTTSTT--THHHHHTCCCSEEEEEESCCC
T ss_pred             CCcCC--cCCEEEEEcHHHHHHHHHhcCCCCEEEEECCcCCCChH--HHHHHHhcCCCeEEEEecCcc
Confidence            88764  356888875            47899999999987653  222221222234677788775

>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=99.55  E-value=4.7e-15  Score=153.30  Aligned_cols=108  Identities=16%  Similarity=0.134  Sum_probs=86.7

Q ss_pred             CCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC------CCeEEEEcccHHHHHHH-HHHHHHhcC--
Q psy2760         192 PFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH------KTRTIYTSPIKALSNQK-YRDFRETFQ--  262 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~------g~ral~l~PtraLa~Q~-~~~l~~~f~--  262 (333)
                      +|.|+++|.++++.+..|+++++++|||+|||++|.++++..+..      +.++||++|+++|+.|+ .++|++.++  
T Consensus         5 ~~~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~~   84 (699)
T 4gl2_A            5 MLQLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKW   84 (699)
T ss_dssp             --CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHHHTTT
T ss_pred             CCCccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHHcCcC
Confidence            458999999999999999999999999999999999999865432      27899999999999999 999999886  


Q ss_pred             -CcEEEeCCCCCCC-------CcceEEecc---------------------CcceEeccccccccc
Q psy2760         263 -DVGLIDDLPPVFP-------DVEKLLEDL---------------------NIGGLDELSIHDFNK  299 (333)
Q Consensus       263 -~vglltGd~~~~~-------~a~ili~t~---------------------~i~liViDe~H~~~~  299 (333)
                       .++.++|+.....       ...++++|+                     ++.++|+||+|.+..
T Consensus        85 ~~v~~~~g~~~~~~~~~~~~~~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~~~~  150 (699)
T 4gl2_A           85 YRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNK  150 (699)
T ss_dssp             SCEEEEC----CCCCHHHHHHSCSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGGCBT
T ss_pred             ceEEEEeCCcchhhHHHhhhcCCCEEEECHHHHHHHHhccccccccceecccCcEEEEECccccCc
Confidence             4788999877653       346777764                     357899999998743

>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=99.54  E-value=1.7e-14  Score=131.78  Aligned_cols=104  Identities=20%  Similarity=0.120  Sum_probs=88.2

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC-C-cEEEe
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ-D-VGLID  268 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~-~-vgllt  268 (333)
                      +++.++++|.+++..+..++++++++|||+|||.++..++...   +.+++|++|+++|+.|+.+++++ |+ . ++.++
T Consensus        90 ~~~~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~---~~~~liv~P~~~L~~q~~~~~~~-~~~~~v~~~~  165 (237)
T 2fz4_A           90 AEISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL---STPTLIVVPTLALAEQWKERLGI-FGEEYVGEFS  165 (237)
T ss_dssp             CCCCCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS---CSCEEEEESSHHHHHHHHHHHGG-GCGGGEEEES
T ss_pred             CCCCcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc---CCCEEEEeCCHHHHHHHHHHHHh-CCCCeEEEEe
Confidence            3458999999999999888899999999999999998877543   67899999999999999999988 65 3 78888


Q ss_pred             CCCCCCCCcceEEecc------------CcceEecccccccccc
Q psy2760         269 DLPPVFPDVEKLLEDL------------NIGGLDELSIHDFNKH  300 (333)
Q Consensus       269 Gd~~~~~~a~ili~t~------------~i~liViDe~H~~~~~  300 (333)
                      |+...  ...+++.|+            ...++|+||+|++...
T Consensus       166 g~~~~--~~~i~v~T~~~l~~~~~~~~~~~~llIiDEaH~l~~~  207 (237)
T 2fz4_A          166 GRIKE--LKPLTVSTYDSAYVNAEKLGNRFMLLIFDEVHHLPAE  207 (237)
T ss_dssp             SSCBC--CCSEEEEEHHHHHHTHHHHTTTCSEEEEECSSCCCTT
T ss_pred             CCCCC--cCCEEEEeHHHHHhhHHHhcccCCEEEEECCccCCCh
Confidence            87654  456788775            4789999999999754

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=99.53  E-value=1.7e-14  Score=146.28  Aligned_cols=134  Identities=13%  Similarity=0.113  Sum_probs=100.3

Q ss_pred             CCC-CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEeC
Q psy2760         191 WPF-ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDD  269 (333)
Q Consensus       191 ~~f-~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vglltG  269 (333)
                      |+| .|+++|.++++.+..|+++++.+|||+|||++|.+|++..   +.+++|++|+++|+.|+.+.+++..-.++.++|
T Consensus        21 ~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~---~g~~lvi~P~~aL~~q~~~~l~~~gi~~~~l~~   97 (523)
T 1oyw_A           21 FGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL---NGLTVVVSPLISLMKDQVDQLQANGVAAACLNS   97 (523)
T ss_dssp             TCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS---SSEEEEECSCHHHHHHHHHHHHHTTCCEEEECT
T ss_pred             hCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh---CCCEEEECChHHHHHHHHHHHHHcCCcEEEEeC
Confidence            344 7899999999999999999999999999999999998643   468999999999999999999874334777887


Q ss_pred             CCCCC-----------CCcceEEecc---------------CcceEeccccccccccCcCccccc----chhhh---hhh
Q psy2760         270 LPPVF-----------PDVEKLLEDL---------------NIGGLDELSIHDFNKHLKFWKPKV----QLDDL---FDW  316 (333)
Q Consensus       270 d~~~~-----------~~a~ili~t~---------------~i~liViDe~H~~~~~~R~~~~~~----~l~~l---~~l  316 (333)
                      +....           ....+++.|+               ++.++|+||+|.+...+..++...    .+.+.   +..
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~vViDEaH~i~~~g~~fr~~~~~l~~l~~~~~~~~~  177 (523)
T 1oyw_A           98 TQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPF  177 (523)
T ss_dssp             TSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTSSCCCHHHHGGGGHHHHCTTSCE
T ss_pred             CCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEEEEeCccccCcCCCccHHHHHHHHHHHHhCCCCCE
Confidence            76532           2246777764               567899999999976655444321    11121   345


Q ss_pred             eeccCcchhhh
Q psy2760         317 TMASDATTLEI  327 (333)
Q Consensus       317 ~~~~d~~~~e~  327 (333)
                      +..|++..-++
T Consensus       178 i~lSAT~~~~~  188 (523)
T 1oyw_A          178 MALTATADDTT  188 (523)
T ss_dssp             EEEESCCCHHH
T ss_pred             EEEeCCCCHHH
Confidence            66777665443

>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=99.53  E-value=1.8e-14  Score=138.98  Aligned_cols=107  Identities=16%  Similarity=0.177  Sum_probs=90.1

Q ss_pred             CCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh-cCCCeEEEEcccHHHHHHHHHHHHHhcC----CcEEE
Q psy2760         193 FELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ-NHKTRTIYTSPIKALSNQKYRDFRETFQ----DVGLI  267 (333)
Q Consensus       193 f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l-~~g~ral~l~PtraLa~Q~~~~l~~~f~----~vgll  267 (333)
                      +.|+++|.+++..+..+ ++++++|||+|||+++..++...+ ..+.++||++|+++|+.|+.+++++.++    .++.+
T Consensus         8 ~~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~~~   86 (494)
T 1wp9_A            8 IQPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVAL   86 (494)
T ss_dssp             HCCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEE
T ss_pred             CCccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHHHHHhCcchhheEEe
Confidence            37999999999999888 999999999999999999887554 4678999999999999999999998775    37888


Q ss_pred             eCCCCCCC------CcceEEecc---------------CcceEecccccccccc
Q psy2760         268 DDLPPVFP------DVEKLLEDL---------------NIGGLDELSIHDFNKH  300 (333)
Q Consensus       268 tGd~~~~~------~a~ili~t~---------------~i~liViDe~H~~~~~  300 (333)
                      +|+.....      ...++++|+               ++.++|+||+|.+...
T Consensus        87 ~g~~~~~~~~~~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~  140 (494)
T 1wp9_A           87 TGEKSPEERSKAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGN  140 (494)
T ss_dssp             CSCSCHHHHHHHHHHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTT
T ss_pred             eCCcchhhhhhhccCCCEEEecHHHHHHHHhcCCcchhhceEEEEECCcccCCC
Confidence            88875432      346788775               4678999999998754

>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=99.52  E-value=2e-14  Score=155.10  Aligned_cols=109  Identities=12%  Similarity=0.072  Sum_probs=89.6

Q ss_pred             CCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC-----CCeEEEEcccHHHHHHHHHHHHHhcC----C
Q psy2760         193 FELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH-----KTRTIYTSPIKALSNQKYRDFRETFQ----D  263 (333)
Q Consensus       193 f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~-----g~ral~l~PtraLa~Q~~~~l~~~f~----~  263 (333)
                      +.|+++|.++++.+..|+++++++|||||||++|.++++..+..     +.++||++||++|+.|++++|++.++    .
T Consensus       247 ~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~  326 (936)
T 4a2w_A          247 KKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYS  326 (936)
T ss_dssp             -CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTCC
T ss_pred             CCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHHhcccCce
Confidence            38999999999999999999999999999999999999866544     78899999999999999999988764    2


Q ss_pred             cEEEeCCCCCCCC-------cceEEecc----------------CcceEeccccccccccC
Q psy2760         264 VGLIDDLPPVFPD-------VEKLLEDL----------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       264 vglltGd~~~~~~-------a~ili~t~----------------~i~liViDe~H~~~~~~  301 (333)
                      ++.++|+.....+       ..++|+|+                ++.++|+||+|.+....
T Consensus       327 v~~~~G~~~~~~~~~~~~~~~~IvI~Tp~~L~~~l~~~~~~~l~~~~liViDEaH~~~~~~  387 (936)
T 4a2w_A          327 VQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNH  387 (936)
T ss_dssp             EEEECCC-----CCHHHHHHCSEEEECHHHHHHHHHSSSCCCGGGCSEEEEETGGGCSTTC
T ss_pred             EEEEECCcchhhHHHHhccCCCEEEecHHHHHHHHHcCccccccCCCEEEEECccccCCCc
Confidence            7889998865542       36888875                25789999999987653

>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=99.44  E-value=1.2e-13  Score=150.86  Aligned_cols=108  Identities=16%  Similarity=0.063  Sum_probs=89.4

Q ss_pred             cCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHH-HHhcCCCeEEEEcccHHHHHHHHHHHHHhcC------
Q psy2760         190 TWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIA-LSQNHKTRTIYTSPIKALSNQKYRDFRETFQ------  262 (333)
Q Consensus       190 ~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il-~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~------  262 (333)
                      .++|.| ++|.++++.++.|++++++||||||||+ |.++++ .....+.+++|++|||+||.|+++.+++.+.      
T Consensus        53 ~~g~~p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~~~~~~lil~PtreLa~Q~~~~l~~l~~~~~i~~  130 (1054)
T 1gku_B           53 CVGEPR-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGT  130 (1054)
T ss_dssp             TTCSCC-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHTTSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSG
T ss_pred             hcCCCH-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhhcCCeEEEEeccHHHHHHHHHHHHHHHhhcCCCc
Confidence            456678 9999999999999999999999999998 666665 4456788999999999999999999988664      


Q ss_pred             --CcEEEeCCCCCCC---------CcceEEecc-----------CcceEeccccccccc
Q psy2760         263 --DVGLIDDLPPVFP---------DVEKLLEDL-----------NIGGLDELSIHDFNK  299 (333)
Q Consensus       263 --~vglltGd~~~~~---------~a~ili~t~-----------~i~liViDe~H~~~~  299 (333)
                        .++.++|+.....         ...++++|+           ++.++|+||+|.+.+
T Consensus       131 ~~~v~~~~Gg~~~~~~~~~~~~l~~~~IlV~TP~~L~~~l~~L~~l~~lViDEah~~l~  189 (1054)
T 1gku_B          131 ENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYRELGHFDFIFVDDVDAILK  189 (1054)
T ss_dssp             GGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHCSTTSCCCSEEEESCHHHHHT
T ss_pred             cceEEEEeCCCChhhHHHHHhhccCCCEEEEcHHHHHHHHHHhccCCEEEEeChhhhhh
Confidence              3577888876533         146888886           466999999998765

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.37  E-value=7.3e-13  Score=135.00  Aligned_cols=131  Identities=16%  Similarity=0.104  Sum_probs=76.4

Q ss_pred             CCCCCHHHHHHHHHHHc-----CCcEEEEcCCCCcHHHHHHHHHHHHhc---------CCCeEEEEcccHHHHHHHH-HH
Q psy2760         192 PFELDVFQKQAIIKLEE-----HNHVFVTAHTSAGKTVIAEYAIALSQN---------HKTRTIYTSPIKALSNQKY-RD  256 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~-----g~~vlv~apTGSGKTl~~~l~il~~l~---------~g~ral~l~PtraLa~Q~~-~~  256 (333)
                      ++.|+++|.+|++.+..     ++++++++|||||||++++..+.....         .+.++||++||++|+.|+. +.
T Consensus       176 ~~~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~  255 (590)
T 3h1t_A          176 GYSPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKT  255 (590)
T ss_dssp             ---CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHHHHTTCCSSCSSSCCCEEEEEC-----------C
T ss_pred             CCCchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHHHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHH
Confidence            34899999999998743     467999999999999998776654433         5689999999999999999 66


Q ss_pred             HHHhcCC-cEEEeCCCCCCCCcceEEecc-------------------CcceEeccccccccccC-cCcccccchhhhhh
Q psy2760         257 FRETFQD-VGLIDDLPPVFPDVEKLLEDL-------------------NIGGLDELSIHDFNKHL-KFWKPKVQLDDLFD  315 (333)
Q Consensus       257 l~~~f~~-vglltGd~~~~~~a~ili~t~-------------------~i~liViDe~H~~~~~~-R~~~~~~~l~~l~~  315 (333)
                      ++. |+. ++.++++. ......++++|+                   .+.++|+||+|.+.... ..|+.....+....
T Consensus       256 ~~~-~~~~~~~~~~~~-~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~~~~~~~~il~~~~~~~  333 (590)
T 3h1t_A          256 FTP-FGDARHKIEGGK-VVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARDNSNWREILEYFEPAF  333 (590)
T ss_dssp             CTT-TCSSEEECCC---CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC---------CHHHHHHSTTSE
T ss_pred             HHh-cchhhhhhhccC-CCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccccchHHHHHHHHhCCcce
Confidence            654 554 55555443 334556777765                   25689999999986542 23332222222234


Q ss_pred             heeccCcch
Q psy2760         316 WTMASDATT  324 (333)
Q Consensus       316 l~~~~d~~~  324 (333)
                      .+.+|+++.
T Consensus       334 ~l~lTATP~  342 (590)
T 3h1t_A          334 QIGMTATPL  342 (590)
T ss_dssp             EEEEESSCS
T ss_pred             EEEeccccc
Confidence            777788765

>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=99.34  E-value=3.8e-12  Score=115.28  Aligned_cols=136  Identities=12%  Similarity=0.111  Sum_probs=93.9

Q ss_pred             CCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh-cC----CCeEEEEcccHHHHHHHHHHHHHhcCC---
Q psy2760         192 PFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ-NH----KTRTIYTSPIKALSNQKYRDFRETFQD---  263 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l-~~----g~ral~l~PtraLa~Q~~~~l~~~f~~---  263 (333)
                      ++.++++|.++++.+..|++++++||||||||.++..+++... ..    +.++++++|+++|+.|+.+.+...++.   
T Consensus        59 ~~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~~~~~  138 (235)
T 3llm_A           59 LLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPG  138 (235)
T ss_dssp             TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTTCCTT
T ss_pred             cCChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhccccC
Confidence            3457899999999999999999999999999998888776432 22    348999999999999999999876653   


Q ss_pred             --cEEEeCCCCC--CCCcceEEecc------------CcceEeccccccccccCcCcc--cccchh---hhhhheeccCc
Q psy2760         264 --VGLIDDLPPV--FPDVEKLLEDL------------NIGGLDELSIHDFNKHLKFWK--PKVQLD---DLFDWTMASDA  322 (333)
Q Consensus       264 --vglltGd~~~--~~~a~ili~t~------------~i~liViDe~H~~~~~~R~~~--~~~~l~---~l~~l~~~~d~  322 (333)
                        +|.-......  .....++++|+            ++.++|+||+|..+-.. ++.  ....+.   ...+.+++|++
T Consensus       139 ~~~g~~~~~~~~~~~~~~~Ivv~Tpg~l~~~l~~~l~~~~~lVlDEah~~~~~~-~~~~~~l~~i~~~~~~~~~il~SAT  217 (235)
T 3llm_A          139 KSCGYSVRFESILPRPHASIMFCTVGVLLRKLEAGIRGISHVIVDEIHERDINT-DFLLVVLRDVVQAYPEVRIVLMSAT  217 (235)
T ss_dssp             SSEEEEETTEEECCCSSSEEEEEEHHHHHHHHHHCCTTCCEEEECCTTSCCHHH-HHHHHHHHHHHHHCTTSEEEEEECS
T ss_pred             ceEEEeechhhccCCCCCeEEEECHHHHHHHHHhhhcCCcEEEEECCccCCcch-HHHHHHHHHHHhhCCCCeEEEEecC
Confidence              3322211111  13456888876            67899999999731111 111  001111   22457888887


Q ss_pred             chhhhh
Q psy2760         323 TTLEIF  328 (333)
Q Consensus       323 ~~~e~~  328 (333)
                      -..+.|
T Consensus       218 ~~~~~~  223 (235)
T 3llm_A          218 IDTSMF  223 (235)
T ss_dssp             SCCHHH
T ss_pred             CCHHHH
Confidence            766654

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.31  E-value=2.6e-12  Score=134.37  Aligned_cols=101  Identities=15%  Similarity=0.103  Sum_probs=79.5

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEeCCCCCCC-----CcceEE
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFP-----DVEKLL  281 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vglltGd~~~~~-----~a~ili  281 (333)
                      ++|++++++||||||||+.++..+..    ..+++|++|||+||.|+++++++....+++++|+.....     ...+++
T Consensus       153 l~rk~vlv~apTGSGKT~~al~~l~~----~~~gl~l~PtR~LA~Qi~~~l~~~g~~v~lltG~~~~iv~TpGr~~~il~  228 (677)
T 3rc3_A          153 MQRKIIFHSGPTNSGKTYHAIQKYFS----AKSGVYCGPLKLLAHEIFEKSNAAGVPCDLVTGEERVTVQPNGKQASHVS  228 (677)
T ss_dssp             SCCEEEEEECCTTSSHHHHHHHHHHH----SSSEEEEESSHHHHHHHHHHHHHTTCCEEEECSSCEECCSTTCCCCSEEE
T ss_pred             cCCCEEEEEcCCCCCHHHHHHHHHHh----cCCeEEEeCHHHHHHHHHHHHHhcCCcEEEEECCeeEEecCCCcccceeE
Confidence            57899999999999999954444332    345699999999999999999886446999999876532     245777


Q ss_pred             ecc-------CcceEeccccccccccCcCcccccchh
Q psy2760         282 EDL-------NIGGLDELSIHDFNKHLKFWKPKVQLD  311 (333)
Q Consensus       282 ~t~-------~i~liViDe~H~~~~~~R~~~~~~~l~  311 (333)
                      +|+       .+.++|+||+|.+.+..|++.+...+.
T Consensus       229 ~T~e~~~l~~~v~lvVIDEaH~l~d~~~g~~~~~~l~  265 (677)
T 3rc3_A          229 CTVEMCSVTTPYEVAVIDEIQMIRDPARGWAWTRALL  265 (677)
T ss_dssp             EEGGGCCSSSCEEEEEECSGGGGGCTTTHHHHHHHHH
T ss_pred             ecHhHhhhcccCCEEEEecceecCCccchHHHHHHHH
Confidence            764       458999999999999999998875444

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.26  E-value=1.6e-12  Score=128.62  Aligned_cols=118  Identities=10%  Similarity=0.012  Sum_probs=76.7

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHH-HHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEeCCCCCC--CCcceEEec-
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIA-LSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVF--PDVEKLLED-  283 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il-~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vglltGd~~~~--~~a~ili~t-  283 (333)
                      .|++++++||||||||++|+++++ .....+.+++|++||++|+.|+++.+..  -.++..+|.....  +...+.+.+ 
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~~g~~~lvl~Pt~~La~Q~~~~~~~--~~v~~~~~~~~~~~~~~~~~~~~~~   78 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVKKRLRTVILAPTRVVASEMYEALRG--EPIRYMTPAVQSERTGNEIVDFMCH   78 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTT--SCEEEC---------CCCSEEEEEH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEECcHHHHHHHHHHHhCC--CeEEEEecCccccCCCCceEEEEch
Confidence            378999999999999999999888 5567788999999999999999987752  1367666653322  122222222 


Q ss_pred             -------------cCcceEeccccccccc---cCcCcccccchhhhhhheeccCcchhhh
Q psy2760         284 -------------LNIGGLDELSIHDFNK---HLKFWKPKVQLDDLFDWTMASDATTLEI  327 (333)
Q Consensus       284 -------------~~i~liViDe~H~~~~---~~R~~~~~~~l~~l~~l~~~~d~~~~e~  327 (333)
                                   .++.++|+||+|.++.   ..|++-.........+.+++|+++.-++
T Consensus        79 ~~l~~~l~~~~~~~~l~~vViDEaH~~~~~~~~~~~~l~~~~~~~~~~~l~~SAT~~~~~  138 (431)
T 2v6i_A           79 STFTMKLLQGVRVPNYNLYIMDEAHFLDPASVAARGYIETRVSMGDAGAIFMTATPPGTT  138 (431)
T ss_dssp             HHHHHHHHHTCCCCCCSEEEEESTTCCSHHHHHHHHHHHHHHHTTSCEEEEEESSCTTCC
T ss_pred             HHHHHHHhcCccccCCCEEEEeCCccCCccHHHHHHHHHHHhhCCCCcEEEEeCCCCcch
Confidence                         2689999999999842   2222222221112356788888776443

>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=99.25  E-value=1.4e-12  Score=136.08  Aligned_cols=102  Identities=9%  Similarity=-0.049  Sum_probs=84.3

Q ss_pred             CHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-cEEEeCCCCCC
Q psy2760         196 DVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-VGLIDDLPPVF  274 (333)
Q Consensus       196 ~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-vglltGd~~~~  274 (333)
                      +++|.+++..+..+++++++||||||||++|.++++.   .+.+++|++|||+||.|+++++.+.++. ++..+|+....
T Consensus       219 ~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~---~g~~vLVl~PTReLA~Qia~~l~~~~g~~vg~~vG~~~~~  295 (666)
T 3o8b_A          219 FTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAA---QGYKVLVLNPSVAATLGFGAYMSKAHGIDPNIRTGVRTIT  295 (666)
T ss_dssp             CCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHH---TTCCEEEEESCHHHHHHHHHHHHHHHSCCCEEECSSCEEC
T ss_pred             HHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHH---CCCeEEEEcchHHHHHHHHHHHHHHhCCCeeEEECcEecc
Confidence            4445555555668899999999999999999988764   4679999999999999999999887764 89999988777


Q ss_pred             CCcceEEecc------------CcceEecccccccccc
Q psy2760         275 PDVEKLLEDL------------NIGGLDELSIHDFNKH  300 (333)
Q Consensus       275 ~~a~ili~t~------------~i~liViDe~H~~~~~  300 (333)
                      ....++++|+            ++.++|+||+|+++..
T Consensus       296 ~~~~IlV~TPGrLl~~~~l~l~~l~~lVlDEAH~l~~~  333 (666)
T 3o8b_A          296 TGAPVTYSTYGKFLADGGCSGGAYDIIICDECHSTDST  333 (666)
T ss_dssp             CCCSEEEEEHHHHHHTTSCCTTSCSEEEETTTTCCSHH
T ss_pred             CCCCEEEECcHHHHhCCCcccCcccEEEEccchhcCcc
Confidence            7788899876            4788999999988644

>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=99.20  E-value=1.9e-11  Score=129.66  Aligned_cols=106  Identities=12%  Similarity=0.012  Sum_probs=85.9

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC----CcEE
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ----DVGL  266 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~----~vgl  266 (333)
                      ++|.|+++|..+++.+++|+  ++.++||+|||++|.+|++.....|.++++++||++||.|..+.+...+.    .++.
T Consensus        80 lG~~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL~g~~vlVltptreLA~qd~e~~~~l~~~lgl~v~~  157 (844)
T 1tf5_A           80 TGMFPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGL  157 (844)
T ss_dssp             HSCCCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTTSSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEE
T ss_pred             cCCCCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHHHHhhcCCeEEE
Confidence            35579999999999999998  89999999999999999985444678999999999999999988766543    2788


Q ss_pred             EeCCCCCCCC-----cceEEecc----------------------CcceEecccccccc
Q psy2760         267 IDDLPPVFPD-----VEKLLEDL----------------------NIGGLDELSIHDFN  298 (333)
Q Consensus       267 ltGd~~~~~~-----a~ili~t~----------------------~i~liViDe~H~~~  298 (333)
                      +.|+.+...+     ..++++|+                      ++.++|+||++.+-
T Consensus       158 i~gg~~~~~r~~~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mL  216 (844)
T 1tf5_A          158 NLNSMSKDEKREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSIL  216 (844)
T ss_dssp             CCTTSCHHHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHH
T ss_pred             EeCCCCHHHHHHhcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhh
Confidence            8888754322     35788775                      24578999999764

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.20  E-value=3.1e-11  Score=122.89  Aligned_cols=65  Identities=22%  Similarity=0.233  Sum_probs=58.3

Q ss_pred             CCCCHHHHHHHHH----HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHh
Q psy2760         193 FELDVFQKQAIIK----LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRET  260 (333)
Q Consensus       193 f~l~~~Q~~ai~~----l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~  260 (333)
                      |.++++|.+++..    +..|+++++.||||+|||++|++|++.   .+.+++|++||++|+.|+.+++...
T Consensus         2 ~~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~---~~~~v~i~~pt~~l~~q~~~~~~~l   70 (551)
T 3crv_A            2 VKLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLE---VKPKVLFVVRTHNEFYPIYRDLTKI   70 (551)
T ss_dssp             CSCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHH---HCSEEEEEESSGGGHHHHHHHHTTC
T ss_pred             CCCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHh---CCCeEEEEcCCHHHHHHHHHHHHHH
Confidence            5789999998775    468999999999999999999999886   5789999999999999999988664

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.20  E-value=7e-13  Score=138.59  Aligned_cols=133  Identities=10%  Similarity=-0.035  Sum_probs=85.3

Q ss_pred             CCCHHHH-----HHHHHHH------cCCcEEEEcCCCCcHHHHHHHHHHHH-hcCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy2760         194 ELDVFQK-----QAIIKLE------EHNHVFVTAHTSAGKTVIAEYAIALS-QNHKTRTIYTSPIKALSNQKYRDFRETF  261 (333)
Q Consensus       194 ~l~~~Q~-----~ai~~l~------~g~~vlv~apTGSGKTl~~~l~il~~-l~~g~ral~l~PtraLa~Q~~~~l~~~f  261 (333)
                      .|+++|+     ++++.++      .|++++++||||||||++|+++++.. ...+.+++|++|||+||.|+++.++. +
T Consensus       215 ~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~~~~~~lilaPTr~La~Q~~~~l~~-~  293 (673)
T 2wv9_A          215 YVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQKRLRTAVLAPTRVVAAEMAEALRG-L  293 (673)
T ss_dssp             EEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTT-S
T ss_pred             ccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEccHHHHHHHHHHHHhc-C
Confidence            5778888     8888766      89999999999999999999998855 45678999999999999999998864 2


Q ss_pred             CCcEEEeCCCC-C-CCCcceEEe--------------ccCcceEecccccccccc---CcCcccccchhhhhhheeccCc
Q psy2760         262 QDVGLIDDLPP-V-FPDVEKLLE--------------DLNIGGLDELSIHDFNKH---LKFWKPKVQLDDLFDWTMASDA  322 (333)
Q Consensus       262 ~~vglltGd~~-~-~~~a~ili~--------------t~~i~liViDe~H~~~~~---~R~~~~~~~l~~l~~l~~~~d~  322 (333)
                       .++..++... . .+..-+...              ..++.++|+||+|.++..   .+++..........+.+++|++
T Consensus       294 -~i~~~~~~l~~v~tp~~ll~~l~~~~l~~~l~~~~~l~~l~lvViDEaH~~~~~~~~~~~~l~~~~~~~~~~vl~~SAT  372 (673)
T 2wv9_A          294 -PVRYLTPAVQREHSGNEIVDVMCHATLTHRLMSPLRVPNYNLFVMDEAHFTDPASIAARGYIATRVEAGEAAAIFMTAT  372 (673)
T ss_dssp             -CCEECCC---CCCCSCCCEEEEEHHHHHHHHHSSSCCCCCSEEEEESTTCCCHHHHHHHHHHHHHHHTTSCEEEEECSS
T ss_pred             -CeeeecccccccCCHHHHHHHHHhhhhHHHHhcccccccceEEEEeCCcccCccHHHHHHHHHHhccccCCcEEEEcCC
Confidence             2333333221 1 111111111              136899999999998321   1222211100123567888887


Q ss_pred             chhhhh
Q psy2760         323 TTLEIF  328 (333)
Q Consensus       323 ~~~e~~  328 (333)
                      ..-++.
T Consensus       373 ~~~~i~  378 (673)
T 2wv9_A          373 PPGTSD  378 (673)
T ss_dssp             CTTCCC
T ss_pred             CChhhh
Confidence            765443

>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=99.20  E-value=5.2e-12  Score=125.85  Aligned_cols=121  Identities=11%  Similarity=-0.044  Sum_probs=77.6

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHHHHHHHH-hcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEeCCCCC--CCCcceEEe
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAEYAIALS-QNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPV--FPDVEKLLE  282 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~l~il~~-l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vglltGd~~~--~~~a~ili~  282 (333)
                      +..+++++++||||||||++|.++++.. ...+.+++|++|||+|+.|++++++. + .++..++....  .+...+.+.
T Consensus        18 l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~~~~~lvl~Ptr~La~Q~~~~l~g-~-~v~~~~~~~~~~~t~~~~i~~~   95 (459)
T 2z83_A           18 LRKRQMTVLDLHPGSGKTRKILPQIIKDAIQQRLRTAVLAPTRVVAAEMAEALRG-L-PVRYQTSAVQREHQGNEIVDVM   95 (459)
T ss_dssp             GSTTCEEEECCCTTSCTTTTHHHHHHHHHHHTTCCEEEEECSHHHHHHHHHHTTT-S-CEEECC--------CCCSEEEE
T ss_pred             HhcCCcEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEECchHHHHHHHHHHhcC-c-eEeEEecccccCCCCCcEEEEE
Confidence            5778999999999999999999998854 34778999999999999999998852 1 23332222211  122222222


Q ss_pred             c--------------cCcceEeccccccccc---cCcCcccccchhhhhhheeccCcchhhhh
Q psy2760         283 D--------------LNIGGLDELSIHDFNK---HLKFWKPKVQLDDLFDWTMASDATTLEIF  328 (333)
Q Consensus       283 t--------------~~i~liViDe~H~~~~---~~R~~~~~~~l~~l~~l~~~~d~~~~e~~  328 (333)
                      +              .++.++|+||+|.++.   ..+++..........+.+++|++..-++.
T Consensus        96 ~~~~l~~~l~~~~~l~~~~~iViDEaH~~~~~~~~~~~~~~~~~~~~~~~~il~SAT~~~~~~  158 (459)
T 2z83_A           96 CHATLTHRLMSPNRVPNYNLFVMDEAHFTDPASIAARGYIATKVELGEAAAIFMTATPPGTTD  158 (459)
T ss_dssp             EHHHHHHHHHSCC-CCCCSEEEESSTTCCSHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCC
T ss_pred             chHHHHHHhhccccccCCcEEEEECCccCCchhhHHHHHHHHHhccCCccEEEEEcCCCcchh
Confidence            2              2678999999997531   11222222211123567888887765543

>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=99.19  E-value=5.1e-12  Score=125.49  Aligned_cols=130  Identities=10%  Similarity=-0.077  Sum_probs=83.7

Q ss_pred             CCCHHHHHHHHHHHcCCcE-EEEcCCCCcHHHHHHHHHHH-HhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEeCCC
Q psy2760         194 ELDVFQKQAIIKLEEHNHV-FVTAHTSAGKTVIAEYAIAL-SQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLP  271 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~v-lv~apTGSGKTl~~~l~il~-~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vglltGd~  271 (333)
                      .++++|+ +++.++.++++ +++||||||||++|+++++. ....+.+++|++|||+|+.|+++.+.. + .++...+..
T Consensus         4 q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~lvl~Ptr~La~Q~~~~l~g-~-~v~~~~~~~   80 (451)
T 2jlq_A            4 MGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALLRRLRTLILAPTRVVAAEMEEALRG-L-PIRYQTPAV   80 (451)
T ss_dssp             CCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTT-S-CEEECCTTC
T ss_pred             CCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHhcCCcEEEECCCHHHHHHHHHHhcC-c-eeeeeeccc
Confidence            4566664 67777777766 99999999999999998874 455778999999999999999988742 1 233322222


Q ss_pred             C--CCCCcceEEecc--------------CcceEeccccccccccCcCccccc----chhhhhhheeccCcchhhh
Q psy2760         272 P--VFPDVEKLLEDL--------------NIGGLDELSIHDFNKHLKFWKPKV----QLDDLFDWTMASDATTLEI  327 (333)
Q Consensus       272 ~--~~~~a~ili~t~--------------~i~liViDe~H~~~~~~R~~~~~~----~l~~l~~l~~~~d~~~~e~  327 (333)
                      .  ..+...+.+.|.              ++.++|+||+|..+. ........    ......+.+++|++..-++
T Consensus        81 ~~~~~~~~~i~~~t~~~l~~~l~~~~~l~~~~~iViDEah~~~~-~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~  155 (451)
T 2jlq_A           81 KSDHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFTDP-CSVAARGYISTRVEMGEAAAIFMTATPPGST  155 (451)
T ss_dssp             SCCCCSSCCEEEEEHHHHHHHHHHCSCCCCCSEEEEETTTCCSH-HHHHHHHHHHHHHHTTSCEEEEECSSCTTCC
T ss_pred             cccCCCCceEEEEChHHHHHHhhCcccccCCCEEEEeCCccCCc-chHHHHHHHHHhhcCCCceEEEEccCCCccc
Confidence            1  122334545542              678999999998722 11111111    0111345778887765443

>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=99.18  E-value=1.9e-11  Score=129.66  Aligned_cols=105  Identities=14%  Similarity=0.023  Sum_probs=85.9

Q ss_pred             CCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC----CcEEE
Q psy2760         192 PFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ----DVGLI  267 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~----~vgll  267 (333)
                      +..|+++|..+++.+++|+  ++.++||+|||++|.+|++.....|.++++++|||+||.|+++.+...+.    .++.+
T Consensus        72 g~~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l~g~~vlVltPTreLA~Q~~e~~~~l~~~lgl~v~~i  149 (853)
T 2fsf_A           72 GMRHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNALTGKGVHVVTVNDYLAQRDAENNRPLFEFLGLTVGIN  149 (853)
T ss_dssp             SCCCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTTSSCCEEEESSHHHHHHHHHHHHHHHHHTTCCEEEC
T ss_pred             CCCCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHHcCCcEEEEcCCHHHHHHHHHHHHHHHHhcCCeEEEE
Confidence            4479999999999999998  89999999999999999986555678999999999999999988876543    27888


Q ss_pred             eCCCCCCC-----CcceEEecc----------------------CcceEecccccccc
Q psy2760         268 DDLPPVFP-----DVEKLLEDL----------------------NIGGLDELSIHDFN  298 (333)
Q Consensus       268 tGd~~~~~-----~a~ili~t~----------------------~i~liViDe~H~~~  298 (333)
                      +|+.+...     ...++++|+                      ++.++|+||+|.+-
T Consensus       150 ~GG~~~~~r~~~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~mL  207 (853)
T 2fsf_A          150 LPGMPAPAKREAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSIL  207 (853)
T ss_dssp             CTTCCHHHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHHHT
T ss_pred             eCCCCHHHHHHhcCCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHHHH
Confidence            89876431     135788875                      34668999999664

>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=99.16  E-value=1.5e-11  Score=122.06  Aligned_cols=119  Identities=14%  Similarity=0.095  Sum_probs=77.5

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHHHHHHHH-hcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEeCCCCC-CCCcceE--E
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAEYAIALS-QNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPV-FPDVEKL--L  281 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~l~il~~-l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vglltGd~~~-~~~a~il--i  281 (333)
                      +.+|++++++||||||||++|+++++.. ...+.+++|++||++||.|+++.++. + .++..++.... .....++  +
T Consensus         5 l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~~~~~lil~Ptr~La~Q~~~~l~~-~-~v~~~~~~~~~v~Tp~~l~~~l   82 (440)
T 1yks_A            5 LKKGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHG-L-DVKFHTQAFSAHGSGREVIDAM   82 (440)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTT-S-CEEEESSCCCCCCCSSCCEEEE
T ss_pred             hhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhcCCeEEEEcchHHHHHHHHHHHhc-C-CeEEecccceeccCCccceeee
Confidence            3568999999999999999999988864 45677999999999999999998864 2 24444444311 1111111  1


Q ss_pred             e-------------ccCcceEecccccccccc---CcCcccccchhhhhhheeccCcchhh
Q psy2760         282 E-------------DLNIGGLDELSIHDFNKH---LKFWKPKVQLDDLFDWTMASDATTLE  326 (333)
Q Consensus       282 ~-------------t~~i~liViDe~H~~~~~---~R~~~~~~~l~~l~~l~~~~d~~~~e  326 (333)
                      .             ..++.++|+||+|.++..   .+++..........+.+++|++..-.
T Consensus        83 ~~~~l~~~~~~~~~~~~l~~vViDEah~~~~~~~~~~~~~~~~~~~~~~~~l~~SAT~~~~  143 (440)
T 1yks_A           83 CHATLTYRMLEPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRARANESATILMTATPPGT  143 (440)
T ss_dssp             EHHHHHHHHTSSSCCCCCSEEEETTTTCCSHHHHHHHHHHHHHHHTTSCEEEEECSSCTTC
T ss_pred             cccchhHhhhCcccccCccEEEEECccccCcchHHHHHHHHHHhccCCceEEEEeCCCCch
Confidence            1             136899999999998211   11222111111235678888876544

>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=99.15  E-value=1e-10  Score=116.20  Aligned_cols=108  Identities=9%  Similarity=0.072  Sum_probs=83.0

Q ss_pred             CCCCHHHHHHHHHH----HcCCcEEEEcCCCCcHHHHHHHHHHHHh--cCCCeEEEEcccHHHHHHHHHHHHHhcCC--c
Q psy2760         193 FELDVFQKQAIIKL----EEHNHVFVTAHTSAGKTVIAEYAIALSQ--NHKTRTIYTSPIKALSNQKYRDFRETFQD--V  264 (333)
Q Consensus       193 f~l~~~Q~~ai~~l----~~g~~vlv~apTGSGKTl~~~l~il~~l--~~g~ral~l~PtraLa~Q~~~~l~~~f~~--v  264 (333)
                      ..|+|+|.+++..+    ..+++++++.+||+|||++++..+....  ....++|||+| .+|+.|+.+++++.++.  +
T Consensus        36 ~~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i~~~~~~~~~~~~LIv~P-~~l~~qw~~e~~~~~~~~~v  114 (500)
T 1z63_A           36 ANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKENELTPSLVICP-LSVLKNWEEELSKFAPHLRF  114 (500)
T ss_dssp             SCCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHHTTCCSSEEEEEC-STTHHHHHHHHHHHCTTSCE
T ss_pred             ccchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHHHHHHhcCCCCCEEEEcc-HHHHHHHHHHHHHHCCCceE
Confidence            37999999998765    5688999999999999999876665433  33478999999 57999999999886654  6


Q ss_pred             EEEeCCCCCC--CCcceEEecc------------CcceEeccccccccccC
Q psy2760         265 GLIDDLPPVF--PDVEKLLEDL------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       265 glltGd~~~~--~~a~ili~t~------------~i~liViDe~H~~~~~~  301 (333)
                      .+++|+....  ....+++.|+            ...++|+||+|.+.+..
T Consensus       115 ~~~~g~~~~~~~~~~~ivi~t~~~l~~~~~l~~~~~~~vIvDEaH~~kn~~  165 (500)
T 1z63_A          115 AVFHEDRSKIKLEDYDIILTTYAVLLRDTRLKEVEWKYIVIDEAQNIKNPQ  165 (500)
T ss_dssp             EECSSSTTSCCGGGSSEEEEEHHHHTTCHHHHTCCEEEEEEETGGGGSCTT
T ss_pred             EEEecCchhccccCCcEEEeeHHHHhccchhcCCCcCEEEEeCccccCCHh
Confidence            7777765432  2245777765            45789999999997654

>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=99.15  E-value=9.6e-11  Score=126.91  Aligned_cols=133  Identities=16%  Similarity=0.103  Sum_probs=94.8

Q ss_pred             CCCCCCHHHHHHHHHHHc--CCcEEEEcCCCCcHHHHHHHHHHHHhcCC--CeEEEEcccHHHHHHHHHHHHHhcCC-cE
Q psy2760         191 WPFELDVFQKQAIIKLEE--HNHVFVTAHTSAGKTVIAEYAIALSQNHK--TRTIYTSPIKALSNQKYRDFRETFQD-VG  265 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~--g~~vlv~apTGSGKTl~~~l~il~~l~~g--~ral~l~PtraLa~Q~~~~l~~~f~~-vg  265 (333)
                      ..+.|+|+|.+++..+..  +.+++++.+||+|||++++..+......+  .+++||+|+ +|+.|+..++.+.|+. +.
T Consensus       150 ~~~~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g~~~rvLIVvP~-sLl~Qw~~E~~~~f~l~v~  228 (968)
T 3dmq_A          150 QRTSLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPE-TLQHQWLVEMLRRFNLRFA  228 (968)
T ss_dssp             CSSCCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTSSCCCEEEECCT-TTHHHHHHHHHHHSCCCCE
T ss_pred             CCCCCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEeCH-HHHHHHHHHHHHHhCCCEE
Confidence            356899999999988744  55899999999999999988877655444  489999999 9999999999888864 66


Q ss_pred             EEeCCC---------CCCCCcceEEecc----------------CcceEeccccccccccCcC----cccccchhhhh-h
Q psy2760         266 LIDDLP---------PVFPDVEKLLEDL----------------NIGGLDELSIHDFNKHLKF----WKPKVQLDDLF-D  315 (333)
Q Consensus       266 lltGd~---------~~~~~a~ili~t~----------------~i~liViDe~H~~~~~~R~----~~~~~~l~~l~-~  315 (333)
                      +++|+.         .......++++|+                +..++|+||+|.+......    |+....+.... .
T Consensus       229 v~~~~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~dlVIvDEAH~~kn~~~~~s~~~~~l~~L~~~~~~  308 (968)
T 3dmq_A          229 LFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQAIEQLAEHVPG  308 (968)
T ss_dssp             ECCHHHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCCCEEEECCSSCCCCBTTBCCHHHHHHHHHHTTCSS
T ss_pred             EEccchhhhhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCCCEEEehhhHhhcCCCCcchHHHHHHHHHhhcCCc
Confidence            665433         2222346777764                4788999999999654322    22111111111 3


Q ss_pred             heeccCcch
Q psy2760         316 WTMASDATT  324 (333)
Q Consensus       316 l~~~~d~~~  324 (333)
                      .++++++|.
T Consensus       309 ~L~LTATPi  317 (968)
T 3dmq_A          309 VLLLTATPE  317 (968)
T ss_dssp             EEESCSSCS
T ss_pred             EEEEEcCCc
Confidence            677778773

>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=99.12  E-value=1.6e-11  Score=127.07  Aligned_cols=130  Identities=10%  Similarity=-0.097  Sum_probs=84.6

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHH-hcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEeCCC-
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALS-QNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLP-  271 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~-l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vglltGd~-  271 (333)
                      .++|+|+++++.+.+|++++++||||||||++|.++++.. ...+.+++|++|||+||.|+++.++.  ..++ +.+.. 
T Consensus       171 ~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~~~~~vLvl~PtreLa~Qi~~~l~~--~~v~-~~~~~l  247 (618)
T 2whx_A          171 IGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALRG--LPIR-YQTPAV  247 (618)
T ss_dssp             CCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTT--SCEE-ECCTTS
T ss_pred             cCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHhCCCeEEEEcChHHHHHHHHHHhcC--Ccee-Eecccc
Confidence            3455665567778999999999999999999999988854 35678999999999999999988752  1244 33332 


Q ss_pred             C--CCCCcceEEec--------------cCcceEeccccccccccCc-Ccccccchh--hhhhheeccCcchhh
Q psy2760         272 P--VFPDVEKLLED--------------LNIGGLDELSIHDFNKHLK-FWKPKVQLD--DLFDWTMASDATTLE  326 (333)
Q Consensus       272 ~--~~~~a~ili~t--------------~~i~liViDe~H~~~~~~R-~~~~~~~l~--~l~~l~~~~d~~~~e  326 (333)
                      .  ..+...+.+.+              .++.++|+||+|.++.... .+.......  ...+.+++|++..-+
T Consensus       248 ~~~~tp~~~i~~~t~~~l~~~l~~~~~l~~~~~iViDEah~~~~~~~~~~~~i~~~l~~~~~q~il~SAT~~~~  321 (618)
T 2whx_A          248 KSDHTGREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFTDPCSVAARGYISTRVEMGEAAAIFMTATPPGS  321 (618)
T ss_dssp             SCCCCSSSCEEEEEHHHHHHHHHHCSSCCCCSEEEEESTTCCSHHHHHHHHHHHHHHHHTSCEEEEECSSCTTC
T ss_pred             eeccCCCceEEEEChHHHHHHHhccccccCCeEEEEECCCCCCccHHHHHHHHHHHhcccCccEEEEECCCchh
Confidence            1  12222222222              3678899999999732110 011111111  224577888776544

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.12  E-value=2.3e-10  Score=116.27  Aligned_cols=65  Identities=17%  Similarity=0.253  Sum_probs=54.6

Q ss_pred             CCCCCHHHHHHHHH----HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         192 PFELDVFQKQAIIK----LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~----l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      +|.++++|.+++..    +..|+++++.||||+|||++|++|++.   .+.+++|++||++|+.|+.+++.+
T Consensus         5 ~~~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~---~~~~~~~~~~t~~l~~q~~~~~~~   73 (540)
T 2vl7_A            5 KLQLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQ---LKKKVLIFTRTHSQLDSIYKNAKL   73 (540)
T ss_dssp             ----CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHH---HTCEEEEEESCHHHHHHHHHHHGG
T ss_pred             CCCCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHh---CCCcEEEEcCCHHHHHHHHHHHHh
Confidence            46899999998765    478999999999999999999998764   367999999999999999999876

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.10  E-value=8.7e-11  Score=125.11  Aligned_cols=106  Identities=14%  Similarity=0.032  Sum_probs=85.8

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC----cEE
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD----VGL  266 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vgl  266 (333)
                      +++.|+++|..+++.+++|+  ++.+.||+|||++|.+|++.....|.++++++||+.||.|.++.+...+..    +++
T Consensus        76 lG~~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~G~qv~VvTPTreLA~Qdae~m~~l~~~lGLsv~~  153 (997)
T 2ipc_A           76 LGMRHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALTGKGVHVVTVNDYLARRDAEWMGPVYRGLGLSVGV  153 (997)
T ss_dssp             TCCCCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTTCSCCEEEESSHHHHHHHHHHHHHHHHTTTCCEEE
T ss_pred             hCCCCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHhCCCEEEEeCCHHHHHHHHHHHHHHHHhcCCeEEE
Confidence            56689999999999999998  899999999999999999755456788999999999999999888776542    788


Q ss_pred             EeCCCCCCC-----CcceEEecc-------------------------CcceEecccccccc
Q psy2760         267 IDDLPPVFP-----DVEKLLEDL-------------------------NIGGLDELSIHDFN  298 (333)
Q Consensus       267 ltGd~~~~~-----~a~ili~t~-------------------------~i~liViDe~H~~~  298 (333)
                      ++|+.+...     ...++++|+                         ++.++|+||+|.+-
T Consensus       154 i~Gg~~~~~r~~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDsmL  215 (997)
T 2ipc_A          154 IQHASTPAERRKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSIL  215 (997)
T ss_dssp             CCTTCCHHHHHHHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHHHT
T ss_pred             EeCCCCHHHHHHHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHHHH
Confidence            898876321     235777664                         35678889998653

>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=99.09  E-value=9.6e-11  Score=124.74  Aligned_cols=106  Identities=11%  Similarity=-0.058  Sum_probs=85.3

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC----CcEE
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ----DVGL  266 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~----~vgl  266 (333)
                      +++.|+++|..+++.+++|+  ++.++||+|||++|.+|++.....|.++++++||++||.|..+.+...+.    .+++
T Consensus       108 lG~rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~g~~v~VvTpTreLA~Qdae~m~~l~~~lGLsv~~  185 (922)
T 1nkt_A          108 LDQRPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALAGNGVHIVTVNDYLAKRDSEWMGRVHRFLGLQVGV  185 (922)
T ss_dssp             HSCCCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTTTSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEE
T ss_pred             cCCCCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHhCCCeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEE
Confidence            35579999999999999998  99999999999999999975444578999999999999999988766543    2788


Q ss_pred             EeCCCCCCC-----CcceEEecc----------------------CcceEecccccccc
Q psy2760         267 IDDLPPVFP-----DVEKLLEDL----------------------NIGGLDELSIHDFN  298 (333)
Q Consensus       267 ltGd~~~~~-----~a~ili~t~----------------------~i~liViDe~H~~~  298 (333)
                      ++|+.+...     ...++++|+                      ++.++|+||++.+-
T Consensus       186 i~gg~~~~~r~~~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmL  244 (922)
T 1nkt_A          186 ILATMTPDERRVAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSIL  244 (922)
T ss_dssp             CCTTCCHHHHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHH
T ss_pred             EeCCCCHHHHHHhcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHH
Confidence            888876432     135777764                      35678999999664

>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=98.91  E-value=1.5e-09  Score=115.04  Aligned_cols=116  Identities=13%  Similarity=0.026  Sum_probs=80.5

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHH-HcCCcEEEEcCCCCcHHHHHHHHHH---HHhcC--CCeEEEEcc
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKL-EEHNHVFVTAHTSAGKTVIAEYAIA---LSQNH--KTRTIYTSP  245 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l-~~g~~vlv~apTGSGKTl~~~l~il---~~l~~--g~ral~l~P  245 (333)
                      ++++.+...++..+ .      .|.+.|++++..+ ..+++++++||||||||+.  +|++   .....  +.++++++|
T Consensus        78 ~l~~~~~~~l~~r~-~------lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTtl--lp~ll~~~~~~~~~g~~ilvl~P  148 (773)
T 2xau_A           78 EFTPKYVDILKIRR-E------LPVHAQRDEFLKLYQNNQIMVFVGETGSGKTTQ--IPQFVLFDEMPHLENTQVACTQP  148 (773)
T ss_dssp             BCCHHHHHHHHHHT-T------SGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHH--HHHHHHHHHCGGGGTCEEEEEES
T ss_pred             CCCHHHHHHHHHhh-c------CChHHHHHHHHHHHhCCCeEEEECCCCCCHHHH--HHHHHHHhccccCCCceEEecCc
Confidence            56667766665444 1      4777888888885 6778899999999999993  3333   12222  678999999


Q ss_pred             cHHHHHHHHHHHHHhcCC-cEEEeC-----CCCCCCCcceEEecc--------------CcceEecccccc
Q psy2760         246 IKALSNQKYRDFRETFQD-VGLIDD-----LPPVFPDVEKLLEDL--------------NIGGLDELSIHD  296 (333)
Q Consensus       246 traLa~Q~~~~l~~~f~~-vglltG-----d~~~~~~a~ili~t~--------------~i~liViDe~H~  296 (333)
                      +|+|+.|+.+++.+.++. ++...|     +........+++.|+              ++.++|+||+|.
T Consensus       149 ~r~La~q~~~~l~~~~~~~v~~~vG~~i~~~~~~~~~~~I~v~T~G~l~r~l~~~~~l~~~~~lIlDEah~  219 (773)
T 2xau_A          149 RRVAAMSVAQRVAEEMDVKLGEEVGYSIRFENKTSNKTILKYMTDGMLLREAMEDHDLSRYSCIILDEAHE  219 (773)
T ss_dssp             CHHHHHHHHHHHHHHTTCCBTTTEEEEETTEEECCTTCSEEEEEHHHHHHHHHHSTTCTTEEEEEECSGGG
T ss_pred             hHHHHHHHHHHHHHHhCCchhheecceeccccccCCCCCEEEECHHHHHHHHhhCccccCCCEEEecCccc
Confidence            999999999988776652 222112     112223456777765              578899999995

>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=98.82  E-value=6.1e-09  Score=113.54  Aligned_cols=103  Identities=13%  Similarity=0.111  Sum_probs=73.7

Q ss_pred             CCCCHHHHHHHHHHHc--------------CCcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcccHHHHHHHHH
Q psy2760         193 FELDVFQKQAIIKLEE--------------HNHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSPIKALSNQKYR  255 (333)
Q Consensus       193 f~l~~~Q~~ai~~l~~--------------g~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~PtraLa~Q~~~  255 (333)
                      ..|+++|.+|++.+..              +++++++++||||||++++. ++..+.   ...++|||+|+++|+.|+.+
T Consensus       270 ~~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~~~-l~~ll~~~~~~~rvLvlvpr~eL~~Q~~~  348 (1038)
T 2w00_A          270 LVMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTSFK-AARLATELDFIDKVFFVVDRKDLDYQTMK  348 (1038)
T ss_dssp             EECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHHHH-HHHHHTTCTTCCEEEEEECGGGCCHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHHHH-HHHHHHhcCCCceEEEEeCcHHHHHHHHH
Confidence            3699999999998643              46899999999999999844 444332   23699999999999999999


Q ss_pred             HHHHhcCCcEEEeCCCCC--------CCCcceEEecc-----------------CcceEecccccccc
Q psy2760         256 DFRETFQDVGLIDDLPPV--------FPDVEKLLEDL-----------------NIGGLDELSIHDFN  298 (333)
Q Consensus       256 ~l~~~f~~vglltGd~~~--------~~~a~ili~t~-----------------~i~liViDe~H~~~  298 (333)
                      .|+. |.... +.|+.+.        .....++++|+                 ...++|+||+|...
T Consensus       349 ~f~~-f~~~~-v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~~~~~~lvIiDEAHrs~  414 (1038)
T 2w00_A          349 EYQR-FSPDS-VNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQ  414 (1038)
T ss_dssp             HHHT-TSTTC-SSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGGGGSCEEEEEESCCTTH
T ss_pred             HHHH-hcccc-cccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccchhccccccEEEEEccchhc
Confidence            9976 43311 1122111        12356777764                 23578999999864

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=98.81  E-value=1e-08  Score=108.74  Aligned_cols=107  Identities=16%  Similarity=0.053  Sum_probs=82.0

Q ss_pred             CCCCHHHHHHHHHH----HcCCcEEEEcCCCCcHHHHHHHHHHHH---hcCCCeEEEEcccHHHHHHHHHHHHHhcCC--
Q psy2760         193 FELDVFQKQAIIKL----EEHNHVFVTAHTSAGKTVIAEYAIALS---QNHKTRTIYTSPIKALSNQKYRDFRETFQD--  263 (333)
Q Consensus       193 f~l~~~Q~~ai~~l----~~g~~vlv~apTGSGKTl~~~l~il~~---l~~g~ral~l~PtraLa~Q~~~~l~~~f~~--  263 (333)
                      ..|+++|.+++.-+    ..+++++++.+||+|||+.++..+...   .....++|+|+| .+|+.|+.++|.+.++.  
T Consensus       235 ~~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P-~sll~qW~~E~~~~~p~~~  313 (800)
T 3mwy_W          235 GELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVP-LSTMPAWLDTFEKWAPDLN  313 (800)
T ss_dssp             SCCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECC-TTTHHHHHHHHHHHSTTCC
T ss_pred             CCcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEEC-chHHHHHHHHHHHHCCCce
Confidence            37999999999765    488999999999999999987766533   244667999999 78999999999887755  


Q ss_pred             cEEEeCCCCC-------------------CCCcceEEecc-------------CcceEecccccccccc
Q psy2760         264 VGLIDDLPPV-------------------FPDVEKLLEDL-------------NIGGLDELSIHDFNKH  300 (333)
Q Consensus       264 vglltGd~~~-------------------~~~a~ili~t~-------------~i~liViDe~H~~~~~  300 (333)
                      +.+++|+...                   .....+++.|.             ...++|+||+|.+.+.
T Consensus       314 v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~l~~~~w~~vIvDEaH~lkn~  382 (800)
T 3mwy_W          314 CICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNA  382 (800)
T ss_dssp             EEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHHHHTSEEEEEEETTGGGGCCS
T ss_pred             EEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHHHhcCCcceeehhhhhhhcCc
Confidence            5666665431                   12345777775             4578999999999644

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=98.81  E-value=7e-09  Score=107.37  Aligned_cols=68  Identities=22%  Similarity=0.288  Sum_probs=57.6

Q ss_pred             CCCCHHHHHHHHH----HHcCCcEEEEcCCCCcHHHHHHHHHHHHh-cCCCeEEEEcccHHHHHHHHHHHHHh
Q psy2760         193 FELDVFQKQAIIK----LEEHNHVFVTAHTSAGKTVIAEYAIALSQ-NHKTRTIYTSPIKALSNQKYRDFRET  260 (333)
Q Consensus       193 f~l~~~Q~~ai~~----l~~g~~vlv~apTGSGKTl~~~l~il~~l-~~g~ral~l~PtraLa~Q~~~~l~~~  260 (333)
                      |.+++.|.+++..    +..|+++++.||||+|||++|++|++... ..+.+++|++||++|+.|+.+++...
T Consensus         2 ~~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~~~kvli~t~T~~l~~Qi~~el~~l   74 (620)
T 4a15_A            2 YENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSERKLKVLYLVRTNSQEEQVIKELRSL   74 (620)
T ss_dssp             ---CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHHTCEEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhcCCeEEEECCCHHHHHHHHHHHHHH
Confidence            4789999999875    57899999999999999999999988554 35789999999999999999988663

>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=98.68  E-value=3.1e-08  Score=102.60  Aligned_cols=106  Identities=17%  Similarity=0.100  Sum_probs=78.0

Q ss_pred             CCCHHHHHHHHHH---------HcCCcEEEEcCCCCcHHHHHHHHHHHHhcC-------CCeEEEEcccHHHHHHHHHHH
Q psy2760         194 ELDVFQKQAIIKL---------EEHNHVFVTAHTSAGKTVIAEYAIALSQNH-------KTRTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       194 ~l~~~Q~~ai~~l---------~~g~~vlv~apTGSGKTl~~~l~il~~l~~-------g~ral~l~PtraLa~Q~~~~l  257 (333)
                      .|+|+|.+++..+         ..+..++++.+||+|||+.++..+...+..       ..++|+|+|+ +|+.|+.+++
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~~~~~p~~~~~LiV~P~-sll~qW~~E~  133 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEV  133 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHhCccccCCCCcEEEEecH-HHHHHHHHHH
Confidence            6999999999886         245678999999999999988777644332       2468999997 8999999999


Q ss_pred             HHhcCC---cEEEeCCCCC---------------CCCcceEEecc-------------CcceEecccccccccc
Q psy2760         258 RETFQD---VGLIDDLPPV---------------FPDVEKLLEDL-------------NIGGLDELSIHDFNKH  300 (333)
Q Consensus       258 ~~~f~~---vglltGd~~~---------------~~~a~ili~t~-------------~i~liViDe~H~~~~~  300 (333)
                      .+.++.   +..+.|+...               .....+++.|.             ...++|+||+|.+.+.
T Consensus       134 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~~~l~~~~~~~vI~DEaH~ikn~  207 (644)
T 1z3i_X          134 GKWLGGRVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAEVLHKGKVGLVICDEGHRLKNS  207 (644)
T ss_dssp             HHHHGGGCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTTTTTTSCCCEEEETTGGGCCTT
T ss_pred             HHHcCCCeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhHHHhhcCCccEEEEECceecCCh
Confidence            886553   3344444321               11245777764             4578999999998654

>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=98.10  E-value=6.2e-06  Score=84.98  Aligned_cols=64  Identities=16%  Similarity=0.136  Sum_probs=53.6

Q ss_pred             CHHHHHHHHHHHcCCcEEEEcCCCCcHH--HHHHHHHHHHh--cCCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         196 DVFQKQAIIKLEEHNHVFVTAHTSAGKT--VIAEYAIALSQ--NHKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       196 ~~~Q~~ai~~l~~g~~vlv~apTGSGKT--l~~~l~il~~l--~~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      .+.|++|+..+..++.+++.|++|+|||  +.++++.+...  ..+.++++++||..+|.++.+.+..
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~~~~~vll~APTg~AA~~L~e~~~~  218 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGK  218 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHTH
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhhcCCCeEEEEeCChhHHHHHHHHHHH
Confidence            6899999999999999999999999999  55566666544  4567899999999999999877654

>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=97.76  E-value=1.6e-05  Score=81.54  Aligned_cols=104  Identities=13%  Similarity=-0.015  Sum_probs=69.8

Q ss_pred             CCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC----cEEE
Q psy2760         192 PFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD----VGLI  267 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vgll  267 (333)
                      ++.+++.|++|+..+..+..+++.||.|+|||.+....+......+.++++++||...+..+.+........    ++..
T Consensus       187 ~~~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl~~ApT~~Aa~~L~e~~~~~a~Tih~ll~~~  266 (574)
T 3e1s_A          187 RKGLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPTGKAARRLGEVTGRTASTVHRLLGYG  266 (574)
T ss_dssp             TTTCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHHTSCEEEHHHHTTEE
T ss_pred             cCCCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEecCcHHHHHHhHhhhcccHHHHHHHHcCC
Confidence            557899999999999889999999999999998765444444467889999999998888776543110000    1111


Q ss_pred             eCCCCCCCCcceEEeccCcceEecccccccccc
Q psy2760         268 DDLPPVFPDVEKLLEDLNIGGLDELSIHDFNKH  300 (333)
Q Consensus       268 tGd~~~~~~a~ili~t~~i~liViDe~H~~~~~  300 (333)
                      ..+...+..     ......++++||+++++..
T Consensus       267 ~~~~~~~~~-----~~~~~dvlIIDEasml~~~  294 (574)
T 3e1s_A          267 PQGFRHNHL-----EPAPYDLLIVDEVSMMGDA  294 (574)
T ss_dssp             TTEESCSSS-----SCCSCSEEEECCGGGCCHH
T ss_pred             cchhhhhhc-----ccccCCEEEEcCccCCCHH
Confidence            100000000     1124578899999998754

>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=97.65  E-value=5.7e-05  Score=79.55  Aligned_cols=77  Identities=19%  Similarity=0.122  Sum_probs=64.4

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcC----CcEE
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQ----DVGL  266 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~----~vgl  266 (333)
                      .++.++..|......+..|+  +....||+|||+++.+|+......|..+.+++|++.||.|-.+.+...+.    .||+
T Consensus        72 lg~r~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~G~~vhVvT~ndyLA~rdae~m~~l~~~Lglsvg~  149 (822)
T 3jux_A           72 LGMRPFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALIGKGVHLVTVNDYLARRDALWMGPVYLFLGLRVGV  149 (822)
T ss_dssp             TSCCCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTTSSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEE
T ss_pred             hCCCCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhcCCceEEEeccHHHHHhHHHHHHHHHHHhCCEEEE
Confidence            45678999999888888887  88999999999999999875555688899999999999998877766543    3787


Q ss_pred             EeC
Q psy2760         267 IDD  269 (333)
Q Consensus       267 ltG  269 (333)
                      ++.
T Consensus       150 i~~  152 (822)
T 3jux_A          150 INS  152 (822)
T ss_dssp             EET
T ss_pred             EcC
Confidence            776

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=97.64  E-value=0.00013  Score=75.48  Aligned_cols=67  Identities=15%  Similarity=0.152  Sum_probs=58.9

Q ss_pred             CCCHHHHHHHHHHHcCC-cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHh
Q psy2760         194 ELDVFQKQAIIKLEEHN-HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRET  260 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~-~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~  260 (333)
                      .|++.|++|+..++..+ -.+|.||.|+|||.+....|.+....+.++++++||..=|+++.+++...
T Consensus       189 ~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~~l~~~~~~ILv~a~TN~AvD~i~erL~~~  256 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNLVERLALC  256 (646)
T ss_dssp             TCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEcCchHHHHHHHHHHHhc
Confidence            68999999999876544 67999999999999988777777888999999999999999999998663

>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=97.49  E-value=0.00028  Score=72.76  Aligned_cols=66  Identities=14%  Similarity=0.148  Sum_probs=56.7

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc-CCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN-HKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~-~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      .+++.|.+|+..+..+..+++.||+|+|||.+....+..... .+.++++++||..-++++.+++.+
T Consensus       180 ~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~~~i~~l~~~~~~~ilv~a~tn~A~~~l~~~l~~  246 (624)
T 2gk6_A          180 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQ  246 (624)
T ss_dssp             CCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHHHHHHHHHTSSSCCEEEEESSHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEeCcHHHHHHHHHHHHh
Confidence            689999999999887888999999999999987655544444 678999999999999999998865

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=97.34  E-value=0.00043  Score=73.61  Aligned_cols=67  Identities=18%  Similarity=0.268  Sum_probs=56.9

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc-CCCeEEEEcccHHHHHHHHHHHHHh
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN-HKTRTIYTSPIKALSNQKYRDFRET  260 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~-~g~ral~l~PtraLa~Q~~~~l~~~  260 (333)
                      .+++.|++|+..+..+..++|.||.|+|||.+....+..... .+.++++++||..-++++.+++.+.
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 QLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             CCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             cCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHHhCCCCeEEEEcCcHHHHHHHHHHHHhh
Confidence            689999999999887778999999999999887655543333 6789999999999999999998763

>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=97.32  E-value=0.00038  Score=70.95  Aligned_cols=67  Identities=15%  Similarity=0.132  Sum_probs=56.0

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC----CCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH----KTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~----g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      .+++-|++|+.  ..+..++|.|+.|||||.+...-+...+..    ..+++++++|+..+.++.+++.+.++
T Consensus         9 ~Ln~~Q~~av~--~~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~~~   79 (647)
T 3lfu_A            9 SLNDKQREAVA--APRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLMG   79 (647)
T ss_dssp             TCCHHHHHHHT--CCSSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHHHC
T ss_pred             cCCHHHHHHHh--CCCCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHHHHHHHHHHHHHhc
Confidence            58999999997  346789999999999999988776655443    25899999999999999999988654

>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=97.22  E-value=0.00079  Score=66.56  Aligned_cols=64  Identities=20%  Similarity=0.217  Sum_probs=49.5

Q ss_pred             CCCHHHHHHHHHHH----c-CCcEEEEcCCCCcHHHHHHHHHHHHhcCCC-eEEEEcccHHHHHHHHHHH
Q psy2760         194 ELDVFQKQAIIKLE----E-HNHVFVTAHTSAGKTVIAEYAIALSQNHKT-RTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~----~-g~~vlv~apTGSGKTl~~~l~il~~l~~g~-ral~l~PtraLa~Q~~~~l  257 (333)
                      .|++-|++|+..+.    . ...+++.|+.|+|||.+....+......+. ++++++||...+..+.+.+
T Consensus        25 ~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll~~~~~~l~~~~~~~il~~a~T~~Aa~~l~~~~   94 (459)
T 3upu_A           25 DLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLTKFIIEALISTGETGIILAAPTHAAKKILSKLS   94 (459)
T ss_dssp             CCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHHHHHHHHHHHTTCCCEEEEESSHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCceEEEecCcHHHHHHHHhhh
Confidence            79999999999753    2 239999999999999877655544444554 7999999988887776554

>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=97.21  E-value=0.00082  Score=71.48  Aligned_cols=66  Identities=14%  Similarity=0.148  Sum_probs=56.1

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc-CCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN-HKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~-~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      .+++.|++|+..+..+...++.||.|+|||.+....+..... .+.++++++||..-++++.+++.+
T Consensus       356 ~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~~~i~~l~~~~~~~ilv~a~tn~A~~~l~~~l~~  422 (800)
T 2wjy_A          356 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQ  422 (800)
T ss_dssp             CCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHHHHHHHHHHTTCSSCEEEEESSHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHHHHHHHHHHHcCCCcEEEEcCcHHHHHHHHHHHHH
Confidence            689999999999888888999999999999886655544443 678999999999999999998865

>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=97.14  E-value=0.00077  Score=70.08  Aligned_cols=69  Identities=28%  Similarity=0.261  Sum_probs=55.3

Q ss_pred             CCCCCHHHHHHHHHH----HcCC-cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC
Q psy2760         192 PFELDVFQKQAIIKL----EEHN-HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD  263 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l----~~g~-~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~  263 (333)
                      +|.|++.|.+++..+    ..|. ..++.+.||||||+++...+...   +..+|+|+|+..+|.|++.+|+..|++
T Consensus         6 ~~~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~~~~~~---~~~~lvv~~~~~~A~ql~~el~~~~~~   79 (664)
T 1c4o_A            6 GPSPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAKVIEAL---GRPALVLAPNKILAAQLAAEFRELFPE   79 (664)
T ss_dssp             SCCCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHH---TCCEEEEESSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHHHHHHh---CCCEEEEecCHHHHHHHHHHHHHHCCC
Confidence            568999999998874    3443 57789999999998876544322   346999999999999999999998765

>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=96.94  E-value=0.0062  Score=62.27  Aligned_cols=73  Identities=11%  Similarity=0.148  Sum_probs=58.5

Q ss_pred             cCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHH-HHh-cCCCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         190 TWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIA-LSQ-NHKTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       190 ~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il-~~l-~~g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      ..||.++++|+..+..+...+.+++..+-|+|||.+....++ ... .++.++++++|++..|.++++.++..+.
T Consensus       159 ~~~~~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~~~~~i~~va~t~~qA~~~~~~i~~~i~  233 (592)
T 3cpe_A          159 VIKVQLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNKDKAVGILAHKGSMSAEVLDRTKQAIE  233 (592)
T ss_dssp             SBBCCCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTSSSCEEEEEESSHHHHHHHHHHHHHHHT
T ss_pred             cccCcCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhCCCCeEEEEECCHHHHHHHHHHHHHHHH
Confidence            357899999999998876678899999999999998665433 233 4556899999999999999987766543

>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=96.70  E-value=0.0025  Score=65.81  Aligned_cols=67  Identities=18%  Similarity=0.100  Sum_probs=55.1

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc----CCCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN----HKTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~----~g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      .|++-|++|+..  .+.+++|.|+.|||||.+...-+...+.    ...++++++.|+..|.++.+++.+.++
T Consensus         2 ~L~~~Q~~av~~--~~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~Aa~em~~Rl~~~l~   72 (673)
T 1uaa_A            2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLG   72 (673)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CCCHHHHHHHhC--CCCCEEEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHcC
Confidence            479999999874  3678999999999999998776654432    346899999999999999999988654

>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=96.67  E-value=0.0027  Score=70.34  Aligned_cols=68  Identities=16%  Similarity=0.147  Sum_probs=56.3

Q ss_pred             CCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCC------CeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         193 FELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHK------TRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       193 f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g------~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      ..+++-|.+++..  .+.+++|.|+.|||||.+...-++..+..+      .+++++++|++.|.++.+++.+.++
T Consensus         9 ~~~t~eQ~~~i~~--~~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~aa~e~~~ri~~~l~   82 (1232)
T 3u4q_A            9 STWTDDQWNAIVS--TGQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAEALE   82 (1232)
T ss_dssp             -CCCHHHHHHHHC--CSSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHhC--CCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHHHHHHHHHHHHHHH
Confidence            3689999999875  378999999999999999887776655443      4799999999999999999877553

>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=96.63  E-value=0.0036  Score=65.51  Aligned_cols=67  Identities=13%  Similarity=0.122  Sum_probs=55.3

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc----CCCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN----HKTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~----~g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      .|++-|++|+..  .+.+++|.|+.|||||.+...-+.+.+.    ...++++++.|+..|.++.+++.+.++
T Consensus        11 ~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vTFTnkAA~Em~~Rl~~~l~   81 (724)
T 1pjr_A           11 HLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLG   81 (724)
T ss_dssp             TSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHHG
T ss_pred             hCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHhc
Confidence            589999999875  4578999999999999998876665543    235799999999999999999987654

>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=96.51  E-value=0.0066  Score=63.00  Aligned_cols=69  Identities=29%  Similarity=0.350  Sum_probs=54.8

Q ss_pred             CCCCCHHHHHHHHHH----HcCC-cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC
Q psy2760         192 PFELDVFQKQAIIKL----EEHN-HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD  263 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l----~~g~-~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~  263 (333)
                      +|.|+..|.+++..+    ..|. ..++.+.||||||++....+.. .  +..+|+|+|+..+|.|.+.+|+..|++
T Consensus        10 ~~~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~a~~~~~-~--~~~~lvv~~~~~~A~~l~~el~~~~~~   83 (661)
T 2d7d_A           10 KYQPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSNLIKE-V--NKPTLVIAHNKTLAGQLYSEFKEFFPN   83 (661)
T ss_dssp             SCCCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHH-H--CCCEEEECSSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHHHHHHHH-h--CCCEEEEECCHHHHHHHHHHHHHHcCC
Confidence            678999999998864    3443 5778899999999876544322 2  346999999999999999999997765

>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=96.04  E-value=0.02  Score=55.87  Aligned_cols=70  Identities=11%  Similarity=0.122  Sum_probs=56.7

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHH-H-hcCCCeEEEEcccHHHHHHHHHHHHHh
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIAL-S-QNHKTRTIYTSPIKALSNQKYRDFRET  260 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~-~-l~~g~ral~l~PtraLa~Q~~~~l~~~  260 (333)
                      .||.++++|+..+..+...+.+++..+-+.|||.+....++. . ...+.++++++|++..|..+++.++..
T Consensus       160 ~p~~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~~~g~~v~~vA~t~~qA~~vf~~i~~m  231 (385)
T 2o0j_A          160 IKVQLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNKDKAVGILAHKGSMSAEVLDRTKQA  231 (385)
T ss_dssp             EECCCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHSSSSCEEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHhCCCCeEEEEeCCHHHHHHHHHHHHHH
Confidence            578999999999988765677999999999999987665543 2 345678999999999999888776554

>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=95.37  E-value=0.027  Score=47.64  Aligned_cols=61  Identities=20%  Similarity=0.198  Sum_probs=40.2

Q ss_pred             CHHHHHHHHHH---------HcCCcEEEEcCCCCcHHHHHHHHHHHHh-cCCCeEEEEcccHHHHHHHHHHH
Q psy2760         196 DVFQKQAIIKL---------EEHNHVFVTAHTSAGKTVIAEYAIALSQ-NHKTRTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       196 ~~~Q~~ai~~l---------~~g~~vlv~apTGSGKTl~~~l~il~~l-~~g~ral~l~PtraLa~Q~~~~l  257 (333)
                      ++.|++++..+         ..|+.+++.||+|+|||..+....-... ..|..++|+ +..++..+....+
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~-~~~~~~~~~~~~~   86 (180)
T 3ec2_A           16 NVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFF-DTKDLIFRLKHLM   86 (180)
T ss_dssp             SHHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEE-EHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEE-EHHHHHHHHHHHh
Confidence            56777777664         2578999999999999988765433322 456566654 4555555555444

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=94.82  E-value=0.056  Score=48.55  Aligned_cols=87  Identities=20%  Similarity=0.152  Sum_probs=42.5

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-cEEEeCCCCCCCCcceEEeccC
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-VGLIDDLPPVFPDVEKLLEDLN  285 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-vglltGd~~~~~~a~ili~t~~  285 (333)
                      ..+.+++++||+|+|||.++..........+...++ ++..++..+....  ..|+. -+.++|.......   .+...+
T Consensus        27 ~~~~~vll~G~~GtGKt~la~~i~~~~~~~~~~~~~-v~~~~~~~~~~~~--~l~g~~~~~~~g~~~~~~~---~l~~a~  100 (265)
T 2bjv_A           27 PLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFIS-LNCAALNENLLDS--ELFGHEAGAFTGAQKRHPG---RFERAD  100 (265)
T ss_dssp             TSCSCEEEECCTTSCHHHHHHHHHHTSTTTTSCEEE-EEGGGSCHHHHHH--HHHCCC---------CCCC---HHHHTT
T ss_pred             CCCCCEEEECCCCCcHHHHHHHHHHhcCccCCCeEE-EecCCCChhHHHH--HhcCCcccccccccccccc---hhhhcC
Confidence            457899999999999998875533222222333444 4444443332221  23443 3444443322110   011123


Q ss_pred             cceEeccccccccc
Q psy2760         286 IGGLDELSIHDFNK  299 (333)
Q Consensus       286 i~liViDe~H~~~~  299 (333)
                      -+.+++||+|.+..
T Consensus       101 ~~~l~lDEi~~l~~  114 (265)
T 2bjv_A          101 GGTLFLDELATAPM  114 (265)
T ss_dssp             TSEEEEESGGGSCH
T ss_pred             CcEEEEechHhcCH
Confidence            46788999998764

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=94.47  E-value=0.18  Score=41.44  Aligned_cols=22  Identities=27%  Similarity=0.318  Sum_probs=18.3

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      ..+++++||+|+|||.++....
T Consensus        43 ~~~vll~G~~G~GKT~la~~~~   64 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIVEGLA   64 (187)
T ss_dssp             SCEEEEESCGGGCHHHHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHHHHH
Confidence            5689999999999998876543

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=93.96  E-value=0.075  Score=46.47  Aligned_cols=50  Identities=18%  Similarity=0.206  Sum_probs=35.3

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFR  258 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~  258 (333)
                      .|..+++.||+|+|||..+...+......+.+++|+.-.. -..++.+++.
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~~e~-~~~~~~~~~~   71 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVALEE-HPVQVRQNMA   71 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEESSS-CHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEccC-CHHHHHHHHH
Confidence            4788999999999999997765555555677888886432 2345554443

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=93.44  E-value=0.14  Score=43.79  Aligned_cols=35  Identities=9%  Similarity=0.133  Sum_probs=25.4

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS  244 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~  244 (333)
                      ++++++||+|+|||..+....-.....+.+++++.
T Consensus        55 ~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~~   89 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVY   89 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEE
Confidence            78999999999999987654433444566666653

>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=92.89  E-value=0.092  Score=47.25  Aligned_cols=41  Identities=17%  Similarity=0.045  Sum_probs=33.7

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIK  247 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Ptr  247 (333)
                      ..|.-++++|++|+|||..++-.+......|.+++++.|..
T Consensus        10 ~~G~i~litG~mGsGKTT~ll~~~~r~~~~g~kVli~~~~~   50 (223)
T 2b8t_A           10 KIGWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKI   50 (223)
T ss_dssp             -CCEEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECC
T ss_pred             CCcEEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEEecc
Confidence            34667889999999999998887777777888999997764

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=92.81  E-value=0.13  Score=44.49  Aligned_cols=40  Identities=15%  Similarity=0.080  Sum_probs=31.9

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIK  247 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Ptr  247 (333)
                      .|+-.+++||.|+|||..++-.+......+.+++++.|..
T Consensus         2 ~g~i~vi~G~~gsGKTT~ll~~~~~~~~~g~~v~~~~~~~   41 (184)
T 2orw_A            2 SGKLTVITGPMYSGKTTELLSFVEIYKLGKKKVAVFKPKI   41 (184)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHHHHTTCEEEEEEEC-
T ss_pred             ccEEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeecc
Confidence            3667889999999999998766666666788899988873

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=92.73  E-value=0.085  Score=49.14  Aligned_cols=87  Identities=17%  Similarity=0.146  Sum_probs=43.4

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-cEEEeCCCCCCCCcceEEeccC
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-VGLIDDLPPVFPDVEKLLEDLN  285 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-vglltGd~~~~~~a~ili~t~~  285 (333)
                      ..+.+++++|++|+|||.++........+.+...+++ ...++......  .+.|+. -|.++|.......   .+...+
T Consensus        23 ~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~~~v~v-~~~~~~~~l~~--~~lfg~~~g~~tg~~~~~~g---~~~~a~   96 (304)
T 1ojl_A           23 PSDATVLIHGDSGTGKELVARALHACSARSDRPLVTL-NCAALNESLLE--SELFGHEKGAFTGADKRREG---RFVEAD   96 (304)
T ss_dssp             STTSCEEEESCTTSCHHHHHHHHHHHSSCSSSCCCEE-ECSSCCHHHHH--HHHTCCCSSCCC---CCCCC---HHHHHT
T ss_pred             CCCCcEEEECCCCchHHHHHHHHHHhCcccCCCeEEE-eCCCCChHHHH--HHhcCccccccCchhhhhcC---HHHhcC
Confidence            4567999999999999988765332222223333333 22222222221  134554 3444444331110   011123


Q ss_pred             cceEeccccccccc
Q psy2760         286 IGGLDELSIHDFNK  299 (333)
Q Consensus       286 i~liViDe~H~~~~  299 (333)
                      -+.+++||++.+..
T Consensus        97 ~g~L~LDEi~~l~~  110 (304)
T 1ojl_A           97 GGTLFLDEIGDISP  110 (304)
T ss_dssp             TSEEEEESCTTCCH
T ss_pred             CCEEEEeccccCCH
Confidence            35678999998753

>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=92.46  E-value=0.14  Score=44.08  Aligned_cols=37  Identities=16%  Similarity=0.293  Sum_probs=25.8

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS  244 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~  244 (333)
                      .+.+++++||+|+|||..+....-.....+.+++++.
T Consensus        51 ~~~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~   87 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLIHAACARANELERRSFYIP   87 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEE
Confidence            4679999999999999987654433333455555553

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=92.13  E-value=0.15  Score=47.60  Aligned_cols=36  Identities=8%  Similarity=0.098  Sum_probs=27.6

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHh-cCCCeEEEEc
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQ-NHKTRTIYTS  244 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l-~~g~ral~l~  244 (333)
                      +.++++.||+|+|||..+........ ..+.+++|+.
T Consensus       152 ~~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~  188 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLH  188 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEE
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEE
Confidence            68999999999999988765444444 5677777764

>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=92.09  E-value=0.14  Score=44.85  Aligned_cols=39  Identities=13%  Similarity=-0.032  Sum_probs=32.7

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIK  247 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Ptr  247 (333)
                      |+-.+++||.|||||..++-.+......+.+++++-|..
T Consensus         8 g~i~v~~G~mgsGKTT~ll~~a~r~~~~g~kV~v~k~~~   46 (191)
T 1xx6_A            8 GWVEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPEI   46 (191)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEEC-
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEecc
Confidence            567788999999999988877777777889999998874

>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=91.98  E-value=0.15  Score=49.31  Aligned_cols=43  Identities=19%  Similarity=0.249  Sum_probs=34.2

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSN  251 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~  251 (333)
                      ..|+++.|+||||||......+.+.+..|.+++++=|..++..
T Consensus        53 ~~h~~i~G~tGsGKs~~~~~li~~~~~~g~~viv~Dpkge~~~   95 (437)
T 1e9r_A           53 PRHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPNGDMLS   95 (437)
T ss_dssp             GGCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEETTHHHH
T ss_pred             cceEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeCCCchhH
Confidence            5799999999999999854344455667888888889888764

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=91.58  E-value=0.17  Score=43.47  Aligned_cols=37  Identities=22%  Similarity=0.263  Sum_probs=27.3

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS  244 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~  244 (333)
                      .|..+++.||+|+|||..+...+......+.+++|+.
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~v~~~~   58 (235)
T 2w0m_A           22 QGFFIALTGEPGTGKTIFSLHFIAKGLRDGDPCIYVT   58 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHHHHHHHTCCEEEEE
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            4788999999999999877654433334466777775

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=91.20  E-value=0.19  Score=41.79  Aligned_cols=37  Identities=16%  Similarity=0.258  Sum_probs=26.3

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS  244 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~  244 (333)
                      .|..+++.||+|+|||..+....-.....|.+++|+.
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~   71 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYID   71 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEc
Confidence            5889999999999999876654433333455666654

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=91.05  E-value=0.22  Score=40.70  Aligned_cols=23  Identities=22%  Similarity=0.315  Sum_probs=19.8

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~  229 (333)
                      ..+.++++.||+|+|||.++...
T Consensus        22 ~~~~~vll~G~~GtGKt~lA~~i   44 (145)
T 3n70_A           22 ETDIAVWLYGAPGTGRMTGARYL   44 (145)
T ss_dssp             TCCSCEEEESSTTSSHHHHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHHHHH
Confidence            56789999999999999988653

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=91.01  E-value=0.18  Score=41.19  Aligned_cols=22  Identities=18%  Similarity=0.282  Sum_probs=18.8

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHH
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAE  227 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~  227 (333)
                      ...+.++++.||+|+|||.++.
T Consensus        24 ~~~~~~vll~G~~GtGKt~lA~   45 (143)
T 3co5_A           24 AKRTSPVFLTGEAGSPFETVAR   45 (143)
T ss_dssp             HTCSSCEEEEEETTCCHHHHHG
T ss_pred             hCCCCcEEEECCCCccHHHHHH
Confidence            3567899999999999998764

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=90.92  E-value=0.42  Score=44.58  Aligned_cols=40  Identities=23%  Similarity=0.176  Sum_probs=31.3

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEccc
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPI  246 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Pt  246 (333)
                      ..|.-++++|++|+|||..++..+......+.+++|++-.
T Consensus        66 ~~G~l~li~G~pG~GKTtl~l~ia~~~a~~g~~vl~~slE  105 (315)
T 3bh0_A           66 KRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSLE  105 (315)
T ss_dssp             CTTCEEEEECCTTSSHHHHHHHHHHHHHTTTCEEEEEESS
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEECC
Confidence            4578899999999999988777665555566789998743

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=90.79  E-value=0.16  Score=44.25  Aligned_cols=50  Identities=18%  Similarity=0.204  Sum_probs=34.3

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHH-HhcCCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIAL-SQNHKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~-~l~~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      |.-++++|++|+|||..++-.+.. ....+..++|++-. .-..++.+++..
T Consensus        30 G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s~E-~~~~~~~~~~~~   80 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTLE-ERARDLRREMAS   80 (251)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEESS-SCHHHHHHHHHT
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeeccc-CCHHHHHHHHHH
Confidence            778999999999999988765543 34556778887643 224455555543

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=90.35  E-value=0.37  Score=39.48  Aligned_cols=22  Identities=27%  Similarity=0.315  Sum_probs=18.2

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      +.+++++||+|+|||.++....
T Consensus        43 ~~~~ll~G~~G~GKT~l~~~~~   64 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAIVEGLA   64 (195)
T ss_dssp             SCEEEEECCTTSCHHHHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHHHHH
Confidence            4689999999999999875443

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=90.23  E-value=0.34  Score=45.32  Aligned_cols=41  Identities=12%  Similarity=0.071  Sum_probs=31.2

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcC------CCeEEEEcccHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNH------KTRTIYTSPIKA  248 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~------g~ral~l~Ptra  248 (333)
                      .|..++++||+|+|||..+...+......      +.+++|+.-...
T Consensus       106 ~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~  152 (324)
T 2z43_A          106 TRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGT  152 (324)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSC
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCC
Confidence            46789999999999999987766554433      678999865543

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=90.22  E-value=0.27  Score=46.98  Aligned_cols=41  Identities=20%  Similarity=0.261  Sum_probs=33.1

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKA  248 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Ptra  248 (333)
                      .+.++++.||||||||......+......+.+++++=|..+
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~~~~~~~~~~~~~~~~D~~~~   74 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKMLLLREYMQGSRVIIIDPERE   74 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEESSCC
T ss_pred             ccCceEEEcCCCCCHHHHHHHHHHHHHHCCCEEEEEeCCcC
Confidence            36799999999999998877666556667888888888765

>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=90.12  E-value=0.5  Score=44.20  Aligned_cols=37  Identities=11%  Similarity=0.111  Sum_probs=27.2

Q ss_pred             CCHHHHHHHHHH----HcCC---cEEEEcCCCCcHHHHHHHHHH
Q psy2760         195 LDVFQKQAIIKL----EEHN---HVFVTAHTSAGKTVIAEYAIA  231 (333)
Q Consensus       195 l~~~Q~~ai~~l----~~g~---~vlv~apTGSGKTl~~~l~il  231 (333)
                      ++|||.+++..+    .+|+   .++++||.|+|||.++....-
T Consensus         3 ~~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~la~   46 (334)
T 1a5t_A            3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSR   46 (334)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHHHHH
Confidence            467787777664    3444   489999999999998876443

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=89.84  E-value=0.18  Score=50.05  Aligned_cols=44  Identities=18%  Similarity=0.121  Sum_probs=34.5

Q ss_pred             cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         211 HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      -.++.|+.|+|||....-.+    . ..+.++++||+++++++.+++.+
T Consensus       163 v~~I~G~aGsGKTt~I~~~~----~-~~~~lVlTpT~~aa~~l~~kl~~  206 (446)
T 3vkw_A          163 VVLVDGVPGCGKTKEILSRV----N-FEEDLILVPGRQAAEMIRRRANA  206 (446)
T ss_dssp             EEEEEECTTSCHHHHHHHHC----C-TTTCEEEESCHHHHHHHHHHHTT
T ss_pred             EEEEEcCCCCCHHHHHHHHh----c-cCCeEEEeCCHHHHHHHHHHhhh
Confidence            45889999999998764322    2 25679999999999998888854

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=89.70  E-value=0.32  Score=41.61  Aligned_cols=35  Identities=17%  Similarity=0.065  Sum_probs=27.3

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSP  245 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~P  245 (333)
                      .|.-+++.||+|+|||..+...+.   ..+.+++|+.-
T Consensus        19 ~G~~~~i~G~~GsGKTtl~~~l~~---~~~~~v~~i~~   53 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLALQTGL---LSGKKVAYVDT   53 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHH---HHCSEEEEEES
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH---HcCCcEEEEEC
Confidence            467899999999999998766544   45678888753

>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=89.62  E-value=0.27  Score=47.29  Aligned_cols=42  Identities=29%  Similarity=0.236  Sum_probs=33.0

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALS  250 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa  250 (333)
                      |.-+++.||+|+|||..+...+......+.+++|+.....+.
T Consensus        61 G~i~~I~GppGsGKSTLal~la~~~~~~gg~VlyId~E~s~~  102 (356)
T 3hr8_A           61 GRIVEIFGQESSGKTTLALHAIAEAQKMGGVAAFIDAEHALD  102 (356)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEecccccc
Confidence            678999999999999988776665556678899987654443

>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=89.61  E-value=0.52  Score=46.69  Aligned_cols=52  Identities=10%  Similarity=0.080  Sum_probs=37.6

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc--ccHHHHHHHHHHHHHh
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS--PIKALSNQKYRDFRET  260 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~--PtraLa~Q~~~~l~~~  260 (333)
                      +..++++|++|+|||..+.-.+......|.+++++.  |.|.-+.++.+.+.+.
T Consensus       100 p~vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv~~D~~R~aa~eqL~~~~~~  153 (443)
T 3dm5_A          100 PTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSDTWRPGAYHQLRQLLDR  153 (443)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECCCSSTHHHHHHHHHHGG
T ss_pred             CeEEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEEeCCCcchhHHHHHHHHHHh
Confidence            357889999999999987665544455678887775  6677666666666553

>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=89.60  E-value=0.52  Score=43.83  Aligned_cols=51  Identities=12%  Similarity=0.197  Sum_probs=33.0

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHH-HHHhcCCCeEEEEc--ccHHHHHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAI-ALSQNHKTRTIYTS--PIKALSNQKYRDFRE  259 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~i-l~~l~~g~ral~l~--PtraLa~Q~~~~l~~  259 (333)
                      ++.+++.||+|+|||..+.... ......|.+++++.  +.+.-+.++...+.+
T Consensus       105 g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~~D~~r~~a~eqL~~~~~  158 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFITTDTYRIAAVEQLKTYAE  158 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEECCCSSTTHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEecCcccchHHHHHHHHHH
Confidence            6788999999999998765533 33334677777763  445545544444433

>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=89.36  E-value=0.53  Score=46.10  Aligned_cols=34  Identities=21%  Similarity=0.326  Sum_probs=24.6

Q ss_pred             CCHHHHHHHHHH--HcCCcEEEEcCCCCcHHHHHHH
Q psy2760         195 LDVFQKQAIIKL--EEHNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       195 l~~~Q~~ai~~l--~~g~~vlv~apTGSGKTl~~~l  228 (333)
                      +.+-+..++..+  ..|..+++.||||||||...-.
T Consensus       151 ~~~~~~~~L~~l~~~~ggii~I~GpnGSGKTTlL~a  186 (418)
T 1p9r_A          151 MTAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTLYA  186 (418)
T ss_dssp             CCHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHH
Confidence            355566666665  3456789999999999987544

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=89.34  E-value=0.29  Score=46.91  Aligned_cols=40  Identities=23%  Similarity=0.203  Sum_probs=32.5

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKA  248 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Ptra  248 (333)
                      |+.+++.|++|+|||..++..+......+.+++|+.....
T Consensus        63 G~ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid~E~s  102 (356)
T 1u94_A           63 GRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHA  102 (356)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSCC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCCCC
Confidence            6789999999999999998776666667788999876433

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=89.27  E-value=0.37  Score=45.91  Aligned_cols=38  Identities=21%  Similarity=0.161  Sum_probs=31.8

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEccc
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPI  246 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Pt  246 (333)
                      |+-+++.||+|+|||..++..+......+.+++|+.-.
T Consensus        61 G~iv~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~~E   98 (349)
T 2zr9_A           61 GRVIEIYGPESSGKTTVALHAVANAQAAGGIAAFIDAE   98 (349)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECC
Confidence            78899999999999999888776666678889998644

>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=89.25  E-value=0.4  Score=44.24  Aligned_cols=48  Identities=21%  Similarity=0.313  Sum_probs=30.8

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l  257 (333)
                      +.+++++||+|+|||..+....-.....+.+++|+.. ..+..+....+
T Consensus        37 ~~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~~-~~~~~~~~~~~   84 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSA-DDFAQAMVEHL   84 (324)
T ss_dssp             CSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEH-HHHHHHHHHHH
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEH-HHHHHHHHHHH
Confidence            4689999999999998876544333334667777653 33444444333

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=89.13  E-value=0.54  Score=47.26  Aligned_cols=33  Identities=18%  Similarity=0.138  Sum_probs=24.2

Q ss_pred             CCHHHHHHHHH-HHcCCcEEEEcCCCCcHHHHHH
Q psy2760         195 LDVFQKQAIIK-LEEHNHVFVTAHTSAGKTVIAE  227 (333)
Q Consensus       195 l~~~Q~~ai~~-l~~g~~vlv~apTGSGKTl~~~  227 (333)
                      +.+.+..-+.. +..|.+++++||||||||...-
T Consensus       245 ~~~~~l~~l~~~v~~g~~i~I~GptGSGKTTlL~  278 (511)
T 2oap_1          245 VPSGVLAYLWLAIEHKFSAIVVGETASGKTTTLN  278 (511)
T ss_dssp             SCHHHHHHHHHHHHTTCCEEEEESTTSSHHHHHH
T ss_pred             CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHHH
Confidence            34444444444 4788899999999999998754

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=88.77  E-value=0.73  Score=41.48  Aligned_cols=42  Identities=12%  Similarity=0.012  Sum_probs=31.7

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKA  248 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Ptra  248 (333)
                      ..|.-.+++||-|||||...+-.+......+.+++++-|...
T Consensus        26 ~~G~I~vitG~M~sGKTT~Llr~~~r~~~~g~kvli~kp~~D   67 (219)
T 3e2i_A           26 HSGWIECITGSMFSGKSEELIRRLRRGIYAKQKVVVFKPAID   67 (219)
T ss_dssp             -CCEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEEC--
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHHHHHcCCceEEEEeccC
Confidence            346677889999999998776666666677889999988753

>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=88.70  E-value=0.59  Score=46.13  Aligned_cols=51  Identities=8%  Similarity=0.057  Sum_probs=35.3

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc--ccHHHHHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS--PIKALSNQKYRDFRE  259 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~--PtraLa~Q~~~~l~~  259 (333)
                      +..++++||+|+|||..+...+......|.+++++.  +.|.-+.++...+.+
T Consensus        97 ~~vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv~~D~~r~~a~eqL~~~~~  149 (433)
T 3kl4_A           97 PFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVAADVYRPAAYDQLLQLGN  149 (433)
T ss_dssp             SEEEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEEEECCSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEecCccchhHHHHHHHHHH
Confidence            467889999999999987664444445677887765  456555555555544

>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=88.67  E-value=0.57  Score=40.66  Aligned_cols=38  Identities=16%  Similarity=0.129  Sum_probs=27.8

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhc------CCCeEEEEcc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQN------HKTRTIYTSP  245 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~------~g~ral~l~P  245 (333)
                      .|.-+++.||+|+|||..+...+.....      .+.+++|+.-
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~   66 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDT   66 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEES
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEEC
Confidence            4788999999999999988765543222      2567888753

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=88.35  E-value=0.49  Score=44.71  Aligned_cols=41  Identities=12%  Similarity=0.056  Sum_probs=30.8

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhc------CCCeEEEEcccHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQN------HKTRTIYTSPIKA  248 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~------~g~ral~l~Ptra  248 (333)
                      .|.-+++.||+|+|||..+...+.....      .+.+++|+.-...
T Consensus       121 ~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~  167 (343)
T 1v5w_A          121 SMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENT  167 (343)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCC
Confidence            4678899999999999998776654333      4678999875543

>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=88.17  E-value=0.58  Score=41.37  Aligned_cols=36  Identities=19%  Similarity=0.092  Sum_probs=32.7

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS  244 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~  244 (333)
                      .-.+++.+++|.|||.+++-..+.+...|.|++|+-
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g~G~rV~~vQ   63 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQ   63 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            458999999999999999998889999999999984

>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=87.64  E-value=0.54  Score=45.23  Aligned_cols=39  Identities=18%  Similarity=0.130  Sum_probs=31.5

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIK  247 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Ptr  247 (333)
                      |.-+++.|++|+|||..++..+......+.+++|+....
T Consensus        74 G~li~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~~E~  112 (366)
T 1xp8_A           74 GRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEH  112 (366)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSC
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEECCC
Confidence            678999999999999988876666556677899987543

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=87.49  E-value=0.99  Score=40.79  Aligned_cols=39  Identities=18%  Similarity=0.096  Sum_probs=27.6

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcC----------CCeEEEEccc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNH----------KTRTIYTSPI  246 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~----------g~ral~l~Pt  246 (333)
                      .|.-+++.||+|+|||..+...+......          +.+++|+.-.
T Consensus        29 ~G~i~~i~G~~GsGKTtl~~~l~~~~~~g~~~~g~~~~~~~~v~~~~~e   77 (279)
T 1nlf_A           29 AGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAE   77 (279)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEESS
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHhcCCCcCCCccCCCccEEEEECC
Confidence            48899999999999999877654322221          3568887643

>1sxj_A Activator 1 95 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=87.38  E-value=0.97  Score=45.01  Aligned_cols=33  Identities=12%  Similarity=0.085  Sum_probs=23.6

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcc
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSP  245 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~P  245 (333)
                      +.++++||+|+|||.++.... ..+  +..++.+..
T Consensus        78 ~~lLL~GppGtGKTtla~~la-~~l--~~~~i~in~  110 (516)
T 1sxj_A           78 RAAMLYGPPGIGKTTAAHLVA-QEL--GYDILEQNA  110 (516)
T ss_dssp             SEEEEECSTTSSHHHHHHHHH-HHT--TCEEEEECT
T ss_pred             cEEEEECCCCCCHHHHHHHHH-HHc--CCCEEEEeC
Confidence            689999999999998876433 222  556666643

>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=87.27  E-value=0.34  Score=46.35  Aligned_cols=42  Identities=2%  Similarity=0.014  Sum_probs=33.6

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcC--CCeEEEEcccHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNH--KTRTIYTSPIKALSN  251 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~--g~ral~l~PtraLa~  251 (333)
                      | .+++.+|.|+|||..++..+......  +.+++|+....++..
T Consensus        29 G-iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~   72 (333)
T 3io5_A           29 G-LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITP   72 (333)
T ss_dssp             E-EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCH
T ss_pred             C-eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhH
Confidence            5 68999999999999998877655554  789999987666643

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=87.11  E-value=0.56  Score=41.45  Aligned_cols=82  Identities=12%  Similarity=-0.033  Sum_probs=51.0

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEccc---HHHHHHHHHHHHHhcCCcEEEeCCCCCCCCcceEEecc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPI---KALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLLEDL  284 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Pt---raLa~Q~~~~l~~~f~~vglltGd~~~~~~a~ili~t~  284 (333)
                      .|+-.+++||.|||||...+-++-.....+.+++|+.|.   |.- +.+..+......  ........ +...    ...
T Consensus        19 ~g~l~fiyG~MgsGKTt~Ll~~i~n~~~~~~kvl~~kp~~D~R~~-~~i~S~~g~~~~--A~~~~~~~-d~~~----~~~   90 (195)
T 1w4r_A           19 RGQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYS-SSFCTHDRNTME--ALPACLLR-DVAQ----EAL   90 (195)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEETTCCCGG-GSCCHHHHHHSE--EEEESSGG-GGHH----HHH
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEccccCccch-hhhhhccCCccc--ceecCCHH-HHHH----hcc
Confidence            477789999999999988888877777778999999887   543 333333322111  11111110 0000    112


Q ss_pred             CcceEeccccccc
Q psy2760         285 NIGGLDELSIHDF  297 (333)
Q Consensus       285 ~i~liViDe~H~~  297 (333)
                      ++.++.+||+|.+
T Consensus        91 ~~DvIlIDEaQFf  103 (195)
T 1w4r_A           91 GVAVIGIDEGQFF  103 (195)
T ss_dssp             TCSEEEESSGGGC
T ss_pred             CCCEEEEEchhhh
Confidence            4567889999988

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=86.82  E-value=1.1  Score=41.93  Aligned_cols=51  Identities=12%  Similarity=0.158  Sum_probs=31.0

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc--ccHHHHHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS--PIKALSNQKYRDFRE  259 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~--PtraLa~Q~~~~l~~  259 (333)
                      ++.+++.+|+|+|||..+..........+.+++++.  +.|.-+.++.+.+.+
T Consensus       104 ~~vi~ivG~~GsGKTTl~~~LA~~l~~~g~kV~lv~~D~~r~~a~eqL~~~~~  156 (306)
T 1vma_A          104 PFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAADTFRAAAIEQLKIWGE  156 (306)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEECTTCHHHHHHHHHHHH
T ss_pred             CeEEEEEcCCCChHHHHHHHHHHHHHhcCCEEEEEccccccHHHHHHHHHHHH
Confidence            567889999999999876553332233466776654  334444444444433

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=86.76  E-value=0.68  Score=45.58  Aligned_cols=40  Identities=23%  Similarity=0.176  Sum_probs=31.9

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEccc
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPI  246 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Pt  246 (333)
                      ..|.-++++|++|+|||..++-.+......|.+++|++-.
T Consensus       195 ~~G~liiIaG~pG~GKTtlal~ia~~~a~~g~~vl~fSlE  234 (444)
T 3bgw_A          195 KRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSLE  234 (444)
T ss_dssp             CSSCEEEEEECSSSSHHHHHHHHHHHHHHTTCEEEEECSS
T ss_pred             CCCcEEEEEeCCCCChHHHHHHHHHHHHHcCCEEEEEECC
Confidence            4577899999999999998877666555558889998643

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=86.61  E-value=0.77  Score=41.60  Aligned_cols=21  Identities=29%  Similarity=0.305  Sum_probs=17.6

Q ss_pred             CCcEEEEcCCCCcHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~  229 (333)
                      +.+++++||+|+|||.++...
T Consensus        67 ~~~vll~G~~GtGKT~la~~l   87 (309)
T 3syl_A           67 TLHMSFTGNPGTGKTTVALKM   87 (309)
T ss_dssp             CCEEEEEECTTSSHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHH
Confidence            347999999999999988653

>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=86.59  E-value=0.69  Score=41.44  Aligned_cols=40  Identities=15%  Similarity=0.018  Sum_probs=32.7

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKA  248 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Ptra  248 (333)
                      |+-.+++|+-|||||..++-.+..+...+.+++++-|.+.
T Consensus        28 G~l~vitG~MgsGKTT~lL~~a~r~~~~g~kVli~k~~~d   67 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPCID   67 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEECC--
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEeccC
Confidence            5566789999999999988888778888999999988754

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=86.55  E-value=0.57  Score=42.70  Aligned_cols=22  Identities=23%  Similarity=0.323  Sum_probs=18.6

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l  228 (333)
                      ..|..+++.||||||||...-.
T Consensus        23 ~~g~~v~i~Gp~GsGKSTll~~   44 (261)
T 2eyu_A           23 RKMGLILVTGPTGSGKSTTIAS   44 (261)
T ss_dssp             CSSEEEEEECSTTCSHHHHHHH
T ss_pred             CCCCEEEEECCCCccHHHHHHH
Confidence            4578899999999999987654

>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=86.48  E-value=1.1  Score=41.57  Aligned_cols=36  Identities=17%  Similarity=0.285  Sum_probs=24.6

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcC--------CCeEEEEc
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNH--------KTRTIYTS  244 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~--------g~ral~l~  244 (333)
                      .+.++++||+|+|||..+....-.....        +..++++.
T Consensus        45 ~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~   88 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVN   88 (384)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEE
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEE
Confidence            4579999999999999875543322111        56667664

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=86.31  E-value=0.79  Score=41.70  Aligned_cols=38  Identities=11%  Similarity=0.100  Sum_probs=27.7

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHH-HhcCCCeEEEEc
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIAL-SQNHKTRTIYTS  244 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~-~l~~g~ral~l~  244 (333)
                      ..|.-+++.||+|+|||..+...+.. ....|.+++|+.
T Consensus        33 ~~G~~~~i~G~~G~GKTTl~~~ia~~~~~~~G~~v~~~~   71 (296)
T 1cr0_A           33 RGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAM   71 (296)
T ss_dssp             CTTCEEEEEESTTSSHHHHHHHHHHHHHHTSCCCEEEEE
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHHcCCeEEEEe
Confidence            45889999999999999887654433 333465787764

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=85.90  E-value=0.51  Score=39.86  Aligned_cols=23  Identities=13%  Similarity=0.203  Sum_probs=19.1

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      .|+-++++||+|||||...-...
T Consensus         4 ~g~~i~i~GpsGsGKSTL~~~L~   26 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIKNTLI   26 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHH
Confidence            47889999999999999876543

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=85.86  E-value=0.81  Score=38.45  Aligned_cols=36  Identities=28%  Similarity=0.218  Sum_probs=24.7

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEE
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYT  243 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l  243 (333)
                      .+..++++|+.|||||.++....-.....+.++.++
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~~~l~~~~~~~~~~   47 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLADLLQKEGYRVEVL   47 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEe
Confidence            367899999999999998766443333345555544

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=85.78  E-value=0.56  Score=53.71  Aligned_cols=47  Identities=21%  Similarity=0.140  Sum_probs=40.9

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKY  254 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~  254 (333)
                      .|+.+.+.+|.|||||..++..+..+...|.+++|+.+-.+|.....
T Consensus      1430 rg~~iei~g~~~sGkttl~~~~~a~~~~~g~~~~~i~~e~~~~~~~~ 1476 (1706)
T 3cmw_A         1430 MGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYA 1476 (1706)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTTSCCCHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEEecCCCCCHHHH
Confidence            46889999999999999999999888888999999998877766653

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=85.61  E-value=0.94  Score=38.85  Aligned_cols=39  Identities=18%  Similarity=0.115  Sum_probs=26.9

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhc------CCCeEEEEccc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQN------HKTRTIYTSPI  246 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~------~g~ral~l~Pt  246 (333)
                      .|.-+.+.||+|||||..+...+-....      .+.+++|+...
T Consensus        24 ~G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~   68 (231)
T 4a74_A           24 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTE   68 (231)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECC
Confidence            5778999999999999887654432221      24567777543

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=84.95  E-value=0.59  Score=40.50  Aligned_cols=23  Identities=13%  Similarity=0.229  Sum_probs=19.1

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      .|+-++++||+|||||.++....
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L~   29 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAVF   29 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHHHHHH
Confidence            47789999999999999876543

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=84.92  E-value=0.8  Score=40.29  Aligned_cols=33  Identities=24%  Similarity=0.252  Sum_probs=27.9

Q ss_pred             CHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHH
Q psy2760         196 DVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       196 ~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l  228 (333)
                      +.-|..++..+..|..+.+.||+|||||...-+
T Consensus         9 ~~g~~~~l~~i~~Ge~~~liG~nGsGKSTLl~~   41 (208)
T 3b85_A            9 TLGQKHYVDAIDTNTIVFGLGPAGSGKTYLAMA   41 (208)
T ss_dssp             SHHHHHHHHHHHHCSEEEEECCTTSSTTHHHHH
T ss_pred             CHhHHHHHHhccCCCEEEEECCCCCCHHHHHHH
Confidence            345677888889999999999999999988655

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=84.88  E-value=0.89  Score=44.76  Aligned_cols=20  Identities=25%  Similarity=0.361  Sum_probs=17.1

Q ss_pred             CcEEEEcCCCCcHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~  229 (333)
                      .+++++||+|+|||.++...
T Consensus        51 ~~vLL~GppGtGKTtlAr~i   70 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLAEVI   70 (447)
T ss_dssp             CEEEEECSTTSSHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHH
Confidence            37999999999999987653

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=84.72  E-value=1  Score=40.76  Aligned_cols=34  Identities=21%  Similarity=0.161  Sum_probs=22.3

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEE
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYT  243 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l  243 (333)
                      .++++.||+|+|||.++....-.....+...+++
T Consensus        48 ~~~ll~G~~GtGKt~la~~la~~~~~~~~~~~~~   81 (311)
T 4fcw_A           48 GSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRI   81 (311)
T ss_dssp             EEEEEESCSSSSHHHHHHHHHHHHHSCGGGEEEE
T ss_pred             eEEEEECCCCcCHHHHHHHHHHHHcCCCcceEEe
Confidence            4799999999999998865433333333334443

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=84.69  E-value=1  Score=42.91  Aligned_cols=39  Identities=21%  Similarity=0.161  Sum_probs=31.1

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcc
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSP  245 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~P  245 (333)
                      ..|.-+++.|++|+|||..++-.+......+.+++|++.
T Consensus        44 ~~G~LiiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~fSl   82 (338)
T 4a1f_A           44 NKGSLVIIGARPSMGKTSLMMNMVLSALNDDRGVAVFSL   82 (338)
T ss_dssp             CTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCEEEEEES
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeC
Confidence            457789999999999999887766555557888999864

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=84.45  E-value=0.5  Score=39.51  Aligned_cols=22  Identities=18%  Similarity=0.326  Sum_probs=18.6

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      ++.++++|++|||||.++....
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La   26 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLA   26 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHH
Confidence            5689999999999999887543

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=84.37  E-value=1.3  Score=41.02  Aligned_cols=23  Identities=22%  Similarity=0.400  Sum_probs=18.8

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      .+.+++++||+|+|||..+....
T Consensus        43 ~~~~vll~G~~G~GKT~l~~~~~   65 (387)
T 2v1u_A           43 KPSNALLYGLTGTGKTAVARLVL   65 (387)
T ss_dssp             CCCCEEECBCTTSSHHHHHHHHH
T ss_pred             CCCcEEEECCCCCCHHHHHHHHH
Confidence            35689999999999999876543

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=84.35  E-value=0.66  Score=39.70  Aligned_cols=24  Identities=25%  Similarity=0.340  Sum_probs=19.6

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      ..++.++++|++|||||.++....
T Consensus        23 ~~~~~i~l~G~~GsGKsTl~~~La   46 (199)
T 3vaa_A           23 NAMVRIFLTGYMGAGKTTLGKAFA   46 (199)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHHHH
T ss_pred             CCCCEEEEEcCCCCCHHHHHHHHH
Confidence            457899999999999999986543

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=84.33  E-value=0.73  Score=53.56  Aligned_cols=42  Identities=24%  Similarity=0.209  Sum_probs=35.4

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKAL  249 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraL  249 (333)
                      .++++++++|+|+|||..+...+..+...|.+++|+....++
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~~e~~~ 1467 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHAL 1467 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSCC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEEccccc
Confidence            378999999999999999988777777788999999866443

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=84.16  E-value=0.78  Score=43.97  Aligned_cols=23  Identities=22%  Similarity=0.299  Sum_probs=18.9

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~  229 (333)
                      ..|..++++||||||||...-..
T Consensus       134 ~~g~~i~ivG~~GsGKTTll~~l  156 (372)
T 2ewv_A          134 RKMGLILVTGPTGSGKSTTIASM  156 (372)
T ss_dssp             SSSEEEEEECSSSSSHHHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHHHHH
Confidence            45778999999999999876543

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=84.07  E-value=0.58  Score=41.05  Aligned_cols=37  Identities=19%  Similarity=0.210  Sum_probs=24.7

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHh-----cCCCeEEEEccc
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQ-----NHKTRTIYTSPI  246 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l-----~~g~ral~l~Pt  246 (333)
                      .-.+++|+.|||||..+..-+....     ..|.+.+|++..
T Consensus         6 mi~l~tG~pGsGKT~~a~~~~~~~~~~~~~~~g~r~v~~~~~   47 (199)
T 2r2a_A            6 EICLITGTPGSGKTLKMVSMMANDEMFKPDENGIRRKVFTNI   47 (199)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCGGGSCCTTSCCCCEEECC
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHhhcccccCceEEEEecC
Confidence            3578999999999998765444332     344366665544

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=83.80  E-value=1.2  Score=41.20  Aligned_cols=49  Identities=12%  Similarity=0.107  Sum_probs=32.7

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHh------------cCC----CeEEEEcccHHH-HHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQ------------NHK----TRTIYTSPIKAL-SNQKYRDF  257 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l------------~~g----~ral~l~PtraL-a~Q~~~~l  257 (333)
                      |.-++++|++|+|||..+...+....            ..|    .+++|+.-...+ ..++.+.+
T Consensus        98 g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~~~  163 (322)
T 2i1q_A           98 QSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMA  163 (322)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHHHH
Confidence            67899999999999998877655421            223    688988755433 33444333

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=83.62  E-value=2  Score=35.60  Aligned_cols=33  Identities=15%  Similarity=0.120  Sum_probs=21.8

Q ss_pred             cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEE
Q psy2760         211 HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYT  243 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l  243 (333)
                      .++++|+.|||||..+-...-..-..|..+.++
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~~~g~~~~~~   35 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILDNQGINNKII   35 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCceEEEE
Confidence            578999999999998865443222234445444

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=83.59  E-value=1.1  Score=43.70  Aligned_cols=40  Identities=15%  Similarity=-0.008  Sum_probs=30.2

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHh-cCCCeEEEEccc
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQ-NHKTRTIYTSPI  246 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l-~~g~ral~l~Pt  246 (333)
                      ..|.-++++|++|+|||..++..+.... ..+.+++|++..
T Consensus       198 ~~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~slE  238 (444)
T 2q6t_A          198 GPGSLNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYSLE  238 (444)
T ss_dssp             CTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEESS
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEECC
Confidence            4567889999999999988876555444 357789988643

>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=83.58  E-value=2  Score=39.84  Aligned_cols=34  Identities=21%  Similarity=0.307  Sum_probs=23.9

Q ss_pred             cEEEEcCCCCcHHHHHHHHHHHHhcC-CCeEEEEc
Q psy2760         211 HVFVTAHTSAGKTVIAEYAIALSQNH-KTRTIYTS  244 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~il~~l~~-g~ral~l~  244 (333)
                      +++++||+|+|||..+....-..... +..++++.
T Consensus        46 ~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~   80 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTLRKLWELYKDKTTARFVYIN   80 (389)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEe
Confidence            79999999999999876543333333 45667664

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=83.58  E-value=0.73  Score=43.93  Aligned_cols=23  Identities=22%  Similarity=0.362  Sum_probs=20.0

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHHH
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~l  228 (333)
                      +..|..++++||||||||...-.
T Consensus       172 i~~G~~i~ivG~sGsGKSTll~~  194 (361)
T 2gza_A          172 VQLERVIVVAGETGSGKTTLMKA  194 (361)
T ss_dssp             HHTTCCEEEEESSSSCHHHHHHH
T ss_pred             HhcCCEEEEECCCCCCHHHHHHH
Confidence            47899999999999999987654

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=83.47  E-value=0.56  Score=38.02  Aligned_cols=20  Identities=20%  Similarity=0.386  Sum_probs=16.8

Q ss_pred             CcEEEEcCCCCcHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~  229 (333)
                      ..++++||+|||||.++...
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHH
Confidence            35789999999999988654

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=83.47  E-value=0.7  Score=39.12  Aligned_cols=23  Identities=13%  Similarity=0.237  Sum_probs=19.4

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~  229 (333)
                      ..|..+++.||+|||||..+-..
T Consensus         4 ~~g~~i~l~G~~GsGKSTl~~~L   26 (207)
T 2j41_A            4 EKGLLIVLSGPSGVGKGTVRKRI   26 (207)
T ss_dssp             CCCCEEEEECSTTSCHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHH
Confidence            45788999999999999987653

>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=83.47  E-value=2  Score=42.82  Aligned_cols=52  Identities=8%  Similarity=0.041  Sum_probs=41.2

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD  263 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~  263 (333)
                      +....+.+-||||||++....+.   ..+..+++|+|+...|.|+++.|+..++.
T Consensus        14 ~~~~~l~g~~gs~ka~~~a~l~~---~~~~p~lvv~~~~~~A~~l~~~l~~~~~~   65 (483)
T 3hjh_A           14 GEQRLLGELTGAACATLVAEIAE---RHAGPVVLIAPDMQNALRLHDEISQFTDQ   65 (483)
T ss_dssp             TCEEEEECCCTTHHHHHHHHHHH---HSSSCEEEEESSHHHHHHHHHHHHHTCSS
T ss_pred             CCeEEEeCCCchHHHHHHHHHHH---HhCCCEEEEeCCHHHHHHHHHHHHhhCCC
Confidence            67889999999999986543331   23556899999999999999999886654

>1c9k_A COBU, adenosylcobinamide kinase; alpha/beta structure rossmann fold P-loop, transferase; HET: 5GP; 2.20A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1cbu_A

Probab=83.43  E-value=0.59  Score=40.68  Aligned_cols=42  Identities=21%  Similarity=0.340  Sum_probs=26.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHH
Q psy2760         212 VFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       212 vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l  257 (333)
                      ++|.|++|||||..+.-..   .. +.+++|++.....-.++.+++
T Consensus         2 ilV~Gg~~SGKS~~A~~la---~~-~~~~~yiaT~~~~d~e~~~rI   43 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALI---GD-APQVLYIATSQILDDEMAARI   43 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHH---CS-CSSEEEEECCCC------CHH
T ss_pred             EEEECCCCCcHHHHHHHHH---hc-CCCeEEEecCCCCCHHHHHHH
Confidence            6899999999998887533   22 667899987555444444333

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=83.40  E-value=0.77  Score=38.87  Aligned_cols=22  Identities=27%  Similarity=0.377  Sum_probs=18.7

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~  229 (333)
                      .|.-+.+.||+|||||...-..
T Consensus         6 ~g~ii~l~Gp~GsGKSTl~~~L   27 (205)
T 3tr0_A            6 KANLFIISAPSGAGKTSLVRAL   27 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHHHHH
Confidence            5788999999999999987653

>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=83.35  E-value=1.4  Score=43.02  Aligned_cols=48  Identities=17%  Similarity=0.195  Sum_probs=30.3

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHh--cCCCeEEEEcccHHHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQ--NHKTRTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l--~~g~ral~l~PtraLa~Q~~~~l  257 (333)
                      +.+++++||+|+|||..+....-...  ..+.+++|+... .+..+....+
T Consensus       130 ~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~~-~~~~~~~~~~  179 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSE-KFLNDLVDSM  179 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEHH-HHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHH-HHHHHHHHHH
Confidence            46899999999999988754332222  236677776543 3444444433

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=83.18  E-value=0.73  Score=39.68  Aligned_cols=22  Identities=18%  Similarity=0.283  Sum_probs=17.6

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~  229 (333)
                      .|+.+.+.||+|||||...-..
T Consensus         3 ~g~~i~lvGpsGaGKSTLl~~L   24 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLLKKL   24 (198)
T ss_dssp             --CCEEEECCTTSSHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHH
Confidence            4788999999999999987654

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=83.15  E-value=1.1  Score=42.18  Aligned_cols=22  Identities=27%  Similarity=0.477  Sum_probs=18.7

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~  229 (333)
                      .+.+++++||+|+|||.++...
T Consensus        50 ~~~~vll~GppGtGKT~la~~i   71 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLAETL   71 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHHH
Confidence            4578999999999999987653

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=83.12  E-value=0.63  Score=38.53  Aligned_cols=21  Identities=24%  Similarity=0.336  Sum_probs=17.9

Q ss_pred             CCcEEEEcCCCCcHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~  229 (333)
                      ++.++++|+.|||||.++-..
T Consensus         3 ~~~i~l~G~~GsGKST~a~~L   23 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIVRCL   23 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHH
Confidence            567899999999999988653

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=83.07  E-value=0.64  Score=42.89  Aligned_cols=23  Identities=13%  Similarity=0.213  Sum_probs=20.1

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHHH
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~l  228 (333)
                      +..+.++++.||+|+|||..+..
T Consensus        43 l~~~~~vll~G~pGtGKT~la~~   65 (331)
T 2r44_A           43 ICTGGHILLEGVPGLAKTLSVNT   65 (331)
T ss_dssp             HHHTCCEEEESCCCHHHHHHHHH
T ss_pred             HHcCCeEEEECCCCCcHHHHHHH
Confidence            56789999999999999988754

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=82.90  E-value=1.2  Score=43.50  Aligned_cols=39  Identities=21%  Similarity=0.164  Sum_probs=30.0

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHh-cCCCeEEEEcc
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQ-NHKTRTIYTSP  245 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l-~~g~ral~l~P  245 (333)
                      ..|.-+++.|++|+|||..+...+.... ..|.+++|+..
T Consensus       201 ~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s~  240 (454)
T 2r6a_A          201 QRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSL  240 (454)
T ss_dssp             CTTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEES
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEEC
Confidence            4678899999999999998876555443 35678888864

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=82.67  E-value=1.5  Score=42.72  Aligned_cols=39  Identities=10%  Similarity=0.081  Sum_probs=28.3

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhc------CCCeEEEEccc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQN------HKTRTIYTSPI  246 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~------~g~ral~l~Pt  246 (333)
                      .|.-+.+.||.|+|||..+...++....      .+.+++|+.-.
T Consensus       177 ~Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E  221 (400)
T 3lda_A          177 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTE  221 (400)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESS
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCC
Confidence            5678999999999999988754433322      35678888543

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=82.65  E-value=1  Score=43.12  Aligned_cols=22  Identities=27%  Similarity=0.285  Sum_probs=17.9

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l  228 (333)
                      ..+..++++||||||||...-.
T Consensus       121 ~~~g~i~I~GptGSGKTTlL~~  142 (356)
T 3jvv_A          121 VPRGLVLVTGPTGSGKSTTLAA  142 (356)
T ss_dssp             CSSEEEEEECSTTSCHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHH
Confidence            4556899999999999987654

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=82.60  E-value=0.66  Score=44.39  Aligned_cols=22  Identities=14%  Similarity=0.173  Sum_probs=18.0

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      ++.++++||||||||.++....
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA   61 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLA   61 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHH
Confidence            3578999999999999876543

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=82.59  E-value=1.9  Score=40.62  Aligned_cols=52  Identities=13%  Similarity=0.163  Sum_probs=31.2

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEE-ccc-HHHHHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYT-SPI-KALSNQKYRDFRE  259 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l-~Pt-raLa~Q~~~~l~~  259 (333)
                      .|.-+.+.||+|||||.......-.....+.++++. .++ +.-+.++...+.+
T Consensus       128 ~g~vi~lvG~nGaGKTTll~~Lag~l~~~~g~V~l~g~D~~r~~a~eql~~~~~  181 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIAKLANWLKNHGFSVVIAASDTFRAGAIEQLEEHAK  181 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEECCSSTTHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEEeecccccchHHHHHHHHH
Confidence            467889999999999987654333223345566554 233 3334444555544

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=82.53  E-value=1.5  Score=40.96  Aligned_cols=35  Identities=20%  Similarity=0.185  Sum_probs=23.8

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEE
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYT  243 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l  243 (333)
                      |..+.+.||+|||||.......-.....+.++.+.
T Consensus       102 g~vi~lvG~nGsGKTTll~~Lagll~~~~g~V~l~  136 (304)
T 1rj9_A          102 GRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFC  136 (304)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEE
Confidence            67889999999999987655333222345566654

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=82.34  E-value=1.4  Score=37.62  Aligned_cols=24  Identities=21%  Similarity=0.268  Sum_probs=19.7

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      ..|..+.+.||.|||||.++-...
T Consensus        23 ~~g~~i~l~G~sGsGKSTl~~~La   46 (200)
T 3uie_A           23 QKGCVIWVTGLSGSGKSTLACALN   46 (200)
T ss_dssp             SCCEEEEEECSTTSSHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHH
Confidence            457789999999999999876543

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=82.19  E-value=1  Score=44.45  Aligned_cols=39  Identities=5%  Similarity=-0.075  Sum_probs=31.0

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHHHhcC-CCeEEEEcc
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIALSQNH-KTRTIYTSP  245 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~~l~~-g~ral~l~P  245 (333)
                      ..|.-+++.|++|+|||..++-.+...... |.+++|++-
T Consensus       240 ~~G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s~  279 (503)
T 1q57_A          240 RGGEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAML  279 (503)
T ss_dssp             CTTCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEES
T ss_pred             CCCeEEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEec
Confidence            457789999999999999887766655554 778999864

>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=82.14  E-value=2.5  Score=38.60  Aligned_cols=48  Identities=13%  Similarity=0.253  Sum_probs=28.2

Q ss_pred             CHHHHHHHHHH-HcCC---cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEccc
Q psy2760         196 DVFQKQAIIKL-EEHN---HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPI  246 (333)
Q Consensus       196 ~~~Q~~ai~~l-~~g~---~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Pt  246 (333)
                      .....+.+..+ ..++   .+++.+|+|+|||.++.... ..+  +...+++.+.
T Consensus        31 ~~~~~~~l~~~l~~~~~~~~~L~~G~~G~GKT~la~~la-~~l--~~~~~~i~~~   82 (324)
T 3u61_B           31 PAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALC-HDV--NADMMFVNGS   82 (324)
T ss_dssp             CHHHHHHHHHHHHTTCCCSEEEECSSTTSSHHHHHHHHH-HHT--TEEEEEEETT
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEeeCcCCCCHHHHHHHHH-HHh--CCCEEEEccc
Confidence            34444445443 3343   45777889999998876532 222  4556666554

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=82.05  E-value=1.5  Score=39.71  Aligned_cols=33  Identities=24%  Similarity=0.220  Sum_probs=25.3

Q ss_pred             cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEE
Q psy2760         211 HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYT  243 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l  243 (333)
                      ++++.++.|+|||..+..........|.+++++
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~~~G~~V~v~   40 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQLRQGVRVMAG   40 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCCEEEE
Confidence            689999999999999776555555667776543

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=82.05  E-value=1.3  Score=41.66  Aligned_cols=62  Identities=15%  Similarity=0.180  Sum_probs=36.0

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc--ccHHHHHHHHHHHHHh--cCCcEEE-eCC
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS--PIKALSNQKYRDFRET--FQDVGLI-DDL  270 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~--PtraLa~Q~~~~l~~~--f~~vgll-tGd  270 (333)
                      ++-+++.+++|+|||..+..........+.+++++-  +.+.-+.+....+.+.  ..+++++ .+.
T Consensus       105 ~~vI~ivG~~G~GKTT~~~~LA~~l~~~g~kVllid~D~~r~~a~~ql~~~~~~~~~~~l~vip~~~  171 (320)
T 1zu4_A          105 LNIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIAAADTFRAGATQQLEEWIKTRLNNKVDLVKANK  171 (320)
T ss_dssp             CEEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEECCCSCHHHHHHHHHHHTTTSCTTEEEECCSS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCCCcchhHHHHHHHHHhccccCCceEEeCCC
Confidence            667889999999999876553332334567777763  3344333333344220  2246777 444

>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=82.01  E-value=1.3  Score=40.16  Aligned_cols=41  Identities=10%  Similarity=-0.025  Sum_probs=34.5

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKA  248 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~Ptra  248 (333)
                      .|+-.+++|+-|||||..++-.+..+...|.+++++-|.+.
T Consensus        18 ~g~l~v~~G~MgsGKTT~lL~~~~r~~~~g~kvli~kp~~D   58 (234)
T 2orv_A           18 RGQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKD   58 (234)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEEETTC
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEeecCC
Confidence            36677888988999999988888888888999999988753

>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=81.97  E-value=1.8  Score=39.79  Aligned_cols=36  Identities=22%  Similarity=0.521  Sum_probs=24.5

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcC---CCeEEEEc
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNH---KTRTIYTS  244 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~---g~ral~l~  244 (333)
                      +..++++||+|+|||..+....-.....   +..++++.
T Consensus        45 ~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~   83 (386)
T 2qby_A           45 PNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYIN   83 (386)
T ss_dssp             CCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEE
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEE
Confidence            5689999999999999876533222221   45666664

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=81.96  E-value=0.87  Score=37.48  Aligned_cols=22  Identities=27%  Similarity=0.493  Sum_probs=18.3

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~  229 (333)
                      .+..+++.||.|||||.++-..
T Consensus         3 ~~~~i~l~G~~GsGKSTl~~~L   24 (173)
T 1kag_A            3 EKRNIFLVGPMGAGKSTIGRQL   24 (173)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHHH
Confidence            3578999999999999987653

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=81.75  E-value=0.91  Score=45.52  Aligned_cols=27  Identities=19%  Similarity=0.288  Sum_probs=22.1

Q ss_pred             HHHHHHcCCcEEEEcCCCCcHHHHHHH
Q psy2760         202 AIIKLEEHNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       202 ai~~l~~g~~vlv~apTGSGKTl~~~l  228 (333)
                      +...+..+.+++++||+|+|||..+..
T Consensus        34 l~~al~~~~~VLL~GpPGtGKT~LAra   60 (500)
T 3nbx_X           34 CLLAALSGESVFLLGPPGIAKSLIARR   60 (500)
T ss_dssp             HHHHHHHTCEEEEECCSSSSHHHHHHH
T ss_pred             HHHHHhcCCeeEeecCchHHHHHHHHH
Confidence            334457899999999999999988754

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=81.72  E-value=0.98  Score=38.75  Aligned_cols=24  Identities=13%  Similarity=0.212  Sum_probs=19.9

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      ..|+.++++||+|||||.++-...
T Consensus        10 ~~~~~i~l~G~sGsGKsTl~~~L~   33 (204)
T 2qor_A           10 ARIPPLVVCGPSGVGKGTLIKKVL   33 (204)
T ss_dssp             CCCCCEEEECCTTSCHHHHHHHHH
T ss_pred             ccCCEEEEECCCCCCHHHHHHHHH
Confidence            467899999999999999876543

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=81.72  E-value=0.79  Score=38.40  Aligned_cols=23  Identities=30%  Similarity=0.432  Sum_probs=19.1

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~  229 (333)
                      ..|..+++.||.|||||..+-..
T Consensus         7 ~~g~~i~l~G~~GsGKSTl~~~L   29 (191)
T 1zp6_A            7 LGGNILLLSGHPGSGKSTIAEAL   29 (191)
T ss_dssp             CTTEEEEEEECTTSCHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHH
Confidence            45778999999999999987543

>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=81.63  E-value=1.9  Score=35.98  Aligned_cols=21  Identities=24%  Similarity=0.292  Sum_probs=17.2

Q ss_pred             CcEEEEcCCCCcHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~i  230 (333)
                      .+++++||+|+|||..+....
T Consensus        39 ~~~ll~G~~G~GKT~l~~~l~   59 (226)
T 2chg_A           39 PHLLFSGPPGTGKTATAIALA   59 (226)
T ss_dssp             CCEEEECSTTSSHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHH
Confidence            369999999999998875533

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=81.61  E-value=1.7  Score=40.31  Aligned_cols=51  Identities=8%  Similarity=0.084  Sum_probs=32.0

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc--ccHHHHHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS--PIKALSNQKYRDFRE  259 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~--PtraLa~Q~~~~l~~  259 (333)
                      ++.+++.+++|+|||..+..........+.+++++.  +.|..+.++.+.+.+
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~~g~~v~l~~~D~~r~~a~~ql~~~~~  150 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKKKGFKVGLVGADVYRPAALEQLQQLGQ  150 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHHTTCCEEEEECCCSSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEecCCCCHHHHHHHHHHhc
Confidence            567788999999999876554333334566777653  345555554444443

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=81.60  E-value=2.4  Score=41.59  Aligned_cols=51  Identities=18%  Similarity=0.234  Sum_probs=33.0

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc--ccHHHHHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS--PIKALSNQKYRDFRE  259 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~--PtraLa~Q~~~~l~~  259 (333)
                      ++.+++++++|+|||..+..........+.+++++.  +.+..+.++...+.+
T Consensus        98 ~~vi~i~G~~GsGKTT~~~~LA~~l~~~g~~Vllvd~D~~r~aa~~qL~~~~~  150 (425)
T 2ffh_A           98 RNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGE  150 (425)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECCSSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEeeccccCchhHHHHHHhcc
Confidence            567888899999999876654433334567777654  455555554444443

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=81.52  E-value=0.77  Score=38.19  Aligned_cols=22  Identities=27%  Similarity=0.359  Sum_probs=18.4

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      +..++++|+.|||||.++-...
T Consensus         3 ~~~I~i~G~~GsGKsT~~~~L~   24 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSSQLAM   24 (192)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHH
Confidence            6789999999999999876533

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=81.38  E-value=0.79  Score=38.75  Aligned_cols=22  Identities=27%  Similarity=0.440  Sum_probs=18.7

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~  229 (333)
                      .+..++++|+.|||||.++-..
T Consensus         9 ~~~~I~l~G~~GsGKSTv~~~L   30 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMAEMI   30 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHH
Confidence            3678999999999999997653

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=81.29  E-value=0.83  Score=38.09  Aligned_cols=22  Identities=18%  Similarity=0.285  Sum_probs=18.8

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~  229 (333)
                      .++.++++|+.|||||.++...
T Consensus        10 ~~~~i~i~G~~GsGKst~~~~l   31 (180)
T 3iij_A           10 LLPNILLTGTPGVGKTTLGKEL   31 (180)
T ss_dssp             CCCCEEEECSTTSSHHHHHHHH
T ss_pred             cCCeEEEEeCCCCCHHHHHHHH
Confidence            3678999999999999988653

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=81.03  E-value=0.8  Score=40.27  Aligned_cols=21  Identities=19%  Similarity=0.314  Sum_probs=17.8

Q ss_pred             CCcEEEEcCCCCcHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~  229 (333)
                      .+.++++||+|+|||.++...
T Consensus        39 ~~~vll~G~~GtGKT~la~~l   59 (262)
T 2qz4_A           39 PKGALLLGPPGCGKTLLAKAV   59 (262)
T ss_dssp             CCEEEEESCTTSSHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHH
Confidence            568999999999999887643

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=80.90  E-value=0.71  Score=41.56  Aligned_cols=19  Identities=26%  Similarity=0.204  Sum_probs=16.0

Q ss_pred             cEEEEcCCCCcHHHHHHHH
Q psy2760         211 HVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~  229 (333)
                      .++++||+|||||.++...
T Consensus         3 li~I~G~~GSGKSTla~~L   21 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAIQI   21 (253)
T ss_dssp             EEEEECCTTSSHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHH
Confidence            4789999999999987653

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=80.74  E-value=0.8  Score=41.07  Aligned_cols=22  Identities=18%  Similarity=0.330  Sum_probs=18.5

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~  229 (333)
                      .++.++++||+|+|||.++...
T Consensus        50 ~~~~~ll~G~~GtGKT~la~~l   71 (285)
T 3h4m_A           50 PPKGILLYGPPGTGKTLLAKAV   71 (285)
T ss_dssp             CCSEEEEESSSSSSHHHHHHHH
T ss_pred             CCCeEEEECCCCCcHHHHHHHH
Confidence            4678999999999999887543

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=80.70  E-value=1.1  Score=40.38  Aligned_cols=22  Identities=27%  Similarity=0.357  Sum_probs=18.5

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~  229 (333)
                      .+.+++++||+|+|||.++...
T Consensus        49 ~~~~vll~G~~GtGKT~la~~l   70 (310)
T 1ofh_A           49 TPKNILMIGPTGVGKTEIARRL   70 (310)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHH
T ss_pred             CCceEEEECCCCCCHHHHHHHH
Confidence            3678999999999999887643

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=80.63  E-value=1.6  Score=40.70  Aligned_cols=37  Identities=14%  Similarity=0.172  Sum_probs=24.9

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS  244 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~  244 (333)
                      .|..+.+.||+|||||.......-.....+.++.+..
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag~l~~~~g~V~l~g  135 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAHRLKNEGTKVLMAA  135 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            3678899999999999876553322223456666653

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=80.58  E-value=2.2  Score=41.80  Aligned_cols=46  Identities=15%  Similarity=0.162  Sum_probs=30.7

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcC-CCeEEEEc--ccHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNH-KTRTIYTS--PIKALSNQKYR  255 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~-g~ral~l~--PtraLa~Q~~~  255 (333)
                      +.+++++++|+|||.++.-........ |.+++++.  |.|..+.++..
T Consensus       101 ~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd~D~~r~~a~~ql~  149 (433)
T 2xxa_A          101 AVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADVYRPAAIKQLE  149 (433)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEECCCSSTTHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEecCCCCccHHHHHH
Confidence            577888999999998876644433444 78887764  44554444433

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=80.54  E-value=0.92  Score=42.74  Aligned_cols=22  Identities=27%  Similarity=0.351  Sum_probs=19.0

Q ss_pred             HHcCCcEEEEcCCCCcHHHHHH
Q psy2760         206 LEEHNHVFVTAHTSAGKTVIAE  227 (333)
Q Consensus       206 l~~g~~vlv~apTGSGKTl~~~  227 (333)
                      +..|..+++.||||||||...-
T Consensus       168 i~~g~~v~i~G~~GsGKTTll~  189 (330)
T 2pt7_A          168 IAIGKNVIVCGGTGSGKTTYIK  189 (330)
T ss_dssp             HHHTCCEEEEESTTSCHHHHHH
T ss_pred             ccCCCEEEEECCCCCCHHHHHH
Confidence            4689999999999999998543

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=80.51  E-value=1  Score=40.65  Aligned_cols=21  Identities=19%  Similarity=0.306  Sum_probs=18.2

Q ss_pred             CCcEEEEcCCCCcHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~  229 (333)
                      ++.++++||+|+|||.++...
T Consensus        54 ~~~vll~Gp~GtGKT~la~~l   74 (297)
T 3b9p_A           54 AKGLLLFGPPGNGKTLLARAV   74 (297)
T ss_dssp             CSEEEEESSSSSCHHHHHHHH
T ss_pred             CCeEEEECcCCCCHHHHHHHH
Confidence            578999999999999987643

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=80.31  E-value=1  Score=41.91  Aligned_cols=22  Identities=27%  Similarity=0.324  Sum_probs=18.2

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      +++++++||+|+|||.++....
T Consensus        70 ~~~vLl~GppGtGKT~la~~la   91 (368)
T 3uk6_A           70 GRAVLIAGQPGTGKTAIAMGMA   91 (368)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHH
Confidence            3589999999999999876543

>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=80.17  E-value=1.7  Score=36.55  Aligned_cols=34  Identities=21%  Similarity=0.197  Sum_probs=22.4

Q ss_pred             CHHHHHHHHH-HHcCC---cEEEEcCCCCcHHHHHHHH
Q psy2760         196 DVFQKQAIIK-LEEHN---HVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       196 ~~~Q~~ai~~-l~~g~---~vlv~apTGSGKTl~~~l~  229 (333)
                      +..+.+.+.. +..++   .++++||+|+|||..+...
T Consensus        28 ~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~l~~~~   65 (250)
T 1njg_A           28 QEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLL   65 (250)
T ss_dssp             CHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHHHHHHH
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHH
Confidence            3334444443 34444   6899999999999887543

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=80.13  E-value=0.91  Score=43.14  Aligned_cols=22  Identities=23%  Similarity=0.208  Sum_probs=17.3

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      ++-++++||||||||.++....
T Consensus         3 ~~~i~i~GptgsGKt~la~~La   24 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLA   24 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHH
T ss_pred             CcEEEEECCCcCCHHHHHHHHH
Confidence            3457889999999998876543

---

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	333
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	5e-06
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	1e-05
d1a1va1	136	c.37.1.14 (A:190-325) HCV helicase domain {Human h	3e-05
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	8e-05
d2eyqa3	233	c.37.1.19 (A:546-778) Transcription-repair couplin	0.001
d2fz4a1	206	c.37.1.19 (A:24-229) DNA repair protein RAD25 {Arc	0.004

>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 = 44.9 bits (105), Expect = 5e-06
 Identities = 14/69 (20%), Positives = 19/69 (27%)

Query: 198 FQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDF 257
            QK    ++        TA T  GKT               R     P   L  Q     
Sbjct: 47  IQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFPTSLLVIQAAETI 106

Query: 258 RETFQDVGL 266
           R+  +  G+
Sbjct: 107 RKYAEKAGV 115

>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 = 44.1 bits (103), Expect = 1e-05
 Identities = 9/57 (15%), Positives = 19/57 (33%), Gaps = 1/57 (1%)

Query: 206 LEEHNHVFVTAHTSAGKT-VIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETF 261
             +     +  H  AGKT       +  +     RT+  +P + ++ +     R   
Sbjct: 6   FRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAPTRVVAAEMEEALRGLP 62

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 136

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 = 41.0 bits (95), Expect = 3e-05
 Identities = 8/58 (13%), Positives = 17/58 (29%), Gaps = 3/58 (5%)

Query: 206 LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD 263
            +      + A T +GK+     A A       + +  +P  A +        +    
Sbjct: 5   PQSFQVAHLHAPTGSGKSTKVPAAYA---AQGYKVLVLNPSVAATLGFGAYMSKAHGV 59

>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 = 40.7 bits (94), Expect = 8e-05
 Identities = 20/66 (30%), Positives = 39/66 (59%)

Query: 194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQK 253
           EL   Q +A+ K+    ++ +   T+AGKT++AE A+        +++Y  P++AL+ +K
Sbjct: 25  ELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGEK 84

Query: 254 YRDFRE 259
           Y  F++
Sbjct: 85  YESFKK 90

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]} Length = 233

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]

 Score = 37.8 bits (87), Expect = 0.001
 Identities = 15/96 (15%), Positives = 29/96 (30%)

Query: 171 LDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAI 230
               +              T      +    + +         V      GKT +A  A 
Sbjct: 38  FKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAA 97

Query: 231 ALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGL 266
            L+ ++  +     P   L+ Q Y +FR+ F +  +
Sbjct: 98  FLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPV 133

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]} 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: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 35.6 bits (81), Expect = 0.004
 Identities = 17/80 (21%), Positives = 30/80 (37%), Gaps = 3/80 (3%)

Query: 184 VPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYT 243
           +P         L  +Q++A+ +        +   T +GKT +A  AI       T T+  
Sbjct: 60  IPTPYFDAEISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAI---NELSTPTLIV 116

Query: 244 SPIKALSNQKYRDFRETFQD 263
            P  AL+ Q         ++
Sbjct: 117 VPTLALAEQWKERLGIFGEE 136

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	333
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.79
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.77
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.76
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.75
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.74
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.73
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.73
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.73
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.72
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.71
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.71
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.69
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.63
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.62
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.58
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.5
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.48
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.46
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.43
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.35
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	98.25
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	98.09
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	97.89
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.68
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	97.25
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	97.09
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.68
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	95.54
d1okkd2	207	GTPase domain of the signal recognition particle r	95.41
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	95.1
d1ls1a2	207	GTPase domain of the signal sequence recognition p	94.53
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	94.23
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	94.16
d2qy9a2	211	GTPase domain of the signal recognition particle r	94.1
d1vmaa2	213	GTPase domain of the signal recognition particle r	94.04
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	93.77
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	93.4
d1j8yf2	211	GTPase domain of the signal sequence recognition p	92.96
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	92.72
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	92.64
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	92.36
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	92.13
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	91.96
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	91.82
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	91.8
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	91.59
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	90.92
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	90.82
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	90.45
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	90.14
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	90.11
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	90.07
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	90.07
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	89.81
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	89.53
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	89.47
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	89.41
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	89.4
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	89.34
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	89.01
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	88.93
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	88.84
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	88.71
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	88.66
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	88.6
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	88.21
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	87.92
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	87.41
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	87.38
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	86.99
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	86.55
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	86.51
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	86.19
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	85.88
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	85.66
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	85.36
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	85.19
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	84.92
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	84.55
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	84.52
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	84.11
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	84.05
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	83.86
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	83.42
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	83.25
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	83.1
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	82.46
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	82.08
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	82.05
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	81.55
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	81.45
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	81.28
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	81.04
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	80.82
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	80.63
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	80.43
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	80.17
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	80.16

>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=99.79  E-value=4e-20  Score=162.28  Aligned_cols=145  Identities=19%  Similarity=0.207  Sum_probs=112.3

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSN  251 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~  251 (333)
                      .+++.+.++++..|+.      +|+|+|.+|+..+.+|+++++++|||||||.++.++++..+.++.+++|++|+++|+.
T Consensus         9 ~~~~~~~~~l~~~g~~------~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~~~~vl~l~P~~~L~~   82 (202)
T d2p6ra3           9 SISSYAVGILKEEGIE------ELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAG   82 (202)
T ss_dssp             HHHHHHHHHHHCC---------CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEESSHHHHH
T ss_pred             hhhHHHHHHHHHcCCC------CCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhccCcceeecccHHHHH
Confidence            3566777777766655      7999999999999999999999999999999999999988888899999999999999


Q ss_pred             HHHHHHHHhcCC---cEEEeCCCCCCCC----cceEEecc---------------CcceEeccccccccccCcCcccccc
Q psy2760         252 QKYRDFRETFQD---VGLIDDLPPVFPD----VEKLLEDL---------------NIGGLDELSIHDFNKHLKFWKPKVQ  309 (333)
Q Consensus       252 Q~~~~l~~~f~~---vglltGd~~~~~~----a~ili~t~---------------~i~liViDe~H~~~~~~R~~~~~~~  309 (333)
                      |+.+++++.++.   ++..+|+......    ..+++.++               .+.++++||+|.+....|+......
T Consensus        83 q~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~~~~~~~~ii~DE~h~~~~~~r~~~~~~~  162 (202)
T d2p6ra3          83 EKYESFKKWEKIGLRIGISTGDYESRDEHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEIL  162 (202)
T ss_dssp             HHHHHHTTTTTTTCCEEEECSSCBCCSSCSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTTTHHHHHHH
T ss_pred             HHHHHHHHHhhccccceeeccCcccccccccccceeeeccHHHHHHHhccchhhhhhhhccccHHHHhcccccchHHHHH
Confidence            999999876553   6777777654432    34455443               5689999999999988888766542


Q ss_pred             hhh------hhhheeccCc
Q psy2760         310 LDD------LFDWTMASDA  322 (333)
Q Consensus       310 l~~------l~~l~~~~d~  322 (333)
                      +..      .++++++|++
T Consensus       163 l~~i~~~~~~~~~l~lSAT  181 (202)
T d2p6ra3         163 VTKMRRMNKALRVIGLSAT  181 (202)
T ss_dssp             HHHHHHHCTTCEEEEEECC
T ss_pred             HHHHHhcCCCCcEEEEcCC
Confidence            221      2356777765

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1.2e-18  Score=156.92  Aligned_cols=124  Identities=12%  Similarity=0.013  Sum_probs=103.8

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh---cCCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ---NHKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l---~~g~ral~l~Ptra  248 (333)
                      +|++.+...++..|+.      .|+++|++||+.++.|+|+++.||||||||++|++|++..+   ..+.++++++|||+
T Consensus        23 ~L~~~l~~~L~~~g~~------~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~~~~~~lil~Ptre   96 (222)
T d2j0sa1          23 GLREDLLRGIYAYGFE------KPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRE   96 (222)
T ss_dssp             CCCHHHHHHHHHHTCC------SCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHH
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccccccCceeEEecchHH
Confidence            5788888888777776      89999999999999999999999999999999999999765   34678999999999


Q ss_pred             HHHHHHHHHHHhcCC----cEEEeCCCCCC-------CCcceEEecc---------------CcceEeccccccccccC
Q psy2760         249 LSNQKYRDFRETFQD----VGLIDDLPPVF-------PDVEKLLEDL---------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       249 La~Q~~~~l~~~f~~----vglltGd~~~~-------~~a~ili~t~---------------~i~liViDe~H~~~~~~  301 (333)
                      ||.|+++.+++....    +..+.|+....       ....++++|+               ++.++|+||+|.+-+.+
T Consensus        97 La~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~  175 (222)
T d2j0sa1          97 LAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKG  175 (222)
T ss_dssp             HHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHTSTT
T ss_pred             HHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccccccccccceeeeecchhHhhhcC
Confidence            999999999774432    56677776643       2346888886               57799999999887665

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.4e-18  Score=155.69  Aligned_cols=126  Identities=13%  Similarity=0.005  Sum_probs=101.7

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh---cCCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ---NHKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l---~~g~ral~l~Ptra  248 (333)
                      +|++.+.+.+...|+.      .|+++|++||+.++.|+|++++||||||||++|++|++..+   ..+.++++++||++
T Consensus        18 ~L~~~l~~~L~~~g~~------~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~~~~~alil~Pt~e   91 (218)
T d2g9na1          18 NLSESLLRGIYAYGFE------KPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRE   91 (218)
T ss_dssp             CCCHHHHHHHHHHTCC------SCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHH
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecccccCccEEEEcccch
Confidence            5888998888776666      79999999999999999999999999999999999999765   35688999999999


Q ss_pred             HHHHHHHHHHHhcCC----cEEEeCCCCCC--------CCcceEEecc---------------CcceEeccccccccccC
Q psy2760         249 LSNQKYRDFRETFQD----VGLIDDLPPVF--------PDVEKLLEDL---------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       249 La~Q~~~~l~~~f~~----vglltGd~~~~--------~~a~ili~t~---------------~i~liViDe~H~~~~~~  301 (333)
                      ||.|+++.++.....    +..+.|+....        ....++|+|+               ++.++|+||+|.+.+.+
T Consensus        92 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~~~l~~lVlDEaD~ll~~~  171 (218)
T d2g9na1          92 LAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRG  171 (218)
T ss_dssp             HHHHHHHHHHHHHTTTTCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHTTSSCSTTCCEEEEESHHHHHHTT
T ss_pred             hhhhHHHHHhhhccccceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhcCCcccccceEEEeeecchhhcCc
Confidence            999999999876553    34444433222        1246888886               58899999999987765


Q ss_pred             cC
Q psy2760         302 KF  303 (333)
Q Consensus       302 R~  303 (333)
                      .+
T Consensus       172 f~  173 (218)
T d2g9na1         172 FK  173 (218)
T ss_dssp             CH
T ss_pred             hH
Confidence            33

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=6.9e-18  Score=149.55  Aligned_cols=124  Identities=9%  Similarity=-0.021  Sum_probs=101.4

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh---cCCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ---NHKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l---~~g~ral~l~Ptra  248 (333)
                      +|++.+.+.+...|+.      .|+++|++||+.+++|+|++++||||||||++|++|++...   ..+.++++++||++
T Consensus         9 ~L~~~l~~~l~~~g~~------~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil~pt~e   82 (206)
T d1veca_           9 CLKRELLMGIFEMGWE------KPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRE   82 (206)
T ss_dssp             CCCHHHHHHHHTTTCC------SCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHH
T ss_pred             CcCHHHHHHHHHCCCC------CCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhcccccccCcceEEEeecch
Confidence            5788888877777776      89999999999999999999999999999999999999765   45678999999999


Q ss_pred             HHHHHHHHHHHhcCC-----cEEEeCCCCC-------CCCcceEEecc---------------CcceEeccccccccccC
Q psy2760         249 LSNQKYRDFRETFQD-----VGLIDDLPPV-------FPDVEKLLEDL---------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       249 La~Q~~~~l~~~f~~-----vglltGd~~~-------~~~a~ili~t~---------------~i~liViDe~H~~~~~~  301 (333)
                      |+.|+++.+......     +....|+...       .....++++|+               ++.++|+||+|.+-+.+
T Consensus        83 l~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~ll~~~  162 (206)
T d1veca_          83 LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQD  162 (206)
T ss_dssp             HHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHHHTSTT
T ss_pred             hhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHhccCeEEeCCccccccccchhccccccceEEEeccccccccc
Confidence            999999998765432     3455555432       23456888886               57889999999877654

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=5e-18  Score=150.56  Aligned_cols=122  Identities=11%  Similarity=0.001  Sum_probs=101.2

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~Ptra  248 (333)
                      +|++.+.+.+...|+.      .|+++|++|++.+++|+|+++.||||||||++|++|++....   .+.++++++|||+
T Consensus         7 ~L~~~l~~~l~~~g~~------~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~Ptre   80 (207)
T d1t6na_           7 LLKPELLRAIVDCGFE------HPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRE   80 (207)
T ss_dssp             CCCHHHHHHHHHTTCC------CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHH
T ss_pred             CcCHHHHHHHHHCCCC------CCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeecccCCCceEEEEeccch
Confidence            6788888887777766      899999999999999999999999999999999999997653   4568999999999


Q ss_pred             HHHHHHHHHHHhcCC-----cEEEeCCCCCC--------CCcceEEecc---------------CcceEeccccccccc
Q psy2760         249 LSNQKYRDFRETFQD-----VGLIDDLPPVF--------PDVEKLLEDL---------------NIGGLDELSIHDFNK  299 (333)
Q Consensus       249 La~Q~~~~l~~~f~~-----vglltGd~~~~--------~~a~ili~t~---------------~i~liViDe~H~~~~  299 (333)
                      |+.|+.+.++.....     ++.++|+....        ....++|+|+               ++.++|+||+|.+-+
T Consensus        81 L~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~~~~l~~l~~lVlDEaD~ll~  159 (207)
T d1t6na_          81 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLE  159 (207)
T ss_dssp             HHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHHHHS
T ss_pred             hhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccCCceeccccceeehhhhhhhhh
Confidence            999999998775432     56677876643        2346888876               577899999996643

>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=99.73  E-value=5.9e-18  Score=153.67  Aligned_cols=141  Identities=21%  Similarity=0.252  Sum_probs=117.8

Q ss_pred             cccCCCCCCHHHHHHHHHH----HcC--CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy2760         188 AHTWPFELDVFQKQAIIKL----EEH--NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETF  261 (333)
Q Consensus       188 ~~~~~f~l~~~Q~~ai~~l----~~g--~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f  261 (333)
                      ...+||.+++-|.+++..+    .++  .+.+++|.||||||.+|+.++...+..|.++++++||..|+.|++++|+++|
T Consensus        49 ~~~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~Pt~~La~Q~~~~~~~~~  128 (233)
T d2eyqa3          49 CDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRF  128 (233)
T ss_dssp             HHTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHHS
T ss_pred             hhccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEccHHHhHHHHHHHHHHHH
Confidence            4568999999999999885    333  4789999999999999999999999999999999999999999999999988


Q ss_pred             CC----cEEEeCCCCCC-----------CCcceEEecc----------CcceEeccccccccccCcCcccccchhhhhhh
Q psy2760         262 QD----VGLIDDLPPVF-----------PDVEKLLEDL----------NIGGLDELSIHDFNKHLKFWKPKVQLDDLFDW  316 (333)
Q Consensus       262 ~~----vglltGd~~~~-----------~~a~ili~t~----------~i~liViDe~H~~~~~~R~~~~~~~l~~l~~l  316 (333)
                      +.    +.+++|..+..           ....++|.|.          +++++|+||-|.|+...|..  .+.....+.+
T Consensus       129 ~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~~~~~f~~LgLiIiDEeH~fg~kQ~~~--l~~~~~~~~~  206 (233)
T d2eyqa3         129 ANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIVDEEHRFGVRHKER--IKAMRANVDI  206 (233)
T ss_dssp             TTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEEEEESGGGSCHHHHHH--HHHHHTTSEE
T ss_pred             hhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhccCCccccccceeeechhhhhhHHHHH--HHhhCCCCCE
Confidence            75    67888887642           3456888875          68999999999998776532  2223455789


Q ss_pred             eeccCcchhhhhhc
Q psy2760         317 TMASDATTLEIFTY  330 (333)
Q Consensus       317 ~~~~d~~~~e~~~~  330 (333)
                      +++|++|+.|++..
T Consensus       207 l~~SATPiprtl~~  220 (233)
T d2eyqa3         207 LTLTATPIPRTLNM  220 (233)
T ss_dssp             EEEESSCCCHHHHH
T ss_pred             EEEecchhHHHHHH
Confidence            99999999999864

>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=99.73  E-value=3.4e-18  Score=153.32  Aligned_cols=108  Identities=16%  Similarity=0.074  Sum_probs=87.9

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC--------cE
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD--------VG  265 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~--------vg  265 (333)
                      .|+++|+++++.++.|++++++||||+|||++++++++....++.+++|++||++|++|+++++++.+..        ++
T Consensus        43 ~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~~~rvliv~Pt~~La~Q~~~~l~~~~~~~~~~~~~~~~  122 (237)
T d1gkub1          43 EPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIG  122 (237)
T ss_dssp             SCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEE
T ss_pred             CCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHhcCeEEEEeccHHHHHHHHHHHHHHHHHcCCceEEEEe
Confidence            6899999999999999999999999999999999999888888999999999999999999999886553        23


Q ss_pred             EEeCCCCCC---------CCcceEEecc-----------CcceEeccccccccccC
Q psy2760         266 LIDDLPPVF---------PDVEKLLEDL-----------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       266 lltGd~~~~---------~~a~ili~t~-----------~i~liViDe~H~~~~~~  301 (333)
                      ...++....         ....+++.|+           ++.++|+||+|.+....
T Consensus       123 ~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~~~~~~~~~~vVvDE~d~~l~~~  178 (237)
T d1gkub1         123 YYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYRELGHFDFIFVDDVDAILKAS  178 (237)
T ss_dssp             ECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHCSTTSCCCSEEEESCHHHHHTST
T ss_pred             eeecccchhhhhhhhccccccceeccChHHHHHhhhhcCCCCEEEEEChhhhhhcc
Confidence            333333221         1235788775           57889999999875443

>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=99.73  E-value=8.2e-18  Score=155.35  Aligned_cols=140  Identities=21%  Similarity=0.234  Sum_probs=114.2

Q ss_pred             cccCCCCCCHHHHHHHHHHH------cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhc
Q psy2760         188 AHTWPFELDVFQKQAIIKLE------EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETF  261 (333)
Q Consensus       188 ~~~~~f~l~~~Q~~ai~~l~------~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f  261 (333)
                      ...+||.+|+-|++|+..+.      ...+.+++|.||||||.+|+.++..+...|.++++++||..||.|+++.|+++|
T Consensus        77 ~~~LPFeLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~~m~Pt~~La~Qh~~~~~~~f  156 (264)
T d1gm5a3          77 IKSLPFKLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTVESF  156 (264)
T ss_dssp             HHHSSSCCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHHHHHHHHH
T ss_pred             HhhccccCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhcccceeEEeehHhhhHHHHHHHHHhh
Confidence            35688999999999999862      334789999999999999999999999999999999999999999999999999


Q ss_pred             CC----cEEEeCCCCC-----------CCCcceEEecc----------CcceEeccccccccccCcCcccccchhhhhhh
Q psy2760         262 QD----VGLIDDLPPV-----------FPDVEKLLEDL----------NIGGLDELSIHDFNKHLKFWKPKVQLDDLFDW  316 (333)
Q Consensus       262 ~~----vglltGd~~~-----------~~~a~ili~t~----------~i~liViDe~H~~~~~~R~~~~~~~l~~l~~l  316 (333)
                      +.    +++++|+.+.           +.+..++|+|.          +++++|+||-|.|+...|..-...+  ..+..
T Consensus       157 ~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~~~~f~~LglviiDEqH~fgv~Qr~~l~~~~--~~~~~  234 (264)
T d1gm5a3         157 SKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVIIDEQHRFGVKQREALMNKG--KMVDT  234 (264)
T ss_dssp             TCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEEEESCCCC-----CCCCSSS--SCCCE
T ss_pred             hhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcCCCCccccceeeeccccccchhhHHHHHHhC--cCCCE
Confidence            63    7888988775           34567889876          7899999999999998886544332  34778


Q ss_pred             eeccCcchhhhhh
Q psy2760         317 TMASDATTLEIFT  329 (333)
Q Consensus       317 ~~~~d~~~~e~~~  329 (333)
                      +++|++|+.+.+.
T Consensus       235 l~~SATPiprtl~  247 (264)
T d1gm5a3         235 LVMSATPIPRSMA  247 (264)
T ss_dssp             EEEESSCCCHHHH
T ss_pred             EEEECCCCHHHHH
Confidence            9999999998864

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=99.72  E-value=1.5e-17  Score=150.72  Aligned_cols=130  Identities=14%  Similarity=0.067  Sum_probs=103.4

Q ss_pred             ccchhhccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh----------
Q psy2760         165 TEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ----------  234 (333)
Q Consensus       165 ~~w~~~~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l----------  234 (333)
                      ..|.+ .+|++.+.+.+...|+.      .|+++|++|++.+++|+|++++||||||||++|++|++..+          
T Consensus        21 ~~F~~-l~l~~~l~~~L~~~g~~------~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~   93 (238)
T d1wrba1          21 ENFDE-LKLDPTIRNNILLASYQ------RPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRY   93 (238)
T ss_dssp             CSSGG-GSCCCSTTTTTTTTTCC------SCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC-----
T ss_pred             CCHHH-CCCCHHHHHHHHHCCCC------CCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccccc
Confidence            34433 36788887776666655      89999999999999999999999999999999999999654          


Q ss_pred             --cCCCeEEEEcccHHHHHHHHHHHHHhcCC----cEEEeCCCCCCC-------CcceEEecc---------------Cc
Q psy2760         235 --NHKTRTIYTSPIKALSNQKYRDFRETFQD----VGLIDDLPPVFP-------DVEKLLEDL---------------NI  286 (333)
Q Consensus       235 --~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vglltGd~~~~~-------~a~ili~t~---------------~i  286 (333)
                        ..+.++++++||++||.|+++.+......    +..++|+.....       ...++|+|+               ++
T Consensus        94 ~~~~~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~~~~~l~~v  173 (238)
T d1wrba1          94 SKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFC  173 (238)
T ss_dssp             -CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTC
T ss_pred             cCCCCceEEEeccchhhhcchheeeeecccCCCcEEEEEeccchhhHHHhhcccCCceeecCHHHHHhHHccCceecccc
Confidence              23568999999999999999988775433    566777765432       246888886               67


Q ss_pred             ceEeccccccccccC
Q psy2760         287 GGLDELSIHDFNKHL  301 (333)
Q Consensus       287 ~liViDe~H~~~~~~  301 (333)
                      .++|+||+|.+-+.+
T Consensus       174 ~~lViDEaD~ll~~~  188 (238)
T d1wrba1         174 KYIVLDEADRMLDMG  188 (238)
T ss_dssp             CEEEEETHHHHHHTT
T ss_pred             ceeeeehhhhhhhhc
Confidence            889999999776554

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.71  E-value=1.2e-17  Score=147.88  Aligned_cols=146  Identities=12%  Similarity=0.072  Sum_probs=111.0

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcC-CcEEEEcCCCCcHHHHHHHHHHHHh--cCCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEH-NHVFVTAHTSAGKTVIAEYAIALSQ--NHKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g-~~vlv~apTGSGKTl~~~l~il~~l--~~g~ral~l~Ptra  248 (333)
                      +|++++.+.+...|+.      .|+++|+++++.+..| +|++++||||||||++|.++++...  ..+.+++|++||++
T Consensus        10 ~l~~~l~~~l~~~g~~------~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~~~~~~~lil~pt~~   83 (208)
T d1hv8a1          10 NLSDNILNAIRNKGFE------KPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRE   83 (208)
T ss_dssp             SCCHHHHHHHHHHTCC------SCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHH
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHHcCCCCeeeechhcccccceeecccccccccccCcceEEEeeccc
Confidence            6888888887776666      7999999999998776 5999999999999999999998644  46789999999999


Q ss_pred             HHHHHHHHHHHhcCC----cEEEeCCCCCCC------CcceEEecc---------------CcceEeccccccccccCcC
Q psy2760         249 LSNQKYRDFRETFQD----VGLIDDLPPVFP------DVEKLLEDL---------------NIGGLDELSIHDFNKHLKF  303 (333)
Q Consensus       249 La~Q~~~~l~~~f~~----vglltGd~~~~~------~a~ili~t~---------------~i~liViDe~H~~~~~~R~  303 (333)
                      ||.|+++.+++.+..    ++..+|+.....      +.+++|+|+               ++.++|+||+|.+-+.+++
T Consensus        84 l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~~IlV~TP~~l~~~l~~~~~~~~~l~~lViDEad~l~~~~~~  163 (208)
T d1hv8a1          84 LAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKNANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFI  163 (208)
T ss_dssp             HHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHHTCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHHHHHTTTTH
T ss_pred             cchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhcCCCCEEEEChHHHHHHHHcCCCCcccCcEEEEEChHHhhcCCCh
Confidence            999999999886653    677888765432      347889885               5789999999977555433


Q ss_pred             cccccchhh----hhhheeccCcch
Q psy2760         304 WKPKVQLDD----LFDWTMASDATT  324 (333)
Q Consensus       304 ~~~~~~l~~----l~~l~~~~d~~~  324 (333)
                      -... ++.+    ..+.++.|++=+
T Consensus       164 ~~i~-~I~~~~~~~~Q~i~~SAT~~  187 (208)
T d1hv8a1         164 KDVE-KILNACNKDKRILLFSATMP  187 (208)
T ss_dssp             HHHH-HHHHTSCSSCEEEEECSSCC
T ss_pred             HHHH-HHHHhCCCCCeEEEEEccCC
Confidence            2111 1221    234666676533

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.71  E-value=3.9e-17  Score=145.44  Aligned_cols=125  Identities=14%  Similarity=0.048  Sum_probs=100.4

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh---cCCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ---NHKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l---~~g~ral~l~Ptra  248 (333)
                      +|++.+.+.++..|+.      .|+++|++||+.++.|+|++++||||||||++|++|++..+   ..+.++++++||++
T Consensus        16 ~l~~~l~~~L~~~g~~------~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~lil~pt~e   89 (212)
T d1qdea_          16 ELDENLLRGVFGYGFE------EPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRE   89 (212)
T ss_dssp             TCCHHHHHHHHHHTCC------SCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHH
T ss_pred             CCCHHHHHHHHHCCCC------CCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhccCCCcceEEEcccHH
Confidence            6899999988877777      89999999999999999999999999999999999999775   35678999999999


Q ss_pred             HHHHHHHHHHHhcCC----cEEEeCCCCCC------CCcceEEecc---------------CcceEeccccccccccCc
Q psy2760         249 LSNQKYRDFRETFQD----VGLIDDLPPVF------PDVEKLLEDL---------------NIGGLDELSIHDFNKHLK  302 (333)
Q Consensus       249 La~Q~~~~l~~~f~~----vglltGd~~~~------~~a~ili~t~---------------~i~liViDe~H~~~~~~R  302 (333)
                      |+.|++..+......    +....|+....      ....++|+|+               ++.++|+||+|.+-+.++
T Consensus        90 l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvI~TP~~l~~~~~~~~~~l~~l~~lVlDEad~lld~~f  168 (212)
T d1qdea_          90 LALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGF  168 (212)
T ss_dssp             HHHHHHHHHHHHTTTSCCCEEEECC----------CTTCSEEEECHHHHHHHHHTTSSCCTTCCEEEEETHHHHHHTTC
T ss_pred             HhhhhhhhhcccccccccceeeEeeccchhHHHHHhcCCcEEEECCCccccccccCceecCcceEEeehhhhhhcccch
Confidence            999999998775432    33344443322      1346888876               588999999998876653

>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=99.69  E-value=3.8e-17  Score=143.04  Aligned_cols=143  Identities=13%  Similarity=0.118  Sum_probs=101.7

Q ss_pred             cCChhhhhhhhccccccccCCC-CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPF-ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALS  250 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f-~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa  250 (333)
                      +|++...++++.      .|+| .|+|+|.+|++.+.+|+|+++++|||||||++|.++++.   ...+++|++|+++|+
T Consensus         8 ~l~~~~~~~l~~------~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~---~~~~~~~v~P~~~L~   78 (206)
T d1oywa2           8 NLESGAKQVLQE------TFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALL---LNGLTVVVSPLISLM   78 (206)
T ss_dssp             SHHHHHHHHHHH------TTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHH---SSSEEEEECSCHHHH
T ss_pred             CCCHHHHHHHHH------hcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhh---ccCceEEeccchhhh
Confidence            345555555532      3455 789999999999999999999999999999999998864   467899999999999


Q ss_pred             HHHHHHHHHhcCCcEEEeCCCCCC-----------CCcceEEecc---------------CcceEeccccccccccCcCc
Q psy2760         251 NQKYRDFRETFQDVGLIDDLPPVF-----------PDVEKLLEDL---------------NIGGLDELSIHDFNKHLKFW  304 (333)
Q Consensus       251 ~Q~~~~l~~~f~~vglltGd~~~~-----------~~a~ili~t~---------------~i~liViDe~H~~~~~~R~~  304 (333)
                      +|+.+.|+..+...+...+.....           ....+++.|+               ++.++++||+|.+...++..
T Consensus        79 ~q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~~~~~~~~v~~lviDEaH~~~~~~~~~  158 (206)
T d1oywa2          79 KDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCISQWGHDF  158 (206)
T ss_dssp             HHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEESSGGGGCTTSSCC
T ss_pred             hhHHHHHHhhcccccccccccccccchhHHHHHhcCCceEEEEechhhhchhhcccchhheeeeeeeeeeeeeeccccch
Confidence            999999988666554444332211           1234555543               57889999999987766543


Q ss_pred             ccc----cchhh---hhhheeccCcc
Q psy2760         305 KPK----VQLDD---LFDWTMASDAT  323 (333)
Q Consensus       305 ~~~----~~l~~---l~~l~~~~d~~  323 (333)
                      ++.    ..+..   .++.++.|++-
T Consensus       159 ~~~~~~~~~l~~~~~~~~ii~lSATl  184 (206)
T d1oywa2         159 RPEYAALGQLRQRFPTLPFMALTATA  184 (206)
T ss_dssp             CHHHHGGGGHHHHCTTSCEEEEESCC
T ss_pred             HHHHHHHHHHHHhCCCCceEEEEeCC
Confidence            332    11111   24566777763

>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=99.63  E-value=2.8e-16  Score=136.06  Aligned_cols=107  Identities=15%  Similarity=0.157  Sum_probs=84.5

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHH-hcCCCeEEEEcccHHHHHHHHHHHHHhcCC----cEEEe
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALS-QNHKTRTIYTSPIKALSNQKYRDFRETFQD----VGLID  268 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~-l~~g~ral~l~PtraLa~Q~~~~l~~~f~~----vgllt  268 (333)
                      .|+++|.+++..+. ++|+++++|||||||+++.+++... ...+.+++|++|+++|+.|+++.+++.+..    ++...
T Consensus         9 ~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~~~~~il~i~P~~~L~~q~~~~~~~~~~~~~~~v~~~~   87 (200)
T d1wp9a1           9 QPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALT   87 (200)
T ss_dssp             CCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEEC
T ss_pred             CCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHhcCCcEEEEcCchHHHHHHHHHHHHhhcccccceeeee
Confidence            68999999998875 5689999999999999998877643 356788999999999999999999998763    56666


Q ss_pred             CCCCCCC------CcceEEecc---------------CcceEeccccccccccC
Q psy2760         269 DLPPVFP------DVEKLLEDL---------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       269 Gd~~~~~------~a~ili~t~---------------~i~liViDe~H~~~~~~  301 (333)
                      ++.....      ...+++.|+               ++.++|+||+|.+....
T Consensus        88 ~~~~~~~~~~~~~~~~i~i~t~~~~~~~~~~~~~~~~~~~~vIiDE~H~~~~~~  141 (200)
T d1wp9a1          88 GEKSPEERSKAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNY  141 (200)
T ss_dssp             SCSCHHHHHHHHHHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTC
T ss_pred             cccchhHHHHhhhcccccccccchhHHHHhhhhhhccccceEEEEehhhhhcch
Confidence            6654322      124566654               57899999999887554

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.62  E-value=1.3e-15  Score=134.18  Aligned_cols=125  Identities=12%  Similarity=0.004  Sum_probs=104.3

Q ss_pred             ccCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh---cCCCeEEEEcccH
Q psy2760         171 LDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ---NHKTRTIYTSPIK  247 (333)
Q Consensus       171 ~~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l---~~g~ral~l~Ptr  247 (333)
                      .+|++.+...++..|+.      .|+++|++|++.+++|+|+++.||||||||++|++|++...   ..+.++++++|++
T Consensus         6 l~L~~~l~~~L~~~g~~------~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~~~~~~~~~~~~~   79 (206)
T d1s2ma1           6 FYLKRELLMGIFEAGFE------KPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTR   79 (206)
T ss_dssp             GCCCHHHHHHHHHTTCC------SCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSH
T ss_pred             cCCCHHHHHHHHHCCCC------CCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccccccccceeeccch
Confidence            47888998888777766      89999999999999999999999999999999999998664   4567899999999


Q ss_pred             HHHHHHHHHHHHhcCC----cEEEeCCCCCC-------CCcceEEecc---------------CcceEeccccccccccC
Q psy2760         248 ALSNQKYRDFRETFQD----VGLIDDLPPVF-------PDVEKLLEDL---------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       248 aLa~Q~~~~l~~~f~~----vglltGd~~~~-------~~a~ili~t~---------------~i~liViDe~H~~~~~~  301 (333)
                      +++.|....+......    +...+|+....       ....++|+|+               ++.++|+||+|.+-+.+
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~lV~DEaD~l~~~~  159 (206)
T d1s2ma1          80 ELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRD  159 (206)
T ss_dssp             HHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHHHSSHH
T ss_pred             hhhhhhhhhhhhcccccCeeEEeecCccchhhHHHHhcccceEEEECCcccccccccceeecccceEEEeechhhhhhhh
Confidence            9999999888764432    67788876542       4467888886               57889999999887654

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.58  E-value=5.7e-15  Score=129.36  Aligned_cols=145  Identities=10%  Similarity=-0.022  Sum_probs=106.7

Q ss_pred             cCChhhhhhhhccccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhc---CCCeEEEEcccHH
Q psy2760         172 DVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN---HKTRTIYTSPIKA  248 (333)
Q Consensus       172 ~L~~~l~~~~~~~~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~---~g~ral~l~Ptra  248 (333)
                      +|++.+.+.++..|+.      .|+++|++||+.+++|+|++++||||||||++|++|++....   .....++++|++.
T Consensus         7 ~L~~~l~~~l~~~g~~------~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~~~~~~~~~~~~~~   80 (209)
T d1q0ua_           7 PFQPFIIEAIKTLRFY------KPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRE   80 (209)
T ss_dssp             CCCHHHHHHHHHTTCC------SCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHH
T ss_pred             CcCHHHHHHHHHCCCC------CCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccccccccccccccccc
Confidence            6888888887776665      799999999999999999999999999999999999986653   3567899999999


Q ss_pred             HHHHHHHHHHHhcCC--------cEEEeCCCCC-------CCCcceEEecc---------------CcceEecccccccc
Q psy2760         249 LSNQKYRDFRETFQD--------VGLIDDLPPV-------FPDVEKLLEDL---------------NIGGLDELSIHDFN  298 (333)
Q Consensus       249 La~Q~~~~l~~~f~~--------vglltGd~~~-------~~~a~ili~t~---------------~i~liViDe~H~~~  298 (333)
                      ++.+.+..+......        +..+.|+...       .....++++|+               ++.++|+||+|.+.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~~~~~~~~~l~~lViDEad~ll  160 (209)
T d1q0ua_          81 LATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLML  160 (209)
T ss_dssp             HHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSHHHHH
T ss_pred             hhHHHHHHHHhhhccccccccccccccccchhhHHHHHHhccCceEEEecCchhhhhhhhhccccccceEEEEeeccccc
Confidence            999999887664432        3334444322       22346888876               58889999999988


Q ss_pred             ccCcCccccc---chhhhhhheeccCc
Q psy2760         299 KHLKFWKPKV---QLDDLFDWTMASDA  322 (333)
Q Consensus       299 ~~~R~~~~~~---~l~~l~~l~~~~d~  322 (333)
                      +.+++-....   .+-...+.++.|++
T Consensus       161 ~~~f~~~v~~I~~~~~~~~Q~il~SAT  187 (209)
T d1q0ua_         161 DMGFITDVDQIAARMPKDLQMLVFSAT  187 (209)
T ss_dssp             HTTCHHHHHHHHHTSCTTCEEEEEESC
T ss_pred             ccccHHHHHHHHHHCCCCCEEEEEEcc
Confidence            7654322221   01123456666653

>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=99.50  E-value=6e-14  Score=123.43  Aligned_cols=102  Identities=21%  Similarity=0.145  Sum_probs=81.3

Q ss_pred             CCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC--cEEEeC
Q psy2760         192 PFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD--VGLIDD  269 (333)
Q Consensus       192 ~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~--vglltG  269 (333)
                      .+.|+++|++|+..+..+++.++.+|||+|||++++..+.   ..+.++||++|+++|++|+.+++.+ |+.  ++...|
T Consensus        68 ~~~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~~~---~~~~~~Liv~p~~~L~~q~~~~~~~-~~~~~~~~~~~  143 (206)
T d2fz4a1          68 EISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAIN---ELSTPTLIVVPTLALAEQWKERLGI-FGEEYVGEFSG  143 (206)
T ss_dssp             CCCCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHH---HSCSCEEEEESSHHHHHHHHHHHGG-GCGGGEEEESS
T ss_pred             CCCcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhHHH---HhcCceeEEEcccchHHHHHHHHHh-hcccchhhccc
Confidence            4589999999999998888999999999999998765543   2356899999999999999999976 543  677777


Q ss_pred             CCCCCCCcceEEecc------------CcceEeccccccccc
Q psy2760         270 LPPVFPDVEKLLEDL------------NIGGLDELSIHDFNK  299 (333)
Q Consensus       270 d~~~~~~a~ili~t~------------~i~liViDe~H~~~~  299 (333)
                      +...  ...+++.+.            ...++|+||+|.+..
T Consensus       144 ~~~~--~~~i~i~t~~~~~~~~~~~~~~~~lvIiDEaH~~~a  183 (206)
T d2fz4a1         144 RIKE--LKPLTVSTYDSAYVNAEKLGNRFMLLIFDEVHHLPA  183 (206)
T ss_dssp             SCBC--CCSEEEEEHHHHHHTHHHHTTTCSEEEEECSSCCCT
T ss_pred             cccc--ccccccceehhhhhhhHhhCCcCCEEEEECCeeCCc
Confidence            6543  234566654            467899999999864

>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=99.48  E-value=7.1e-14  Score=129.27  Aligned_cols=116  Identities=18%  Similarity=0.145  Sum_probs=86.9

Q ss_pred             ccccccCCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHH-hcCCCeEEEEcccHHHHHHHHHHHHHhcCC
Q psy2760         185 PIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALS-QNHKTRTIYTSPIKALSNQKYRDFRETFQD  263 (333)
Q Consensus       185 ~~~~~~~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~-l~~g~ral~l~PtraLa~Q~~~~l~~~f~~  263 (333)
                      .......++.|+++|.+|+..+..+++.++.+|||+|||+++...+... ...+.++||++|+++|+.|+.++|.+.+..
T Consensus       104 ~~~~~~~~~~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i~~~~~~~~~~k~Liivp~~~Lv~Q~~~~f~~~~~~  183 (282)
T d1rifa_         104 EIYSGNKRIEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLF  183 (282)
T ss_dssp             CCEETTEECCCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSSHHHHHHHHHHHHHHTSC
T ss_pred             cccccCCccccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHHHHHhhhcccceEEEEEcCchhHHHHHHHHHHhhcc
Confidence            3333344678999999999999888899999999999999987655433 344578999999999999999999875432


Q ss_pred             ----cEEEeCCCCCC----CCcceEEecc------------CcceEecccccccccc
Q psy2760         264 ----VGLIDDLPPVF----PDVEKLLEDL------------NIGGLDELSIHDFNKH  300 (333)
Q Consensus       264 ----vglltGd~~~~----~~a~ili~t~------------~i~liViDe~H~~~~~  300 (333)
                          ++.+.++....    ....+++.|+            +..++|+||+|.+...
T Consensus       184 ~~~~~~~~~~g~~~~~~~~~~~~i~i~t~qs~~~~~~~~~~~f~~VIvDEaH~~~a~  240 (282)
T d1rifa_         184 SHAMIKKIGGGASKDDKYKNDAPVVVGTWQTVVKQPKEWFSQFGMMMNDECHLATGK  240 (282)
T ss_dssp             CGGGEEECSTTCSSTTCCCTTCSEEEECHHHHTTSCGGGGGGEEEEEEETGGGCCHH
T ss_pred             ccccceeecceecccccccccceEEEEeeehhhhhcccccCCCCEEEEECCCCCCch
Confidence                45555544332    2235666654            5789999999988643

>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=99.46  E-value=5.3e-15  Score=134.86  Aligned_cols=94  Identities=15%  Similarity=-0.030  Sum_probs=67.9

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHH-HhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEeCCCCCCCCcceEEecc-
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIAL-SQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLLEDL-  284 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~-~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vglltGd~~~~~~a~ili~t~-  284 (333)
                      .+|+++++.||||||||++|+.+++. ...++.+++|++|||+||+|++++|++....+....++........+++.|+ 
T Consensus         7 ~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~~~~~lvi~Ptr~La~q~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~t~~   86 (305)
T d2bmfa2           7 RKKRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIRAEHTGREIVDLMCHA   86 (305)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHTTTSCCBCCC--------CCCSEEEEEHH
T ss_pred             hcCCcEEEEECCCCCHHHHHHHHHHHHHHhcCCEEEEEccHHHHHHHHHHHHhcCCcceeeeEEeecccCccccccCCcH
Confidence            46899999999999999998877763 4567889999999999999999998764433332222333334445555553 


Q ss_pred             -------------CcceEecccccccccc
Q psy2760         285 -------------NIGGLDELSIHDFNKH  300 (333)
Q Consensus       285 -------------~i~liViDe~H~~~~~  300 (333)
                                   ++.++|+||+|.+...
T Consensus        87 ~l~~~~~~~~~~~~~~~vViDE~H~~~~~  115 (305)
T d2bmfa2          87 TFTMRLLSPIRVPNYNLIIMDEAHFTDPA  115 (305)
T ss_dssp             HHHHHHTSSSCCCCCSEEEEESTTCCSHH
T ss_pred             HHHHHHhcCccccceeEEEeeeeeecchh
Confidence                         6889999999988654

>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=99.43  E-value=1.3e-14  Score=116.68  Aligned_cols=117  Identities=11%  Similarity=-0.043  Sum_probs=76.9

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHH-HHhcCCCeEEEEcccHHHHHHHHHHHHHhcCCcEEEeCCCCCCCCcceEEecc-
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIA-LSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLLEDL-  284 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il-~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~vglltGd~~~~~~a~ili~t~-  284 (333)
                      ..|+++++++|||||||.++..+++ .....+.++++++|+++|++|..+.+......+....+.............+. 
T Consensus         5 ~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~~~~vli~~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (140)
T d1yksa1           5 KKGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGLDVKFHTQAFSAHGSGREVIDAMCHA   84 (140)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTTSCEEEESSCCCCCCCSSCCEEEEEHH
T ss_pred             HcCCcEEEEcCCCCChhHHHHHHHHHHhhhcCceeeeeecchhHHHHHHHHhhhhhhhhcccccccccccccchhhhhHH
Confidence            5689999999999999998877665 44567889999999999999999877443222222223323333333333321 


Q ss_pred             -------------CcceEeccccccccccC---cCcccccchhhhhhheeccCcc
Q psy2760         285 -------------NIGGLDELSIHDFNKHL---KFWKPKVQLDDLFDWTMASDAT  323 (333)
Q Consensus       285 -------------~i~liViDe~H~~~~~~---R~~~~~~~l~~l~~l~~~~d~~  323 (333)
                                   ++.++|+||+|++...+   |+|..........+.+.+|+++
T Consensus        85 ~l~~~~~~~~~~~~~~lvIiDEaH~~~~~~~~~~~~~~~~~~~~~~~~l~lTATP  139 (140)
T d1yksa1          85 TLTYRMLEPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRARANESATILMTATP  139 (140)
T ss_dssp             HHHHHHTSSSCCCCCSEEEETTTTCCSHHHHHHHHHHHHHHHTTSCEEEEECSSC
T ss_pred             HHHHHHhccccccceeEEEEccccccChhhHHHHHHHHHHhhCCCCCEEEEEcCC
Confidence                         78999999999875443   3333222223345677777765

>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=99.35  E-value=8.7e-13  Score=107.57  Aligned_cols=89  Identities=9%  Similarity=-0.017  Sum_probs=70.0

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC-cEEEeCCCCCCCCcceEEecc---
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD-VGLIDDLPPVFPDVEKLLEDL---  284 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~-vglltGd~~~~~~a~ili~t~---  284 (333)
                      .+..++.||||||||+++...+   ...+.+++|++|+++|++|+.+.+.+.+.. .+...++........+.+.+.   
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~~---~~~~~~vli~~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAAY---AAQGYKVLVLNPSVAATLGFGAYMSKAHGVDPNIRTGVRTITTGSPITYSTYGKF   84 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHHH---HTTTCCEEEEESCHHHHHHHHHHHHHHHSCCCEEECSSCEECCCCSEEEEEHHHH
T ss_pred             CCEEEEEeCCCCCHHHHHHHHH---HHcCCcEEEEcChHHHHHHHHHHHHHHhhccccccccccccccccceEEEeeeee
Confidence            4678999999999998764433   466889999999999999999999887765 666666665555555666543   


Q ss_pred             ---------CcceEecccccccccc
Q psy2760         285 ---------NIGGLDELSIHDFNKH  300 (333)
Q Consensus       285 ---------~i~liViDe~H~~~~~  300 (333)
                               ++.++|+||+|.++..
T Consensus        85 ~~~~~~~~~~~~~vIiDE~H~~~~~  109 (136)
T d1a1va1          85 LADGGCSGGAYDIIICDECHSTDAT  109 (136)
T ss_dssp             HHTTGGGGCCCSEEEEETTTCCSHH
T ss_pred             ccccchhhhcCCEEEEecccccCHH
Confidence                     5789999999998654

>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=98.25  E-value=2.7e-06  Score=74.24  Aligned_cols=107  Identities=9%  Similarity=0.083  Sum_probs=72.8

Q ss_pred             CCCHHHHHHHHHH----HcCCcEEEEcCCCCcHHHHHHHHHHHHh--cCCCeEEEEcccHHHHHHHHHHHHHhcCC--cE
Q psy2760         194 ELDVFQKQAIIKL----EEHNHVFVTAHTSAGKTVIAEYAIALSQ--NHKTRTIYTSPIKALSNQKYRDFRETFQD--VG  265 (333)
Q Consensus       194 ~l~~~Q~~ai~~l----~~g~~vlv~apTGSGKTl~~~l~il~~l--~~g~ral~l~PtraLa~Q~~~~l~~~f~~--vg  265 (333)
                      .|+++|.+++.-+    ..+..++++-.+|.|||+.++..+....  ....++++++| ..+..|+.+++.+.+..  +.
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~~~~~~~~~~~~~~LIv~p-~~l~~~W~~e~~~~~~~~~~~   90 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKENELTPSLVICP-LSVLKNWEEELSKFAPHLRFA   90 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHHTTCCSSEEEEEC-STTHHHHHHHHHHHCTTSCEE
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHhhhhhhhcccccccceecc-hhhhhHHHHHHHhhcccccce
Confidence            6899999998653    4556789999999999999876554332  33467899888 57888999999876554  22


Q ss_pred             EEeCCCCC--CCCcceEEecc------------CcceEeccccccccccC
Q psy2760         266 LIDDLPPV--FPDVEKLLEDL------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       266 lltGd~~~--~~~a~ili~t~------------~i~liViDe~H~~~~~~  301 (333)
                      ...+....  .....+++.+.            ...++|+||.|++....
T Consensus        91 ~~~~~~~~~~~~~~~vvi~~~~~~~~~~~l~~~~~~~vI~DEah~~k~~~  140 (230)
T d1z63a1          91 VFHEDRSKIKLEDYDIILTTYAVLLRDTRLKEVEWKYIVIDEAQNIKNPQ  140 (230)
T ss_dssp             ECSSSTTSCCGGGSSEEEEEHHHHTTCHHHHTCCEEEEEEETGGGGSCTT
T ss_pred             eeccccchhhccCcCEEEeeHHHHHhHHHHhcccceEEEEEhhhcccccc
Confidence            22221111  12235555543            45679999999996543

>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=98.09  E-value=6.7e-06  Score=74.55  Aligned_cols=107  Identities=17%  Similarity=0.084  Sum_probs=70.4

Q ss_pred             CCCHHHHHHHHHH---------HcCCcEEEEcCCCCcHHHHHHHHHHHHhc-------CCCeEEEEcccHHHHHHHHHHH
Q psy2760         194 ELDVFQKQAIIKL---------EEHNHVFVTAHTSAGKTVIAEYAIALSQN-------HKTRTIYTSPIKALSNQKYRDF  257 (333)
Q Consensus       194 ~l~~~Q~~ai~~l---------~~g~~vlv~apTGSGKTl~~~l~il~~l~-------~g~ral~l~PtraLa~Q~~~~l  257 (333)
                      .|+|||.+++.-+         ..+..++++=..|.|||+.++..+.....       ...++|+|+|. .|+.|+.+++
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia~l~~l~~~~~~~~~~~~~~LIV~P~-sl~~qW~~Ei  133 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEV  133 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHHHHHHHHHHhcccccCCCCcEEEEccc-hhhHHHHHHH
Confidence            5899999998743         23456888889999999865543332221       12468999998 5889999999


Q ss_pred             HHhcCC---cEEEeCCCCC---------------CCCcceEEecc-------------CcceEeccccccccccC
Q psy2760         258 RETFQD---VGLIDDLPPV---------------FPDVEKLLEDL-------------NIGGLDELSIHDFNKHL  301 (333)
Q Consensus       258 ~~~f~~---vglltGd~~~---------------~~~a~ili~t~-------------~i~liViDe~H~~~~~~  301 (333)
                      .+.++.   +..+.|+...               .....+++.+.             ...++|+||.|++.+..
T Consensus       134 ~k~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~~l~~~~~~~vI~DEaH~ikn~~  208 (298)
T d1z3ix2         134 GKWLGGRVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAEVLHKGKVGLVICDEGHRLKNSD  208 (298)
T ss_dssp             HHHHGGGCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTTTTTTSCCCEEEETTGGGCCTTC
T ss_pred             HhhcCCceeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccchhcccccceeeeeccccccccccc
Confidence            886653   3334444321               11123455432             35689999999997553

>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=97.89  E-value=8.5e-06  Score=72.49  Aligned_cols=67  Identities=18%  Similarity=0.092  Sum_probs=53.4

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHh----cCCCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQ----NHKTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l----~~g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      .|+|-|++|+..  ...+++|.|+.|||||.+...-+...+    .+..+++++++|+++|+.+..++.+.++
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~a~~~i~~~~~~~~~   71 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLG   71 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHHHHHHHHHHHHHhcC
Confidence            478999999964  356799999999999998776554332    2335899999999999999999877664

>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=97.68  E-value=4.2e-05  Score=68.67  Aligned_cols=67  Identities=13%  Similarity=0.127  Sum_probs=54.5

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcC----CCeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH----KTRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~----g~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      .|++-|++++..  .+.+++|.|+.|||||.+....+...+..    ..+++++++++..+..+..++.+...
T Consensus        11 ~L~~eQ~~~v~~--~~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~aa~~~~~~~~~~~~   81 (318)
T d1pjra1          11 HLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLG   81 (318)
T ss_dssp             TSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHHG
T ss_pred             hCCHHHHHHHhC--CCCCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHHHHHHHHHHHHhhcc
Confidence            489999999974  45679999999999999998876644432    24799999999999999999877543

>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=97.25  E-value=0.00022  Score=66.69  Aligned_cols=66  Identities=12%  Similarity=0.104  Sum_probs=51.0

Q ss_pred             CCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHH--HHHHh--cCCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYA--IALSQ--NHKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~--il~~l--~~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      .....|++|+..+..++.+++.||.|+|||.+....  .+...  ..+.++++++||..=|..+.+....
T Consensus       148 ~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~~~  217 (359)
T d1w36d1         148 DEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGK  217 (359)
T ss_dssp             TSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHTH
T ss_pred             ccccHHHHHHHHHHcCCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHHHH
Confidence            457899999999989999999999999999875432  22222  4567899999998777777766543

>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=96.68  E-value=0.0022  Score=60.91  Aligned_cols=70  Identities=30%  Similarity=0.347  Sum_probs=54.9

Q ss_pred             CCCCCCHHHHHHHHHH----HcC-CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC
Q psy2760         191 WPFELDVFQKQAIIKL----EEH-NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD  263 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l----~~g-~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~  263 (333)
                      -+|.|.-.|=+||..+    ..| ++.++.|-||||||++..-.+ ..  .+..+|+|+|+..+|.|++++|+..+++
T Consensus         8 ~~~~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA~l~-~~--~~rp~LVVt~n~~~A~qL~~dL~~~l~~   82 (413)
T d1t5la1           8 APYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVI-AQ--VNKPTLVIAHNKTLAGQLYSELKEFFPH   82 (413)
T ss_dssp             CSSCCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHHHHH-HH--HTCCEEEECSSHHHHHHHHHHHHHHCTT
T ss_pred             cCCCCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHHHHH-HH--hCCCEEEEeCCHHHHHHHHHHHHHHcCC
Confidence            3678888888888774    444 678999999999997654322 22  2556999999999999999999998875

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=95.54  E-value=0.021  Score=51.02  Aligned_cols=81  Identities=15%  Similarity=0.070  Sum_probs=59.6

Q ss_pred             CCCCCCHHHHHHHHHHHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHh---cC-CcEE
Q psy2760         191 WPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRET---FQ-DVGL  266 (333)
Q Consensus       191 ~~f~l~~~Q~~ai~~l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~---f~-~vgl  266 (333)
                      ++..+++.|...--.+..|+  +....||-|||+++.+|+......|..+-++...--||..=.+.+...   ++ .||.
T Consensus        77 lG~RhyDVQLiGgi~L~~G~--iaem~TGEGKTL~a~l~a~l~al~g~~vhvvTvNdyLA~RDae~m~~iy~~lGlsvg~  154 (273)
T d1tf5a3          77 TGMFPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGL  154 (273)
T ss_dssp             HSCCCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTTSSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEE
T ss_pred             hceEEehhHHHHHHHHHhhh--heeecCCCcchhHHHHHHHHHHhcCCCceEEecCccccchhhhHHhHHHHHcCCCccc
Confidence            34568888888777788885  779999999999999988766666778888888777887655554443   33 3677


Q ss_pred             EeCCCCC
Q psy2760         267 IDDLPPV  273 (333)
Q Consensus       267 ltGd~~~  273 (333)
                      .+.+...
T Consensus       155 ~~~~~~~  161 (273)
T d1tf5a3         155 NLNSMSK  161 (273)
T ss_dssp             CCTTSCH
T ss_pred             cccccCH
Confidence            6665443

>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=95.41  E-value=0.013  Score=50.28  Aligned_cols=54  Identities=15%  Similarity=0.223  Sum_probs=39.6

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc--ccHHHHHHHHHHHHHhcC
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS--PIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~--PtraLa~Q~~~~l~~~f~  262 (333)
                      ++-++++||||+|||....-...+....|.++.+++  ..|+=+.++.+.+.+..+
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~~~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~   61 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLS   61 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEECCCCSSTTHHHHHHHHHHHHT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEeccccccchhhHhhcccccC
Confidence            566788999999999986543344445667777665  358888888888877653

>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=95.10  E-value=0.0088  Score=54.63  Aligned_cols=52  Identities=21%  Similarity=0.157  Sum_probs=35.8

Q ss_pred             HHHHHHHHH-HHcCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHH
Q psy2760         197 VFQKQAIIK-LEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKAL  249 (333)
Q Consensus       197 ~~Q~~ai~~-l~~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraL  249 (333)
                      +.+...+.. +..++|++++|+||||||... .+++.......|++.+--+.+|
T Consensus       153 ~~~~~~l~~~v~~~~nili~G~tgSGKTT~l-~al~~~i~~~~rivtiEd~~El  205 (323)
T d1g6oa_         153 EQAISAIKDGIAIGKNVIVCGGTGSGKTTYI-KSIMEFIPKEERIISIEDTEEI  205 (323)
T ss_dssp             HHHHHHHHHHHHHTCCEEEEESTTSSHHHHH-HHHGGGSCTTCCEEEEESSCCC
T ss_pred             HHHHHHHHHHHHhCCCEEEEeeccccchHHH-HHHhhhcccccceeeccchhhh
Confidence            344445554 478899999999999999874 4555555556667666555554

>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=94.53  E-value=0.031  Score=47.70  Aligned_cols=51  Identities=16%  Similarity=0.212  Sum_probs=37.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc--ccHHHHHHHHHHHHHhcC
Q psy2760         212 VFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS--PIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       212 vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~--PtraLa~Q~~~~l~~~f~  262 (333)
                      ++++||||+|||....-...+...++.++.+++  ..|.=|.++.+.+.+..+
T Consensus        13 i~lvGp~GvGKTTTiaKLA~~~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~   65 (207)
T d1ls1a2          13 WFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVG   65 (207)
T ss_dssp             EEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEECCSSCHHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEecccccchHHHHHHHHHHhcC
Confidence            566999999998875443333445677777665  369999999988888664

>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=94.16  E-value=0.02  Score=45.14  Aligned_cols=30  Identities=27%  Similarity=0.380  Sum_probs=21.4

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcCCCe
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTR  239 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~g~r  239 (333)
                      |++++.||+|+|||......+......+.+
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l~~~~~~   31 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVLKSSGVP   31 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHHHTTCC
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHCCCE
Confidence            689999999999999766544433334433

>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=94.10  E-value=0.052  Score=46.51  Aligned_cols=51  Identities=8%  Similarity=0.141  Sum_probs=36.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc--ccHHHHHHHHHHHHHhcC
Q psy2760         212 VFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS--PIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       212 vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~--PtraLa~Q~~~~l~~~f~  262 (333)
                      ++++||||+|||....-...+....+.++.+++  ..|.=|.++.+.+.+..+
T Consensus        12 i~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~   64 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTFRAAAVEQLQVWGQRNN   64 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTTTCCEEEECCCTTCHHHHHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEecccccccchhhhhhhhhhcC
Confidence            567999999999886543334445566766665  348888888888877653

>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=94.04  E-value=0.045  Score=46.95  Aligned_cols=52  Identities=12%  Similarity=0.175  Sum_probs=36.0

Q ss_pred             cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc--ccHHHHHHHHHHHHHhcC
Q psy2760         211 HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS--PIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~--PtraLa~Q~~~~l~~~f~  262 (333)
                      -++++||||+|||....-...+...++.++.+++  ..|.=|.++.+.+.+..+
T Consensus        13 vi~lvGptGvGKTTTiAKLAa~~~~~~~kV~lit~Dt~R~gA~eQL~~~a~~l~   66 (213)
T d1vmaa2          13 VIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAADTFRAAAIEQLKIWGERVG   66 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEECTTCHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEeecccccchhHHHHHHhhhcC
Confidence            4677999999999885443333445566665554  458888888888877553

>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=93.77  E-value=0.032  Score=51.31  Aligned_cols=42  Identities=19%  Similarity=0.248  Sum_probs=34.1

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALS  250 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa  250 (333)
                      .+|++|.|+||||||......+.+....+..++++=|.-++.
T Consensus        50 ~~H~~I~G~tGsGKT~~l~~li~~~~~~g~~~iiiD~kge~~   91 (433)
T d1e9ra_          50 PRHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPNGDML   91 (433)
T ss_dssp             GGCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEETTHHH
T ss_pred             cceEEEEeCCCCcHHHHHHHHHHHHHhCCCCEEEEeCChhHH
Confidence            579999999999999876555666777888888888887653

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

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: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=93.40  E-value=0.041  Score=46.27  Aligned_cols=38  Identities=21%  Similarity=0.284  Sum_probs=32.6

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSP  245 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~P  245 (333)
                      .|.-+++.|++|+|||..+.--+......+.+++|++-
T Consensus        25 ~gsl~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is~   62 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLVSRFVENACANKERAILFAY   62 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEES
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhccccceeec
Confidence            36789999999999999998877777788888999864

>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=92.96  E-value=0.076  Score=45.38  Aligned_cols=52  Identities=6%  Similarity=0.086  Sum_probs=31.7

Q ss_pred             cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEc--ccHHHHHHHHHHHHHhcC
Q psy2760         211 HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS--PIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~--PtraLa~Q~~~~l~~~f~  262 (333)
                      -++++||||+|||....-...+....|.++.+++  ..|.=+.++.+.+.+..+
T Consensus        14 vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~Dt~R~ga~eQL~~~a~~l~   67 (211)
T d1j8yf2          14 VIMLVGVQGTGKATTAGKLAYFYKKKGFKVGLVGADVYRPAALEQLQQLGQQIG   67 (211)
T ss_dssp             EEEEECSCCC----HHHHHHHHHHHTTCCEEEEECCCSSHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEEeeccccchhHHHHHhccccC
Confidence            4667999999999885443333445566666554  248888888888877554

>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=92.72  E-value=0.075  Score=49.40  Aligned_cols=38  Identities=16%  Similarity=0.253  Sum_probs=29.0

Q ss_pred             CCCHHHHHHHHHHHcC--CcEEEEcCCCCcHHHHHHHHHH
Q psy2760         194 ELDVFQKQAIIKLEEH--NHVFVTAHTSAGKTVIAEYAIA  231 (333)
Q Consensus       194 ~l~~~Q~~ai~~l~~g--~~vlv~apTGSGKTl~~~l~il  231 (333)
                      .+.+.|.+.+..+...  --++++||||||||......+.
T Consensus       141 G~~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl~~~l~  180 (401)
T d1p9ra_         141 GMTAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTLYAGLQ  180 (401)
T ss_dssp             CCCHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHhhhhceEEEEcCCCCCccHHHHHHhh
Confidence            4688899888887433  3588999999999988655443

>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=92.64  E-value=0.1  Score=44.66  Aligned_cols=71  Identities=8%  Similarity=-0.057  Sum_probs=58.9

Q ss_pred             HHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC--cEEEeCCCCCC-----------CCcceEEecc---------Cc
Q psy2760         229 AIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD--VGLIDDLPPVF-----------PDVEKLLEDL---------NI  286 (333)
Q Consensus       229 ~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~--vglltGd~~~~-----------~~a~ili~t~---------~i  286 (333)
                      +|...+.+|.++.||+|..+-+......+++.|++  +++++|..+..           ...+++++|+         +.
T Consensus        23 ~I~~El~rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~TtvIEvGiDvpnA  102 (211)
T d2eyqa5          23 AILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTA  102 (211)
T ss_dssp             HHHHHHTTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESSTTGGGSCCTTE
T ss_pred             HHHHHHHcCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehhhhhccCCCCC
Confidence            45567789999999999999999999999999986  89999988753           4457999986         56


Q ss_pred             ceEeccccccccc
Q psy2760         287 GGLDELSIHDFNK  299 (333)
Q Consensus       287 ~liViDe~H~~~~  299 (333)
                      ..||+..++.|+-
T Consensus       103 ~~iiI~~a~rfGL  115 (211)
T d2eyqa5         103 NTIIIERADHFGL  115 (211)
T ss_dssp             EEEEETTTTSSCH
T ss_pred             cEEEEecchhccc
Confidence            7788888887753

>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=92.36  E-value=0.21  Score=46.57  Aligned_cols=67  Identities=27%  Similarity=0.270  Sum_probs=49.3

Q ss_pred             CCCHHHHHHHHH----HHcCC-cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHHHHHhcCC
Q psy2760         194 ELDVFQKQAIIK----LEEHN-HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD  263 (333)
Q Consensus       194 ~l~~~Q~~ai~~----l~~g~-~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~l~~~f~~  263 (333)
                      .|..-|-+||..    +..|. .+.+.|.+||+|+++..-. ...  .++.+++|+|+...|.++++.|+..+++
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~A~l-~~~--~~rp~LvVt~~~~~A~~l~~dL~~~l~~   79 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAKV-IEA--LGRPALVLAPNKILAAQLAAEFRELFPE   79 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHH-HHH--HTCCEEEEESSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHHHHH-HHH--hCCCEEEEeCCHHHHHHHHHHHHHhcCc
Confidence            456667666666    45555 4789999999999654322 222  2456899999999999999999987765

>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=92.13  E-value=0.041  Score=49.27  Aligned_cols=21  Identities=29%  Similarity=0.393  Sum_probs=18.5

Q ss_pred             cCCcEEEEcCCCCcHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l  228 (333)
                      ..++++++||||+|||+.+-.
T Consensus        48 ~~~~iLl~GPpG~GKT~lAka   68 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIARR   68 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHHHH
T ss_pred             CCceEEEECCCCCCHHHHHHH
Confidence            468999999999999999864

>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=91.96  E-value=0.033  Score=52.85  Aligned_cols=20  Identities=30%  Similarity=0.414  Sum_probs=18.0

Q ss_pred             CCcEEEEcCCCCcHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l  228 (333)
                      .+|+|+.||||+|||+.+--
T Consensus        49 ksNILliGPTGvGKTlLAr~   68 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIARR   68 (443)
T ss_dssp             CCCEEEECCTTSSHHHHHHH
T ss_pred             cccEEEECCCCCCHHHHHHH
Confidence            57999999999999999864

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {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: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=91.82  E-value=0.07  Score=43.53  Aligned_cols=34  Identities=29%  Similarity=0.259  Sum_probs=26.1

Q ss_pred             CcEEEEcC-CCCcHHHHHHHHHHHHhcCCCeEEEE
Q psy2760         210 NHVFVTAH-TSAGKTVIAEYAIALSQNHKTRTIYT  243 (333)
Q Consensus       210 ~~vlv~ap-TGSGKTl~~~l~il~~l~~g~ral~l  243 (333)
                      |.++|+|. ||.|||.+....+....+.|.|++++
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~G~rVl~i   36 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGY   36 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHCCCeEEEE
Confidence            45667666 79999999877665556778888886

>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=91.80  E-value=0.054  Score=41.56  Aligned_cols=22  Identities=23%  Similarity=0.427  Sum_probs=18.8

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      .+++++.||.|||||.++-...
T Consensus         2 ~k~I~l~G~~GsGKSTvak~La   23 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGRQLA   23 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHH
Confidence            4789999999999999887643

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

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: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=91.59  E-value=0.1  Score=44.86  Aligned_cols=39  Identities=10%  Similarity=0.078  Sum_probs=30.7

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHHHH-HhcCCCeEEEEcc
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAIAL-SQNHKTRTIYTSP  245 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~il~-~l~~g~ral~l~P  245 (333)
                      ..|.-+++.|+||+|||..+...+.. +...|.+++|++.
T Consensus        33 ~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~   72 (277)
T d1cr2a_          33 RGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAML   72 (277)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEES
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEeee
Confidence            34788999999999999777665554 4567889999874

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {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: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=90.92  E-value=0.11  Score=43.24  Aligned_cols=38  Identities=18%  Similarity=0.171  Sum_probs=27.7

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHh------cCCCeEEEEcc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQ------NHKTRTIYTSP  245 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l------~~g~ral~l~P  245 (333)
                      .|+-+++.||+|+|||..++.-+....      ..+.+++|+.-
T Consensus        35 ~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~   78 (254)
T d1pzna2          35 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDT   78 (254)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEES
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEec
Confidence            367899999999999999877655433      23566777643

>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=90.82  E-value=0.057  Score=42.55  Aligned_cols=22  Identities=27%  Similarity=0.410  Sum_probs=19.0

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      +.+++++||.|||||.++-...
T Consensus         5 ~~~I~i~G~~GsGKTT~~~~La   26 (174)
T d1y63a_           5 GINILITGTPGTGKTSMAEMIA   26 (174)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHHHHHH
Confidence            6789999999999999986644

>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=90.45  E-value=0.11  Score=43.43  Aligned_cols=37  Identities=11%  Similarity=0.120  Sum_probs=28.0

Q ss_pred             CCCHHHHHHHHHH----HcCC---cEEEEcCCCCcHHHHHHHHH
Q psy2760         194 ELDVFQKQAIIKL----EEHN---HVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       194 ~l~~~Q~~ai~~l----~~g~---~vlv~apTGSGKTl~~~l~i  230 (333)
                      .++|||..++..+    ..++   .++++||.|+|||.++..-+
T Consensus         2 ~~yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a   45 (207)
T d1a5ta2           2 RWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALS   45 (207)
T ss_dssp             CCCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHH
T ss_pred             CCCcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHH
Confidence            4578888887764    3443   48999999999999887644

>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=90.14  E-value=0.082  Score=48.66  Aligned_cols=20  Identities=25%  Similarity=0.521  Sum_probs=17.5

Q ss_pred             CCcEEEEcCCCCcHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l  228 (333)
                      -.|+|..||||+|||..+-.
T Consensus        68 ~~niLfiGPTGvGKTElAk~   87 (364)
T d1um8a_          68 KSNILLIGPTGSGKTLMAQT   87 (364)
T ss_dssp             CCCEEEECCTTSSHHHHHHH
T ss_pred             CcceeeeCCCCccHHHHHHH
Confidence            46899999999999999854

>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=90.11  E-value=0.23  Score=41.31  Aligned_cols=19  Identities=21%  Similarity=0.221  Sum_probs=17.0

Q ss_pred             CcEEEEcCCCCcHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l  228 (333)
                      .++++.||+|+|||.++-.
T Consensus        44 ~~lll~GppGtGKT~l~~~   62 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTLRK   62 (276)
T ss_dssp             CEEEEECCTTSSHHHHHHH
T ss_pred             CceEEECCCCCCHHHHHHH
Confidence            6899999999999988755

>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=90.07  E-value=0.28  Score=44.50  Aligned_cols=54  Identities=11%  Similarity=0.065  Sum_probs=41.3

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcC---------C---CeEEEEcccHHHHHHHHHHHHHhcC
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNH---------K---TRTIYTSPIKALSNQKYRDFRETFQ  262 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~---------g---~ral~l~PtraLa~Q~~~~l~~~f~  262 (333)
                      ..+++|.|+-|||||.+...-++..+..         +   .+++.|+=|+.=|.++.+++.+.++
T Consensus        16 ~g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~~L~   81 (485)
T d1w36b1          16 QGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNIH   81 (485)
T ss_dssp             SSCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHHHHH
Confidence            3578999999999999877766654421         1   2488999999989998888877654

>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=90.07  E-value=0.27  Score=41.34  Aligned_cols=46  Identities=20%  Similarity=0.307  Sum_probs=30.7

Q ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRD  256 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~~~~  256 (333)
                      ..++++||+|+|||.......-.....+.+++|+ +...+..+....
T Consensus        37 n~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~-~~~~~~~~~~~~   82 (213)
T d1l8qa2          37 NPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYS-SADDFAQAMVEH   82 (213)
T ss_dssp             SSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEE-EHHHHHHHHHHH
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHhccCccceEEe-chHHHHHHHHHH
Confidence            3489999999999977655444455566777775 455555554443

>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=89.81  E-value=0.074  Score=41.82  Aligned_cols=22  Identities=32%  Similarity=0.493  Sum_probs=18.5

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~  229 (333)
                      .|+-+++.||+|||||.++...
T Consensus         3 ~g~iI~l~G~~GsGKSTia~~L   24 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIAEAL   24 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHH
Confidence            4778899999999999987543

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-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: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=89.53  E-value=0.18  Score=44.28  Aligned_cols=41  Identities=24%  Similarity=0.230  Sum_probs=33.4

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKAL  249 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraL  249 (333)
                      |+-+.+.+|+|+|||..++..+..+...+.+++|+--.-++
T Consensus        54 g~itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyidtE~~~   94 (263)
T d1u94a1          54 GRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHAL   94 (263)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCC
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEEcccccc
Confidence            67889999999999999999888777778888887543333

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {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: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=89.47  E-value=0.19  Score=39.05  Aligned_cols=35  Identities=17%  Similarity=0.098  Sum_probs=26.1

Q ss_pred             cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcc
Q psy2760         211 HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSP  245 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~P  245 (333)
                      -+.++|+.|||||......+-....+|.++.++..
T Consensus         4 vi~itG~~GSGKTTL~~~L~~~l~~~g~~v~v~~~   38 (170)
T d1np6a_           4 LLAFAAWSGTGKTTLLKKLIPALCARGIRPGLIKH   38 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEecc
Confidence            36789999999999877666555566777776643

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

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: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=89.41  E-value=0.16  Score=41.42  Aligned_cols=38  Identities=11%  Similarity=0.114  Sum_probs=28.1

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHH-HHhcCCCeEEEEcc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIA-LSQNHKTRTIYTSP  245 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il-~~l~~g~ral~l~P  245 (333)
                      .|.-+++.|++|+|||..+.--+. .....+.+++|+..
T Consensus        25 ~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s~   63 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTF   63 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEES
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCcccccc
Confidence            378899999999999988765333 34455567888764

>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=89.40  E-value=0.062  Score=42.12  Aligned_cols=21  Identities=24%  Similarity=0.321  Sum_probs=18.0

Q ss_pred             CCcEEEEcCCCCcHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~  229 (333)
                      -+.+++.||+|||||..+-..
T Consensus         7 ~K~I~i~G~~GsGKTTla~~L   27 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKL   27 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHH
Confidence            368999999999999988653

>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=89.34  E-value=0.26  Score=41.44  Aligned_cols=24  Identities=25%  Similarity=0.285  Sum_probs=19.3

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIA  231 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il  231 (333)
                      ...|+++.|+.|.|||.+....+.
T Consensus        42 ~k~n~lLvG~pGVGKTalv~~LA~   65 (195)
T d1jbka_          42 TKNNPVLIGEPGVGKTAIVEGLAQ   65 (195)
T ss_dssp             SSCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCCCeEEEecCCcccHHHHHHHHH
Confidence            445999999999999998765443

>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=89.01  E-value=0.11  Score=40.45  Aligned_cols=21  Identities=19%  Similarity=0.360  Sum_probs=17.6

Q ss_pred             CcEEEEcCCCCcHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~i  230 (333)
                      .+++++||.|||||.++....
T Consensus         5 ~~I~i~G~pGsGKTTia~~La   25 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELA   25 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHH
Confidence            578999999999999876543

>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=88.93  E-value=0.088  Score=40.86  Aligned_cols=20  Identities=15%  Similarity=0.240  Sum_probs=16.6

Q ss_pred             CcEEEEcCCCCcHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~  229 (333)
                      +-++++||+|||||.++-..
T Consensus         3 klI~i~G~~GsGKTTva~~L   22 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRL   22 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHH
Confidence            45789999999999997543

>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=88.84  E-value=0.09  Score=40.58  Aligned_cols=19  Identities=16%  Similarity=0.239  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCCcHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l  228 (333)
                      +-++++|++|||||..+-.
T Consensus         3 klIii~G~pGsGKTTla~~   21 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWARE   21 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHH
Confidence            3478899999999998653

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {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: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.71  E-value=0.13  Score=42.21  Aligned_cols=37  Identities=11%  Similarity=0.137  Sum_probs=27.1

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHHh------cCCCeEEEEc
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALSQ------NHKTRTIYTS  244 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~l------~~g~ral~l~  244 (333)
                      .|+-+++.||+|+|||..++-.+..+.      ..+..++|+.
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~   75 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYID   75 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEE
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEe
Confidence            468999999999999998876544322      2356778874

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

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: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=88.66  E-value=0.22  Score=38.95  Aligned_cols=23  Identities=26%  Similarity=0.339  Sum_probs=18.4

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIA  231 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il  231 (333)
                      ++-+++.|+.|||||..+-...-
T Consensus         1 ~kiI~i~G~~GsGKsT~~~~L~~   23 (190)
T d1khta_           1 NKVVVVTGVPGVGSTTSSQLAMD   23 (190)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            36689999999999998765443

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {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: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=88.60  E-value=0.31  Score=41.94  Aligned_cols=23  Identities=26%  Similarity=0.387  Sum_probs=19.4

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~  229 (333)
                      ..+..|++.|++|+|||.++-..
T Consensus        21 ~~~~pvlI~Ge~GtGK~~~A~~i   43 (247)
T d1ny5a2          21 CAECPVLITGESGVGKEVVARLI   43 (247)
T ss_dssp             TCCSCEEEECSTTSSHHHHHHHH
T ss_pred             CCCCCEEEECCCCcCHHHHHHHH
Confidence            56789999999999999877543

>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=88.21  E-value=0.14  Score=42.95  Aligned_cols=21  Identities=29%  Similarity=0.482  Sum_probs=17.9

Q ss_pred             CcEEEEcCCCCcHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~i  230 (333)
                      .+++++||+|+|||.++-..+
T Consensus        36 ~~~L~~GPpGtGKT~lA~~la   56 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLAHIIA   56 (238)
T ss_dssp             CCEEEESSTTSSHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHH
Confidence            479999999999999886543

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic 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: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.92  E-value=0.17  Score=39.99  Aligned_cols=26  Identities=15%  Similarity=0.034  Sum_probs=21.1

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAIALS  233 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~il~~  233 (333)
                      .|+-+++.||+|+|||..++-.+...
T Consensus        22 ~G~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHHH
Confidence            37889999999999999887655543

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=87.41  E-value=0.13  Score=40.10  Aligned_cols=22  Identities=23%  Similarity=0.320  Sum_probs=18.3

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~  229 (333)
                      +.+-|+++|+.|||||.++...
T Consensus         2 ~~kiI~l~G~~GsGKsTva~~L   23 (178)
T d1qhxa_           2 TTRMIILNGGSSAGKSGIVRCL   23 (178)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHH
Confidence            3567899999999999988653

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=87.38  E-value=0.1  Score=43.98  Aligned_cols=19  Identities=16%  Similarity=0.305  Sum_probs=16.2

Q ss_pred             CcEEEEcCCCCcHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l  228 (333)
                      +.++++||+|+|||..+-.
T Consensus        33 ~~ilL~GpPGtGKT~la~~   51 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSLRSA   51 (273)
T ss_dssp             EEEEEECCTTSCTHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHH
Confidence            4599999999999998753

>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=86.99  E-value=0.13  Score=40.18  Aligned_cols=24  Identities=25%  Similarity=0.311  Sum_probs=19.6

Q ss_pred             HcCCcEEEEcCCCCcHHHHHHHHH
Q psy2760         207 EEHNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       207 ~~g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      .+|..|+++|+.|||||.++-...
T Consensus         4 ~~g~~I~l~G~~GsGKTTia~~La   27 (183)
T d1m8pa3           4 TQGFTIFLTGYMNSGKDAIARALQ   27 (183)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHH
Confidence            357789999999999999986543

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {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: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.55  E-value=0.39  Score=39.55  Aligned_cols=51  Identities=14%  Similarity=0.155  Sum_probs=33.6

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhc------CCCeEEEEcccHHHHHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQN------HKTRTIYTSPIKALSNQKYRDFRE  259 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~------~g~ral~l~PtraLa~Q~~~~l~~  259 (333)
                      |+-++++|++|+|||..++.-+.....      .+..++++.....+..+....+..
T Consensus        37 G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (258)
T d1v5wa_          37 MAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIAD   93 (258)
T ss_dssp             SEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHHHHHHHHh
Confidence            778999999999999998876654332      234567666554444444444433

>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=86.51  E-value=0.17  Score=42.39  Aligned_cols=20  Identities=25%  Similarity=0.418  Sum_probs=17.4

Q ss_pred             CcEEEEcCCCCcHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~  229 (333)
                      .+++++||+|+|||.++..-
T Consensus        36 ~~~Ll~GPpG~GKTtla~~l   55 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLAHVI   55 (239)
T ss_dssp             CCEEEECCTTSCHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHH
Confidence            58999999999999888653

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {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: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=86.19  E-value=0.36  Score=42.45  Aligned_cols=45  Identities=22%  Similarity=0.179  Sum_probs=36.0

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQK  253 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa~Q~  253 (333)
                      |+-..+.+|.|+|||..++..+..+...+.+++|+--..++..+.
T Consensus        60 g~i~e~~G~~~~GKT~l~l~~~~~~q~~g~~~vyIDtE~~~~~e~  104 (269)
T d1mo6a1          60 GRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDY  104 (269)
T ss_dssp             SSEEEEECSSSSSHHHHHHHHHHHHHHTTCEEEEEESSCCCCHHH
T ss_pred             ceeEEEecCCCcHHHHHHHHHHHHHhcCCCEEEEEECCccCCHHH
Confidence            788999999999999999888887777788888876555554443

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

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: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=85.88  E-value=0.39  Score=42.11  Aligned_cols=42  Identities=21%  Similarity=0.175  Sum_probs=33.6

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEEcccHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALS  250 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l~PtraLa  250 (333)
                      |+-..+.+|.|||||..++..+..+...|.+++|+=-..++.
T Consensus        57 g~itei~G~~~sGKT~l~l~~~~~aqk~g~~v~yiDtE~~~~   98 (268)
T d1xp8a1          57 GRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHALD   98 (268)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCC
T ss_pred             ceEEEEecCCccchHHHHHHHHHHHHhCCCEEEEEECCccCC
Confidence            678899999999999999888877777788888875443333

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {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: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=85.66  E-value=0.41  Score=37.86  Aligned_cols=19  Identities=21%  Similarity=0.254  Sum_probs=15.4

Q ss_pred             EEEEcCCCCcHHHHHHHHH
Q psy2760         212 VFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       212 vlv~apTGSGKTl~~~l~i  230 (333)
                      |.|+||+|||||.++-...
T Consensus        25 IgI~G~~GSGKSTla~~L~   43 (198)
T d1rz3a_          25 LGIDGLSRSGKTTLANQLS   43 (198)
T ss_dssp             EEEEECTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            4489999999999886543

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

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: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=85.36  E-value=0.16  Score=41.54  Aligned_cols=25  Identities=16%  Similarity=0.036  Sum_probs=21.2

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAIALS  233 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~il~~  233 (333)
                      |.-+++.|++|+|||..++-.+...
T Consensus        34 G~l~~i~G~~G~GKT~~~l~~a~~~   58 (258)
T d2i1qa2          34 QSVTEFAGVFGSGKTQIMHQSCVNL   58 (258)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            6789999999999999988766644

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

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: Campylobacter jejuni [TaxId: 197]

Probab=85.19  E-value=0.2  Score=39.77  Aligned_cols=20  Identities=15%  Similarity=0.326  Sum_probs=17.3

Q ss_pred             CcEEEEcCCCCcHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~  229 (333)
                      +++++.|+.|||||.++-..
T Consensus         1 k~I~liG~~GsGKsTi~k~L   20 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTLARAL   20 (161)
T ss_dssp             CCEEEECCTTSCHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHH
Confidence            57899999999999998654

>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=84.92  E-value=0.24  Score=41.19  Aligned_cols=20  Identities=25%  Similarity=0.290  Sum_probs=17.1

Q ss_pred             CcEEEEcCCCCcHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~  229 (333)
                      .+++++||+|+|||.++...
T Consensus        46 ~~lll~Gp~G~GKTtla~~i   65 (231)
T d1iqpa2          46 PHLLFAGPPGVGKTTAALAL   65 (231)
T ss_dssp             CEEEEESCTTSSHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHH
Confidence            47999999999999887653

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {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: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=84.55  E-value=0.2  Score=39.13  Aligned_cols=21  Identities=19%  Similarity=0.338  Sum_probs=17.2

Q ss_pred             CCcEEEEcCCCCcHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~  229 (333)
                      ++-++++||.|||||.++-..
T Consensus         6 ~~iivl~G~~GsGKsT~a~~L   26 (171)
T d1knqa_           6 HHIYVLMGVSGSGKSAVASEV   26 (171)
T ss_dssp             SEEEEEECSTTSCHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHH
Confidence            445788999999999998763

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

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: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=84.52  E-value=0.48  Score=37.03  Aligned_cols=33  Identities=15%  Similarity=0.120  Sum_probs=22.1

Q ss_pred             cEEEEcCCCCcHHHHHHHHHHHHhcCCCeEEEE
Q psy2760         211 HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYT  243 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~il~~l~~g~ral~l  243 (333)
                      -+++.|+.|||||.++-...-....++..+..+
T Consensus         3 iivi~G~~GsGKTT~~~~La~~L~~~~~~~~~~   35 (194)
T d1nksa_           3 IGIVTGIPGVGKSTVLAKVKEILDNQGINNKII   35 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEE
Confidence            367899999999998866543333445555444

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

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: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=84.11  E-value=0.19  Score=43.33  Aligned_cols=19  Identities=26%  Similarity=0.363  Sum_probs=16.6

Q ss_pred             CcEEEEcCCCCcHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l  228 (333)
                      +.+|++||+|+|||.++-.
T Consensus        41 ~~vLL~GppGtGKT~la~a   59 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALAAK   59 (246)
T ss_dssp             EEEEEECSTTSSHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHH
Confidence            4699999999999998765

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {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 C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=84.05  E-value=0.29  Score=40.98  Aligned_cols=19  Identities=21%  Similarity=0.256  Sum_probs=16.7

Q ss_pred             CcEEEEcCCCCcHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l  228 (333)
                      ++++++||+|+|||.++..
T Consensus        53 ~~lll~GPpG~GKTt~a~~   71 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTAAHL   71 (253)
T ss_dssp             SEEEEECSTTSSHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            5799999999999988764

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

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: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=83.86  E-value=0.34  Score=39.01  Aligned_cols=22  Identities=18%  Similarity=0.072  Sum_probs=18.7

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      |..+++.||+|||||..+-...
T Consensus         3 ~~riil~G~pGSGKsT~a~~La   24 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQAPKLA   24 (190)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHH
Confidence            6788899999999999987643

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {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: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.42  E-value=0.34  Score=39.34  Aligned_cols=21  Identities=10%  Similarity=0.330  Sum_probs=17.7

Q ss_pred             CcEEEEcCCCCcHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~i  230 (333)
                      +.++++||+|||||.+.-..+
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~   22 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLF   22 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHH
Confidence            578999999999999876544

>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=83.25  E-value=0.32  Score=40.14  Aligned_cols=21  Identities=19%  Similarity=0.169  Sum_probs=17.2

Q ss_pred             CcEEEEcCCCCcHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~i  230 (333)
                      .+++++||+|+|||..+...+
T Consensus        34 ~~lll~Gp~G~GKTtl~~~i~   54 (237)
T d1sxjd2          34 PHMLFYGPPGTGKTSTILALT   54 (237)
T ss_dssp             CCEEEECSTTSSHHHHHHHHH
T ss_pred             CeEEEECCCCCChHHHHHHHH
Confidence            368999999999998776544

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {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: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.10  E-value=0.34  Score=38.41  Aligned_cols=22  Identities=27%  Similarity=0.291  Sum_probs=18.5

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      |..++++|+.|||||.++-...
T Consensus        19 g~vI~L~G~pGSGKTTiAk~La   40 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSMALE   40 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHH
Confidence            5678899999999999987644

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {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: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=82.46  E-value=0.39  Score=37.95  Aligned_cols=19  Identities=26%  Similarity=0.277  Sum_probs=16.6

Q ss_pred             cEEEEcCCCCcHHHHHHHH
Q psy2760         211 HVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~  229 (333)
                      ++++.||.|||||..+...
T Consensus         2 ~I~i~G~pGSGKsT~a~~L   20 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAEKI   20 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            5899999999999998653

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {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: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=82.08  E-value=0.43  Score=38.27  Aligned_cols=22  Identities=14%  Similarity=0.253  Sum_probs=18.5

Q ss_pred             CCcEEEEcCCCCcHHHHHHHHH
Q psy2760         209 HNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       209 g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      |+-++++||.|||||.+.-..+
T Consensus         2 G~iivl~GpsG~GK~tl~~~L~   23 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTVVRCLR   23 (182)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHH
Confidence            6789999999999999875543

>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=82.05  E-value=0.37  Score=39.73  Aligned_cols=35  Identities=17%  Similarity=0.152  Sum_probs=23.6

Q ss_pred             CHHHHHHHHHH-HcCC--cEEEEcCCCCcHHHHHHHHH
Q psy2760         196 DVFQKQAIIKL-EEHN--HVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       196 ~~~Q~~ai~~l-~~g~--~vlv~apTGSGKTl~~~l~i  230 (333)
                      .+...+.+..+ ..++  +++++||+|+|||.++...+
T Consensus        19 ~~~~~~~L~~~i~~~~~~~lLl~Gp~G~GKttl~~~la   56 (227)
T d1sxjc2          19 QNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALA   56 (227)
T ss_dssp             CHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEECCCCCChhHHHHHHH
Confidence            34445555553 3343  68999999999998776543

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {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: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=81.55  E-value=0.44  Score=37.31  Aligned_cols=18  Identities=22%  Similarity=0.484  Sum_probs=15.1

Q ss_pred             cEEEEcCCCCcHHHHHHH
Q psy2760         211 HVFVTAHTSAGKTVIAEY  228 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l  228 (333)
                      .+++.||+|+|||.....
T Consensus         2 ki~I~G~~G~GKSTLl~~   19 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLVKK   19 (178)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             EEEEECCCCcHHHHHHHH
Confidence            589999999999997533

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

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: Maize (Zea mays) [TaxId: 4577]

Probab=81.45  E-value=0.39  Score=38.65  Aligned_cols=20  Identities=20%  Similarity=0.323  Sum_probs=17.1

Q ss_pred             CcEEEEcCCCCcHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYA  229 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~  229 (333)
                      ..+++.||.|||||..+...
T Consensus         4 m~I~i~GppGsGKsT~a~~L   23 (189)
T d1zaka1           4 LKVMISGAPASGKGTQCELI   23 (189)
T ss_dssp             CCEEEEESTTSSHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHH
Confidence            46899999999999988653

>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=81.28  E-value=0.42  Score=39.52  Aligned_cols=32  Identities=13%  Similarity=0.268  Sum_probs=22.0

Q ss_pred             HHHHHHHH-HcC--CcEEEEcCCCCcHHHHHHHHH
Q psy2760         199 QKQAIIKL-EEH--NHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       199 Q~~ai~~l-~~g--~~vlv~apTGSGKTl~~~l~i  230 (333)
                      ..+.+..+ ..+  .+++++||.|+|||.++...+
T Consensus        23 ~~~~L~~~~~~~~~~~~ll~Gp~G~GKTt~a~~la   57 (224)
T d1sxjb2          23 TIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLA   57 (224)
T ss_dssp             HHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCeEEEECCCCCCchhhHHHHH
Confidence            33444443 344  378999999999999886544

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {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: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=81.04  E-value=0.46  Score=38.70  Aligned_cols=21  Identities=19%  Similarity=0.343  Sum_probs=17.2

Q ss_pred             CcEEEEcCCCCcHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~i  230 (333)
                      +.++++||+|||||.++-..+
T Consensus         1 rpIvl~GPsGsGK~tl~~~L~   21 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTLLKKLF   21 (190)
T ss_dssp             CCEEEECCTTSSHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHH
Confidence            468999999999999876543

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {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: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.82  E-value=0.35  Score=39.05  Aligned_cols=18  Identities=22%  Similarity=0.353  Sum_probs=15.2

Q ss_pred             CcEEEEcCCCCcHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAE  227 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~  227 (333)
                      .-++++|++|||||..+.
T Consensus        15 ~liil~G~pGsGKST~a~   32 (172)
T d1yj5a2          15 EVVVAVGFPGAGKSTFIQ   32 (172)
T ss_dssp             CEEEEECCTTSSHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHH
Confidence            467889999999998764

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

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: Erwinia chrysanthemi [TaxId: 556]

Probab=80.63  E-value=0.5  Score=37.40  Aligned_cols=21  Identities=14%  Similarity=0.302  Sum_probs=17.8

Q ss_pred             CcEEEEcCCCCcHHHHHHHHH
Q psy2760         210 NHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       210 ~~vlv~apTGSGKTl~~~l~i  230 (333)
                      +.+++.|+.|||||.++-...
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA   23 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELA   23 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHH
Confidence            678899999999999887644

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {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: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=80.43  E-value=0.5  Score=37.55  Aligned_cols=20  Identities=20%  Similarity=0.403  Sum_probs=16.8

Q ss_pred             cEEEEcCCCCcHHHHHHHHH
Q psy2760         211 HVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~i  230 (333)
                      ++++.||.|||||..+....
T Consensus         2 ~I~i~G~pGSGKsT~~~~La   21 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIM   21 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            68899999999999986543

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {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: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=80.17  E-value=0.54  Score=39.16  Aligned_cols=23  Identities=22%  Similarity=0.330  Sum_probs=19.2

Q ss_pred             cCCcEEEEcCCCCcHHHHHHHHH
Q psy2760         208 EHNHVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       208 ~g~~vlv~apTGSGKTl~~~l~i  230 (333)
                      +|+-++++||+|+|||.+.-..+
T Consensus         1 ~G~livi~GPSG~GK~tl~~~L~   23 (205)
T d1s96a_           1 QGTLYIVSAPSGAGKSSLIQALL   23 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHH
Confidence            47889999999999999876543

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

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: Bacillus globisporus [TaxId: 1459]

Probab=80.16  E-value=0.52  Score=37.59  Aligned_cols=20  Identities=20%  Similarity=0.326  Sum_probs=16.9

Q ss_pred             cEEEEcCCCCcHHHHHHHHH
Q psy2760         211 HVFVTAHTSAGKTVIAEYAI  230 (333)
Q Consensus       211 ~vlv~apTGSGKTl~~~l~i  230 (333)
                      .+++.||+|||||..+....
T Consensus         2 ~I~i~G~pGSGKsT~a~~La   21 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIV   21 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            58899999999999886543