Citrus Sinensis ID: 042424

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------14
Protein Sequence
MEESQTPGKRKAPKADSHVRGTPKEESTKKQRNPTRSCVHEVAVPSCYTLTTDETTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRGMLY
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccEEccccccEEEEccccccHHHHHHHHHHHHHHcccEEEEcccHHHHHHHHHHHHHHHcccccccccccEEcccccEEEEEHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccccccccccHHHHHEcccccccccccccccccccccccccccHHEEEEEccccEEEEEcccccHHHHHHHHHHHHHHcccEEEEEcHHHHHHHHHHHHHHHHHcccEEEcccEEEcccccEEEEHHHHHHHHcc
Coil and Loop (DISEMBL)
meesqtpgkrkapkadshvrgtpkeestkkqrnptrscvhevavpscytlttdetthgtltnpvyngkTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKdvglmtgdvtlspnascLVMTTEILRGMLY
Flexible Loop (DISEMBL)
meesqtpgkrkapkadshvrgtpkeestkkqrnptrscvhevaVPSCYTlttdetthgtltnpvyngKTAVAEYAIAMAFRDKQRVIYTSSlkalsnqkYRELHKEFKDVGlmtgdvtlspnasclvmtteilrgmly
Low Complexity Region (SEG)
MEESQTPGKRKAPKADSHVRGTPKEESTKKQRNPTRSCVHEVAVPSCYtlttdetthgtltNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRGMLY
Disordered region (IsUnstruct)
*************************************CVHEVAVPSCYTLTTDETTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILR****
Disordered Region (DISOPRED)
*********************************PTRSCVHEVAVPSCYTLTTDETTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRGMLY
Disordered Region (DISEMBL)
*************************************CVHEVAVPSCYTLTTDETTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRGMLY
Disordered Region (DISPRO)
****************SHVRGTPKEESTKKQRNPTRSCVHEVAVPSCYTLTTDETTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRGMLY
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEESQTPGKRKAPKADSHVRGTPKEESTKKQRNPTRSCVHEVAVPSCYTLTTDETTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRGMLY
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	138	2.2.26 [Sep-21-2011]
O14232	1117	ATP-dependent RNA helicas	yes	no	0.521	0.064	0.791	4e-28
P42285	1042	Superkiller viralicidic a	yes	no	0.521	0.069	0.777	4e-28
Q9CZU3	1040	Superkiller viralicidic a	yes	no	0.521	0.069	0.777	5e-28
Q23223	1026	mRNA transport homolog 4	yes	no	0.775	0.104	0.511	1e-27
P47047	1073	ATP-dependent RNA helicas	yes	no	0.521	0.067	0.763	7e-26
O13799	1030	Uncharacterized helicase	no	no	0.521	0.069	0.736	1e-25
Q15477	1246	Helicase SKI2W OS=Homo sa	no	no	0.521	0.057	0.680	2e-22
P35207	1287	Antiviral helicase SKI2 O	no	no	0.521	0.055	0.648	1e-20
O59801	1213	Putative ATP-dependent RN	no	no	0.521	0.059	0.625	2e-20
B9DFG3	1171	DEAD-box ATP-dependent RN	no	no	0.572	0.067	0.481	3e-14

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

 Score =  123 bits (308), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 57/72 (79%), Positives = 64/72 (88%)

Query: 67  GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
           GKT VAEYA+A + RDKQRVIYTS +KALSNQKYREL  EF DVGLMTGDVT++P+A+CL
Sbjct: 225 GKTVVAEYAVAQSLRDKQRVIYTSPIKALSNQKYRELLAEFGDVGLMTGDVTINPDATCL 284

Query: 127 VMTTEILRGMLY 138
           VMTTEILR MLY
Sbjct: 285 VMTTEILRSMLY 296

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: 3EC: .EC: 6EC: .EC: 4EC: .EC: -

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

 Score =  122 bits (307), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 56/72 (77%), Positives = 66/72 (91%)

Query: 67  GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
           GKT  AEYAIA+A R+KQRVI+TS +KALSNQKYRE+++EF+DVGLMTGDVT++P ASCL
Sbjct: 166 GKTVCAEYAIALALREKQRVIFTSPIKALSNQKYREMYEEFQDVGLMTGDVTINPTASCL 225

Query: 127 VMTTEILRGMLY 138
           VMTTEILR MLY
Sbjct: 226 VMTTEILRSMLY 237

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 =  122 bits (307), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 56/72 (77%), Positives = 66/72 (91%)

Query: 67  GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
           GKT  AEYAIA+A R+KQRVI+TS +KALSNQKYRE+++EF+DVGLMTGDVT++P ASCL
Sbjct: 164 GKTVCAEYAIALALREKQRVIFTSPIKALSNQKYREMYEEFQDVGLMTGDVTINPTASCL 223

Query: 127 VMTTEILRGMLY 138
           VMTTEILR MLY
Sbjct: 224 VMTTEILRSMLY 235

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

 Score =  121 bits (304), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 69/135 (51%), Positives = 76/135 (56%), Gaps = 28/135 (20%)

Query: 32  RNPTRSCVHEVAVPSCYTLTTDETTHGTLTNPVY-------------------------- 65
           R    +C HEVA+P            GT     Y                          
Sbjct: 89  RTDNENCTHEVAIPPNAEFAELRENSGTEPAKYYPFQLDAFQKQAILCIDNNQSVLVSAH 148

Query: 66  --NGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNA 123
              GKT VA YAIA   R+KQRVIYTS +KALSNQKYREL +EFKDVGLMTGDVTL+P+A
Sbjct: 149 TSAGKTVVATYAIAKCLREKQRVIYTSPIKALSNQKYRELEEEFKDVGLMTGDVTLNPDA 208

Query: 124 SCLVMTTEILRGMLY 138
           SCLVMTTEILR MLY
Sbjct: 209 SCLVMTTEILRSMLY 223

Caenorhabditis elegans (taxid: 6239)

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 =  115 bits (288), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 55/72 (76%), Positives = 63/72 (87%)

Query: 67  GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
           GKT VAEYAIA + ++KQRVIYTS +KALSNQKYREL  EF DVGLMTGD+T++P+A CL
Sbjct: 176 GKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCL 235

Query: 127 VMTTEILRGMLY 138
           VMTTEILR MLY
Sbjct: 236 VMTTEILRSMLY 247

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 =  114 bits (286), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 53/72 (73%), Positives = 64/72 (88%)

Query: 67  GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
           GKT +AEYAIA A +++QRVIYTS +K+LSNQKYREL  EF DVGLMTGDV+++P+ASCL
Sbjct: 152 GKTVIAEYAIAQALKNRQRVIYTSPIKSLSNQKYRELLSEFGDVGLMTGDVSINPSASCL 211

Query: 127 VMTTEILRGMLY 138
           +MTTEILR MLY
Sbjct: 212 IMTTEILRAMLY 223

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

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

 Score =  104 bits (259), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 49/72 (68%), Positives = 56/72 (77%)

Query: 67  GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
           GKT VAEYAIA+A +   R IYTS +KALSNQK+R+    F DVGL+TGDV L P ASCL
Sbjct: 337 GKTVVAEYAIALAQKHMTRTIYTSPIKALSNQKFRDFRNTFGDVGLLTGDVQLHPEASCL 396

Query: 127 VMTTEILRGMLY 138
           +MTTEILR MLY
Sbjct: 397 IMTTEILRSMLY 408

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: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

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

 Score = 98.2 bits (243), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 48/74 (64%), Positives = 60/74 (81%), Gaps = 2/74 (2%)

Query: 67  GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDV--GLMTGDVTLSPNAS 124
           GKT VAEYAIAMA R+  + IYTS +KALSNQK+R+  + F DV  GL+TGDV ++P+A+
Sbjct: 356 GKTVVAEYAIAMAHRNMTKTIYTSPIKALSNQKFRDFKETFDDVNIGLITGDVQINPDAN 415

Query: 125 CLVMTTEILRGMLY 138
           CL+MTTEILR MLY
Sbjct: 416 CLIMTTEILRSMLY 429

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 = 97.8 bits (242), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 45/72 (62%), Positives = 58/72 (80%)

Query: 67  GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
           GKT VAEYAIA+A +   + IYTS +KALSNQK+R+   +F+DVG++TGDV ++P  SCL
Sbjct: 307 GKTVVAEYAIALAQKHMTKAIYTSPIKALSNQKFRDFKHKFEDVGILTGDVQVNPEGSCL 366

Query: 127 VMTTEILRGMLY 138
           +MTTEILR MLY
Sbjct: 367 LMTTEILRSMLY 378

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

 Score = 77.0 bits (188), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 39/81 (48%), Positives = 54/81 (66%), Gaps = 2/81 (2%)

Query: 60  LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKD--VGLMTGDV 117
           ++ P  +GKT +AE A        +R+ YT+ LKALSNQK+RE  + F D  VGL+TGD 
Sbjct: 174 VSAPTSSGKTLIAEAAAVSTVAKGRRLFYTTPLKALSNQKFREFRETFGDDNVGLLTGDS 233

Query: 118 TLSPNASCLVMTTEILRGMLY 138
            ++ +A  ++MTTEILR MLY
Sbjct: 234 AINKDAQIVIMTTEILRNMLY 254

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	138
359484919	995	PREDICTED: superkiller viralicidic activ	1.0	0.138	0.628	5e-51
147792354	836	hypothetical protein VITISV_043093 [Viti	1.0	0.165	0.628	7e-51
255581147	962	helicase, putative [Ricinus communis] gi	0.971	0.139	0.6	1e-47
297831726	984	HUA enhancer 2 [Arabidopsis lyrata subsp	1.0	0.140	0.597	7e-47
18396436	995	RNA helicase, ATP-dependent, SK12/DOB1 p	0.992	0.137	0.596	2e-45
16024936	991	HUA enhancer 2 [Arabidopsis thaliana]	0.992	0.138	0.596	3e-45
449470374	1014	PREDICTED: superkiller viralicidic activ	1.0	0.136	0.535	3e-45
449527177	865	PREDICTED: superkiller viralicidic activ	1.0	0.159	0.535	4e-45
356513235	982	PREDICTED: LOW QUALITY PROTEIN: superkil	0.978	0.137	0.572	1e-42
357520641	984	ATP-dependent RNA helicase DOB1 [Medicag	0.992	0.139	0.560	1e-42

>gi|359484919|ref|XP_002266524.2| PREDICTED: superkiller viralicidic activity 2-like 2-like [Vitis vinifera]

 Score =  205 bits (521), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 110/175 (62%), Positives = 119/175 (68%), Gaps = 37/175 (21%)

Query: 1   MEESQTPGKRKAPKADSHVRGTPK-EESTKKQRNPTRSCVHEVAVPSCYTLTTDETTHGT 59
           MEES T GKRK P+ +S V+ TPK EES  K+RN TR+CVHE AVP  YT   DE+ HGT
Sbjct: 1   MEESPTLGKRKLPEENSEVKQTPKQEESASKRRNLTRTCVHEAAVPVGYTSNKDESVHGT 60

Query: 60  LTNPVYNGK------------------------------------TAVAEYAIAMAFRDK 83
           L+NPVYNGK                                    TAVAEY+IAMAFRDK
Sbjct: 61  LSNPVYNGKMAKTYPFTLDPFQQVSVACLERNESVLVSAHTSAGKTAVAEYSIAMAFRDK 120

Query: 84  QRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRGMLY 138
           QRVIYTS LKALSNQKYREL +EF DVGLMTGDVTLSPNASCLVMTTEILRGMLY
Sbjct: 121 QRVIYTSPLKALSNQKYRELSQEFSDVGLMTGDVTLSPNASCLVMTTEILRGMLY 175

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147792354|emb|CAN65767.1| hypothetical protein VITISV_043093 [Vitis vinifera]

 Score =  204 bits (520), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 110/175 (62%), Positives = 118/175 (67%), Gaps = 37/175 (21%)

Query: 1   MEESQTPGKRKAPKADSHVRGTPK-EESTKKQRNPTRSCVHEVAVPSCYTLTTDETTHGT 59
           MEES T GKRK P  +S V+ TPK EES  K+RN TR+CVHE AVP  YT   DE+ HGT
Sbjct: 39  MEESPTLGKRKLPXENSEVKQTPKQEESASKRRNLTRTCVHEAAVPVGYTSNKDESVHGT 98

Query: 60  LTNPVYNGK------------------------------------TAVAEYAIAMAFRDK 83
           L+NPVYNGK                                    TAVAEY+IAMAFRDK
Sbjct: 99  LSNPVYNGKMAKTYPFTLDPFQQVSVACLERNESVLVSAHTSAGKTAVAEYSIAMAFRDK 158

Query: 84  QRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRGMLY 138
           QRVIYTS LKALSNQKYREL +EF DVGLMTGDVTLSPNASCLVMTTEILRGMLY
Sbjct: 159 QRVIYTSPLKALSNQKYRELSQEFSDVGLMTGDVTLSPNASCLVMTTEILRGMLY 213

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255581147|ref|XP_002531387.1| helicase, putative [Ricinus communis] gi|223529017|gb|EEF31007.1| helicase, putative [Ricinus communis]

 Score =  194 bits (492), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 105/175 (60%), Positives = 119/175 (68%), Gaps = 41/175 (23%)

Query: 1   MEESQTPG-KRKAPKADSHVRGTPKEESTKKQRNPTRSCVHEVAVPSCYTLTTDETTHGT 59
           MEES TP  KRK    ++ +  TP++ES +K+RN TR+CVHEVAVP  Y  T +E+ HGT
Sbjct: 1   MEESPTPTVKRK----ETEIGDTPQQESAQKRRNLTRTCVHEVAVPIGYVSTKEESIHGT 56

Query: 60  LTNPVYNG------------------------------------KTAVAEYAIAMAFRDK 83
           L+NP +NG                                    KTAVAEYAIAMAFRDK
Sbjct: 57  LSNPEFNGDNAKTYPFELDPFQKVSVACLERNESVLVSAHTSAGKTAVAEYAIAMAFRDK 116

Query: 84  QRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRGMLY 138
           QRVIYTS LKALSNQKYRELH+EF+DVGLMTGDVTLSPNASCLVMTTEILRGMLY
Sbjct: 117 QRVIYTSPLKALSNQKYRELHQEFQDVGLMTGDVTLSPNASCLVMTTEILRGMLY 171

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297831726|ref|XP_002883745.1| HUA enhancer 2 [Arabidopsis lyrata subsp. lyrata] gi|297329585|gb|EFH60004.1| HUA enhancer 2 [Arabidopsis lyrata subsp. lyrata]

 Score =  191 bits (485), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 104/174 (59%), Positives = 113/174 (64%), Gaps = 36/174 (20%)

Query: 1   MEESQTPGKRKAPKADSHVRGTPKEESTKKQRNPTRSCVHEVAVPSCYTLTTDETTHGTL 60
           MEE +T GKRK  ++      TP  E T K+R+  R+CVHEVAVP+ YT T +ET HGTL
Sbjct: 1   MEEPETLGKRKVSESSKLSDETPTPEPTTKRRSLIRACVHEVAVPNDYTPTKEETIHGTL 60

Query: 61  TNPVYNG------------------------------------KTAVAEYAIAMAFRDKQ 84
            NPV+NG                                    KTAVAEYAIAMAFRDKQ
Sbjct: 61  DNPVFNGDMAKTYPFKLDPFQSVSVACLERKESILVSAHTSAGKTAVAEYAIAMAFRDKQ 120

Query: 85  RVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRGMLY 138
           RVIYTS LKALSNQKYREL  EFKDVGLMTGDVTLSPNASCLVMTTEILR MLY
Sbjct: 121 RVIYTSPLKALSNQKYRELQHEFKDVGLMTGDVTLSPNASCLVMTTEILRAMLY 174

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18396436|ref|NP_565338.1| RNA helicase, ATP-dependent, SK12/DOB1 protein [Arabidopsis thaliana] gi|20197305|gb|AAC67203.2| expressed protein [Arabidopsis thaliana] gi|28973761|gb|AAO64196.1| putative DEAD/DEAH box RNA helicase (HUA ENHANCER2) [Arabidopsis thaliana] gi|330250934|gb|AEC06028.1| RNA helicase, ATP-dependent, SK12/DOB1 protein [Arabidopsis thaliana]

 Score =  186 bits (472), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 105/176 (59%), Positives = 115/176 (65%), Gaps = 39/176 (22%)

Query: 1   MEESQTPGKRKAPKADSHVRG--TPKEESTKKQRNPTRSCVHEVAVPSCYTLTTDETTHG 58
           MEE +T GKRK  ++ S +R   TP  E   K+R+  R+CVHEVAVP+ YT T +ET HG
Sbjct: 5   MEEPETLGKRKESES-SKLRSDETPTPEPRTKRRSLKRACVHEVAVPNDYTPTKEETIHG 63

Query: 59  TLTNPVYNG------------------------------------KTAVAEYAIAMAFRD 82
           TL NPV+NG                                    KTAVAEYAIAMAFRD
Sbjct: 64  TLDNPVFNGDMAKTYPFKLDPFQSVSVACLERKESILVSAHTSAGKTAVAEYAIAMAFRD 123

Query: 83  KQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRGMLY 138
           KQRVIYTS LKALSNQKYREL  EFKDVGLMTGDVTLSPNASCLVMTTEILR MLY
Sbjct: 124 KQRVIYTSPLKALSNQKYRELQHEFKDVGLMTGDVTLSPNASCLVMTTEILRAMLY 179

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|16024936|gb|AAL11446.1| HUA enhancer 2 [Arabidopsis thaliana]

 Score =  186 bits (472), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 105/176 (59%), Positives = 115/176 (65%), Gaps = 39/176 (22%)

Query: 1   MEESQTPGKRKAPKADSHVRG--TPKEESTKKQRNPTRSCVHEVAVPSCYTLTTDETTHG 58
           MEE +T GKRK  ++ S +R   TP  E   K+R+  R+CVHEVAVP+ YT T +ET HG
Sbjct: 1   MEEPETLGKRKESES-SKLRSDETPTPEPRTKRRSLKRACVHEVAVPNDYTPTKEETIHG 59

Query: 59  TLTNPVYNG------------------------------------KTAVAEYAIAMAFRD 82
           TL NPV+NG                                    KTAVAEYAIAMAFRD
Sbjct: 60  TLDNPVFNGDMAKTYPFKLDPFQSVSVACLERKESILVSAHTSAGKTAVAEYAIAMAFRD 119

Query: 83  KQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRGMLY 138
           KQRVIYTS LKALSNQKYREL  EFKDVGLMTGDVTLSPNASCLVMTTEILR MLY
Sbjct: 120 KQRVIYTSPLKALSNQKYRELQHEFKDVGLMTGDVTLSPNASCLVMTTEILRAMLY 175

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449470374|ref|XP_004152892.1| PREDICTED: superkiller viralicidic activity 2-like 2-like [Cucumis sativus]

 Score =  186 bits (471), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 106/198 (53%), Positives = 117/198 (59%), Gaps = 60/198 (30%)

Query: 1   MEESQTPGKRKAPKADSHV------------------------RGTPKEESTKKQRNPTR 36
           MEES   GKRK  + +S V                        + TP +E+   +R+ TR
Sbjct: 1   MEESPILGKRKDSEEESAVAETGNTQETSSSKRPKESKNLEDEKTTPSQETVSNRRSLTR 60

Query: 37  SCVHEVAVPSCYTLTTDETTHGTLTNPVYNG----------------------------- 67
           +CVHEVAVP  Y+ T DE+ HGTL NPVYNG                             
Sbjct: 61  TCVHEVAVPVGYSSTKDESVHGTLPNPVYNGTMAKTYPFTLDPFQQVSVSCLERNESILV 120

Query: 68  -------KTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLS 120
                  KTAVAEYAIAMAFRDKQRVIYTS LKALSNQKYREL +EFKDVGLMTGDVTLS
Sbjct: 121 SAHTSAGKTAVAEYAIAMAFRDKQRVIYTSPLKALSNQKYRELSQEFKDVGLMTGDVTLS 180

Query: 121 PNASCLVMTTEILRGMLY 138
           PNASCLVMTTEILRGMLY
Sbjct: 181 PNASCLVMTTEILRGMLY 198

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449527177|ref|XP_004170589.1| PREDICTED: superkiller viralicidic activity 2-like 2-like, partial [Cucumis sativus]

 Score =  185 bits (470), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 106/198 (53%), Positives = 117/198 (59%), Gaps = 60/198 (30%)

Query: 1   MEESQTPGKRKAPKADSHV------------------------RGTPKEESTKKQRNPTR 36
           MEES   GKRK  + +S V                        + TP +E+   +R+ TR
Sbjct: 1   MEESPILGKRKDSEEESAVAETGNTQETSSSKRPKESKNLEDEKTTPSQETVSNRRSLTR 60

Query: 37  SCVHEVAVPSCYTLTTDETTHGTLTNPVYNG----------------------------- 67
           +CVHEVAVP  Y+ T DE+ HGTL NPVYNG                             
Sbjct: 61  TCVHEVAVPVGYSSTKDESVHGTLPNPVYNGTMAKTYPFTLDPFQQVSVSCLERNESILV 120

Query: 68  -------KTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLS 120
                  KTAVAEYAIAMAFRDKQRVIYTS LKALSNQKYREL +EFKDVGLMTGDVTLS
Sbjct: 121 SAHTSAGKTAVAEYAIAMAFRDKQRVIYTSPLKALSNQKYRELSQEFKDVGLMTGDVTLS 180

Query: 121 PNASCLVMTTEILRGMLY 138
           PNASCLVMTTEILRGMLY
Sbjct: 181 PNASCLVMTTEILRGMLY 198

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356513235|ref|XP_003525319.1| PREDICTED: LOW QUALITY PROTEIN: superkiller viralicidic activity 2-like 2-like [Glycine max]

 Score =  177 bits (449), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 99/173 (57%), Positives = 110/173 (63%), Gaps = 38/173 (21%)

Query: 2   EESQTPGKRKAPKADSHVRGTPKEESTKKQRNPTRSCVHEVAVPSCYTLTTDETTHGTLT 61
           +ES T GKR+ P  D  V  T      KK R+  R+CVHEVAVPS Y  + DE  HGTL+
Sbjct: 7   KESLTLGKRREP--DLPVTVTETTSMPKKARSSERTCVHEVAVPSGYVSSKDEDLHGTLS 64

Query: 62  NPVYNG------------------------------------KTAVAEYAIAMAFRDKQR 85
           NP++NG                                    KTAVAEYAIAM+FRDKQR
Sbjct: 65  NPLHNGPMAKSYPFTLDPFQQVSIACLERNESVLVSAHTSDGKTAVAEYAIAMSFRDKQR 124

Query: 86  VIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRGMLY 138
           VIYTS LKALSNQKYREL +EF DVGLMTGDVTLSPNA+CLVMTTEILRGMLY
Sbjct: 125 VIYTSPLKALSNQKYRELSQEFTDVGLMTGDVTLSPNATCLVMTTEILRGMLY 177

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357520641|ref|XP_003630609.1| ATP-dependent RNA helicase DOB1 [Medicago truncatula] gi|355524631|gb|AET05085.1| ATP-dependent RNA helicase DOB1 [Medicago truncatula]

 Score =  177 bits (449), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 97/173 (56%), Positives = 109/173 (63%), Gaps = 36/173 (20%)

Query: 2   EESQTPGKRKAPKADSHVRGTPKEESTKKQRNPTRSCVHEVAVPSCYTLTTDETTHGTLT 61
           +ES T GKR  P+  S   G       KK R+   +CVHEVAVP  YT T DE+ HGTL+
Sbjct: 9   QESTTLGKRSEPEPVSTADGGDTSSQPKKCRSSECTCVHEVAVPINYTSTKDESLHGTLS 68

Query: 62  NPVYNG------------------------------------KTAVAEYAIAMAFRDKQR 85
           NP++NG                                    KTA+AEYAIAM+FRDKQR
Sbjct: 69  NPLHNGTMAKTYPFTLDPFQQVSIACLERNESVLVSAHTSAGKTAIAEYAIAMSFRDKQR 128

Query: 86  VIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRGMLY 138
           VIYTS LKALSNQKYREL +EF DVGLMTGDVTLSPNA+CLVMTTEILRGMLY
Sbjct: 129 VIYTSPLKALSNQKYRELSQEFTDVGLMTGDVTLSPNATCLVMTTEILRGMLY 181

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

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	138
TAIR|locus:2063648	995	HEN2 "hua enhancer 2" [Arabido	0.521	0.072	0.944	9e-40
UNIPROTKB|P42285	1042	SKIV2L2 "Superkiller viralicid	0.521	0.069	0.777	3.3e-27
UNIPROTKB|G3MYJ7	605	SKIV2L2 "Uncharacterized prote	0.521	0.119	0.777	5.7e-27
WB|WBGene00012342	1026	mtr-4 [Caenorhabditis elegans	0.521	0.070	0.819	5.8e-27
ZFIN|ZDB-GENE-040426-2854	1034	skiv2l2 "superkiller viralicid	0.521	0.069	0.777	3.2e-26
UNIPROTKB|F1MJX4	937	SKIV2L2 "Uncharacterized prote	0.521	0.076	0.777	3.8e-26
MGI|MGI:1919448	1040	Skiv2l2 "superkiller viralicid	0.521	0.069	0.777	5.4e-26
UNIPROTKB|E2RCI5	1042	SKIV2L2 "Uncharacterized prote	0.521	0.069	0.777	5.4e-26
UNIPROTKB|F1SLL6	1046	SKIV2L2 "Uncharacterized prote	0.521	0.068	0.777	5.4e-26
TAIR|locus:2026001	988	MTR4 "homolog of yeast MTR4" [	0.521	0.072	0.75	6.8e-25

TAIR|locus:2063648 HEN2 "hua enhancer 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 335 (123.0 bits), Expect = 9.0e-40, Sum P(2) = 9.0e-40
 Identities = 68/72 (94%), Positives = 68/72 (94%)

Query:    67 GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
             GKTAVAEYAIAMAFRDKQRVIYTS LKALSNQKYREL  EFKDVGLMTGDVTLSPNASCL
Sbjct:   108 GKTAVAEYAIAMAFRDKQRVIYTSPLKALSNQKYRELQHEFKDVGLMTGDVTLSPNASCL 167

Query:   127 VMTTEILRGMLY 138
             VMTTEILR MLY
Sbjct:   168 VMTTEILRAMLY 179

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;ISS

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

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

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

GO:0003724 "RNA helicase activity" evidence=ISS

GO:0010093 "specification of floral organ identity" evidence=IMP

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0005829 "cytosol" evidence=IDA

GO:0000278 "mitotic cell cycle" evidence=RCA

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

GO:0003002 "regionalization" evidence=RCA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA

GO:0006396 "RNA processing" evidence=RCA

GO:0007155 "cell adhesion" evidence=RCA

GO:0009640 "photomorphogenesis" evidence=RCA

GO:0009793 "embryo development ending in seed dormancy" evidence=RCA

GO:0009845 "seed germination" evidence=RCA

GO:0009909 "regulation of flower development" evidence=RCA

GO:0009933 "meristem structural organization" evidence=RCA

GO:0010090 "trichome morphogenesis" evidence=RCA

GO:0010162 "seed dormancy process" evidence=RCA

GO:0010182 "sugar mediated signaling pathway" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0010388 "cullin deneddylation" evidence=RCA

GO:0016567 "protein ubiquitination" evidence=RCA

GO:0016571 "histone methylation" evidence=RCA

GO:0016579 "protein deubiquitination" evidence=RCA

GO:0019915 "lipid storage" evidence=RCA

GO:0030422 "production of siRNA involved in RNA interference" evidence=RCA

GO:0033043 "regulation of organelle organization" evidence=RCA

GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=RCA

GO:0043687 "post-translational protein modification" evidence=RCA

GO:0045010 "actin nucleation" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

GO:0048449 "floral organ formation" evidence=RCA

GO:0050826 "response to freezing" evidence=RCA

UNIPROTKB|P42285 SKIV2L2 "Superkiller viralicidic activity 2-like 2" [Homo sapiens (taxid:9606)]

 Score = 294 (108.6 bits), Expect = 3.3e-27, Sum P(3) = 3.3e-27
 Identities = 56/72 (77%), Positives = 66/72 (91%)

Query:    67 GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
             GKT  AEYAIA+A R+KQRVI+TS +KALSNQKYRE+++EF+DVGLMTGDVT++P ASCL
Sbjct:   166 GKTVCAEYAIALALREKQRVIFTSPIKALSNQKYREMYEEFQDVGLMTGDVTINPTASCL 225

Query:   127 VMTTEILRGMLY 138
             VMTTEILR MLY
Sbjct:   226 VMTTEILRSMLY 237

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

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

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

GO:0000178 "exosome (RNase complex)" evidence=IDA

GO:0000460 "maturation of 5.8S rRNA" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

UNIPROTKB|G3MYJ7 SKIV2L2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 294 (108.6 bits), Expect = 5.7e-27, Sum P(2) = 5.7e-27
 Identities = 56/72 (77%), Positives = 66/72 (91%)

Query:    67 GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
             GKT  AEYAIA+A R+KQRVI+TS +KALSNQKYRE+++EF+DVGLMTGDVT++P ASCL
Sbjct:   164 GKTVCAEYAIALALREKQRVIFTSPIKALSNQKYREMYEEFQDVGLMTGDVTINPTASCL 223

Query:   127 VMTTEILRGMLY 138
             VMTTEILR MLY
Sbjct:   224 VMTTEILRSMLY 235

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

WB|WBGene00012342 mtr-4 [Caenorhabditis elegans (taxid:6239)]

 Score = 297 (109.6 bits), Expect = 5.8e-27, Sum P(2) = 5.8e-27
 Identities = 59/72 (81%), Positives = 64/72 (88%)

Query:    67 GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
             GKT VA YAIA   R+KQRVIYTS +KALSNQKYREL +EFKDVGLMTGDVTL+P+ASCL
Sbjct:   152 GKTVVATYAIAKCLREKQRVIYTSPIKALSNQKYRELEEEFKDVGLMTGDVTLNPDASCL 211

Query:   127 VMTTEILRGMLY 138
             VMTTEILR MLY
Sbjct:   212 VMTTEILRSMLY 223

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

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

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

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0002009 "morphogenesis of an epithelium" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0042127 "regulation of cell proliferation" evidence=IMP

GO:0040020 "regulation of meiosis" evidence=IMP

GO:0040022 "feminization of hermaphroditic germ-line" evidence=IMP

GO:0007281 "germ cell development" evidence=IMP

ZFIN|ZDB-GENE-040426-2854 skiv2l2 "superkiller viralicidic activity 2-like 2" [Danio rerio (taxid:7955)]

 Score = 294 (108.6 bits), Expect = 3.2e-26, Sum P(2) = 3.2e-26
 Identities = 56/72 (77%), Positives = 66/72 (91%)

Query:    67 GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
             GKT  AEYAIA+A R+KQRVI+TS +KALSNQKYRE+++EF+DVGLMTGDVT++P ASCL
Sbjct:   154 GKTVCAEYAIALALREKQRVIFTSPIKALSNQKYREMYEEFQDVGLMTGDVTINPTASCL 213

Query:   127 VMTTEILRGMLY 138
             VMTTEILR MLY
Sbjct:   214 VMTTEILRSMLY 225

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

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

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

GO:0005575 "cellular_component" evidence=ND

GO:0031101 "fin regeneration" evidence=IMP

GO:0051781 "positive regulation of cell division" evidence=IMP

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|F1MJX4 SKIV2L2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 294 (108.6 bits), Expect = 3.8e-26, Sum P(2) = 3.8e-26
 Identities = 56/72 (77%), Positives = 66/72 (91%)

Query:    67 GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
             GKT  AEYAIA+A R+KQRVI+TS +KALSNQKYRE+++EF+DVGLMTGDVT++P ASCL
Sbjct:   164 GKTVCAEYAIALALREKQRVIFTSPIKALSNQKYREMYEEFQDVGLMTGDVTINPTASCL 223

Query:   127 VMTTEILRGMLY 138
             VMTTEILR MLY
Sbjct:   224 VMTTEILRSMLY 235

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

GO:0000460 "maturation of 5.8S rRNA" evidence=IEA

GO:0000178 "exosome (RNase complex)" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

MGI|MGI:1919448 Skiv2l2 "superkiller viralicidic activity 2-like 2 (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 294 (108.6 bits), Expect = 5.4e-26, Sum P(2) = 5.4e-26
 Identities = 56/72 (77%), Positives = 66/72 (91%)

Query:    67 GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
             GKT  AEYAIA+A R+KQRVI+TS +KALSNQKYRE+++EF+DVGLMTGDVT++P ASCL
Sbjct:   164 GKTVCAEYAIALALREKQRVIFTSPIKALSNQKYREMYEEFQDVGLMTGDVTINPTASCL 223

Query:   127 VMTTEILRGMLY 138
             VMTTEILR MLY
Sbjct:   224 VMTTEILRSMLY 235

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000460 "maturation of 5.8S rRNA" evidence=ISO

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

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

GO:0008380 "RNA splicing" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

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

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

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

UNIPROTKB|E2RCI5 SKIV2L2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 294 (108.6 bits), Expect = 5.4e-26, Sum P(2) = 5.4e-26
 Identities = 56/72 (77%), Positives = 66/72 (91%)

Query:    67 GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
             GKT  AEYAIA+A R+KQRVI+TS +KALSNQKYRE+++EF+DVGLMTGDVT++P ASCL
Sbjct:   166 GKTVCAEYAIALALREKQRVIFTSPIKALSNQKYREMYEEFQDVGLMTGDVTINPTASCL 225

Query:   127 VMTTEILRGMLY 138
             VMTTEILR MLY
Sbjct:   226 VMTTEILRSMLY 237

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1SLL6 SKIV2L2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 294 (108.6 bits), Expect = 5.4e-26, Sum P(2) = 5.4e-26
 Identities = 56/72 (77%), Positives = 66/72 (91%)

Query:    67 GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
             GKT  AEYAIA+A R+KQRVI+TS +KALSNQKYRE+++EF+DVGLMTGDVT++P ASCL
Sbjct:   167 GKTVCAEYAIALALREKQRVIFTSPIKALSNQKYREMYEEFQDVGLMTGDVTINPTASCL 226

Query:   127 VMTTEILRGMLY 138
             VMTTEILR MLY
Sbjct:   227 VMTTEILRSMLY 238

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

GO:0000460 "maturation of 5.8S rRNA" evidence=IEA

GO:0000178 "exosome (RNase complex)" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

TAIR|locus:2026001 MTR4 "homolog of yeast MTR4" [Arabidopsis thaliana (taxid:3702)]

 Score = 280 (103.6 bits), Expect = 6.8e-25, Sum P(2) = 6.8e-25
 Identities = 54/72 (75%), Positives = 61/72 (84%)

Query:    67 GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
             GKT VA YAIAM+ ++ QRVIYTS +KALSNQKYR+  +EF DVGLMTGDVT+ PNASCL
Sbjct:    94 GKTVVASYAIAMSLKENQRVIYTSPIKALSNQKYRDFKEEFSDVGLMTGDVTIDPNASCL 153

Query:   127 VMTTEILRGMLY 138
             VMTTEILR M Y
Sbjct:   154 VMTTEILRSMQY 165

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

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

GO:0006364 "rRNA processing" evidence=IMP

GO:0031125 "rRNA 3'-end processing" evidence=IMP

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

GO:0000724 "double-strand break repair via homologous recombination" evidence=RCA

GO:0000741 "karyogamy" evidence=RCA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA

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

GO:0006606 "protein import into nucleus" evidence=RCA

GO:0009560 "embryo sac egg cell differentiation" evidence=RCA

GO:0009640 "photomorphogenesis" evidence=RCA

GO:0009909 "regulation of flower development" evidence=RCA

GO:0010074 "maintenance of meristem identity" evidence=RCA

GO:0010212 "response to ionizing radiation" evidence=RCA

GO:0010388 "cullin deneddylation" evidence=RCA

GO:0016567 "protein ubiquitination" evidence=RCA

GO:0016571 "histone methylation" evidence=RCA

GO:0016579 "protein deubiquitination" evidence=RCA

GO:0030422 "production of siRNA involved in RNA interference" evidence=RCA

GO:0035196 "production of miRNAs involved in gene silencing by miRNA" evidence=RCA

GO:0043687 "post-translational protein modification" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

GO:0048825 "cotyledon development" evidence=RCA

GO:0051301 "cell division" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9CZU3	SK2L2_MOUSE	3, ., 6, ., 4, ., 1, 3	0.7777	0.5217	0.0692	yes	no
P42285	SK2L2_HUMAN	3, ., 6, ., 4, ., 1, 3	0.7777	0.5217	0.0690	yes	no
P47047	MTR4_YEAST	3, ., 6, ., 4, ., 1, 3	0.7638	0.5217	0.0671	yes	no
O14232	MTR4_SCHPO	3, ., 6, ., 4, ., -	0.7916	0.5217	0.0644	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00017018001	SubName- Full=Chromosome chr11 scaffold_14, whole genome shotgun sequence; (995 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00034559001	SubName- Full=Chromosome chr9 scaffold_7, whole genome shotgun sequence; (840 aa)				•					0.488
	GSVIVG00033408001	SubName- Full=Chromosome chr19 scaffold_66, whole genome shotgun sequence; (430 aa)				•			•		0.485
	GSVIVG00038815001	SubName- Full=Chromosome chr5 scaffold_98, whole genome shotgun sequence; (1139 aa)				•					0.454
	GSVIVG00018638001	SubName- Full=Chromosome chr12 scaffold_18, whole genome shotgun sequence; (452 aa)				•					0.451
	GSVIVG00020673001	SubName- Full=Chromosome chr14 scaffold_21, whole genome shotgun sequence; (607 aa)				•					0.442
	GSVIVG00021307001	SubName- Full=Chromosome chr8 scaffold_23, whole genome shotgun sequence; (586 aa)				•					0.432
	GSVIVG00000661001	SubName- Full=Chromosome chr8 scaffold_106, whole genome shotgun sequence; (701 aa)				•					0.424
	GSVIVG00025547001	RecName- Full=DNA-directed RNA polymerase; EC=2.7.7.6; (1518 aa)				•					0.423
	GSVIVG00021672001	SubName- Full=Chromosome chr8 scaffold_23, whole genome shotgun sequence; (315 aa)				•	•				0.422
	GSVIVG00019329001	SubName- Full=Chromosome chr7 scaffold_20, whole genome shotgun sequence; (943 aa)				•			•		0.420

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	138
COG4581	1041	COG4581, COG4581, Superfamily II RNA helicase [DNA	3e-35
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	8e-09
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	4e-07
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	1e-06
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	9e-06
COG1202	830	COG1202, COG1202, Superfamily II helicase, archaea	8e-05
PRK01172	674	PRK01172, PRK01172, ski2-like helicase; Provisiona	2e-04
PRK00254	720	PRK00254, PRK00254, ski2-like helicase; Provisiona	4e-04
PRK02362	737	PRK02362, PRK02362, ski2-like helicase; Provisiona	0.004

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

 Score =  127 bits (322), Expect = 3e-35
 Identities = 55/76 (72%), Positives = 63/76 (82%), Gaps = 4/76 (5%)

Query: 67  GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDV----GLMTGDVTLSPN 122
           GKT VAEYAIA+A RD QRVIYTS +KALSNQKYR+L  +F DV    GLMTGDV+++P+
Sbjct: 146 GKTVVAEYAIALALRDGQRVIYTSPIKALSNQKYRDLLAKFGDVADMVGLMTGDVSINPD 205

Query: 123 ASCLVMTTEILRGMLY 138
           A CLVMTTEILR MLY
Sbjct: 206 APCLVMTTEILRNMLY 221

Length = 1041

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

 Score = 50.7 bits (122), Expect = 8e-09
 Identities = 25/86 (29%), Positives = 34/86 (39%), Gaps = 15/86 (17%)

Query: 67  GKTAVAEYAIAMAFRDKQ---RVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTL 119
           GKT      I  A   K+   + +  +  + L+ Q Y EL K FK     V L+TG  +L
Sbjct: 26  GKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQIYEELKKLFKILGLRVALLTGGTSL 85

Query: 120 SP--------NASCLVMTTEILRGML 137
                      A  LV T   L  +L
Sbjct: 86  KEQARKLKKGKADILVGTPGRLLDLL 111

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

 Score = 47.4 bits (113), Expect = 4e-07
 Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 10/74 (13%)

Query: 67  GKTAVAEYAIAMAF-RDKQRVIYTSSLKALSNQKYRELHKEFKDVGL----MTGDVTLSP 121
           GKT +A  AI         +V+Y   LKAL+ +KY E     +++G+     TGD  L  
Sbjct: 59  GKTLIALLAILSTLLEGGGKVVYIVPLKALAEEKYEEF-SRLEELGIRVGISTGDYDLDD 117

Query: 122 ----NASCLVMTTE 131
                   +V T E
Sbjct: 118 ERLARYDVIVTTPE 131

Length = 766

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

 Score = 45.2 bits (107), Expect = 1e-06
 Identities = 23/85 (27%), Positives = 28/85 (32%), Gaps = 14/85 (16%)

Query: 67  GKTAVAEYAIAMAFR--DKQRVIYTSSLKALSNQKYRELHKEFKD-----VGLMTGDVT- 118
           GKT  A      A +     RV+     + L+ Q   EL K         VGL  GD   
Sbjct: 36  GKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKR 95

Query: 119 ------LSPNASCLVMTTEILRGML 137
                  S     LV T   L  +L
Sbjct: 96  EQLRKLESGKTDILVTTPGRLLDLL 120

Length = 201

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

 Score = 42.3 bits (100), Expect = 9e-06
 Identities = 20/83 (24%), Positives = 29/83 (34%), Gaps = 12/83 (14%)

Query: 67  GKTAVAEYAIAMAFR--DKQRVIYTSSLKALSNQKYRELHKEFK---DVGLMTGDVT--- 118
           GKT  A   I          +V+  +  + L+NQ    L + F     VG + G  +   
Sbjct: 12  GKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKVGYLIGGTSIKQ 71

Query: 119 ----LSPNASCLVMTTEILRGML 137
               LS     +V T   L   L
Sbjct: 72  QEKLLSGKTDIVVGTPGRLLDEL 94

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

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

 Score = 40.5 bits (95), Expect = 8e-05
 Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 16/81 (19%)

Query: 67  GKTAVAEYA-IAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTG---------- 115
           GKT + E A I       +++++   L AL+NQKY +  + +  +GL             
Sbjct: 244 GKTLIGELAGIPRLLSGGKKMLFLVPLVALANQKYEDFKERYSKLGLKVAIRVGMSRIKT 303

Query: 116 -----DVTLSPNASCLVMTTE 131
                 V  SP+A  +V T E
Sbjct: 304 REEPVVVDTSPDADIIVGTYE 324

Length = 830

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

 Score = 39.5 bits (92), Expect = 2e-04
 Identities = 22/84 (26%), Positives = 39/84 (46%), Gaps = 9/84 (10%)

Query: 63  PVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMT----GDVT 118
           P   GKT +A  AI   F    + IY   L++L+ +KY EL +  + +G+      GD  
Sbjct: 45  PTAAGKTLIAYSAIYETFLAGLKSIYIVPLRSLAMEKYEELSR-LRSLGMRVKISIGDYD 103

Query: 119 LSP----NASCLVMTTEILRGMLY 138
             P        +++T+E    +++
Sbjct: 104 DPPDFIKRYDVVILTSEKADSLIH 127

Length = 674

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

 Score = 38.6 bits (90), Expect = 4e-04
 Identities = 25/61 (40%), Positives = 35/61 (57%), Gaps = 10/61 (16%)

Query: 63  PVYNGKTAVAEYAIAMA---FRDKQRVIYTSSLKALSNQKYRELHKEFKDVGL----MTG 115
           P  +GKT VAE  I M     R+  + +Y   LKAL+ +KYRE  K+++ +GL     TG
Sbjct: 47  PTASGKTLVAE--IVMVNKLLREGGKAVYLVPLKALAEEKYREF-KDWEKLGLRVAMTTG 103

Query: 116 D 116
           D
Sbjct: 104 D 104

Length = 720

>gnl|CDD|235032 PRK02362, PRK02362, ski2-like helicase; Provisional

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 5/58 (8%)

Query: 63  PVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGD 116
           P  +GKT +AE A+  A     + +Y   L+AL+++K+ E  + F+     VG+ TGD
Sbjct: 47  PTASGKTLIAELAMLKAIARGGKALYIVPLRALASEKFEEF-ERFEELGVRVGISTGD 103

Length = 737

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	138
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.89
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.82
COG1204	766	Superfamily II helicase [General function predicti	99.79
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.79
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.76
PRK02362	737	ski2-like helicase; Provisional	99.7
PRK01172	674	ski2-like helicase; Provisional	99.62
PRK00254	720	ski2-like helicase; Provisional	99.6
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.59
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.49
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.48
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.48
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.48
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.47
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.47
PRK13767	876	ATP-dependent helicase; Provisional	99.46
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.46
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.45
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.45
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.45
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.45
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.44
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.43
PTZ00424	401	helicase 45; Provisional	99.43
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.43
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.42
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.42
COG1205	851	Distinct helicase family with a unique C-terminal	99.41
PTZ00110	545	helicase; Provisional	99.38
COG1202	830	Superfamily II helicase, archaea-specific [General	99.36
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.35
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.35
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.31
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.31
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.29
KOG0354	746	consensus DEAD-box like helicase [General function	99.28
PRK13766	773	Hef nuclease; Provisional	99.27
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	99.24
PHA02558	501	uvsW UvsW helicase; Provisional	99.24
PRK05580	679	primosome assembly protein PriA; Validated	99.24
PRK10689	1147	transcription-repair coupling factor; Provisional	99.22
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	99.21
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	99.19
PRK09401	1176	reverse gyrase; Reviewed	99.18
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.18
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.16
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.15
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	99.13
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	99.1
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.1
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.05
KOG0343	758	consensus RNA Helicase [RNA processing and modific	99.05
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.05
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.03
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.03
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.02
PRK14701	1638	reverse gyrase; Provisional	99.01
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	98.98
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	98.97
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.95
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	98.95
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	98.95
PRK09694	878	helicase Cas3; Provisional	98.95
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	98.94
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	98.94
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	98.93
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	98.9
KOG0346	569	consensus RNA helicase [RNA processing and modific	98.85
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	98.84
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	98.84
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	98.84
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	98.84
PRK09200	790	preprotein translocase subunit SecA; Reviewed	98.83
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	98.83
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	98.78
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	98.78
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	98.74
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	98.69
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	98.68
COG1198	730	PriA Primosomal protein N' (replication factor Y)	98.68
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.68
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	98.66
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	98.66
KOG0347	731	consensus RNA helicase [RNA processing and modific	98.63
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	98.6
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	98.59
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.59
PRK12904	830	preprotein translocase subunit SecA; Reviewed	98.52
KOG0334	997	consensus RNA helicase [RNA processing and modific	98.51
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	98.43
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	98.36
PHA02653	675	RNA helicase NPH-II; Provisional	98.34
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	98.31
PRK14873	665	primosome assembly protein PriA; Provisional	98.31
PRK13107	908	preprotein translocase subunit SecA; Reviewed	98.26
COG4096	875	HsdR Type I site-specific restriction-modification	98.22
PF13245	76	AAA_19: Part of AAA domain	98.19
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.15
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	98.15
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	98.13
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.09
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	98.02
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	97.98
KOG4284	980	consensus DEAD box protein [Transcription]	97.98
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	97.97
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	97.95
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	97.94
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	97.94
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	97.84
PRK12326	764	preprotein translocase subunit SecA; Reviewed	97.8
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	97.77
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	97.66
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	97.65
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	97.61
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	97.6
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	97.57
KOG0327	397	consensus Translation initiation factor 4F, helica	97.54
PRK04914	956	ATP-dependent helicase HepA; Validated	97.52
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	97.51
KOG1123	776	consensus RNA polymerase II transcription initiati	97.5
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.43
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	97.43
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	97.42
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	97.4
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	97.36
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.34
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	97.3
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	97.3
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	97.3
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	97.14
PRK15483	986	type III restriction-modification system StyLTI en	97.13
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	97.07
KOG0353	695	consensus ATP-dependent DNA helicase [General func	97.05
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.05
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.82
TIGR00376	637	DNA helicase, putative. The gene product may repre	96.81
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	96.78
COG0610	962	Type I site-specific restriction-modification syst	96.75
PRK08727	233	hypothetical protein; Validated	96.74
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.7
PF12846	304	AAA_10: AAA-like domain	96.66
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	96.65
CHL00122	870	secA preprotein translocase subunit SecA; Validate	96.55
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	96.52
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	96.51
PRK04328	249	hypothetical protein; Provisional	96.37
PRK08181	269	transposase; Validated	96.29
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.28
PRK06526	254	transposase; Provisional	96.28
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	96.28
PRK08533	230	flagellar accessory protein FlaH; Reviewed	96.24
PRK05973	237	replicative DNA helicase; Provisional	96.24
TIGR02237	209	recomb_radB DNA repair and recombination protein R	96.23
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	96.19
smart00382	148	AAA ATPases associated with a variety of cellular	96.17
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	96.09
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	96.08
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	96.06
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	96.03
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	96.03
PRK12377	248	putative replication protein; Provisional	96.0
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	95.99
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	95.99
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	95.98
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	95.94
PRK04296	190	thymidine kinase; Provisional	95.93
PRK06067	234	flagellar accessory protein FlaH; Validated	95.92
PRK06835	329	DNA replication protein DnaC; Validated	95.9
KOG1802	935	consensus RNA helicase nonsense mRNA reducing fact	95.89
PRK09183	259	transposase/IS protein; Provisional	95.82
cd01394	218	radB RadB. The archaeal protein radB shares simila	95.75
PRK09354	349	recA recombinase A; Provisional	95.75
cd00983	325	recA RecA is a bacterial enzyme which has roles in	95.74
COG1484	254	DnaC DNA replication protein [DNA replication, rec	95.73
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	95.73
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	95.71
cd03115	173	SRP The signal recognition particle (SRP) mediates	95.67
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	95.67
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.66
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.64
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	95.64
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	95.58
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	95.58
PRK05642	234	DNA replication initiation factor; Validated	95.58
KOG1803	649	consensus DNA helicase [Replication, recombination	95.5
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	95.49
PRK06921	266	hypothetical protein; Provisional	95.48
PRK08084	235	DNA replication initiation factor; Provisional	95.43
PRK07952	244	DNA replication protein DnaC; Validated	95.4
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	95.36
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	95.33
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.28
PRK06893	229	DNA replication initiation factor; Validated	95.25
COG3451	796	VirB4 Type IV secretory pathway, VirB4 components	95.22
COG4889	1518	Predicted helicase [General function prediction on	95.19
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	95.16
PRK08116	268	hypothetical protein; Validated	95.15
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.0
PRK08903	227	DnaA regulatory inactivator Hda; Validated	94.97
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	94.97
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	94.94
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	94.91
PRK11054	684	helD DNA helicase IV; Provisional	94.89
PRK09302	509	circadian clock protein KaiC; Reviewed	94.85
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	94.79
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	94.78
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	94.7
PRK12422	445	chromosomal replication initiation protein; Provis	94.67
TIGR02746	797	TraC-F-type type-IV secretion system protein TraC.	94.65
PRK00149	450	dnaA chromosomal replication initiation protein; R	94.61
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	94.6
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	94.59
PRK10416	318	signal recognition particle-docking protein FtsY;	94.52
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	94.51
KOG4439	901	consensus RNA polymerase II transcription terminat	94.51
COG0593	408	DnaA ATPase involved in DNA replication initiation	94.5
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	94.49
PRK08939	306	primosomal protein DnaI; Reviewed	94.46
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	94.46
TIGR03744	893	traC_PFL_4706 conjugative transfer ATPase, PFL_470	94.44
PRK09302	509	circadian clock protein KaiC; Reviewed	94.43
PRK13851	344	type IV secretion system protein VirB11; Provision	94.42
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	94.42
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	94.39
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	94.36
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	94.29
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	94.28
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	94.28
PRK10536	262	hypothetical protein; Provisional	94.27
PRK10867	433	signal recognition particle protein; Provisional	94.13
PRK14974	336	cell division protein FtsY; Provisional	94.07
TIGR00959	428	ffh signal recognition particle protein. This mode	94.02
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	93.98
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	93.94
PRK00771	437	signal recognition particle protein Srp54; Provisi	93.85
PRK13833	323	conjugal transfer protein TrbB; Provisional	93.85
PRK14086	617	dnaA chromosomal replication initiation protein; P	93.84
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	93.76
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	93.75
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	93.75
PF00004	132	AAA: ATPase family associated with various cellula	93.72
TIGR00929	785	VirB4_CagE type IV secretion/conjugal transfer ATP	93.68
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	93.68
TIGR03783	829	Bac_Flav_CT_G Bacteroides conjugation system ATPas	93.58
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	93.56
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	93.54
PRK05298	652	excinuclease ABC subunit B; Provisional	93.5
PRK13873	811	conjugal transfer ATPase TrbE; Provisional	93.48
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	93.45
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	93.44
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	93.42
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	93.42
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	93.36
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	93.34
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	93.31
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	93.28
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	93.26
PRK13891	852	conjugal transfer protein TrbE; Provisional	93.25
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	93.2
PRK14087	450	dnaA chromosomal replication initiation protein; P	93.18
PRK11823	446	DNA repair protein RadA; Provisional	93.14
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	93.13
PRK13764	602	ATPase; Provisional	93.11
PRK13700	732	conjugal transfer protein TraD; Provisional	93.06
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	92.97
COG3973	747	Superfamily I DNA and RNA helicases [General funct	92.96
PRK14088	440	dnaA chromosomal replication initiation protein; P	92.94
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	92.93
PF00154	322	RecA: recA bacterial DNA recombination protein; In	92.91
TIGR02236	310	recomb_radA DNA repair and recombination protein R	92.85
PRK10436	462	hypothetical protein; Provisional	92.84
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	92.84
PRK13721	844	conjugal transfer ATP-binding protein TraC; Provis	92.78
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	92.76
PRK09519	790	recA DNA recombination protein RecA; Reviewed	92.74
TIGR00665	434	DnaB replicative DNA helicase. This model describe	92.69
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	92.64
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	92.56
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	92.48
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	92.34
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	92.34
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	92.28
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	92.26
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	92.22
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	92.21
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	92.21
PRK14729	300	miaA tRNA delta(2)-isopentenylpyrophosphate transf	92.15
TIGR02533	486	type_II_gspE general secretory pathway protein E.	91.99
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	91.91
cd01983	99	Fer4_NifH The Fer4_NifH superfamily contains a var	91.88
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	91.83
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	91.83
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	91.76
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	91.75
PRK08506	472	replicative DNA helicase; Provisional	91.74
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	91.69
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	91.67
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	91.62
PRK05595	444	replicative DNA helicase; Provisional	91.61
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	91.47
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	91.43
PRK13768	253	GTPase; Provisional	91.38
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	91.37
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	91.37
PRK04301	317	radA DNA repair and recombination protein RadA; Va	91.36
PHA02542	473	41 41 helicase; Provisional	91.24
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	91.1
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	91.05
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	90.99
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	90.98
PF05729	166	NACHT: NACHT domain	90.9
PRK05748	448	replicative DNA helicase; Provisional	90.83
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	90.75
cd02034	116	CooC The accessory protein CooC, which contains a	90.69
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	90.69
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	90.68
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	90.6
cd03114	148	ArgK-like The function of this protein family is u	90.46
COG0378	202	HypB Ni2+-binding GTPase involved in regulation of	90.4
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	90.33
KOG0387	923	consensus Transcription-coupled repair protein CSB	90.33
PHA00729	226	NTP-binding motif containing protein	90.31
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	90.24
PRK13830	818	conjugal transfer protein TrbE; Provisional	90.21
PRK05541	176	adenylylsulfate kinase; Provisional	90.17
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	90.15
PF13476	202	AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V	90.0
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	89.97
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	89.92
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	89.84
PRK00411	394	cdc6 cell division control protein 6; Reviewed	89.82
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	89.8
PTZ00301	210	uridine kinase; Provisional	89.71
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	89.52
PF13173	128	AAA_14: AAA domain	89.52
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	89.49
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	89.45
PRK14494	229	putative molybdopterin-guanine dinucleotide biosyn	89.43
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	89.41
PRK08760	476	replicative DNA helicase; Provisional	89.4
COG0324	308	MiaA tRNA delta(2)-isopentenylpyrophosphate transf	89.35
PRK00091	307	miaA tRNA delta(2)-isopentenylpyrophosphate transf	89.2
KOG1002	791	consensus Nucleotide excision repair protein RAD16	89.18
CHL00181	287	cbbX CbbX; Provisional	89.18
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	89.14
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	89.14
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	89.05
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	88.95
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	88.92
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	88.86
PF13500	199	AAA_26: AAA domain; PDB: 3OF5_A 2IOJ_A 4A0G_B 4A0R	88.72
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	88.64
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	88.52
PF01656	195	CbiA: CobQ/CobB/MinD/ParA nucleotide binding domai	88.52
PRK13898	800	type IV secretion system ATPase VirB4; Provisional	88.5
COG4240	300	Predicted kinase [General function prediction only	88.48
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	88.47
TIGR00347	166	bioD dethiobiotin synthase. Dethiobiotin synthase	88.42
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	88.4
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	88.39
cd02035	217	ArsA ArsA ATPase functionas as an efflux pump loca	88.31
PRK10689	1147	transcription-repair coupling factor; Provisional	88.31
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	88.28
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	88.26
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	88.21
COG3587	985	Restriction endonuclease [Defense mechanisms]	88.19
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	88.18
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	88.11
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	88.1
PRK12402	337	replication factor C small subunit 2; Reviewed	88.05
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	87.94
PRK13853	789	type IV secretion system protein VirB4; Provisiona	87.73
PLN02165	334	adenylate isopentenyltransferase	87.61
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	87.54
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	87.45
PRK00889	175	adenylylsulfate kinase; Provisional	87.33
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	87.3
PRK07667	193	uridine kinase; Provisional	87.18
PF13555	62	AAA_29: P-loop containing region of AAA domain	87.16
PRK05480	209	uridine/cytidine kinase; Provisional	87.15
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	87.09
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	87.02
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	87.0
PRK06696	223	uridine kinase; Validated	86.96
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	86.94
TIGR00174	287	miaA tRNA isopentenyltransferase (miaA). Catalyzes	86.63
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	86.59
PRK06762	166	hypothetical protein; Provisional	86.58
PRK00300	205	gmk guanylate kinase; Provisional	86.54
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	86.54
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	86.53
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	86.51
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	86.43
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	86.42
PRK07004	460	replicative DNA helicase; Provisional	86.33
PRK09165	497	replicative DNA helicase; Provisional	86.19
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	86.18
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	86.16
PRK05636	505	replicative DNA helicase; Provisional	86.11
PRK07261	171	topology modulation protein; Provisional	85.98
TIGR02773	1158	addB_Gpos ATP-dependent nuclease subunit B. DNA re	85.98
PRK00090	222	bioD dithiobiotin synthetase; Reviewed	85.97
KOG2749	415	consensus mRNA cleavage and polyadenylation factor	85.96
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	85.94
PRK08118	167	topology modulation protein; Reviewed	85.92
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	85.85
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	85.8
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	85.68
PRK13897	606	type IV secretion system component VirD4; Provisio	85.61
PRK00131	175	aroK shikimate kinase; Reviewed	85.5
PRK03846	198	adenylylsulfate kinase; Provisional	85.45
PRK08233	182	hypothetical protein; Provisional	85.41
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	85.41
PF01745	233	IPT: Isopentenyl transferase; InterPro: IPR002648	85.35
PTZ00035	337	Rad51 protein; Provisional	85.31
PHA03333	752	putative ATPase subunit of terminase; Provisional	85.27
PRK06851	367	hypothetical protein; Provisional	85.24
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	85.22
KOG1131	755	consensus RNA polymerase II transcription initiati	85.1
PF02283	167	CobU: Cobinamide kinase / cobinamide phosphate gua	85.04
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	84.99
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	84.94
PHA00350	399	putative assembly protein	84.93
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	84.84
PF06414	199	Zeta_toxin: Zeta toxin; InterPro: IPR010488 This e	84.83
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	84.74
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	84.67
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	84.65
COG0419	908	SbcC ATPase involved in DNA repair [DNA replicatio	84.6
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	84.57
PHA02244	383	ATPase-like protein	84.57
PF02492	178	cobW: CobW/HypB/UreG, nucleotide-binding domain; I	84.49
PRK08840	464	replicative DNA helicase; Provisional	84.37
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	84.36
PRK10865	857	protein disaggregation chaperone; Provisional	84.25
PLN03025	319	replication factor C subunit; Provisional	84.24
PRK08006	471	replicative DNA helicase; Provisional	84.18
PRK06904	472	replicative DNA helicase; Validated	84.15
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	84.13
PRK07773	886	replicative DNA helicase; Validated	84.11
cd00550	254	ArsA_ATPase Oxyanion-translocating ATPase (ArsA).	84.09
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	84.03
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	83.78
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	83.78
PRK08356	195	hypothetical protein; Provisional	83.74
PRK14530	215	adenylate kinase; Provisional	83.71
PRK06321	472	replicative DNA helicase; Provisional	83.59
PRK14737	186	gmk guanylate kinase; Provisional	83.59
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	83.53
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	83.53
PRK03992	389	proteasome-activating nucleotidase; Provisional	83.46
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	83.39
COG2256	436	MGS1 ATPase related to the helicase subunit of the	83.23
PRK09435	332	membrane ATPase/protein kinase; Provisional	83.13
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	83.07
cd02037	169	MRP-like MRP (Multiple Resistance and pH adaptatio	82.92
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	82.91
PTZ00293	211	thymidine kinase; Provisional	82.9
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	82.85
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	82.83
TIGR00235	207	udk uridine kinase. Model contains a number of lon	82.83
PRK14493	274	putative bifunctional molybdopterin-guanine dinucl	82.77
COG1192	259	Soj ATPases involved in chromosome partitioning [C	82.6
PRK13850	670	type IV secretion system protein VirD4; Provisiona	82.53
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	82.51
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	82.39
PRK01184	184	hypothetical protein; Provisional	82.37
PRK06620	214	hypothetical protein; Validated	82.36
PRK06749	428	replicative DNA helicase; Provisional	82.16
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	82.14
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	82.14
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	82.07
TIGR01968	261	minD_bact septum site-determining protein MinD. Th	82.06
PRK10875	615	recD exonuclease V subunit alpha; Provisional	82.06
cd03116	159	MobB Molybdenum is an essential trace element in t	82.04
PLN02840	421	tRNA dimethylallyltransferase	82.04
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	81.95
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	81.91
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	81.88
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	81.86
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	81.73
cd02029	277	PRK_like Phosphoribulokinase-like (PRK-like) is a	81.68
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	81.65
PRK06547	172	hypothetical protein; Provisional	81.56
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	81.48
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	81.41
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	81.38
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	81.35
KOG2028	554	consensus ATPase related to the helicase subunit o	81.29
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	81.26
PRK06217	183	hypothetical protein; Validated	81.24
PRK13822	641	conjugal transfer coupling protein TraG; Provision	81.18
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	81.14
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	81.13
PRK13880	636	conjugal transfer coupling protein TraG; Provision	81.11
COG3857	1108	AddB ATP-dependent nuclease, subunit B [DNA replic	81.04
PF02463	220	SMC_N: RecF/RecN/SMC N terminal domain; InterPro:	81.02
TIGR00609	1087	recB exodeoxyribonuclease V, beta subunit. All pro	80.8
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	80.79
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	80.47

>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]

Probab=99.89  E-value=1.2e-23  Score=186.96  Aligned_cols=103  Identities=67%  Similarity=0.965  Sum_probs=94.9

Q ss_pred             CCcccccccCCC--CccCCCC---------------------------CCCceEECcCCCchHHHHHHHHHHHHHcCCcE
Q 042424           36 RSCVHEVAVPSC--YTLTTDE---------------------------TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRV   86 (138)
Q Consensus        36 ~~~~~~~~~p~~--y~~~~~~---------------------------~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rv   86 (138)
                      +.|.|+++.|++  |.|+..+                           ..+.+++|-|++|||++|+|||+++|+.++|+
T Consensus        96 ~~c~HeVavP~~~dY~p~~~~~~~~~pAk~YPF~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~kQRV  175 (1041)
T KOG0948|consen   96 EGCRHEVAVPPNYDYTPLLPKIFGKPPAKTYPFTLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLREKQRV  175 (1041)
T ss_pred             ccceeeeecCCccccCccccccCCCCcccCCCcccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHhcCeE
Confidence            589999999977  7774321                           13566999999999999999999999999999


Q ss_pred             EEEechHHHHHHHHHHHHHhcCceEEEecCCcCCCCCCEEEecHHHHHHhhC
Q 042424           87 IYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRGMLY  138 (138)
Q Consensus        87 iyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~~~~~IiVtTpe~l~~lL~  138 (138)
                      ||.+|.+||.||+|++|...|++||++|||.++|+++.|+|+|.|+|++|||
T Consensus       176 IYTSPIKALSNQKYREl~~EF~DVGLMTGDVTInP~ASCLVMTTEILRsMLY  227 (1041)
T KOG0948|consen  176 IYTSPIKALSNQKYRELLEEFKDVGLMTGDVTINPDASCLVMTTEILRSMLY  227 (1041)
T ss_pred             EeeChhhhhcchhHHHHHHHhcccceeecceeeCCCCceeeeHHHHHHHHHh
Confidence            9999999999999999999999999999999999999999999999999998

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

Probab=99.82  E-value=1.7e-20  Score=172.30  Aligned_cols=84  Identities=67%  Similarity=0.993  Sum_probs=80.8

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcCce----EEEecCCcCCCCCCEEEecH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDV----GLMTGDVTLSPNASCLVMTT  130 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~~v----~~~tGd~~~~~~~~IiVtTp  130 (138)
                      ..+.++|||||||||++++|||..++++|.|++|++|.|||+||+|++|...|++|    |++|||..+|++++|+|+|.
T Consensus       134 ~esVlV~ApTssGKTvVaeyAi~~al~~~qrviYTsPIKALsNQKyrdl~~~fgdv~~~vGL~TGDv~IN~~A~clvMTT  213 (1041)
T COG4581         134 GESVLVCAPTSSGKTVVAEYAIALALRDGQRVIYTSPIKALSNQKYRDLLAKFGDVADMVGLMTGDVSINPDAPCLVMTT  213 (1041)
T ss_pred             CCcEEEEccCCCCcchHHHHHHHHHHHcCCceEeccchhhhhhhHHHHHHHHhhhhhhhccceecceeeCCCCceEEeeH
Confidence            35778999999999999999999999999999999999999999999999999966    99999999999999999999


Q ss_pred             HHHHHhhC
Q 042424          131 EILRGMLY  138 (138)
Q Consensus       131 e~l~~lL~  138 (138)
                      |+|.+|||
T Consensus       214 EILRnMly  221 (1041)
T COG4581         214 EILRNMLY  221 (1041)
T ss_pred             HHHHHHhc
Confidence            99999998

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.79  E-value=3.4e-19  Score=161.05  Aligned_cols=83  Identities=33%  Similarity=0.486  Sum_probs=76.0

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc-CCcEEEEechHHHHHHHHHHHH--HhcC-ceEEEecCCcCCC----CCCEE
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD-KQRVIYTSSLKALSNQKYRELH--KEFK-DVGLMTGDVTLSP----NASCL  126 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~-~~rviyv~P~kaLv~Q~~~~l~--~~f~-~v~~~tGd~~~~~----~~~Ii  126 (138)
                      +.|.++|+|||||||++|+++|.+.+.+ +.++||++|++||++|++++|+  +.|+ +|++.|||...+.    +++||
T Consensus        47 ~~N~li~aPTgsGKTlIA~lai~~~l~~~~~k~vYivPlkALa~Ek~~~~~~~~~~GirV~~~TgD~~~~~~~l~~~~Vi  126 (766)
T COG1204          47 DENVLISAPTGSGKTLIALLAILSTLLEGGGKVVYIVPLKALAEEKYEEFSRLEELGIRVGISTGDYDLDDERLARYDVI  126 (766)
T ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHHHhcCCcEEEEeChHHHHHHHHHHhhhHHhcCCEEEEecCCcccchhhhccCCEE
Confidence            7899999999999999999999999987 5999999999999999999999  4466 8999999988554    89999


Q ss_pred             EecHHHHHHhh
Q 042424          127 VMTTEILRGML  137 (138)
Q Consensus       127 VtTpe~l~~lL  137 (138)
                      |+|||+|++++
T Consensus       127 VtT~EK~Dsl~  137 (766)
T COG1204         127 VTTPEKLDSLT  137 (766)
T ss_pred             EEchHHhhHhh
Confidence            99999999875

>KOG0947 consensus Cytoplasmic exosomal RNA helicase SKI2, DEAD-box superfamily [RNA processing and modification]

Probab=99.79  E-value=1e-19  Score=164.99  Aligned_cols=83  Identities=58%  Similarity=0.883  Sum_probs=79.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCCCCCCEEEecHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRG  135 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~~~~~IiVtTpe~l~~  135 (138)
                      .+..+.|+|+||||++|+|||..+..++.|.||.+|.|||.||++++|++.|++||++|||..+++++.|+|||.|+|++
T Consensus       313 ~SVFVAAHTSAGKTvVAEYAialaq~h~TR~iYTSPIKALSNQKfRDFk~tF~DvgLlTGDvqinPeAsCLIMTTEILRs  392 (1248)
T KOG0947|consen  313 DSVFVAAHTSAGKTVVAEYAIALAQKHMTRTIYTSPIKALSNQKFRDFKETFGDVGLLTGDVQINPEASCLIMTTEILRS  392 (1248)
T ss_pred             CeEEEEecCCCCcchHHHHHHHHHHhhccceEecchhhhhccchHHHHHHhccccceeecceeeCCCcceEeehHHHHHH
Confidence            35569999999999999999999988999999999999999999999999999999999999999999999999999999


Q ss_pred             hhC
Q 042424          136 MLY  138 (138)
Q Consensus       136 lL~  138 (138)
                      |||
T Consensus       393 MLY  395 (1248)
T KOG0947|consen  393 MLY  395 (1248)
T ss_pred             HHh
Confidence            998

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=99.76  E-value=1.1e-18  Score=159.41  Aligned_cols=82  Identities=24%  Similarity=0.399  Sum_probs=74.8

Q ss_pred             CCCCceEECcCCCchHHHHHHHHHHHHHc----------CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcC
Q 042424           54 ETTHGTLTNPVYNGKTAVAEYAIAMAFRD----------KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTL  119 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~~ai~~~l~~----------~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~  119 (138)
                      .+.|.+||||||||||.+|+++|++.++.          +-++|||+|+||||.++++.|.++|.    .|..+|||...
T Consensus       125 SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~~~~kkl~~~gi~v~ELTGD~ql  204 (1230)
T KOG0952|consen  125 SNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVDKFSKKLAPLGISVRELTGDTQL  204 (1230)
T ss_pred             CCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHHHHhhhcccccceEEEecCcchh
Confidence            66899999999999999999999999883          57999999999999999999999987    78899999865


Q ss_pred             CC----CCCEEEecHHHHHH
Q 042424          120 SP----NASCLVMTTEILRG  135 (138)
Q Consensus       120 ~~----~~~IiVtTpe~l~~  135 (138)
                      ..    +++|||+|||+||-
T Consensus       205 ~~tei~~tqiiVTTPEKwDv  224 (1230)
T KOG0952|consen  205 TKTEIADTQIIVTTPEKWDV  224 (1230)
T ss_pred             hHHHHHhcCEEEecccceee
Confidence            43    89999999999985

>PRK02362 ski2-like helicase; Provisional

Probab=99.70  E-value=1e-16  Score=144.05  Aligned_cols=83  Identities=29%  Similarity=0.471  Sum_probs=74.2

Q ss_pred             CCCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhc---C-ceEEEecCCcCCC----CCCE
Q 042424           54 ETTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEF---K-DVGLMTGDVTLSP----NASC  125 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f---~-~v~~~tGd~~~~~----~~~I  125 (138)
                      ..+|.++++|||||||+++++++++++..+.++||++|+++|++|++++|++ |   + .|+.++||...+.    +.+|
T Consensus        38 ~g~nvlv~APTGSGKTlia~lail~~l~~~~kal~i~P~raLa~q~~~~~~~-~~~~g~~v~~~tGd~~~~~~~l~~~~I  116 (737)
T PRK02362         38 DGKNLLAAIPTASGKTLIAELAMLKAIARGGKALYIVPLRALASEKFEEFER-FEELGVRVGISTGDYDSRDEWLGDNDI  116 (737)
T ss_pred             CCCcEEEECCCcchHHHHHHHHHHHHHhcCCcEEEEeChHHHHHHHHHHHHH-hhcCCCEEEEEeCCcCccccccCCCCE
Confidence            4578899999999999999999999998899999999999999999999997 5   4 7889999876543    6899


Q ss_pred             EEecHHHHHHhh
Q 042424          126 LVMTTEILRGML  137 (138)
Q Consensus       126 iVtTpe~l~~lL  137 (138)
                      +|+|||+|++++
T Consensus       117 iV~Tpek~~~ll  128 (737)
T PRK02362        117 IVATSEKVDSLL  128 (737)
T ss_pred             EEECHHHHHHHH
Confidence            999999999875

>PRK01172 ski2-like helicase; Provisional

Probab=99.62  E-value=2.2e-15  Score=133.96  Aligned_cols=84  Identities=26%  Similarity=0.368  Sum_probs=72.7

Q ss_pred             CCCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhc--C-ceEEEecCCcCCC----CCCEE
Q 042424           54 ETTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEF--K-DVGLMTGDVTLSP----NASCL  126 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f--~-~v~~~tGd~~~~~----~~~Ii  126 (138)
                      ...+.++++|||||||+++++++.+++..+.++||++|+++|++|++++|++..  + .|+..+|+...+.    ..+|+
T Consensus        36 ~~~nvlv~apTGSGKTl~a~lail~~l~~~~k~v~i~P~raLa~q~~~~~~~l~~~g~~v~~~~G~~~~~~~~~~~~dIi  115 (674)
T PRK01172         36 KGENVIVSVPTAAGKTLIAYSAIYETFLAGLKSIYIVPLRSLAMEKYEELSRLRSLGMRVKISIGDYDDPPDFIKRYDVV  115 (674)
T ss_pred             cCCcEEEECCCCchHHHHHHHHHHHHHHhCCcEEEEechHHHHHHHHHHHHHHhhcCCeEEEEeCCCCCChhhhccCCEE
Confidence            346788999999999999999999998889999999999999999999998732  2 6788889875443    68999


Q ss_pred             EecHHHHHHhh
Q 042424          127 VMTTEILRGML  137 (138)
Q Consensus       127 VtTpe~l~~lL  137 (138)
                      |+|||+|++++
T Consensus       116 v~Tpek~~~l~  126 (674)
T PRK01172        116 ILTSEKADSLI  126 (674)
T ss_pred             EECHHHHHHHH
Confidence            99999999875

>PRK00254 ski2-like helicase; Provisional

Probab=99.60  E-value=5.1e-15  Score=132.80  Aligned_cols=84  Identities=30%  Similarity=0.437  Sum_probs=71.6

Q ss_pred             CCCCceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEechHHHHHHHHHHHHHh--cC-ceEEEecCCcCCC----CCCE
Q 042424           54 ETTHGTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLKALSNQKYRELHKE--FK-DVGLMTGDVTLSP----NASC  125 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~kaLv~Q~~~~l~~~--f~-~v~~~tGd~~~~~----~~~I  125 (138)
                      ..+|.++++|||||||+++++++++.+. .+.++||++|+++|++|++++|++.  ++ .|+.++||...+.    +.+|
T Consensus        38 ~g~nvlv~apTGsGKT~~~~l~il~~l~~~~~~~l~l~P~~aLa~q~~~~~~~~~~~g~~v~~~~Gd~~~~~~~~~~~~I  117 (720)
T PRK00254         38 EGKNLVLAIPTASGKTLVAEIVMVNKLLREGGKAVYLVPLKALAEEKYREFKDWEKLGLRVAMTTGDYDSTDEWLGKYDI  117 (720)
T ss_pred             CCCcEEEECCCCcHHHHHHHHHHHHHHHhcCCeEEEEeChHHHHHHHHHHHHHHhhcCCEEEEEeCCCCCchhhhccCCE
Confidence            4578889999999999999998888765 5889999999999999999999862  23 7888999876442    6799


Q ss_pred             EEecHHHHHHhh
Q 042424          126 LVMTTEILRGML  137 (138)
Q Consensus       126 iVtTpe~l~~lL  137 (138)
                      +|+|||+|++++
T Consensus       118 iV~Tpe~~~~ll  129 (720)
T PRK00254        118 IIATAEKFDSLL  129 (720)
T ss_pred             EEEcHHHHHHHH
Confidence            999999999875

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

Probab=99.59  E-value=1.1e-14  Score=106.49  Aligned_cols=83  Identities=27%  Similarity=0.365  Sum_probs=70.4

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCC--cEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC--------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQ--RVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS--------  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~--rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~--------  120 (138)
                      .++.++.+|||+|||+++..++...+.+++  +++|++|+++|++|.++++++.+.    ++..++|+...+        
T Consensus        14 ~~~~li~aptGsGKT~~~~~~~l~~~~~~~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (169)
T PF00270_consen   14 GKNVLISAPTGSGKTLAYILPALNRLQEGKDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLHGGQSISEDQREVLS   93 (169)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHTTSSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEESTTSCHHHHHHHHHH
T ss_pred             CCCEEEECCCCCccHHHHHHHHHhhhccCCCceEEEEeeccccccccccccccccccccccccccccccccccccccccc
Confidence            356789999999999999988888777644  999999999999999999999776    577778876532        


Q ss_pred             CCCCEEEecHHHHHHhh
Q 042424          121 PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 ~~~~IiVtTpe~l~~lL  137 (138)
                      .+++|+|+||++|..++
T Consensus        94 ~~~~ilv~T~~~l~~~~  110 (169)
T PF00270_consen   94 NQADILVTTPEQLLDLI  110 (169)
T ss_dssp             TTSSEEEEEHHHHHHHH
T ss_pred             ccccccccCcchhhccc
Confidence            36999999999998765

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 ....

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.49  E-value=1.5e-13  Score=116.09  Aligned_cols=83  Identities=22%  Similarity=0.203  Sum_probs=68.1

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc-------CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC---
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD-------KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS---  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~-------~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~---  120 (138)
                      .++.++++|||+|||+++++++++.+..       +.++||++|+++|+.|.++.++....    +++.++|+...+   
T Consensus        38 g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~Pt~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~  117 (434)
T PRK11192         38 GRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHA  117 (434)
T ss_pred             CCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECCcHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHH
Confidence            3678899999999999999988887642       35899999999999999998887443    678888876432   


Q ss_pred             ----CCCCEEEecHHHHHHhh
Q 042424          121 ----PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 ----~~~~IiVtTpe~l~~lL  137 (138)
                          .+.+|+|+||++|..++
T Consensus       118 ~~l~~~~~IlV~Tp~rl~~~~  138 (434)
T PRK11192        118 EVFSENQDIVVATPGRLLQYI  138 (434)
T ss_pred             HHhcCCCCEEEEChHHHHHHH
Confidence                26789999999998764

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.48  E-value=1.3e-13  Score=117.70  Aligned_cols=83  Identities=17%  Similarity=0.125  Sum_probs=67.2

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcC---------CcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC-
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDK---------QRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS-  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~---------~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~-  120 (138)
                      .++.++++|||+|||+++++++++.+..+         .++||++||++|+.|+++.+++.+.    .+..+.|+...+ 
T Consensus        38 g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil~PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~  117 (456)
T PRK10590         38 GRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINP  117 (456)
T ss_pred             CCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEEeCcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHH
Confidence            36788999999999999999998887531         3799999999999999999988543    445566766543 


Q ss_pred             ------CCCCEEEecHHHHHHhh
Q 042424          121 ------PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 ------~~~~IiVtTpe~l~~lL  137 (138)
                            ...+|+|+||++|.+++
T Consensus       118 ~~~~l~~~~~IiV~TP~rL~~~~  140 (456)
T PRK10590        118 QMMKLRGGVDVLVATPGRLLDLE  140 (456)
T ss_pred             HHHHHcCCCcEEEEChHHHHHHH
Confidence                  26799999999998764

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.48  E-value=1.3e-13  Score=116.34  Aligned_cols=83  Identities=17%  Similarity=0.071  Sum_probs=66.2

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc----------CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcC-
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD----------KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTL-  119 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~----------~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~-  119 (138)
                      ..+.++++|||||||+++++++++.+..          +.++||++|+++|+.|+++++.....    .++.+.|+... 
T Consensus        45 g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~lil~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~  124 (423)
T PRK04837         45 GRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYD  124 (423)
T ss_pred             CCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEEEECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHH
Confidence            4678899999999999999888877632          35799999999999999998877433    56777775432 


Q ss_pred             ------CCCCCEEEecHHHHHHhh
Q 042424          120 ------SPNASCLVMTTEILRGML  137 (138)
Q Consensus       120 ------~~~~~IiVtTpe~l~~lL  137 (138)
                            +.+.+|+|+||+++..++
T Consensus       125 ~~~~~l~~~~~IlV~TP~~l~~~l  148 (423)
T PRK04837        125 KQLKVLESGVDILIGTTGRLIDYA  148 (423)
T ss_pred             HHHHHhcCCCCEEEECHHHHHHHH
Confidence                  225799999999998764

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

Probab=99.48  E-value=7.9e-14  Score=125.99  Aligned_cols=123  Identities=14%  Similarity=0.172  Sum_probs=86.1

Q ss_pred             CCCCCCCCCCCCCCcchhhhhcCCCCCCcccccccCCCCc----cCCCCCCCceEECcCCCchHHHHHHHHHHHHHc--C
Q 042424           10 RKAPKADSHVRGTPKEESTKKQRNPTRSCVHEVAVPSCYT----LTTDETTHGTLTNPVYNGKTAVAEYAIAMAFRD--K   83 (138)
Q Consensus        10 ~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~p~~y~----~~~~~~~~~~l~aPTGsGKTlva~~ai~~~l~~--~   83 (138)
                      +..|+.+-.+...|...+......+.+.-   ...|...|    +.....+|.++++|||||||+++.+++++++.+  +
T Consensus         5 ~~~p~~~a~~~~~~~~l~~~l~~~L~~~g---~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~~~   81 (742)
T TIGR03817         5 EHLPARAGRTAPWPAWAHPDVVAALEAAG---IHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADDPR   81 (742)
T ss_pred             eecCCCCcccCCCCCcCCHHHHHHHHHcC---CCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhCCC
Confidence            45677777777777665544222221110   00111111    111234688899999999999999999988854  5


Q ss_pred             CcEEEEechHHHHHHHHHHHHHhc--C-ceEEEecCCcCC------CCCCEEEecHHHHHH
Q 042424           84 QRVIYTSSLKALSNQKYRELHKEF--K-DVGLMTGDVTLS------PNASCLVMTTEILRG  135 (138)
Q Consensus        84 ~rviyv~P~kaLv~Q~~~~l~~~f--~-~v~~~tGd~~~~------~~~~IiVtTpe~l~~  135 (138)
                      .++||++||++|++|++++|++..  + .+..++||...+      .+++|||+||+++..
T Consensus        82 ~~aL~l~PtraLa~q~~~~l~~l~~~~i~v~~~~Gdt~~~~r~~i~~~~~IivtTPd~L~~  142 (742)
T TIGR03817        82 ATALYLAPTKALAADQLRAVRELTLRGVRPATYDGDTPTEERRWAREHARYVLTNPDMLHR  142 (742)
T ss_pred             cEEEEEcChHHHHHHHHHHHHHhccCCeEEEEEeCCCCHHHHHHHhcCCCEEEEChHHHHH
Confidence            689999999999999999999843  2 678889987542      368999999999874

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.

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.47  E-value=1.5e-13  Score=120.92  Aligned_cols=83  Identities=16%  Similarity=0.095  Sum_probs=68.1

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc----------CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD----------KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~----------~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~  120 (138)
                      .++.++++|||||||+++++++++.+..          +.++||++||++|++|+++++.+...    .+..++|+...+
T Consensus        46 G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raLIl~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~  125 (572)
T PRK04537         46 GGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYD  125 (572)
T ss_pred             CCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEEEEeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHH
Confidence            4678899999999999999988887632          35899999999999999999988443    577788876532


Q ss_pred             -------CCCCEEEecHHHHHHhh
Q 042424          121 -------PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 -------~~~~IiVtTpe~l~~lL  137 (138)
                             .+.+|||+||++|..+|
T Consensus       126 ~q~~~l~~~~dIiV~TP~rL~~~l  149 (572)
T PRK04537        126 KQRELLQQGVDVIIATPGRLIDYV  149 (572)
T ss_pred             HHHHHHhCCCCEEEECHHHHHHHH
Confidence                   25789999999998765

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.47  E-value=1.8e-13  Score=112.44  Aligned_cols=80  Identities=21%  Similarity=0.228  Sum_probs=64.8

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcC---------------
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTL---------------  119 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~---------------  119 (138)
                      .++++|||||||+++++++++++..  +.+++|++|+++|++|++++|.+.|+ .++.++|+...               
T Consensus         2 vvi~apTGsGKT~~~~~~~l~~~~~~~~~~ii~v~P~~~L~~q~~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (358)
T TIGR01587         2 LVIEAPTGYGKTEAALLWALHSIKSQKADRVIIALPTRATINAMYRRAKELFGSNLGLLHSSSSFKRIKEMGDSEEFEHL   81 (358)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhhCCCCeEEEEeehHHHHHHHHHHHHHHhCcccEEeeccHHHHHHhccCCchhHHHH
Confidence            3699999999999999888877753  68999999999999999999999887 56655543210               


Q ss_pred             ----------CCCCCEEEecHHHHHHhh
Q 042424          120 ----------SPNASCLVMTTEILRGML  137 (138)
Q Consensus       120 ----------~~~~~IiVtTpe~l~~lL  137 (138)
                                -+..+|+|+||+++...+
T Consensus        82 ~~~~~~~~~~~~~~~I~v~T~~~l~~~~  109 (358)
T TIGR01587        82 FPLYIHSNDKLFLDPITVCTIDQVLKSV  109 (358)
T ss_pred             HHHHhhchhhhhhCCeeeCCHHHHHHHH
Confidence                      125789999999987765

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.

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.46  E-value=2e-13  Score=125.28  Aligned_cols=83  Identities=30%  Similarity=0.336  Sum_probs=66.6

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---------CCcEEEEechHHHHHHHHHHHHHh-------c--------C-c
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---------KQRVIYTSSLKALSNQKYRELHKE-------F--------K-D  109 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---------~~rviyv~P~kaLv~Q~~~~l~~~-------f--------~-~  109 (138)
                      ..|.++++|||||||+++++++++.+..         +.++||++|+++|++|+++.+.+.       +        + .
T Consensus        47 g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtraLa~di~~~L~~~l~~i~~~~~~~g~~~~~i~  126 (876)
T PRK13767         47 GKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRALNNDIHRNLEEPLTEIREIAKERGEELPEIR  126 (876)
T ss_pred             CCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCee
Confidence            4688999999999999999988877642         346999999999999999876531       1        1 5


Q ss_pred             eEEEecCCcCCC-------CCCEEEecHHHHHHhh
Q 042424          110 VGLMTGDVTLSP-------NASCLVMTTEILRGML  137 (138)
Q Consensus       110 v~~~tGd~~~~~-------~~~IiVtTpe~l~~lL  137 (138)
                      +++++||...+.       ..+|+|||||.|..++
T Consensus       127 v~v~~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll  161 (876)
T PRK13767        127 VAIRTGDTSSYEKQKMLKKPPHILITTPESLAILL  161 (876)
T ss_pred             EEEEcCCCCHHHHHHHHhCCCCEEEecHHHHHHHh
Confidence            788899976432       5789999999998765

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.46  E-value=2.6e-13  Score=115.62  Aligned_cols=83  Identities=17%  Similarity=0.172  Sum_probs=68.6

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCCcC-------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDVTL-------  119 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~~~-------  119 (138)
                      ..+.++++|||+|||+++.+++++.+..   +.++++++||++|+.|++++++....     .+..++|+...       
T Consensus        41 g~dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l  120 (460)
T PRK11776         41 GKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSL  120 (460)
T ss_pred             CCCEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHh
Confidence            4678899999999999999999988864   34799999999999999999987432     56777887654       


Q ss_pred             CCCCCEEEecHHHHHHhh
Q 042424          120 SPNASCLVMTTEILRGML  137 (138)
Q Consensus       120 ~~~~~IiVtTpe~l~~lL  137 (138)
                      ..+.+|+|+||++|..++
T Consensus       121 ~~~~~IvV~Tp~rl~~~l  138 (460)
T PRK11776        121 EHGAHIIVGTPGRILDHL  138 (460)
T ss_pred             cCCCCEEEEChHHHHHHH
Confidence            237899999999998765

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.45  E-value=1.7e-13  Score=130.64  Aligned_cols=78  Identities=31%  Similarity=0.356  Sum_probs=63.5

Q ss_pred             EECcCCCchHHHHHHHHHHHHHc-------------CCcEEEEechHHHHHHHHHHHHH----------hc-----C-ce
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRD-------------KQRVIYTSSLKALSNQKYRELHK----------EF-----K-DV  110 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~-------------~~rviyv~P~kaLv~Q~~~~l~~----------~f-----~-~v  110 (138)
                      |++|||||||++++++++..+..             +.++|||+|+|+|++|+++.|+.          .+     + .|
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            58999999999999877666531             46899999999999999999864          11     2 68


Q ss_pred             EEEecCCcCCC-------CCCEEEecHHHHHHhh
Q 042424          111 GLMTGDVTLSP-------NASCLVMTTEILRGML  137 (138)
Q Consensus       111 ~~~tGd~~~~~-------~~~IiVtTpe~l~~lL  137 (138)
                      ++++||...+.       ..+|||+|||+|+.||
T Consensus        81 ~vrtGDt~~~eR~rll~~ppdILVTTPEsL~~LL  114 (1490)
T PRK09751         81 GIRTGDTPAQERSKLTRNPPDILITTPESLYLML  114 (1490)
T ss_pred             EEEECCCCHHHHHHHhcCCCCEEEecHHHHHHHH
Confidence            89999986532       5799999999998875

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

Probab=99.45  E-value=2.1e-13  Score=123.85  Aligned_cols=84  Identities=27%  Similarity=0.321  Sum_probs=71.0

Q ss_pred             CCCCceEECcCCCchHHHHHHHHHHHHHc--------CCcEEEEechHHHHHHHHHHHHHhc---C-ceEEEecCCcCCC
Q 042424           54 ETTHGTLTNPVYNGKTAVAEYAIAMAFRD--------KQRVIYTSSLKALSNQKYRELHKEF---K-DVGLMTGDVTLSP  121 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~~ai~~~l~~--------~~rviyv~P~kaLv~Q~~~~l~~~f---~-~v~~~tGd~~~~~  121 (138)
                      ...|.+++||||||||++|+++++..+.+        |-.+|||+|.|||.+++.+.+....   + .|.+.+||++...
T Consensus        36 ~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn~Di~~rL~~~~~~~G~~v~vRhGDT~~~e  115 (814)
T COG1201          36 SGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALNNDIRRRLEEPLRELGIEVAVRHGDTPQSE  115 (814)
T ss_pred             CCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHHHHHHHHHHHHHHHHcCCccceecCCCChHH
Confidence            45789999999999999999999888753        2468999999999999999987743   3 7899999987643


Q ss_pred             -------CCCEEEecHHHHHHhh
Q 042424          122 -------NASCLVMTTEILRGML  137 (138)
Q Consensus       122 -------~~~IiVtTpe~l~~lL  137 (138)
                             -.+|+|||||.|..+|
T Consensus       116 r~r~~~~PPdILiTTPEsL~lll  138 (814)
T COG1201         116 KQKMLKNPPHILITTPESLAILL  138 (814)
T ss_pred             hhhccCCCCcEEEeChhHHHHHh
Confidence                   5679999999998776

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.45  E-value=4.4e-13  Score=114.82  Aligned_cols=81  Identities=19%  Similarity=0.135  Sum_probs=65.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc----------CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC-
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD----------KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS-  120 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~----------~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~-  120 (138)
                      ++.++++|||||||+++++++++.+.+          +.++||++||++|+.|+++.+++...    .+..++|+...+ 
T Consensus       125 ~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~aLil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~  204 (475)
T PRK01297        125 HDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDK  204 (475)
T ss_pred             CCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceEEEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHH
Confidence            578899999999999999988887643          35899999999999999999987543    566677765321 


Q ss_pred             -------CCCCEEEecHHHHHHh
Q 042424          121 -------PNASCLVMTTEILRGM  136 (138)
Q Consensus       121 -------~~~~IiVtTpe~l~~l  136 (138)
                             ...+|||+||++|..+
T Consensus       205 ~~~~~~~~~~~Iiv~TP~~Ll~~  227 (475)
T PRK01297        205 QLKQLEARFCDILVATPGRLLDF  227 (475)
T ss_pred             HHHHHhCCCCCEEEECHHHHHHH
Confidence                   2578999999999765

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.45  E-value=3.3e-13  Score=119.81  Aligned_cols=78  Identities=26%  Similarity=0.333  Sum_probs=69.0

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC-----------C
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS-----------P  121 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~-----------~  121 (138)
                      +.++++|||||||++++++++.++..|.+++|++||++|+.|+++.|++.+.    ++++++|+....           .
T Consensus       258 ~~Ll~g~TGSGKT~va~l~il~~~~~g~qvlilaPT~~LA~Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g  337 (630)
T TIGR00643       258 NRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASG  337 (630)
T ss_pred             cEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEECCHHHHHHHHHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCC
Confidence            5689999999999999999999998999999999999999999999999765    688899986532           2


Q ss_pred             CCCEEEecHHHHH
Q 042424          122 NASCLVMTTEILR  134 (138)
Q Consensus       122 ~~~IiVtTpe~l~  134 (138)
                      +.+|||+||..+.
T Consensus       338 ~~~IiVgT~~ll~  350 (630)
T TIGR00643       338 QIHLVVGTHALIQ  350 (630)
T ss_pred             CCCEEEecHHHHh
Confidence            5799999999875

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=99.44  E-value=2.7e-13  Score=126.23  Aligned_cols=85  Identities=25%  Similarity=0.312  Sum_probs=72.3

Q ss_pred             CCCCCCceEECcCCCchHHHHHHHHHHHHHcC-----------CcEEEEechHHHHHHHHHHHHHhcC----ceEEEecC
Q 042424           52 TDETTHGTLTNPVYNGKTAVAEYAIAMAFRDK-----------QRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGD  116 (138)
Q Consensus        52 ~~~~~~~~l~aPTGsGKTlva~~ai~~~l~~~-----------~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd  116 (138)
                      +....|.++|||||+|||.+|++.|++.+..+           .+++|++|++||+.++...|.+++.    .|+-+|||
T Consensus       322 l~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLvqE~VgsfSkRla~~GI~V~ElTgD  401 (1674)
T KOG0951|consen  322 LRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALVQEMVGSFSKRLAPLGITVLELTGD  401 (1674)
T ss_pred             hcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeHHHHHHHHHHHHHhhccccCcEEEEeccc
Confidence            34557899999999999999999999888642           3799999999999999999999876    68889999


Q ss_pred             CcCC----CCCCEEEecHHHHHHh
Q 042424          117 VTLS----PNASCLVMTTEILRGM  136 (138)
Q Consensus       117 ~~~~----~~~~IiVtTpe~l~~l  136 (138)
                      ....    ...+|||||||+||-+
T Consensus       402 ~~l~~~qieeTqVIV~TPEK~DiI  425 (1674)
T KOG0951|consen  402 SQLGKEQIEETQVIVTTPEKWDII  425 (1674)
T ss_pred             ccchhhhhhcceeEEeccchhhhh
Confidence            7643    3789999999999743

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.43  E-value=5.2e-13  Score=119.58  Aligned_cols=80  Identities=26%  Similarity=0.334  Sum_probs=70.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcC-----------C
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTL-----------S  120 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~-----------~  120 (138)
                      .+.++++|||||||++++++++.++..|.+++|++||++|++|+++.|++.+.    ++++++|+.+.           +
T Consensus       283 ~~~Ll~~~TGSGKT~va~~~il~~~~~g~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~  362 (681)
T PRK10917        283 MNRLLQGDVGSGKTVVAALAALAAIEAGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIAS  362 (681)
T ss_pred             ceEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhC
Confidence            36789999999999999999999998899999999999999999999998764    68899998763           1


Q ss_pred             CCCCEEEecHHHHHH
Q 042424          121 PNASCLVMTTEILRG  135 (138)
Q Consensus       121 ~~~~IiVtTpe~l~~  135 (138)
                      .+.+|+|+||..+..
T Consensus       363 g~~~IvVgT~~ll~~  377 (681)
T PRK10917        363 GEADIVIGTHALIQD  377 (681)
T ss_pred             CCCCEEEchHHHhcc
Confidence            268999999987753

>PTZ00424 helicase 45; Provisional

Probab=99.43  E-value=5.5e-13  Score=110.74  Aligned_cols=83  Identities=13%  Similarity=0.023  Sum_probs=65.7

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcC-------C
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTL-------S  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~-------~  120 (138)
                      ..+.++++|||||||+++++++.+.+..   +.++||++|+++|++|.++.+.....    .+..+.|+...       .
T Consensus        65 ~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~  144 (401)
T PTZ00424         65 GYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLK  144 (401)
T ss_pred             CCCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECCCHHHHHHHHHHHHHHhhhcCceEEEEECCcCHHHHHHHHc
Confidence            3577899999999999999888887753   57899999999999999998887543    34555665432       1


Q ss_pred             CCCCEEEecHHHHHHhh
Q 042424          121 PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 ~~~~IiVtTpe~l~~lL  137 (138)
                      .+.+|+|+||+++..++
T Consensus       145 ~~~~Ivv~Tp~~l~~~l  161 (401)
T PTZ00424        145 AGVHMVVGTPGRVYDMI  161 (401)
T ss_pred             CCCCEEEECcHHHHHHH
Confidence            25689999999988764

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

Probab=99.43  E-value=2e-13  Score=118.03  Aligned_cols=82  Identities=23%  Similarity=0.263  Sum_probs=73.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc-CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC------CCC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD-KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP------NAS  124 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~-~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~------~~~  124 (138)
                      .|.+++.|||-|||.+|.+.|...+.. ++++||++||+-|+.|+++.+++.++    .+..+||....+.      +++
T Consensus        30 ~NtLvvlPTGLGKT~IA~~V~~~~l~~~~~kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~i~~ltGev~p~~R~~~w~~~k  109 (542)
T COG1111          30 KNTLVVLPTGLGKTFIAAMVIANRLRWFGGKVLFLAPTKPLVLQHAEFCRKVTGIPEDEIAALTGEVRPEEREELWAKKK  109 (542)
T ss_pred             cCeEEEecCCccHHHHHHHHHHHHHHhcCCeEEEecCCchHHHHHHHHHHHHhCCChhheeeecCCCChHHHHHHHhhCC
Confidence            699999999999999999999988875 55899999999999999999999877    6899999987652      899


Q ss_pred             EEEecHHHHHHhh
Q 042424          125 CLVMTTEILRGML  137 (138)
Q Consensus       125 IiVtTpe~l~~lL  137 (138)
                      |+|+||+.+.|-|
T Consensus       110 VfvaTPQvveNDl  122 (542)
T COG1111         110 VFVATPQVVENDL  122 (542)
T ss_pred             EEEeccHHHHhHH
Confidence            9999999987754

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

Probab=99.42  E-value=7.9e-13  Score=114.89  Aligned_cols=83  Identities=17%  Similarity=0.067  Sum_probs=63.9

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHH----------cCCcEEEEechHHHHHHHHHHHHHhcC----c-eEEEecCCc-
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFR----------DKQRVIYTSSLKALSNQKYRELHKEFK----D-VGLMTGDVT-  118 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~----------~~~rviyv~P~kaLv~Q~~~~l~~~f~----~-v~~~tGd~~-  118 (138)
                      .++.++++|||||||++++++++.++.          .+.++||++||++|+.|.++.++....    . +.++.|+.. 
T Consensus       158 g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~~~~~~~~~gG~~~~  237 (518)
T PLN00206        158 GRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMP  237 (518)
T ss_pred             CCCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchH
Confidence            467889999999999999988876652          246899999999999999988877433    2 334445432 


Q ss_pred             -----CCCCCCEEEecHHHHHHhh
Q 042424          119 -----LSPNASCLVMTTEILRGML  137 (138)
Q Consensus       119 -----~~~~~~IiVtTpe~l~~lL  137 (138)
                           .....+|||+||++|..+|
T Consensus       238 ~q~~~l~~~~~IiV~TPgrL~~~l  261 (518)
T PLN00206        238 QQLYRIQQGVELIVGTPGRLIDLL  261 (518)
T ss_pred             HHHHHhcCCCCEEEECHHHHHHHH
Confidence                 1236899999999998775

>cd00268 DEADc DEAD-box helicases

Probab=99.42  E-value=1.1e-12  Score=99.21  Aligned_cols=83  Identities=18%  Similarity=0.100  Sum_probs=66.6

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc-----CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC-----
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD-----KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS-----  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~-----~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~-----  120 (138)
                      .++.++++|||+|||+++.+++.+.+..     +.+++|++|+++|+.|+.+.+++...    .+..++|+....     
T Consensus        36 ~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  115 (203)
T cd00268          36 GRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRK  115 (203)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHH
Confidence            4778899999999999988777666653     45899999999999999999988533    566677765432     


Q ss_pred             --CCCCEEEecHHHHHHhh
Q 042424          121 --PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 --~~~~IiVtTpe~l~~lL  137 (138)
                        .+++|+|+||+.|..++
T Consensus       116 ~~~~~~iiv~T~~~l~~~l  134 (203)
T cd00268         116 LKRGPHIVVATPGRLLDLL  134 (203)
T ss_pred             hcCCCCEEEEChHHHHHHH
Confidence              27899999999988765

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.

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

Probab=99.41  E-value=6.1e-13  Score=121.84  Aligned_cols=82  Identities=21%  Similarity=0.230  Sum_probs=71.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHHHHHHHHHHHHHhcC------ceEEEecCCcCCC------
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKALSNQKYRELHKEFK------DVGLMTGDVTLSP------  121 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~kaLv~Q~~~~l~~~f~------~v~~~tGd~~~~~------  121 (138)
                      +|.+|++|||||||.+++++|++.+.+  ..++||+.||+||++.+.++|++...      .++.++||+....      
T Consensus        86 ~~vvVtTgTgSGKTe~FllPIld~~l~~~~a~AL~lYPtnALa~DQ~~rl~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~  165 (851)
T COG1205          86 RNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNALANDQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIR  165 (851)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhhCcCccEEEEechhhhHhhHHHHHHHHHHhCCCcceeeeecCCCChHHHHHHHh
Confidence            688999999999999999999998876  45779999999999999999998433      5678999987543      


Q ss_pred             -CCCEEEecHHHHHHhh
Q 042424          122 -NASCLVMTTEILRGML  137 (138)
Q Consensus       122 -~~~IiVtTpe~l~~lL  137 (138)
                       ..+||+|||.+|+.+|
T Consensus       166 ~pp~IllTNpdMLh~~l  182 (851)
T COG1205         166 NPPDILLTNPDMLHYLL  182 (851)
T ss_pred             CCCCEEEeCHHHHHHHh
Confidence             7899999999999854

>PTZ00110 helicase; Provisional

Probab=99.38  E-value=1.4e-12  Score=114.13  Aligned_cols=83  Identities=14%  Similarity=0.036  Sum_probs=63.9

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc--------CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcC---
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD--------KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTL---  119 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~--------~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~---  119 (138)
                      .++.++++|||||||++++++++..+..        +..+|+++||++|+.|+++++++...    .+..+.|+...   
T Consensus       167 G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q  246 (545)
T PTZ00110        167 GRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQ  246 (545)
T ss_pred             CCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcEEEEECChHHHHHHHHHHHHHHhcccCccEEEEeCCCCHHHH
Confidence            3678899999999999998877655432        45799999999999999999988432    34455555432   


Q ss_pred             ----CCCCCEEEecHHHHHHhh
Q 042424          120 ----SPNASCLVMTTEILRGML  137 (138)
Q Consensus       120 ----~~~~~IiVtTpe~l~~lL  137 (138)
                          ....+|+|+||++|..+|
T Consensus       247 ~~~l~~~~~IlVaTPgrL~d~l  268 (545)
T PTZ00110        247 IYALRRGVEILIACPGRLIDFL  268 (545)
T ss_pred             HHHHHcCCCEEEECHHHHHHHH
Confidence                226899999999998765

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

Probab=99.36  E-value=1.2e-12  Score=115.16  Aligned_cols=83  Identities=25%  Similarity=0.357  Sum_probs=66.4

Q ss_pred             CCCceEECcCCCchHHHHHHHHHH-HHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCC-----------c
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAM-AFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDV-----------T  118 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~-~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~-----------~  118 (138)
                      ..|.++..+|+||||+++++|-.. ++..|++.+|++|..||+||+|++|+++|+    .+.+..|-.           .
T Consensus       232 G~nllVVSaTasGKTLIgElAGi~~~l~~g~KmlfLvPLVALANQKy~dF~~rYs~LglkvairVG~srIk~~~~pv~~~  311 (830)
T COG1202         232 GENLLVVSATASGKTLIGELAGIPRLLSGGKKMLFLVPLVALANQKYEDFKERYSKLGLKVAIRVGMSRIKTREEPVVVD  311 (830)
T ss_pred             CCceEEEeccCCCcchHHHhhCcHHHHhCCCeEEEEehhHHhhcchHHHHHHHhhcccceEEEEechhhhcccCCccccC
Confidence            367789999999999999876554 455699999999999999999999999987    233332321           2


Q ss_pred             CCCCCCEEEecHHHHHHhh
Q 042424          119 LSPNASCLVMTTEILRGML  137 (138)
Q Consensus       119 ~~~~~~IiVtTpe~l~~lL  137 (138)
                      ...+++|||.|+|-++.+|
T Consensus       312 t~~dADIIVGTYEGiD~lL  330 (830)
T COG1202         312 TSPDADIIVGTYEGIDYLL  330 (830)
T ss_pred             CCCCCcEEEeechhHHHHH
Confidence            2349999999999999886

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.35  E-value=2.5e-12  Score=118.72  Aligned_cols=78  Identities=22%  Similarity=0.222  Sum_probs=66.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC-----------
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS-----------  120 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~-----------  120 (138)
                      .+.++++|||+|||++++.+++.++..|.+++|++||++|+.|+++.|++.|.    .+++++|.....           
T Consensus       473 ~d~Ll~adTGsGKT~val~a~l~al~~g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~  552 (926)
T TIGR00580       473 MDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELAS  552 (926)
T ss_pred             CCEEEECCCCccHHHHHHHHHHHHHHhCCeEEEEeCcHHHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHc
Confidence            46789999999999999999999988899999999999999999999999876    567788765421           


Q ss_pred             CCCCEEEecHHHH
Q 042424          121 PNASCLVMTTEIL  133 (138)
Q Consensus       121 ~~~~IiVtTpe~l  133 (138)
                      .+.+|||+||..+
T Consensus       553 g~~dIVIGTp~ll  565 (926)
T TIGR00580       553 GKIDILIGTHKLL  565 (926)
T ss_pred             CCceEEEchHHHh
Confidence            1578999999655

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.

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.35  E-value=3.6e-12  Score=113.51  Aligned_cols=83  Identities=16%  Similarity=0.086  Sum_probs=66.0

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCCcC-------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDVTL-------  119 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~~~-------  119 (138)
                      ..+.++++|||+|||+++.+++++.+..   +.++||++||++|+.|+++++.+...     .+..+.|+...       
T Consensus        43 g~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l  122 (629)
T PRK11634         43 GRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRAL  122 (629)
T ss_pred             CCCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHh
Confidence            3677899999999999999988887753   45899999999999999999877432     45555565533       


Q ss_pred             CCCCCEEEecHHHHHHhh
Q 042424          120 SPNASCLVMTTEILRGML  137 (138)
Q Consensus       120 ~~~~~IiVtTpe~l~~lL  137 (138)
                      ....+|||+||++|..+|
T Consensus       123 ~~~~~IVVgTPgrl~d~l  140 (629)
T PRK11634        123 RQGPQIVVGTPGRLLDHL  140 (629)
T ss_pred             cCCCCEEEECHHHHHHHH
Confidence            236899999999998765

>TIGR00595 priA primosomal protein N'

Probab=99.31  E-value=5.6e-12  Score=109.73  Aligned_cols=75  Identities=21%  Similarity=0.166  Sum_probs=65.8

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcCC-----------CCCCEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTLS-----------PNASCL  126 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~~-----------~~~~Ii  126 (138)
                      +|.+|||||||.+++.++.+++.+|++++|++|+++|+.|+++.|++.|+ ++.+++|+....           .+.+||
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            37899999999999988888888899999999999999999999999898 788898876431           267899


Q ss_pred             EecHHHH
Q 042424          127 VMTTEIL  133 (138)
Q Consensus       127 VtTpe~l  133 (138)
                      |+|+..+
T Consensus        81 VGTrsal   87 (505)
T TIGR00595        81 IGTRSAL   87 (505)
T ss_pred             ECChHHH
Confidence            9999765

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).

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.31  E-value=1.1e-11  Score=103.30  Aligned_cols=78  Identities=13%  Similarity=0.044  Sum_probs=61.1

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC--------ceEEEecCCcCC--------
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK--------DVGLMTGDVTLS--------  120 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~--------~v~~~tGd~~~~--------  120 (138)
                      +.++++|||||||++++++++.   .+.+++|++|+++|++|++++|++.+.        .+..++|+...+        
T Consensus        16 ~~~i~apTGsGKT~~~~~~~l~---~~~~~~~~~P~~aL~~~~~~~~~~~~~~~~~~~~~~v~~~~g~~~~d~~~~~~~~   92 (357)
T TIGR03158        16 IIFNTAPTGAGKTLAWLTPLLH---GENDTIALYPTNALIEDQTEAIKEFVDVFKPERDVNLLHVSKATLKDIKEYANDK   92 (357)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH---cCCCEEEEeChHHHHHHHHHHHHHHHHhcCCCCCceEEEecCCchHHHHHhhhhh
Confidence            3568999999999999887763   467899999999999999999999762        355667762211        


Q ss_pred             -------------------CCCCEEEecHHHHHHhh
Q 042424          121 -------------------PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 -------------------~~~~IiVtTpe~l~~lL  137 (138)
                                         ....|++|||++|+.++
T Consensus        93 ~~~~~g~~~~~~~r~~~~~~~p~illT~p~~l~~ll  128 (357)
T TIGR03158        93 VGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLT  128 (357)
T ss_pred             cccCccchhhhhHHHHHhcCCCCEEEecHHHHHHHH
Confidence                               13668999999998765

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.

>KOG0350 consensus DEAD-box ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.29  E-value=4.1e-12  Score=110.06  Aligned_cols=82  Identities=22%  Similarity=0.255  Sum_probs=67.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc----CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC-------
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD----KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS-------  120 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~----~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~-------  120 (138)
                      ++..+.||||||||+++...|.+++.+    .-|+++|+|++.|+.|.++.|.+...    .|+.++|.....       
T Consensus       184 rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~LRavVivPtr~L~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL~  263 (620)
T KOG0350|consen  184 RDICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTRELALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLA  263 (620)
T ss_pred             CceEEecCCCCCceeeehhHHHHHHccCCccceEEEEEeeHHHHHHHHHHHHHHhccCCceEEEecccccchHHHHHHHh
Confidence            455599999999999999999999865    46899999999999999999998654    577777765432       


Q ss_pred             --C---CCCEEEecHHHHHHhh
Q 042424          121 --P---NASCLVMTTEILRGML  137 (138)
Q Consensus       121 --~---~~~IiVtTpe~l~~lL  137 (138)
                        +   ..+|+|+||.+|..-|
T Consensus       264 ~~~~~~~~DIlVaTPGRLVDHl  285 (620)
T KOG0350|consen  264 SDPPECRIDILVATPGRLVDHL  285 (620)
T ss_pred             cCCCccccceEEcCchHHHHhc
Confidence              1   5699999999997655

>KOG0354 consensus DEAD-box like helicase [General function prediction only]

Probab=99.28  E-value=1e-11  Score=111.69  Aligned_cols=83  Identities=23%  Similarity=0.249  Sum_probs=68.4

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCC-cCCC------CC
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDV-TLSP------NA  123 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~-~~~~------~~  123 (138)
                      ..|.++++|||+|||++|.+.|..+++.  +.++||++|++-|++|+...|...+.  .+....||. ....      ..
T Consensus        76 gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~~KiVF~aP~~pLv~QQ~a~~~~~~~~~~~T~~l~~~~~~~~r~~i~~s~  155 (746)
T KOG0354|consen   76 GKNTIIALPTGSGKTFIAAVIMKNHFEWRPKGKVVFLAPTRPLVNQQIACFSIYLIPYSVTGQLGDTVPRSNRGEIVASK  155 (746)
T ss_pred             cCCeEEEeecCCCccchHHHHHHHHHhcCCcceEEEeeCCchHHHHHHHHHhhccCcccceeeccCccCCCchhhhhccc
Confidence            4799999999999999999999999885  79999999999999999988887443  454444543 3221      78


Q ss_pred             CEEEecHHHHHHhh
Q 042424          124 SCLVMTTEILRGML  137 (138)
Q Consensus       124 ~IiVtTpe~l~~lL  137 (138)
                      +|+|+||+.+.+.|
T Consensus       156 ~vff~TpQil~ndL  169 (746)
T KOG0354|consen  156 RVFFRTPQILENDL  169 (746)
T ss_pred             ceEEeChHhhhhhc
Confidence            89999999998876

>PRK13766 Hef nuclease; Provisional

Probab=99.27  E-value=2.1e-11  Score=109.76  Aligned_cols=82  Identities=24%  Similarity=0.310  Sum_probs=69.3

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC------CCCC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS------PNAS  124 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~------~~~~  124 (138)
                      +|.++++|||+|||+++.+.+...+. .++++||++|+++|++|+.+.|++.++    .+..++|+...+      .+++
T Consensus        30 ~n~lv~~ptG~GKT~~a~~~i~~~l~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~r~~~~~~~~  109 (773)
T PRK13766         30 KNTLVVLPTGLGKTAIALLVIAERLHKKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTGEVSPEKRAELWEKAK  109 (773)
T ss_pred             CCeEEEcCCCccHHHHHHHHHHHHHHhCCCeEEEEeCcHHHHHHHHHHHHHHhCCCCceEEEEeCCCCHHHHHHHHhCCC
Confidence            58899999999999999888877764 378999999999999999999999765    577888886543      1789


Q ss_pred             EEEecHHHHHHhh
Q 042424          125 CLVMTTEILRGML  137 (138)
Q Consensus       125 IiVtTpe~l~~lL  137 (138)
                      |+|+||+.+.+.+
T Consensus       110 iiv~T~~~l~~~l  122 (773)
T PRK13766        110 VIVATPQVIENDL  122 (773)
T ss_pred             EEEECHHHHHHHH
Confidence            9999999987643

>KOG0331 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.24  E-value=6.9e-11  Score=103.07  Aligned_cols=84  Identities=14%  Similarity=0.050  Sum_probs=66.5

Q ss_pred             CCCCceEECcCCCchHHHHHHHHHHHHHc---------CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC
Q 042424           54 ETTHGTLTNPVYNGKTAVAEYAIAMAFRD---------KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS  120 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~~ai~~~l~~---------~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~  120 (138)
                      ..++.+..+-||||||+.+++.+.+.+..         +-++|+++|||+|+.|..+++.+.-.    ....+.|+....
T Consensus       127 ~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~  206 (519)
T KOG0331|consen  127 SGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKG  206 (519)
T ss_pred             cCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEEcCcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCcc
Confidence            34677799999999999999877777664         56799999999999999999999433    233344555543


Q ss_pred             -------CCCCEEEecHHHHHHhh
Q 042424          121 -------PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 -------~~~~IiVtTpe~l~~lL  137 (138)
                             ...+|+|+||.++..+|
T Consensus       207 ~Q~~~l~~gvdiviaTPGRl~d~l  230 (519)
T KOG0331|consen  207 PQLRDLERGVDVVIATPGRLIDLL  230 (519)
T ss_pred             HHHHHHhcCCcEEEeCChHHHHHH
Confidence                   27899999999998876

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.24  E-value=5.3e-11  Score=103.16  Aligned_cols=79  Identities=14%  Similarity=0.139  Sum_probs=60.2

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCC-cEEEEechHHHHHHHHHHHHHhcC----ce-EEEecCCcCCCCCCEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQ-RVIYTSSLKALSNQKYRELHKEFK----DV-GLMTGDVTLSPNASCLVMT  129 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~-rviyv~P~kaLv~Q~~~~l~~~f~----~v-~~~tGd~~~~~~~~IiVtT  129 (138)
                      .+.++++|||+|||+++...+...+..++ ++++++|+++|++|+.++|++...    .+ ++..| .....+.+|+|+|
T Consensus       130 ~~~il~apTGsGKT~i~~~l~~~~~~~~~~~vLilvpt~eL~~Q~~~~l~~~~~~~~~~~~~i~~g-~~~~~~~~I~VaT  208 (501)
T PHA02558        130 NRRLLNLPTSAGKSLIQYLLSRYYLENYEGKVLIIVPTTSLVTQMIDDFVDYRLFPREAMHKIYSG-TAKDTDAPIVVST  208 (501)
T ss_pred             CceEEEeCCCCCHHHHHHHHHHHHHhcCCCeEEEEECcHHHHHHHHHHHHHhccccccceeEEecC-cccCCCCCEEEee
Confidence            56789999999999998654444444444 999999999999999999998432    33 34444 3444578999999


Q ss_pred             HHHHHH
Q 042424          130 TEILRG  135 (138)
Q Consensus       130 pe~l~~  135 (138)
                      ++.+..
T Consensus       209 ~qsl~~  214 (501)
T PHA02558        209 WQSAVK  214 (501)
T ss_pred             HHHHhh
Confidence            999865

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.24  E-value=3.2e-11  Score=108.23  Aligned_cols=79  Identities=19%  Similarity=0.156  Sum_probs=68.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcCC-----------CCC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTLS-----------PNA  123 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~~-----------~~~  123 (138)
                      .+.++.+|||||||.+++.++..++..|+++++++|+++|+.|+++.|++.|+ .+.+++|+....           .+.
T Consensus       163 ~~~Ll~~~TGSGKT~v~l~~i~~~l~~g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~  242 (679)
T PRK05580        163 SPFLLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEA  242 (679)
T ss_pred             CcEEEECCCCChHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCC
Confidence            45679999999999999989988888899999999999999999999999887 788898876431           257


Q ss_pred             CEEEecHHHHH
Q 042424          124 SCLVMTTEILR  134 (138)
Q Consensus       124 ~IiVtTpe~l~  134 (138)
                      +|+|+|+..+.
T Consensus       243 ~IVVgTrsal~  253 (679)
T PRK05580        243 KVVIGARSALF  253 (679)
T ss_pred             CEEEeccHHhc
Confidence            89999997653

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.22  E-value=3.8e-11  Score=112.91  Aligned_cols=79  Identities=20%  Similarity=0.254  Sum_probs=65.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC-----------
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS-----------  120 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~-----------  120 (138)
                      .+.++++|||+|||.+++.+++.++.+|.++++++||++|+.|+++.|++.|.    .+..++|.....           
T Consensus       622 ~d~Ll~a~TGsGKT~val~aa~~~~~~g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~  701 (1147)
T PRK10689        622 MDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAE  701 (1147)
T ss_pred             CCEEEEcCCCcCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHh
Confidence            46789999999999999988888888899999999999999999999998775    466677654321           


Q ss_pred             CCCCEEEecHHHHH
Q 042424          121 PNASCLVMTTEILR  134 (138)
Q Consensus       121 ~~~~IiVtTpe~l~  134 (138)
                      .+.+|||+||+.+.
T Consensus       702 g~~dIVVgTp~lL~  715 (1147)
T PRK10689        702 GKIDILIGTHKLLQ  715 (1147)
T ss_pred             CCCCEEEECHHHHh
Confidence            25789999998654

>KOG0345 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.21  E-value=4.7e-11  Score=102.88  Aligned_cols=88  Identities=15%  Similarity=0.089  Sum_probs=69.9

Q ss_pred             cCCCCCCCceEECcCCCchHHHHHHHHHHHHHc------CC--cEEEEechHHHHHHHHHHHHHhcC-----ceEEEecC
Q 042424           50 LTTDETTHGTLTNPVYNGKTAVAEYAIAMAFRD------KQ--RVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGD  116 (138)
Q Consensus        50 ~~~~~~~~~~l~aPTGsGKTlva~~ai~~~l~~------~~--rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd  116 (138)
                      |++..+.+.++-+|||||||+++++.++..+.+      ..  .+++++|||+|+.|+.+..+....     ++.++.|.
T Consensus        38 Plll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalIIsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG  117 (567)
T KOG0345|consen   38 PLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPTRELARQIREVAQPFLEHLPNLNCELLVGG  117 (567)
T ss_pred             HHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEEEecCcHHHHHHHHHHHHHHHHhhhccceEEEecC
Confidence            344455777899999999999999999998832      22  589999999999999988776322     57777777


Q ss_pred             CcCCC--------CCCEEEecHHHHHHhh
Q 042424          117 VTLSP--------NASCLVMTTEILRGML  137 (138)
Q Consensus       117 ~~~~~--------~~~IiVtTpe~l~~lL  137 (138)
                      .....        +++|+|+||.+|..++
T Consensus       118 ~~v~~Di~~fkee~~nIlVgTPGRL~di~  146 (567)
T KOG0345|consen  118 RSVEEDIKTFKEEGPNILVGTPGRLLDIL  146 (567)
T ss_pred             ccHHHHHHHHHHhCCcEEEeCchhHHHHH
Confidence            65532        7889999999998875

>KOG0335 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.19  E-value=7.1e-11  Score=102.01  Aligned_cols=82  Identities=23%  Similarity=0.254  Sum_probs=64.5

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc-------------CCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecC
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD-------------KQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGD  116 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~-------------~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd  116 (138)
                      .+..+.||+||||||.++++.+...+.+             .-++++++||++|++|.|.+-++ |.     .+....|+
T Consensus       111 Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~Qi~nea~k-~~~~s~~~~~~~ygg  189 (482)
T KOG0335|consen  111 GRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALILAPTRELVDQIYNEARK-FSYLSGMKSVVVYGG  189 (482)
T ss_pred             CCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCCCCCCceEEEeCcHHHhhHHHHHHHh-hcccccceeeeeeCC
Confidence            4566799999999999999888877653             15799999999999999999888 43     34444454


Q ss_pred             CcC-------CCCCCEEEecHHHHHHhh
Q 042424          117 VTL-------SPNASCLVMTTEILRGML  137 (138)
Q Consensus       117 ~~~-------~~~~~IiVtTpe~l~~lL  137 (138)
                      .+.       ...++|+|+||.+|.+++
T Consensus       190 ~~~~~q~~~~~~gcdIlvaTpGrL~d~~  217 (482)
T KOG0335|consen  190 TDLGAQLRFIKRGCDILVATPGRLKDLI  217 (482)
T ss_pred             cchhhhhhhhccCccEEEecCchhhhhh
Confidence            332       238999999999998875

>PRK09401 reverse gyrase; Reviewed

Probab=99.18  E-value=1.3e-10  Score=109.51  Aligned_cols=83  Identities=17%  Similarity=0.090  Sum_probs=61.8

Q ss_pred             CCCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcC----------
Q 042424           54 ETTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTL----------  119 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~----------  119 (138)
                      ..++.++++|||+|||.+++..+.....++.+++|++||++|+.|+++.|++...    .+..+.|....          
T Consensus        94 ~g~dv~i~ApTGsGKT~f~l~~~~~l~~~g~~alIL~PTreLa~Qi~~~l~~l~~~~~~~~~~~~g~~~~~~~ek~~~~~  173 (1176)
T PRK09401         94 LGESFAIIAPTGVGKTTFGLVMSLYLAKKGKKSYIIFPTRLLVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLE  173 (1176)
T ss_pred             CCCcEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEEeccHHHHHHHHHHHHHHhhhcCceEEEEEccCCcchhHHHHHHH
Confidence            3467889999999999765544333334589999999999999999999998543    34555544321          


Q ss_pred             ---CCCCCEEEecHHHHHHh
Q 042424          120 ---SPNASCLVMTTEILRGM  136 (138)
Q Consensus       120 ---~~~~~IiVtTpe~l~~l  136 (138)
                         ..+.+|+|+||+.+...
T Consensus       174 ~l~~~~~~IlV~Tp~rL~~~  193 (1176)
T PRK09401        174 RLKEGDFDILVTTSQFLSKN  193 (1176)
T ss_pred             HHhcCCCCEEEECHHHHHHH
Confidence               12589999999998764

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.18  E-value=3.6e-10  Score=77.79  Aligned_cols=80  Identities=25%  Similarity=0.281  Sum_probs=64.0

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHH--cCCcEEEEechHHHHHHHHHHHHHhcC---ceEEEecCCcC-------CCCCC
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFR--DKQRVIYTSSLKALSNQKYRELHKEFK---DVGLMTGDVTL-------SPNAS  124 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~--~~~rviyv~P~kaLv~Q~~~~l~~~f~---~v~~~tGd~~~-------~~~~~  124 (138)
                      +.++.+|||+|||.++...+.+.+.  ..++++|++|+++|++|..+.+...+.   .+..+.+....       ..+.+
T Consensus         2 ~~~i~~~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~p~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKVGYLIGGTSIKQQEKLLSGKTD   81 (144)
T ss_pred             CEEEECCCCCchhHHHHHHHHHHHhcccCCCEEEEcCcHHHHHHHHHHHHHHhhCCcEEEEEecCcchhHHHHHhcCCCC
Confidence            4579999999999999877777665  468999999999999999999988763   46666654432       24889


Q ss_pred             EEEecHHHHHHh
Q 042424          125 CLVMTTEILRGM  136 (138)
Q Consensus       125 IiVtTpe~l~~l  136 (138)
                      |+++|++.+...
T Consensus        82 i~i~t~~~~~~~   93 (144)
T cd00046          82 IVVGTPGRLLDE   93 (144)
T ss_pred             EEEECcHHHHHH
Confidence            999999987643

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

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

Probab=99.16  E-value=9.7e-11  Score=102.09  Aligned_cols=84  Identities=19%  Similarity=0.141  Sum_probs=67.8

Q ss_pred             CCCCceEECcCCCchHHHHHHHHHHHHH--cC-C-c-EEEEechHHHHHHHHHHHHHhcC-----ceEEEecCCcCCC--
Q 042424           54 ETTHGTLTNPVYNGKTAVAEYAIAMAFR--DK-Q-R-VIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDVTLSP--  121 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~~ai~~~l~--~~-~-r-viyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~~~~~--  121 (138)
                      ..++.+..++||+|||+++.+++++.+.  .. . . +|+++|||+|+.|.++++.+.-.     .+..+.|......  
T Consensus        65 ~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~  144 (513)
T COG0513          65 AGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQI  144 (513)
T ss_pred             CCCCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHH
Confidence            3477889999999999999999999887  22 2 2 89999999999999999988422     3567777765332  


Q ss_pred             -----CCCEEEecHHHHHHhh
Q 042424          122 -----NASCLVMTTEILRGML  137 (138)
Q Consensus       122 -----~~~IiVtTpe~l~~lL  137 (138)
                           ..+|||+||.++.+++
T Consensus       145 ~~l~~~~~ivVaTPGRllD~i  165 (513)
T COG0513         145 EALKRGVDIVVATPGRLLDLI  165 (513)
T ss_pred             HHHhcCCCEEEECccHHHHHH
Confidence                 5899999999998876

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.15  E-value=2.2e-10  Score=98.41  Aligned_cols=75  Identities=13%  Similarity=0.094  Sum_probs=61.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcCC-----------CCC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTLS-----------PNA  123 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~~-----------~~~  123 (138)
                      ++.++++|||+|||+++.++++   ..+..+|+++|+++|+.|+++.|+. ++ .+..++|+...+           ...
T Consensus        27 ~dvlv~apTGsGKTl~y~lp~l---~~~~~~lVi~P~~~L~~dq~~~l~~-~gi~~~~l~~~~~~~~~~~i~~~~~~~~~  102 (470)
T TIGR00614        27 RDCFVVMPTGGGKSLCYQLPAL---CSDGITLVISPLISLMEDQVLQLKA-SGIPATFLNSSQSKEQQKNVLTDLKDGKI  102 (470)
T ss_pred             CCEEEEcCCCCcHhHHHHHHHH---HcCCcEEEEecHHHHHHHHHHHHHH-cCCcEEEEeCCCCHHHHHHHHHHHhcCCC
Confidence            5778999999999999887764   3477899999999999999999987 55 677777765432           257


Q ss_pred             CEEEecHHHHH
Q 042424          124 SCLVMTTEILR  134 (138)
Q Consensus       124 ~IiVtTpe~l~  134 (138)
                      +|+++|||.+.
T Consensus       103 ~il~~TPe~l~  113 (470)
T TIGR00614       103 KLLYVTPEKCS  113 (470)
T ss_pred             CEEEECHHHHc
Confidence            89999999874

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

>KOG0348 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.13  E-value=1.9e-10  Score=100.59  Aligned_cols=83  Identities=20%  Similarity=0.174  Sum_probs=65.5

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---------CCcEEEEechHHHHHHHHHHHHHhcC------ceEEEecCCcC
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---------KQRVIYTSSLKALSNQKYRELHKEFK------DVGLMTGDVTL  119 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---------~~rviyv~P~kaLv~Q~~~~l~~~f~------~v~~~tGd~~~  119 (138)
                      .++.+|.++||||||+++++.+.+.|..         |.-+++++|||+|+.|.|+.+++...      ...++.|+...
T Consensus       174 grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkK  253 (708)
T KOG0348|consen  174 GRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKK  253 (708)
T ss_pred             CcceEEEcCCCCcccHHHHHHHHHHHHhcCccccccCCceEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccc
Confidence            3566799999999999999999988753         56689999999999999999999655      22334444433


Q ss_pred             C------CCCCEEEecHHHHHHhh
Q 042424          120 S------PNASCLVMTTEILRGML  137 (138)
Q Consensus       120 ~------~~~~IiVtTpe~l~~lL  137 (138)
                      .      ...+|+|+||.+|..-|
T Consensus       254 SEKARLRKGiNILIgTPGRLvDHL  277 (708)
T KOG0348|consen  254 SEKARLRKGINILIGTPGRLVDHL  277 (708)
T ss_pred             cHHHHHhcCceEEEcCchHHHHHH
Confidence            2      28999999999987654

>KOG0949 consensus Predicted helicase, DEAD-box superfamily [General function prediction only]

Probab=99.10  E-value=6.2e-11  Score=108.85  Aligned_cols=94  Identities=28%  Similarity=0.429  Sum_probs=77.2

Q ss_pred             cCCCCccCCC----CCCCceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHHHHHHHHHHHHHhcC---------
Q 042424           44 VPSCYTLTTD----ETTHGTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKALSNQKYRELHKEFK---------  108 (138)
Q Consensus        44 ~p~~y~~~~~----~~~~~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~kaLv~Q~~~~l~~~f~---------  108 (138)
                      .|+.||--+.    .+.+.+|+|||++|||+++.|+|...++.  .+-+||++|++||++|...+...+|.         
T Consensus       511 ~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfisfY~iEKVLResD~~VVIyvaPtKaLVnQvsa~VyaRF~~~t~~rg~s  590 (1330)
T KOG0949|consen  511 CPDEWQRELLDSVDRNESAVIVAPTSAGKTFISFYAIEKVLRESDSDVVIYVAPTKALVNQVSANVYARFDTKTFLRGVS  590 (1330)
T ss_pred             CCcHHHHHHhhhhhcccceEEEeeccCCceeccHHHHHHHHhhcCCCEEEEecchHHHhhhhhHHHHHhhccCccccchh
Confidence            5667873322    23567899999999999999999999985  67899999999999999999999885         


Q ss_pred             ceEEEecCCcCCC-CCCEEEecHHHHHHhh
Q 042424          109 DVGLMTGDVTLSP-NASCLVMTTEILRGML  137 (138)
Q Consensus       109 ~v~~~tGd~~~~~-~~~IiVtTpe~l~~lL  137 (138)
                      -.|.++-|..+++ +++|+||.||.+.++|
T Consensus       591 l~g~ltqEYsinp~nCQVLITvPecleslL  620 (1330)
T KOG0949|consen  591 LLGDLTQEYSINPWNCQVLITVPECLESLL  620 (1330)
T ss_pred             hHhhhhHHhcCCchhceEEEEchHHHHHHh
Confidence            1345566666664 9999999999999987

>TIGR01054 rgy reverse gyrase

Probab=99.10  E-value=3e-10  Score=107.17  Aligned_cols=83  Identities=14%  Similarity=0.091  Sum_probs=61.9

Q ss_pred             CCCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-------ceEEEecCCcCC------
Q 042424           54 ETTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-------DVGLMTGDVTLS------  120 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-------~v~~~tGd~~~~------  120 (138)
                      ..++.++++|||+|||+.++.++.....++.+++|++||++|+.|+++.|++.+.       .++.++|+....      
T Consensus        92 ~G~d~vi~ApTGsGKT~f~l~~~~~l~~~g~~vLIL~PTreLa~Qi~~~l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~  171 (1171)
T TIGR01054        92 RGDSFAIIAPTGVGKTTFGLAMSLFLAKKGKRCYIILPTTLLVIQVAEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFM  171 (1171)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEeCHHHHHHHHHHHHHHHHHhcCCceeeeeeecCCCCHHHHHHHH
Confidence            3467789999999999855433333334588999999999999999999998543       134567765431      


Q ss_pred             -----CCCCEEEecHHHHHHh
Q 042424          121 -----PNASCLVMTTEILRGM  136 (138)
Q Consensus       121 -----~~~~IiVtTpe~l~~l  136 (138)
                           .+.+|+|+||..+...
T Consensus       172 ~~l~~~~~dIlV~Tp~rL~~~  192 (1171)
T TIGR01054       172 ERIENGDFDILITTTMFLSKN  192 (1171)
T ss_pred             HHHhcCCCCEEEECHHHHHHH
Confidence                 2489999999998754

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.

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.05  E-value=4.6e-10  Score=98.76  Aligned_cols=76  Identities=14%  Similarity=0.118  Sum_probs=61.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcCC-----------CCC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTLS-----------PNA  123 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~~-----------~~~  123 (138)
                      ++.++++|||+|||+++.++++   ..++.++|++|+++|+.|+++.|+. ++ .+..++|+...+           ...
T Consensus        29 ~dvlv~~PTG~GKTl~y~lpal---~~~g~~lVisPl~sL~~dq~~~l~~-~gi~~~~~~s~~~~~~~~~~~~~l~~~~~  104 (591)
T TIGR01389        29 RDVLVVMPTGGGKSLCYQVPAL---LLKGLTVVISPLISLMKDQVDQLRA-AGVAAAYLNSTLSAKEQQDIEKALVNGEL  104 (591)
T ss_pred             CCEEEEcCCCccHhHHHHHHHH---HcCCcEEEEcCCHHHHHHHHHHHHH-cCCcEEEEeCCCCHHHHHHHHHHHhCCCC
Confidence            5778999999999999976654   3467899999999999999999988 55 777777765432           257


Q ss_pred             CEEEecHHHHHH
Q 042424          124 SCLVMTTEILRG  135 (138)
Q Consensus       124 ~IiVtTpe~l~~  135 (138)
                      +|+++|||++.+
T Consensus       105 ~il~~tpe~l~~  116 (591)
T TIGR01389       105 KLLYVAPERLEQ  116 (591)
T ss_pred             CEEEEChhHhcC
Confidence            899999999854

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.

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=99.05  E-value=2.8e-10  Score=99.99  Aligned_cols=76  Identities=22%  Similarity=0.166  Sum_probs=64.6

Q ss_pred             EECcCCCchHHHHHHHHHHHHHc-------CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC------C
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRD-------KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP------N  122 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~-------~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~------~  122 (138)
                      =.+-||||||++++..++++|.+       |--+|+|+|||+|+.|.+..+.+.-.    +.|++.|......      .
T Consensus       111 GAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGalIISPTRELA~QtFevL~kvgk~h~fSaGLiiGG~~~k~E~eRi~~  190 (758)
T KOG0343|consen  111 GAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGALIISPTRELALQTFEVLNKVGKHHDFSAGLIIGGKDVKFELERISQ  190 (758)
T ss_pred             cccccCCCceeeehHHHHHHHHHcCCCCCCCceeEEecchHHHHHHHHHHHHHHhhccccccceeecCchhHHHHHhhhc
Confidence            45669999999999999988754       67899999999999999999998533    7899988766543      8


Q ss_pred             CCEEEecHHHHHH
Q 042424          123 ASCLVMTTEILRG  135 (138)
Q Consensus       123 ~~IiVtTpe~l~~  135 (138)
                      .+|+||||.+|+-
T Consensus       191 mNILVCTPGRLLQ  203 (758)
T KOG0343|consen  191 MNILVCTPGRLLQ  203 (758)
T ss_pred             CCeEEechHHHHH
Confidence            8999999999874

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

Probab=99.05  E-value=4.7e-10  Score=100.01  Aligned_cols=78  Identities=26%  Similarity=0.316  Sum_probs=69.8

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC-----------C
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS-----------P  121 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~-----------~  121 (138)
                      +++|.+.-|||||+||++|++.++..|..+..++||.-|++|+|+.+.+.|.    +|+++||..+-.           -
T Consensus       285 ~RLlQGDVGSGKTvVA~laml~ai~~G~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G  364 (677)
T COG1200         285 NRLLQGDVGSGKTVVALLAMLAAIEAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASG  364 (677)
T ss_pred             HHHhccCcCCCHHHHHHHHHHHHHHcCCeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCC
Confidence            6779999999999999999999999999999999999999999999999886    689999977532           2


Q ss_pred             CCCEEEecHHHHH
Q 042424          122 NASCLVMTTEILR  134 (138)
Q Consensus       122 ~~~IiVtTpe~l~  134 (138)
                      +.+|+|.|..-+.
T Consensus       365 ~~~ivVGTHALiQ  377 (677)
T COG1200         365 EIDIVVGTHALIQ  377 (677)
T ss_pred             CCCEEEEcchhhh
Confidence            7899999987654

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]

Probab=99.03  E-value=4.6e-10  Score=105.11  Aligned_cols=88  Identities=24%  Similarity=0.383  Sum_probs=74.7

Q ss_pred             CccCCCCCCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCCcCCC-
Q 042424           48 YTLTTDETTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDVTLSP-  121 (138)
Q Consensus        48 y~~~~~~~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~~~~~-  121 (138)
                      |..+...+.+.++++|+|+|||.||++|+++ -....+++|++|..+++..++++|.+.|+     .+..++|+...+. 
T Consensus      1152 f~~~y~~nd~v~vga~~gsgkt~~ae~a~l~-~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~~G~~~~~l~ge~s~~lk 1230 (1674)
T KOG0951|consen 1152 FTSLYNTNDNVLVGAPNGSGKTACAELALLR-PDTIGRAVYIAPLEEIADEQYRDWEKKFSKLLGLRIVKLTGETSLDLK 1230 (1674)
T ss_pred             EeeeecccceEEEecCCCCchhHHHHHHhcC-CccceEEEEecchHHHHHHHHHHHHHhhccccCceEEecCCccccchH
Confidence            4445556678889999999999999999976 12368999999999999999999999997     4667789887765 


Q ss_pred             ---CCCEEEecHHHHHHh
Q 042424          122 ---NASCLVMTTEILRGM  136 (138)
Q Consensus       122 ---~~~IiVtTpe~l~~l  136 (138)
                         ..+|+|+|||+|+.+
T Consensus      1231 l~~~~~vii~tpe~~d~l 1248 (1674)
T KOG0951|consen 1231 LLQKGQVIISTPEQWDLL 1248 (1674)
T ss_pred             HhhhcceEEechhHHHHH
Confidence               899999999999875

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.03  E-value=1.3e-09  Score=98.58  Aligned_cols=76  Identities=17%  Similarity=0.139  Sum_probs=63.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC--CCCEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP--NASCLVMT  129 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~--~~~IiVtT  129 (138)
                      ++.+|+.|||+|||++++.++...   ++++|+++|+..|++|+.++|.+.+.    .++.++|+.....  ..+|+|+|
T Consensus       274 r~GIIvLPtGaGKTlvai~aa~~l---~k~tLILvps~~Lv~QW~~ef~~~~~l~~~~I~~~tg~~k~~~~~~~~VvVtT  350 (732)
T TIGR00603       274 RSGIIVLPCGAGKSLVGVTAACTV---KKSCLVLCTSAVSVEQWKQQFKMWSTIDDSQICRFTSDAKERFHGEAGVVVST  350 (732)
T ss_pred             CCcEEEeCCCCChHHHHHHHHHHh---CCCEEEEeCcHHHHHHHHHHHHHhcCCCCceEEEEecCcccccccCCcEEEEE
Confidence            467899999999999998766532   68899999999999999999998543    6788888765543  57899999


Q ss_pred             HHHHH
Q 042424          130 TEILR  134 (138)
Q Consensus       130 pe~l~  134 (138)
                      ++.+.
T Consensus       351 Yq~l~  355 (732)
T TIGR00603       351 YSMVA  355 (732)
T ss_pred             HHHhh
Confidence            98874

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).

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.02  E-value=2.2e-09  Score=78.10  Aligned_cols=82  Identities=30%  Similarity=0.302  Sum_probs=63.2

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC--CcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCCc------CCCC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK--QRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDVT------LSPN  122 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~--~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~~------~~~~  122 (138)
                      .+.++++|||+|||.++..++.+.+..+  .+++|++|+.+++.|..+++++.+.     ....+.+...      ...+
T Consensus        25 ~~~~i~~~~GsGKT~~~~~~~~~~~~~~~~~~~l~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  104 (201)
T smart00487       25 RDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESG  104 (201)
T ss_pred             CcEEEECCCCCchhHHHHHHHHHHhcccCCCcEEEEeCCHHHHHHHHHHHHHHhccCCeEEEEEeCCcchHHHHHHHhcC
Confidence            5667999999999998887777776654  8999999999999999999998763     2344444332      1223


Q ss_pred             C-CEEEecHHHHHHhh
Q 042424          123 A-SCLVMTTEILRGML  137 (138)
Q Consensus       123 ~-~IiVtTpe~l~~lL  137 (138)
                      . +|+++|++.+...+
T Consensus       105 ~~~v~~~t~~~l~~~~  120 (201)
T smart00487      105 KTDILVTTPGRLLDLL  120 (201)
T ss_pred             CCCEEEeChHHHHHHH
Confidence            3 99999999887653

>PRK14701 reverse gyrase; Provisional

Probab=99.01  E-value=9.8e-10  Score=106.28  Aligned_cols=82  Identities=11%  Similarity=0.102  Sum_probs=61.9

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC------ceEEEecCCcCC--------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK------DVGLMTGDVTLS--------  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~------~v~~~tGd~~~~--------  120 (138)
                      .++.++++|||+|||+++.........+|.++++++||++|+.|+++.|+....      .+..++|+....        
T Consensus        94 G~d~li~APTGsGKTl~~~~~al~~~~~g~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~  173 (1638)
T PRK14701         94 GKSFSIVAPTGMGKSTFGAFIALFLALKGKKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLER  173 (1638)
T ss_pred             CCCEEEEEcCCCCHHHHHHHHHHHHHhcCCeEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHH
Confidence            467789999999999965544333334678999999999999999999998432      345566765422        


Q ss_pred             ---CCCCEEEecHHHHHHh
Q 042424          121 ---PNASCLVMTTEILRGM  136 (138)
Q Consensus       121 ---~~~~IiVtTpe~l~~l  136 (138)
                         .+.+|+|+||+.+...
T Consensus       174 l~~g~~dILV~TPgrL~~~  192 (1638)
T PRK14701        174 IENGDFDILVTTAQFLARN  192 (1638)
T ss_pred             HhcCCCCEEEECCchhHHh
Confidence               1579999999988653

>KOG0330 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=98.98  E-value=1.7e-09  Score=91.76  Aligned_cols=83  Identities=17%  Similarity=0.141  Sum_probs=67.7

Q ss_pred             CCCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCCcC------
Q 042424           54 ETTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDVTL------  119 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~~~------  119 (138)
                      ..++.+..|-||||||..+.+.|.++|-+   --++++++|+|+|+.|+...|.. ++     .|.++.|....      
T Consensus        97 ~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLtPtRELA~QI~e~fe~-Lg~~iglr~~~lvGG~~m~~q~~~  175 (476)
T KOG0330|consen   97 GGRDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLTPTRELAQQIAEQFEA-LGSGIGLRVAVLVGGMDMMLQANQ  175 (476)
T ss_pred             CCCcEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEEecCcHHHHHHHHHHHHH-hccccCeEEEEEecCchHHHHHHH
Confidence            34667788899999999999999999865   35799999999999999999988 54     46666676542      


Q ss_pred             -CCCCCEEEecHHHHHHhh
Q 042424          120 -SPNASCLVMTTEILRGML  137 (138)
Q Consensus       120 -~~~~~IiVtTpe~l~~lL  137 (138)
                       ....+|||+||.+|...|
T Consensus       176 L~kkPhilVaTPGrL~dhl  194 (476)
T KOG0330|consen  176 LSKKPHILVATPGRLWDHL  194 (476)
T ss_pred             hhcCCCEEEeCcHHHHHHH
Confidence             348899999999987654

>KOG0342 consensus ATP-dependent RNA helicase pitchoune [RNA processing and modification]

Probab=98.97  E-value=1.4e-09  Score=94.11  Aligned_cols=83  Identities=20%  Similarity=0.208  Sum_probs=68.1

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc-------CCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCCcCC--
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD-------KQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDVTLS--  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~-------~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~~~~--  120 (138)
                      .++.+..|-||+|||+++++...+.+.+       +-.+++++|||.|+.|.+.+.++.+.     .|++..|.....  
T Consensus       119 gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e  198 (543)
T KOG0342|consen  119 GKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLIICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVE  198 (543)
T ss_pred             CccceeeeccCCCceeeehhHHHHHHHhcccCCCCCeeEEEecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHH
Confidence            3577799999999999999888777654       56799999999999999999888654     577777776532  


Q ss_pred             -----CCCCEEEecHHHHHHhh
Q 042424          121 -----PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 -----~~~~IiVtTpe~l~~lL  137 (138)
                           ..++|+|+||.+|...|
T Consensus       199 ~~kl~k~~niliATPGRLlDHl  220 (543)
T KOG0342|consen  199 ADKLVKGCNILIATPGRLLDHL  220 (543)
T ss_pred             HHHhhccccEEEeCCchHHhHh
Confidence                 28999999999998754

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

Probab=98.95  E-value=3.4e-09  Score=90.88  Aligned_cols=78  Identities=28%  Similarity=0.279  Sum_probs=63.3

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC---ceEEEecCCcCCCCCCEEEecHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK---DVGLMTGDVTLSPNASCLVMTTE  131 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~---~v~~~tGd~~~~~~~~IiVtTpe  131 (138)
                      .++.++++|||+|||+++..++...   +.++++|+|++.|+.|+++.+.+.+.   .+|.+.|+........|.|+|.+
T Consensus        55 ~~~gvivlpTGaGKT~va~~~~~~~---~~~~Lvlv~~~~L~~Qw~~~~~~~~~~~~~~g~~~~~~~~~~~~~i~vat~q  131 (442)
T COG1061          55 ERRGVIVLPTGAGKTVVAAEAIAEL---KRSTLVLVPTKELLDQWAEALKKFLLLNDEIGIYGGGEKELEPAKVTVATVQ  131 (442)
T ss_pred             CCceEEEeCCCCCHHHHHHHHHHHh---cCCEEEEECcHHHHHHHHHHHHHhcCCccccceecCceeccCCCcEEEEEhH
Confidence            5678899999999999999888765   45599999999999999998888776   47888775433222679999998


Q ss_pred             HHHH
Q 042424          132 ILRG  135 (138)
Q Consensus       132 ~l~~  135 (138)
                      .+..
T Consensus       132 tl~~  135 (442)
T COG1061         132 TLAR  135 (442)
T ss_pred             HHhh
Confidence            8765

>KOG0338 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=98.95  E-value=1.9e-09  Score=94.07  Aligned_cols=82  Identities=21%  Similarity=0.165  Sum_probs=67.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc------CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC----
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD------KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP----  121 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~------~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~----  121 (138)
                      +...-||-||+|||.++.+.++..|..      -.|+|+++||+.|+-|.+...++.-.    .||+..|......    
T Consensus       219 kDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~  298 (691)
T KOG0338|consen  219 KDICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVLVPTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAV  298 (691)
T ss_pred             chhhheecccCCchhhhHHHHHHHHhcCcccCcceeEEEEeccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHH
Confidence            344478899999999999999888753      36899999999999999988887432    6888889876543    


Q ss_pred             ---CCCEEEecHHHHHHhh
Q 042424          122 ---NASCLVMTTEILRGML  137 (138)
Q Consensus       122 ---~~~IiVtTpe~l~~lL  137 (138)
                         ..+|+|+||.+|..-|
T Consensus       299 LRs~PDIVIATPGRlIDHl  317 (691)
T KOG0338|consen  299 LRSRPDIVIATPGRLIDHL  317 (691)
T ss_pred             HhhCCCEEEecchhHHHHh
Confidence               7899999999997654

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=98.95  E-value=2.3e-09  Score=95.05  Aligned_cols=76  Identities=14%  Similarity=0.076  Sum_probs=59.6

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcCC-----------CC
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTLS-----------PN  122 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~~-----------~~  122 (138)
                      .++.++++|||+|||+++.++++   ..+..+|+++|+++|+.|+.+.|+. ++ .+..+.+....+           .+
T Consensus        40 g~dvlv~apTGsGKTl~y~lpal---~~~g~tlVisPl~sL~~dqv~~l~~-~gi~~~~~~s~~~~~~~~~~~~~~~~g~  115 (607)
T PRK11057         40 GRDCLVVMPTGGGKSLCYQIPAL---VLDGLTLVVSPLISLMKDQVDQLLA-NGVAAACLNSTQTREQQLEVMAGCRTGQ  115 (607)
T ss_pred             CCCEEEEcCCCchHHHHHHHHHH---HcCCCEEEEecHHHHHHHHHHHHHH-cCCcEEEEcCCCCHHHHHHHHHHHhCCC
Confidence            36788999999999999876654   3467899999999999999999988 55 555555543221           25


Q ss_pred             CCEEEecHHHHH
Q 042424          123 ASCLVMTTEILR  134 (138)
Q Consensus       123 ~~IiVtTpe~l~  134 (138)
                      .+++++|||++.
T Consensus       116 ~~il~~tPe~l~  127 (607)
T PRK11057        116 IKLLYIAPERLM  127 (607)
T ss_pred             CcEEEEChHHhc
Confidence            689999999986

>PRK09694 helicase Cas3; Provisional

Probab=98.95  E-value=3.2e-09  Score=97.81  Aligned_cols=81  Identities=17%  Similarity=0.115  Sum_probs=62.3

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC--CcEEEEechHHHHHHHHHHHHH----hcC--ceEEEecCCcCC-------
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK--QRVIYTSSLKALSNQKYRELHK----EFK--DVGLMTGDVTLS-------  120 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~--~rviyv~P~kaLv~Q~~~~l~~----~f~--~v~~~tGd~~~~-------  120 (138)
                      +..+|.+|||+|||.+++.++...+..+  .+++|..||+++++|+++++.+    .|.  ++.+.+|....+       
T Consensus       302 gl~ileApTGsGKTEAAL~~A~~l~~~~~~~gi~~aLPT~Atan~m~~Rl~~~~~~~f~~~~v~L~Hg~a~l~~~~~~~~  381 (878)
T PRK09694        302 GLTIIEAPTGSGKTEAALAYAWRLIDQGLADSIIFALPTQATANAMLSRLEALASKLFPSPNLILAHGNSRFNHLFQSLK  381 (878)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHHHHhCCCCeEEEECcHHHHHHHHHHHHHHHHHHhcCCCceEeecCcchhhhhhhhhh
Confidence            4457999999999999988776655543  7999999999999999999875    343  577766643210       


Q ss_pred             ---------------------------CCCCEEEecHHHHHHh
Q 042424          121 ---------------------------PNASCLVMTTEILRGM  136 (138)
Q Consensus       121 ---------------------------~~~~IiVtTpe~l~~l  136 (138)
                                                 .-++|+|||..++...
T Consensus       382 ~~~~~~~~~~~~~~~~~~w~~~~~kr~llapi~V~TiDQlL~a  424 (878)
T PRK09694        382 SRAATEQGQEEAWVQCCEWLSQSNKRVFLGQIGVCTIDQVLIS  424 (878)
T ss_pred             cccccccccchhhhHHHHHHhhhhhhhhcCCEEEcCHHHHHHH
Confidence                                       0279999999998854

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=98.94  E-value=4.3e-10  Score=103.84  Aligned_cols=100  Identities=27%  Similarity=0.250  Sum_probs=82.0

Q ss_pred             CCcccccccCCC-CccCCCCCCCceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHHHHHHHHHHHHHhcC----
Q 042424           36 RSCVHEVAVPSC-YTLTTDETTHGTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKALSNQKYRELHKEFK----  108 (138)
Q Consensus        36 ~~~~~~~~~p~~-y~~~~~~~~~~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~kaLv~Q~~~~l~~~f~----  108 (138)
                      ..|.|....+.. |..+.....+..+.+|||+|||++++.++++++..  +.+++|++|.++|+.+..++|.+++.    
T Consensus       923 ~~~~~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~p~~kvvyIap~kalvker~~Dw~~r~~~~g~ 1002 (1230)
T KOG0952|consen  923 ALYKYFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYYPGSKVVYIAPDKALVKERSDDWSKRDELPGI 1002 (1230)
T ss_pred             HhhcccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccCCCccEEEEcCCchhhcccccchhhhcccCCc
Confidence            557665444444 33343445677899999999999999999999885  79999999999999999999999875    


Q ss_pred             ceEEEecCCcCCC----CCCEEEecHHHHHH
Q 042424          109 DVGLMTGDVTLSP----NASCLVMTTEILRG  135 (138)
Q Consensus       109 ~v~~~tGd~~~~~----~~~IiVtTpe~l~~  135 (138)
                      .+.-++||...+.    +++|+|+|||+|+.
T Consensus      1003 k~ie~tgd~~pd~~~v~~~~~~ittpek~dg 1033 (1230)
T KOG0952|consen 1003 KVIELTGDVTPDVKAVREADIVITTPEKWDG 1033 (1230)
T ss_pred             eeEeccCccCCChhheecCceEEcccccccC
Confidence            4777889887773    89999999999874

>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=98.94  E-value=1e-08  Score=75.15  Aligned_cols=78  Identities=19%  Similarity=0.171  Sum_probs=55.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcCc-eEEEe--------cC------C---
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKD-VGLMT--------GD------V---  117 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~~-v~~~t--------Gd------~---  117 (138)
                      ++.++.+|||||||.++..++.+...   ++++++|+++|++|..++|...... .....        ++      .   
T Consensus        26 ~~~ll~~~tGsGKT~~~~~~~~~l~~---~~l~~~p~~~l~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  102 (184)
T PF04851_consen   26 RRVLLNAPTGSGKTIIALALILELAR---KVLIVAPNISLLEQWYDEFDDFGSEKYNFFEKSIKPAYDSKEFISIQDDIS  102 (184)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHC---EEEEEESSHHHHHHHHHHHHHHSTTSEEEEE--GGGCCE-SEEETTTTEEE
T ss_pred             CCEEEEECCCCCcChhhhhhhhcccc---ceeEecCHHHHHHHHHHHHHHhhhhhhhhcccccccccccccccccccccc
Confidence            56779999999999999876665544   9999999999999999999663331 11110        00      0   


Q ss_pred             ----cCCCCCCEEEecHHHHHHh
Q 042424          118 ----TLSPNASCLVMTTEILRGM  136 (138)
Q Consensus       118 ----~~~~~~~IiVtTpe~l~~l  136 (138)
                          ..+.+.+++++|.+.|...
T Consensus       103 ~~~~~~~~~~~i~~~~~~~l~~~  125 (184)
T PF04851_consen  103 DKSESDNNDKDIILTTYQSLQSD  125 (184)
T ss_dssp             HHHHHCBSS-SEEEEEHHHHHHH
T ss_pred             cccccccccccchhhHHHHHHhh
Confidence                0122788999999998764

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 ....

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=98.93  E-value=3.2e-09  Score=97.88  Aligned_cols=82  Identities=12%  Similarity=0.068  Sum_probs=68.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC-----CCCEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP-----NASCL  126 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~-----~~~Ii  126 (138)
                      .+.+..++||+|||+++.++++..+..+..+++|+|++.|+.|.++.+...+.    +++.+.|+.....     .++|+
T Consensus       108 ~gvIAeaqTGeGKTLAf~LP~l~~aL~g~~v~IVTpTrELA~Qdae~m~~L~k~lGLsV~~i~GG~~~~eq~~~y~~DIV  187 (970)
T PRK12899        108 KGFITEMQTGEGKTLTAVMPLYLNALTGKPVHLVTVNDYLAQRDCEWVGSVLRWLGLTTGVLVSGSPLEKRKEIYQCDVV  187 (970)
T ss_pred             CCeEEEeCCCCChHHHHHHHHHHHHhhcCCeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHHcCCCEE
Confidence            56789999999999999988887666677799999999999999999988654    6777777765432     68999


Q ss_pred             EecHHHH-HHhh
Q 042424          127 VMTTEIL-RGML  137 (138)
Q Consensus       127 VtTpe~l-~~lL  137 (138)
                      |+||.+| ..+|
T Consensus       188 ygTPgRLgfDyL  199 (970)
T PRK12899        188 YGTASEFGFDYL  199 (970)
T ss_pred             EECCChhHHHHh
Confidence            9999999 5544

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=98.90  E-value=7.1e-09  Score=94.94  Aligned_cols=82  Identities=18%  Similarity=0.226  Sum_probs=65.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEe-cCCcCCCCCCEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMT-GDVTLSPNASCLVMT  129 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~t-Gd~~~~~~~~IiVtT  129 (138)
                      ++.++++|||||||..+.+++++....+.+++++.|++.++.|.++.+.+.++     .||... |+...+.+.+|+|+|
T Consensus        21 ~~vvv~A~TGSGKTt~~pl~lL~~~~~~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VGy~vr~~~~~~~~t~I~v~T  100 (812)
T PRK11664         21 PQVLLKAPTGAGKSTWLPLQLLQHGGINGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVGYRMRAESKVGPNTRLEVVT  100 (812)
T ss_pred             CCEEEEcCCCCCHHHHHHHHHHHcCCcCCeEEEECChHHHHHHHHHHHHHHhCcccCceEEEEecCccccCCCCcEEEEC
Confidence            56779999999999999877776533346899999999999999999987665     465544 343445577899999


Q ss_pred             HHHHHHhh
Q 042424          130 TEILRGML  137 (138)
Q Consensus       130 pe~l~~lL  137 (138)
                      +.+|..+|
T Consensus       101 ~G~Llr~l  108 (812)
T PRK11664        101 EGILTRMI  108 (812)
T ss_pred             hhHHHHHH
Confidence            99998765

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=98.85  E-value=6.8e-09  Score=89.34  Aligned_cols=84  Identities=17%  Similarity=0.094  Sum_probs=62.1

Q ss_pred             CCCCceEECcCCCchHHHHHHHHHHHHHc---------CCcEEEEechHHHHHHHHHHHHHhcC------ceEEEecCCc
Q 042424           54 ETTHGTLTNPVYNGKTAVAEYAIAMAFRD---------KQRVIYTSSLKALSNQKYRELHKEFK------DVGLMTGDVT  118 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~~ai~~~l~~---------~~rviyv~P~kaLv~Q~~~~l~~~f~------~v~~~tGd~~  118 (138)
                      ...+.+..|-||||||.+++..+++.+-.         |-.+++++||++|+.|.|..+.+.-.      .+.-++.+..
T Consensus        55 EgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~iLvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~s  134 (569)
T KOG0346|consen   55 EGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVILVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMS  134 (569)
T ss_pred             cCcceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccceeEEEechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccc
Confidence            44677789999999999999998887632         45789999999999999999887322      1111222221


Q ss_pred             C-------CCCCCEEEecHHHHHHhh
Q 042424          119 L-------SPNASCLVMTTEILRGML  137 (138)
Q Consensus       119 ~-------~~~~~IiVtTpe~l~~lL  137 (138)
                      .       ....+|+|+||.++..++
T Consensus       135 dsv~~~~L~d~pdIvV~TP~~ll~~~  160 (569)
T KOG0346|consen  135 DSVNSVALMDLPDIVVATPAKLLRHL  160 (569)
T ss_pred             hHHHHHHHccCCCeEEeChHHHHHHH
Confidence            1       127889999999998764

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

Probab=98.84  E-value=1.2e-08  Score=95.88  Aligned_cols=76  Identities=13%  Similarity=0.100  Sum_probs=59.7

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcCC-------------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTLS-------------  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~~-------------  120 (138)
                      .++.++++|||+|||+++.++++.   .+..+|+|+|+++|+.++...+.. .+ .+..+.|.....             
T Consensus       475 GrDVLVimPTGSGKSLcYQLPAL~---~~GiTLVISPLiSLmqDQV~~L~~-~GI~Aa~L~s~~s~~eq~~ilr~l~s~~  550 (1195)
T PLN03137        475 GYDVFVLMPTGGGKSLTYQLPALI---CPGITLVISPLVSLIQDQIMNLLQ-ANIPAASLSAGMEWAEQLEILQELSSEY  550 (1195)
T ss_pred             CCCEEEEcCCCccHHHHHHHHHHH---cCCcEEEEeCHHHHHHHHHHHHHh-CCCeEEEEECCCCHHHHHHHHHHHHhcC
Confidence            367889999999999999877653   467899999999999988888776 44 566666654321             


Q ss_pred             CCCCEEEecHHHHH
Q 042424          121 PNASCLVMTTEILR  134 (138)
Q Consensus       121 ~~~~IiVtTpe~l~  134 (138)
                      ...+||++|||+|.
T Consensus       551 g~~~ILyvTPERL~  564 (1195)
T PLN03137        551 SKYKLLYVTPEKVA  564 (1195)
T ss_pred             CCCCEEEEChHHhh
Confidence            25789999999974

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=98.84  E-value=1.7e-08  Score=92.60  Aligned_cols=83  Identities=20%  Similarity=0.228  Sum_probs=66.5

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEe-cCCcCCCCCCEEEe
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMT-GDVTLSPNASCLVM  128 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~t-Gd~~~~~~~~IiVt  128 (138)
                      +.+.++++|||||||..+..++++....+.+++++.|++.++.|.++++.+.++     .||... ++.....+.+|+|+
T Consensus        17 ~~~vIi~a~TGSGKTT~vpl~lL~~~~~~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~VGy~vr~~~~~s~~t~I~v~   96 (819)
T TIGR01970        17 HPQVVLEAPPGAGKSTAVPLALLDAPGIGGKIIMLEPRRLAARSAAQRLASQLGEAVGQTVGYRVRGENKVSRRTRLEVV   96 (819)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHhhccCCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEEEEEEccccccCCCCcEEEE
Confidence            356779999999999999988887765567999999999999999999987665     355332 34344457889999


Q ss_pred             cHHHHHHhh
Q 042424          129 TTEILRGML  137 (138)
Q Consensus       129 Tpe~l~~lL  137 (138)
                      |+.+|..+|
T Consensus        97 T~G~Llr~l  105 (819)
T TIGR01970        97 TEGILTRMI  105 (819)
T ss_pred             CCcHHHHHH
Confidence            999998765

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.

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

Probab=98.84  E-value=1.2e-08  Score=85.70  Aligned_cols=80  Identities=25%  Similarity=0.228  Sum_probs=74.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCCcCCCCCCEEEecHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVTLSPNASCLVMTTEIL  133 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~~~~~~~IiVtTpe~l  133 (138)
                      ...++.|-||||||.+.+-+|.+++++|.++.+.+|....+-+.+.+|+..|.  ++..+.||......++++|+|..+|
T Consensus       117 ~~~lv~AV~GaGKTEMif~~i~~al~~G~~vciASPRvDVclEl~~Rlk~aF~~~~I~~Lyg~S~~~fr~plvVaTtHQL  196 (441)
T COG4098         117 EDTLVWAVTGAGKTEMIFQGIEQALNQGGRVCIASPRVDVCLELYPRLKQAFSNCDIDLLYGDSDSYFRAPLVVATTHQL  196 (441)
T ss_pred             CcEEEEEecCCCchhhhHHHHHHHHhcCCeEEEecCcccchHHHHHHHHHhhccCCeeeEecCCchhccccEEEEehHHH
Confidence            46779999999999999999999999999999999999999999999999998  7889999988888899999999998


Q ss_pred             HH
Q 042424          134 RG  135 (138)
Q Consensus       134 ~~  135 (138)
                      ..
T Consensus       197 lr  198 (441)
T COG4098         197 LR  198 (441)
T ss_pred             HH
Confidence            64

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=98.84  E-value=1e-08  Score=94.24  Aligned_cols=78  Identities=15%  Similarity=0.112  Sum_probs=66.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC-----CCCEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP-----NASCL  126 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~-----~~~Ii  126 (138)
                      ...+..++||+|||+++.+++......|+.+.+++|+..|+.|.++.+...+.    .|+.++|+...+.     .++|+
T Consensus        96 ~G~Iaem~TGeGKTL~a~Lpa~~~al~G~~V~VvTpn~yLA~qd~e~m~~l~~~lGLtv~~i~gg~~~~~r~~~y~~dIv  175 (896)
T PRK13104         96 EGNIAEMRTGEGKTLVATLPAYLNAISGRGVHIVTVNDYLAKRDSQWMKPIYEFLGLTVGVIYPDMSHKEKQEAYKADIV  175 (896)
T ss_pred             cCccccccCCCCchHHHHHHHHHHHhcCCCEEEEcCCHHHHHHHHHHHHHHhcccCceEEEEeCCCCHHHHHHHhCCCEE
Confidence            45578999999999999887776556688999999999999999999998765    7888888765432     78999


Q ss_pred             EecHHHH
Q 042424          127 VMTTEIL  133 (138)
Q Consensus       127 VtTpe~l  133 (138)
                      ++||..|
T Consensus       176 ygT~grl  182 (896)
T PRK13104        176 YGTNNEY  182 (896)
T ss_pred             EECChhh
Confidence            9999997

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=98.83  E-value=9.3e-09  Score=93.83  Aligned_cols=77  Identities=19%  Similarity=0.189  Sum_probs=65.8

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCc-CC-----CCCCEE
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVT-LS-----PNASCL  126 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~-~~-----~~~~Ii  126 (138)
                      ..+..+.||+|||+++.+++......|..+.+++|++.||.|.++.+...+.    +|+++.|+.. ..     -.++|+
T Consensus        93 G~Iaem~TGeGKTL~a~lp~~l~al~G~~v~VvTpt~~LA~qd~e~~~~l~~~lGl~v~~i~g~~~~~~~r~~~y~~dIv  172 (790)
T PRK09200         93 GNIAEMQTGEGKTLTATMPLYLNALEGKGVHLITVNDYLAKRDAEEMGQVYEFLGLTVGLNFSDIDDASEKKAIYEADII  172 (790)
T ss_pred             CceeeecCCCcchHHHHHHHHHHHHcCCCeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCcHHHHHHhcCCCEE
Confidence            4489999999999999988875556799999999999999999999988765    7888888776 22     278999


Q ss_pred             EecHHHH
Q 042424          127 VMTTEIL  133 (138)
Q Consensus       127 VtTpe~l  133 (138)
                      ++||..|
T Consensus       173 ygT~~~l  179 (790)
T PRK09200        173 YTTNSEL  179 (790)
T ss_pred             EECCccc
Confidence            9999887

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=98.83  E-value=1.1e-08  Score=92.66  Aligned_cols=77  Identities=16%  Similarity=0.107  Sum_probs=64.3

Q ss_pred             CCceEECcCCCchHHHHHHHHH-HHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC-----CCCE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIA-MAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP-----NASC  125 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~-~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~-----~~~I  125 (138)
                      ...+..++||+|||+++.+++. .++ .|+.+.+++|+..||.|.++.+...|.    +|+.++|+.....     .++|
T Consensus        70 ~G~Iaem~TGeGKTLva~lpa~l~aL-~G~~V~VvTpt~~LA~qdae~~~~l~~~LGLsv~~i~g~~~~~~r~~~y~~dI  148 (745)
T TIGR00963        70 KGKIAEMKTGEGKTLTATLPAYLNAL-TGKGVHVVTVNDYLAQRDAEWMGQVYRFLGLSVGLILSGMSPEERREAYACDI  148 (745)
T ss_pred             CCceeeecCCCccHHHHHHHHHHHHH-hCCCEEEEcCCHHHHHHHHHHHHHHhccCCCeEEEEeCCCCHHHHHHhcCCCE
Confidence            4458999999999999998774 554 588999999999999999999998765    7888888765322     6899


Q ss_pred             EEecHHHH
Q 042424          126 LVMTTEIL  133 (138)
Q Consensus       126 iVtTpe~l  133 (138)
                      +++||..|
T Consensus       149 vyGT~~rl  156 (745)
T TIGR00963       149 TYGTNNEL  156 (745)
T ss_pred             EEECCCch
Confidence            99999977

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

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=98.78  E-value=3.4e-08  Score=89.82  Aligned_cols=77  Identities=16%  Similarity=0.120  Sum_probs=61.7

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhc---C-ceEEEecCCc---CC-------CC
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEF---K-DVGLMTGDVT---LS-------PN  122 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f---~-~v~~~tGd~~---~~-------~~  122 (138)
                      ..++.++||+|||+++.+++......|..+++++|++.|+.|.++.+...+   + +|+...++..   .+       -.
T Consensus        85 G~Iaem~TGeGKTLta~Lpa~l~aL~g~~V~VVTpn~yLA~Rdae~m~~l~~~LGLsv~~~~~~s~~~~~~~~~rr~~y~  164 (762)
T TIGR03714        85 GNIAEMKTGEGKTLTATMPLYLNALTGKGAMLVTTNDYLAKRDAEEMGPVYEWLGLTVSLGVVDDPDEEYDANEKRKIYN  164 (762)
T ss_pred             CceeEecCCcchHHHHHHHHHHHhhcCCceEEeCCCHHHHHHHHHHHHHHHhhcCCcEEEEECCCCccccCHHHHHHhCC
Confidence            468999999999999998776555568899999999999999999887654   3 6777655411   11       17


Q ss_pred             CCEEEecHHHH
Q 042424          123 ASCLVMTTEIL  133 (138)
Q Consensus       123 ~~IiVtTpe~l  133 (138)
                      ++|+++||..|
T Consensus       165 ~dIvygTp~~L  175 (762)
T TIGR03714       165 SDIVYTTNSAL  175 (762)
T ss_pred             CCEEEECchhh
Confidence            89999999998

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.

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

Probab=98.78  E-value=1.8e-08  Score=94.18  Aligned_cols=78  Identities=21%  Similarity=0.222  Sum_probs=66.4

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcC-----------CC
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTL-----------SP  121 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~-----------~~  121 (138)
                      +++||+.-|-|||.||+-|++.|...|+.|.++|||+-|++|+|+.|+++|.    +|.+++.-.+.           +-
T Consensus       617 DRLiCGDVGFGKTEVAmRAAFkAV~~GKQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G  696 (1139)
T COG1197         617 DRLICGDVGFGKTEVAMRAAFKAVMDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEG  696 (1139)
T ss_pred             hheeecCcCCcHHHHHHHHHHHHhcCCCeEEEEcccHHhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcC
Confidence            5679999999999999999999999999999999999999999999999997    67777543221           12


Q ss_pred             CCCEEEecHHHHH
Q 042424          122 NASCLVMTTEILR  134 (138)
Q Consensus       122 ~~~IiVtTpe~l~  134 (138)
                      ..||||.|..-|.
T Consensus       697 ~vDIvIGTHrLL~  709 (1139)
T COG1197         697 KVDIVIGTHRLLS  709 (1139)
T ss_pred             CccEEEechHhhC
Confidence            7899999987654

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=98.74  E-value=2.1e-08  Score=89.91  Aligned_cols=76  Identities=17%  Similarity=0.073  Sum_probs=65.2

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC-----CCCCEEEe
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS-----PNASCLVM  128 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~-----~~~~IiVt  128 (138)
                      .+..+.||+|||+++.+++......|..+++++|++.|+.|.++.+.+.|.    +|+.+.|+....     -.++|+++
T Consensus       119 ~Iae~~TGeGKTla~~lp~~~~al~G~~v~VvTptreLA~qdae~~~~l~~~lGlsv~~i~gg~~~~~r~~~y~~dIvyg  198 (656)
T PRK12898        119 RLAEMQTGEGKTLTATLPAGTAALAGLPVHVITVNDYLAERDAELMRPLYEALGLTVGCVVEDQSPDERRAAYGADITYC  198 (656)
T ss_pred             CeeeeeCCCCcHHHHHHHHHHHhhcCCeEEEEcCcHHHHHHHHHHHHHHHhhcCCEEEEEeCCCCHHHHHHHcCCCEEEE
Confidence            389999999999999988887777799999999999999999999998654    788888876432     27899999


Q ss_pred             cHHHH
Q 042424          129 TTEIL  133 (138)
Q Consensus       129 Tpe~l  133 (138)
                      |...|
T Consensus       199 T~~e~  203 (656)
T PRK12898        199 TNKEL  203 (656)
T ss_pred             CCCch
Confidence            98765

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

Probab=98.69  E-value=3.1e-08  Score=90.89  Aligned_cols=77  Identities=17%  Similarity=0.241  Sum_probs=53.3

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHc----CCcEEEEechHHHHHHHHHHHHHhcC------------------------
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRD----KQRVIYTSSLKALSNQKYRELHKEFK------------------------  108 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~----~~rviyv~P~kaLv~Q~~~~l~~~f~------------------------  108 (138)
                      +.++.+|||||||.++...++ .+..    -+++||++|+++|++|.++++.+...                        
T Consensus        33 ~v~~~apTGSGKTaa~aafll-~~~~~~~~~~rLv~~vPtReLa~Qi~~~~~~~~k~l~~~~~~~~~~~~~~~~~~~~~~  111 (844)
T TIGR02621        33 PESCSTPTGLGKTSIIAAWLL-AVEIGAKVPRRLVYVVNRRTVVDQVTEEAEKIGERLPDVPEVEAALWALCSTRPEKKD  111 (844)
T ss_pred             cceEecCCCCcccHHHHHhhc-cccccccccceEEEeCchHHHHHHHHHHHHHHHHHhcccchhhhhhhhhhcccccccc
Confidence            455789999999985431111 2221    35788899999999999999887431                        


Q ss_pred             ---ceEEEecCCcCCC-------CCCEEEecHHHHH
Q 042424          109 ---DVGLMTGDVTLSP-------NASCLVMTTEILR  134 (138)
Q Consensus       109 ---~v~~~tGd~~~~~-------~~~IiVtTpe~l~  134 (138)
                         .+..+.|....+.       ..+|||+|++++.
T Consensus       112 ~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~D~i~  147 (844)
T TIGR02621       112 RPLAISTLRGQFADNDEWMLDPHRPAVIVGTVDMIG  147 (844)
T ss_pred             CCeEEEEEECCCChHHHHHhcCCCCcEEEECHHHHc
Confidence               2455577765432       5789999987764

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.

>KOG0344 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=98.68  E-value=1.8e-08  Score=88.53  Aligned_cols=82  Identities=21%  Similarity=0.235  Sum_probs=62.8

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc--------CCcEEEEechHHHHHHHHHHHHHhc--C----ceEEEecCCcC-
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD--------KQRVIYTSSLKALSNQKYRELHKEF--K----DVGLMTGDVTL-  119 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~--------~~rviyv~P~kaLv~Q~~~~l~~~f--~----~v~~~tGd~~~-  119 (138)
                      .++.+.|+|||||||+.+.+.+++.|..        |-+++++.|+++|+.|.|+++++.-  .    .+..+..+... 
T Consensus       173 ~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~  252 (593)
T KOG0344|consen  173 KRDVLACAPTGSGKTLAFNLPILQHLKDLSQEKHKVGLRALILSPTRELAAQIYREMRKYSIDEGTSLRAAQFSKPAYPS  252 (593)
T ss_pred             ccceEEeccCCCcchhhhhhHHHHHHHHhhcccCccceEEEEecchHHHHHHHHHHHHhcCCCCCCchhhhhcccccchh
Confidence            4678899999999999999999888753        5789999999999999999999843  1    23333333111 


Q ss_pred             -------CCCCCEEEecHHHHHHh
Q 042424          120 -------SPNASCLVMTTEILRGM  136 (138)
Q Consensus       120 -------~~~~~IiVtTpe~l~~l  136 (138)
                             +..++|+|.||-++..+
T Consensus       253 qk~a~~~~~k~dili~TP~ri~~~  276 (593)
T KOG0344|consen  253 QKPAFLSDEKYDILISTPMRIVGL  276 (593)
T ss_pred             hccchhHHHHHHHHhcCHHHHHHH
Confidence                   12789999999886544

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

Probab=98.68  E-value=3.2e-08  Score=89.67  Aligned_cols=74  Identities=22%  Similarity=0.178  Sum_probs=65.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcCC-----C------CC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTLS-----P------NA  123 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~~-----~------~~  123 (138)
                      ...++-+.||||||.+.+.+|..+|.+|+.+|+++|-.+|..|..++|+.+|+ +|+++++.....     |      ++
T Consensus       218 ~~~Ll~GvTGSGKTEvYl~~i~~~L~~GkqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~~~G~~  297 (730)
T COG1198         218 APFLLDGVTGSGKTEVYLEAIAKVLAQGKQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGEA  297 (730)
T ss_pred             cceeEeCCCCCcHHHHHHHHHHHHHHcCCEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHHhcCCc
Confidence            34569999999999999999999999999999999999999999999999999 888888766432     1      77


Q ss_pred             CEEEec
Q 042424          124 SCLVMT  129 (138)
Q Consensus       124 ~IiVtT  129 (138)
                      .|+|.|
T Consensus       298 ~vVIGt  303 (730)
T COG1198         298 RVVIGT  303 (730)
T ss_pred             eEEEEe
Confidence            888887

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

Probab=98.68  E-value=8.1e-08  Score=90.62  Aligned_cols=81  Identities=16%  Similarity=0.098  Sum_probs=60.3

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHHHHHHHHHHHHHhcC--c--e-EEE--e--cCCcCCCCCC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKALSNQKYRELHKEFK--D--V-GLM--T--GDVTLSPNAS  124 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~kaLv~Q~~~~l~~~f~--~--v-~~~--t--Gd~~~~~~~~  124 (138)
                      ++.+++.|||+|||+++...+.+.++.  .+|+||++|+++|++|..+.|.....  .  + .+.  .  ++...+.+.+
T Consensus       434 r~~Ll~maTGSGKT~tai~li~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~~~~~~~~~~i~~i~~L~~~~~~~~~~  513 (1123)
T PRK11448        434 REILLAMATGTGKTRTAIALMYRLLKAKRFRRILFLVDRSALGEQAEDAFKDTKIEGDQTFASIYDIKGLEDKFPEDETK  513 (1123)
T ss_pred             CCeEEEeCCCCCHHHHHHHHHHHHHhcCccCeEEEEecHHHHHHHHHHHHHhcccccccchhhhhchhhhhhhcccCCCC
Confidence            567899999999999988777666554  47999999999999999999988321  1  1 111  1  2222344789


Q ss_pred             EEEecHHHHHHh
Q 042424          125 CLVMTTEILRGM  136 (138)
Q Consensus       125 IiVtTpe~l~~l  136 (138)
                      |+|+|.+.|.+.
T Consensus       514 I~iaTiQtl~~~  525 (1123)
T PRK11448        514 VHVATVQGMVKR  525 (1123)
T ss_pred             EEEEEHHHHHHh
Confidence            999999988654

>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=98.66  E-value=7.7e-08  Score=84.27  Aligned_cols=81  Identities=21%  Similarity=0.192  Sum_probs=61.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc--------CCcEEEEechHHHHHHHHHHHHHhcC------ceEEEecCCcC--
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD--------KQRVIYTSSLKALSNQKYRELHKEFK------DVGLMTGDVTL--  119 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~--------~~rviyv~P~kaLv~Q~~~~l~~~f~------~v~~~tGd~~~--  119 (138)
                      +..+=.|-||||||-++.+.++.++..        |--.+|++||++|+.|++.+-++ |+      .|+++.|....  
T Consensus       261 rdvigIAktgSgktaAfi~pm~~himdq~eL~~g~gPi~vilvPTrela~Qi~~eaKk-f~K~ygl~~v~~ygGgsk~eQ  339 (731)
T KOG0339|consen  261 RDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVILVPTRELASQIFSEAKK-FGKAYGLRVVAVYGGGSKWEQ  339 (731)
T ss_pred             ccchheeeccCcchhHHHHHHHHHhcchhhhcCCCCCeEEEEeccHHHHHHHHHHHHH-hhhhccceEEEeecCCcHHHH
Confidence            334456779999999998877766532        45689999999999999988777 53      45666554432  


Q ss_pred             ----CCCCCEEEecHHHHHHhh
Q 042424          120 ----SPNASCLVMTTEILRGML  137 (138)
Q Consensus       120 ----~~~~~IiVtTpe~l~~lL  137 (138)
                          ...+.||||||++|..|+
T Consensus       340 ~k~Lk~g~EivVaTPgRlid~V  361 (731)
T KOG0339|consen  340 SKELKEGAEIVVATPGRLIDMV  361 (731)
T ss_pred             HHhhhcCCeEEEechHHHHHHH
Confidence                238999999999998875

>KOG0340 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=98.66  E-value=3.3e-08  Score=83.26  Aligned_cols=82  Identities=18%  Similarity=0.151  Sum_probs=67.3

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCCc-------C
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDVT-------L  119 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~~-------~  119 (138)
                      .++.+=+|-||||||..+.+.|++.|..   |.=++++.||+.|+-|+.+.|.- .+     .+.++.|...       .
T Consensus        44 Grdcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTPTrELA~QiaEQF~a-lGk~l~lK~~vivGG~d~i~qa~~L  122 (442)
T KOG0340|consen   44 GRDCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTPTRELALQIAEQFIA-LGKLLNLKVSVIVGGTDMIMQAAIL  122 (442)
T ss_pred             ccccccccccCCCcchhhhHHHHHhhccCCCcceEEEecchHHHHHHHHHHHHH-hcccccceEEEEEccHHHhhhhhhc
Confidence            3566679999999999999999999875   67789999999999999999987 44     5777777653       2


Q ss_pred             CCCCCEEEecHHHHHHhh
Q 042424          120 SPNASCLVMTTEILRGML  137 (138)
Q Consensus       120 ~~~~~IiVtTpe~l~~lL  137 (138)
                      ..+.+++|+||+++...|
T Consensus       123 ~~rPHvVvatPGRlad~l  140 (442)
T KOG0340|consen  123 SDRPHVVVATPGRLADHL  140 (442)
T ss_pred             ccCCCeEecCcccccccc
Confidence            348899999999986543

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=98.63  E-value=3.1e-08  Score=87.20  Aligned_cols=78  Identities=17%  Similarity=0.184  Sum_probs=61.1

Q ss_pred             EECcCCCchHHHHHHHHHHHHH--------------cCCc--EEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcC
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFR--------------DKQR--VIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTL  119 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~--------------~~~r--viyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~  119 (138)
                      =.|-||||||+++-..|...+.              ++.+  ++++.|||+|+.|+.+.|.....    .+..++|....
T Consensus       224 GaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLav  303 (731)
T KOG0347|consen  224 GAAETGSGKTLAFGIPIVERLLESSDDSQELSNTSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAV  303 (731)
T ss_pred             cccccCCCceeeecchhhhhhhhccchHhhhhhHHhccCcceeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHH
Confidence            3456999999999777766321              1345  89999999999999999887554    57778888653


Q ss_pred             -------CCCCCEEEecHHHHHHhh
Q 042424          120 -------SPNASCLVMTTEILRGML  137 (138)
Q Consensus       120 -------~~~~~IiVtTpe~l~~lL  137 (138)
                             +...+|+|+||.+|..|+
T Consensus       304 qKQqRlL~~~p~IVVATPGRlweli  328 (731)
T KOG0347|consen  304 QKQQRLLNQRPDIVVATPGRLWELI  328 (731)
T ss_pred             HHHHHHHhcCCCEEEecchHHHHHH
Confidence                   337899999999998876

>KOG0333 consensus U5 snRNP-like RNA helicase subunit [RNA processing and modification]

Probab=98.60  E-value=9.8e-08  Score=83.70  Aligned_cols=86  Identities=17%  Similarity=0.119  Sum_probs=64.9

Q ss_pred             CCCCCCCceEECcCCCchHHHHHHHHHHHHHc------------CCcEEEEechHHHHHHHHHHHHHhcC-----ceEEE
Q 042424           51 TTDETTHGTLTNPVYNGKTAVAEYAIAMAFRD------------KQRVIYTSSLKALSNQKYRELHKEFK-----DVGLM  113 (138)
Q Consensus        51 ~~~~~~~~~l~aPTGsGKTlva~~ai~~~l~~------------~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~  113 (138)
                      +...+++.+..+-||||||..++..++..+.+            |..+++++||+.|+.|+.++-.+ |.     .+..+
T Consensus       278 l~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~~~gpyaiilaptReLaqqIeeEt~k-f~~~lg~r~vsv  356 (673)
T KOG0333|consen  278 LGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEGPYAIILAPTRELAQQIEEETNK-FGKPLGIRTVSV  356 (673)
T ss_pred             chhccCCeeeEEeccCCccccchhhHHHHHHcCCCcchhhhcccCceeeeechHHHHHHHHHHHHHH-hcccccceEEEE
Confidence            34456788899999999998887666554322            78999999999999999999877 54     33333


Q ss_pred             ecCCcC-------CCCCCEEEecHHHHHHhh
Q 042424          114 TGDVTL-------SPNASCLVMTTEILRGML  137 (138)
Q Consensus       114 tGd~~~-------~~~~~IiVtTpe~l~~lL  137 (138)
                      .|....       ...+.|+|+||.+|+..|
T Consensus       357 igg~s~EEq~fqls~gceiviatPgrLid~L  387 (673)
T KOG0333|consen  357 IGGLSFEEQGFQLSMGCEIVIATPGRLIDSL  387 (673)
T ss_pred             ecccchhhhhhhhhccceeeecCchHHHHHH
Confidence            344433       238999999999998765

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

Probab=98.59  E-value=1.5e-07  Score=84.47  Aligned_cols=80  Identities=16%  Similarity=0.231  Sum_probs=59.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHH--cCCcEEEEechHHHHHHHHHHHHHhcCc-eEEEe--cCC---cCCCCCCEEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFR--DKQRVIYTSSLKALSNQKYRELHKEFKD-VGLMT--GDV---TLSPNASCLV  127 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~--~~~rviyv~P~kaLv~Q~~~~l~~~f~~-v~~~t--Gd~---~~~~~~~IiV  127 (138)
                      ++.+++.|||||||+++.+++...+.  ...++|+++|.+.|.+|..++|...... +....  ++.   -.+.+.+|+|
T Consensus       264 ~~gli~~~TGsGKT~t~~~la~~l~~~~~~~~vl~lvdR~~L~~Q~~~~f~~~~~~~~~~~~s~~~L~~~l~~~~~~iiv  343 (667)
T TIGR00348       264 RGGLIWHTQGSGKTLTMLFAARKALELLKNPKVFFVVDRRELDYQLMKEFQSLQKDCAERIESIAELKRLLEKDDGGIII  343 (667)
T ss_pred             ceeEEEEecCCCccHHHHHHHHHHHhhcCCCeEEEEECcHHHHHHHHHHHHhhCCCCCcccCCHHHHHHHHhCCCCCEEE
Confidence            56889999999999999887776654  3579999999999999999999984322 11110  000   0122578999


Q ss_pred             ecHHHHHH
Q 042424          128 MTTEILRG  135 (138)
Q Consensus       128 tTpe~l~~  135 (138)
                      +|.+.|..
T Consensus       344 tTiQk~~~  351 (667)
T TIGR00348       344 TTIQKFDK  351 (667)
T ss_pred             EEhHHhhh
Confidence            99999874

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

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

Probab=98.59  E-value=1.9e-07  Score=86.72  Aligned_cols=80  Identities=21%  Similarity=0.200  Sum_probs=58.7

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-----ceEE-EecCCcC---------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-----DVGL-MTGDVTL---------  119 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~-~tGd~~~---------  119 (138)
                      +.+..+.||||.|||...+.+-+..-.+|+|++|++||+.|+.|.++.+++.-.     .+-+ ++|..+.         
T Consensus        97 g~SFaiiAPTGvGKTTfg~~~sl~~a~kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~  176 (1187)
T COG1110          97 GKSFAIIAPTGVGKTTFGLLMSLYLAKKGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALER  176 (1187)
T ss_pred             CCceEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHH
Confidence            356779999999999988643333335689999999999999999999998432     2222 5555332         


Q ss_pred             --CCCCCEEEecHHHHH
Q 042424          120 --SPNASCLVMTTEILR  134 (138)
Q Consensus       120 --~~~~~IiVtTpe~l~  134 (138)
                        +.|.+|+|+|..-+.
T Consensus       177 i~~gdfdIlitTs~FL~  193 (1187)
T COG1110         177 IESGDFDILITTSQFLS  193 (1187)
T ss_pred             HhcCCccEEEEeHHHHH
Confidence              127999999987553

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=98.52  E-value=2.1e-07  Score=85.31  Aligned_cols=77  Identities=16%  Similarity=0.091  Sum_probs=64.5

Q ss_pred             CCceEECcCCCchHHHHHHHHH-HHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC-----CCCE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIA-MAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP-----NASC  125 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~-~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~-----~~~I  125 (138)
                      ...+..+.||+|||+++.+++. .++ .|+.+-+++|+.-||.|.++.+...|.    +|++++|+.+...     .++|
T Consensus        95 ~G~Iaem~TGeGKTLva~lpa~l~aL-~G~~V~IvTpn~yLA~rd~e~~~~l~~~LGlsv~~i~~~~~~~er~~~y~~dI  173 (830)
T PRK12904         95 EGKIAEMKTGEGKTLVATLPAYLNAL-TGKGVHVVTVNDYLAKRDAEWMGPLYEFLGLSVGVILSGMSPEERREAYAADI  173 (830)
T ss_pred             CCchhhhhcCCCcHHHHHHHHHHHHH-cCCCEEEEecCHHHHHHHHHHHHHHHhhcCCeEEEEcCCCCHHHHHHhcCCCe
Confidence            3457899999999999988775 555 477899999999999999999998765    7888888765432     7899


Q ss_pred             EEecHHHH
Q 042424          126 LVMTTEIL  133 (138)
Q Consensus       126 iVtTpe~l  133 (138)
                      +++|+..|
T Consensus       174 ~ygT~~el  181 (830)
T PRK12904        174 TYGTNNEF  181 (830)
T ss_pred             EEECCcch
Confidence            99999988

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=98.51  E-value=1.9e-07  Score=86.32  Aligned_cols=82  Identities=20%  Similarity=0.151  Sum_probs=62.9

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc--------CCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCCcC--
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD--------KQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDVTL--  119 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~--------~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~~~--  119 (138)
                      .+..+-.+-||||||+.+++.++++...        |--+|+++||+.|+.|+++++++...     -|.++ |...+  
T Consensus       402 GrdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~aPtrela~QI~r~~~kf~k~l~ir~v~vy-gg~~~~~  480 (997)
T KOG0334|consen  402 GRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILAPTRELAMQIHREVRKFLKLLGIRVVCVY-GGSGISQ  480 (997)
T ss_pred             CcceEEeeccCCccchhhhcchhhhhhcCCChhhCCCceEEEEcCCHHHHHHHHHHHHHHHhhcCceEEEec-CCccHHH
Confidence            3566688999999999998888876542        56799999999999999999988332     23344 33332  


Q ss_pred             -----CCCCCEEEecHHHHHHhh
Q 042424          120 -----SPNASCLVMTTEILRGML  137 (138)
Q Consensus       120 -----~~~~~IiVtTpe~l~~lL  137 (138)
                           +..+.|+||||.++..+|
T Consensus       481 qiaelkRg~eIvV~tpGRmiD~l  503 (997)
T KOG0334|consen  481 QIAELKRGAEIVVCTPGRMIDIL  503 (997)
T ss_pred             HHHHHhcCCceEEeccchhhhhH
Confidence                 337999999999988765

>KOG0337 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=98.43  E-value=1.8e-07  Score=80.31  Aligned_cols=80  Identities=18%  Similarity=0.154  Sum_probs=63.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc----CCcEEEEechHHHHHHHHHHHHHhcC------ceEEEecCCcC------
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD----KQRVIYTSSLKALSNQKYRELHKEFK------DVGLMTGDVTL------  119 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~----~~rviyv~P~kaLv~Q~~~~l~~~f~------~v~~~tGd~~~------  119 (138)
                      +..+-.+-||||||.+++..++++|..    |.|+++++|++.|+.|..+.+.+ ++      .+.++.||...      
T Consensus        59 ~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~RalilsptreLa~qtlkvvkd-lgrgt~lr~s~~~ggD~~eeqf~~l  137 (529)
T KOG0337|consen   59 RDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALILSPTRELALQTLKVVKD-LGRGTKLRQSLLVGGDSIEEQFILL  137 (529)
T ss_pred             cccceeeecCCcchhhHHHHHHHHHhhccccccceeeccCcHHHHHHHHHHHHH-hccccchhhhhhcccchHHHHHHHh
Confidence            334456779999999999999998875    57999999999999999998888 54      23355566532      


Q ss_pred             CCCCCEEEecHHHHHHh
Q 042424          120 SPNASCLVMTTEILRGM  136 (138)
Q Consensus       120 ~~~~~IiVtTpe~l~~l  136 (138)
                      +.+.+||++||.++..+
T Consensus       138 ~~npDii~ATpgr~~h~  154 (529)
T KOG0337|consen  138 NENPDIIIATPGRLLHL  154 (529)
T ss_pred             ccCCCEEEecCceeeee
Confidence            34899999999987654

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=98.36  E-value=9.4e-07  Score=80.23  Aligned_cols=52  Identities=29%  Similarity=0.369  Sum_probs=42.7

Q ss_pred             CceEECcCCCchHHHHH-HHHHHHHH---cCCcEEEEechHHHHHHHHHHHHHhcC
Q 042424           57 HGTLTNPVYNGKTAVAE-YAIAMAFR---DKQRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~-~ai~~~l~---~~~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      ..++.+|||+|||.+++ ++......   ...|++|+.|++++++++++++++.++
T Consensus       216 ~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~~  271 (733)
T COG1203         216 LVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFG  271 (733)
T ss_pred             cEEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHHHHHHHHHHHhhhc
Confidence            44599999999999997 44444333   268999999999999999999998766

>PHA02653 RNA helicase NPH-II; Provisional

Probab=98.34  E-value=1.1e-06  Score=79.43  Aligned_cols=78  Identities=15%  Similarity=0.086  Sum_probs=55.4

Q ss_pred             CCCceEECcCCCchHHHH---------HHHHHHHH---H---cCCcEEEEechHHHHHHHHHHHHHhcC-------ceEE
Q 042424           55 TTHGTLTNPVYNGKTAVA---------EYAIAMAF---R---DKQRVIYTSSLKALSNQKYRELHKEFK-------DVGL  112 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva---------~~ai~~~l---~---~~~rviyv~P~kaLv~Q~~~~l~~~f~-------~v~~  112 (138)
                      .++.+++|+||||||...         +++.+..+   .   .+.+++++.|+++|+.|+..++.+..+       .+.+
T Consensus       179 gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreLa~qi~~~i~~~vg~~~~~g~~v~v  258 (675)
T PHA02653        179 RKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVALVRLHSITLLKSLGFDEIDGSPISL  258 (675)
T ss_pred             CCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHHHHHHHHHHHHHhCccccCCceEEE
Confidence            467789999999999872         22233322   2   246899999999999999999986443       3566


Q ss_pred             EecCCcCC------CCCCEEEecHHH
Q 042424          113 MTGDVTLS------PNASCLVMTTEI  132 (138)
Q Consensus       113 ~tGd~~~~------~~~~IiVtTpe~  132 (138)
                      ..|+....      ...+|+|+|+..
T Consensus       259 ~~Gg~~~~~~~t~~k~~~Ilv~T~~L  284 (675)
T PHA02653        259 KYGSIPDELINTNPKPYGLVFSTHKL  284 (675)
T ss_pred             EECCcchHHhhcccCCCCEEEEeCcc
Confidence            77776421      145799999754

>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]

Probab=98.31  E-value=3.4e-07  Score=78.35  Aligned_cols=82  Identities=20%  Similarity=0.114  Sum_probs=60.7

Q ss_pred             CCceEECcCCCchHHHHHHH-HHHHHHc----------CCcEEEEechHHHHHHHHHHHHHhcC----------ceEEEe
Q 042424           56 THGTLTNPVYNGKTAVAEYA-IAMAFRD----------KQRVIYTSSLKALSNQKYRELHKEFK----------DVGLMT  114 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a-i~~~l~~----------~~rviyv~P~kaLv~Q~~~~l~~~f~----------~v~~~t  114 (138)
                      ++.+=.+-||||||+++.+. |+.+|.+          |--.++++|.+.|+.|.+.-+...+.          ..+++.
T Consensus       208 RDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~Lci  287 (610)
T KOG0341|consen  208 RDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCI  287 (610)
T ss_pred             CceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCCCeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhh
Confidence            34445566999999999653 3344433          56689999999999999988877543          355666


Q ss_pred             cCCcCC-------CCCCEEEecHHHHHHhh
Q 042424          115 GDVTLS-------PNASCLVMTTEILRGML  137 (138)
Q Consensus       115 Gd~~~~-------~~~~IiVtTpe~l~~lL  137 (138)
                      |.....       ...+|+|+||.+|-.||
T Consensus       288 GG~~v~eql~~v~~GvHivVATPGRL~DmL  317 (610)
T KOG0341|consen  288 GGVPVREQLDVVRRGVHIVVATPGRLMDML  317 (610)
T ss_pred             cCccHHHHHHHHhcCeeEEEcCcchHHHHH
Confidence            766543       37899999999998886

>PRK14873 primosome assembly protein PriA; Provisional

Probab=98.31  E-value=1.4e-06  Score=78.58  Aligned_cols=72  Identities=13%  Similarity=0.033  Sum_probs=61.0

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCCcCC-----------CCCCE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVTLS-----------PNASC  125 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~~~-----------~~~~I  125 (138)
                      ++.+.+|||||.+++.++..++..|+.+|+++|..+|+.|..+.|++.|+  .|.++++.....           .+..|
T Consensus       164 i~~~~~GSGKTevyl~~i~~~l~~Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~~~I  243 (665)
T PRK14873        164 VWQALPGEDWARRLAAAAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQARV  243 (665)
T ss_pred             HhhcCCCCcHHHHHHHHHHHHHHcCCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCCCcE
Confidence            34444699999999999999999999999999999999999999999996  688898766432           15789


Q ss_pred             EEecH
Q 042424          126 LVMTT  130 (138)
Q Consensus       126 iVtTp  130 (138)
                      +|.|-
T Consensus       244 ViGtR  248 (665)
T PRK14873        244 VVGTR  248 (665)
T ss_pred             EEEcc
Confidence            99883

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=98.26  E-value=1.9e-06  Score=79.65  Aligned_cols=78  Identities=15%  Similarity=0.083  Sum_probs=64.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC-----CCCEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP-----NASCL  126 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~-----~~~Ii  126 (138)
                      ...+..++||.|||+++.+++......|+.+.+|.|+.-|+.|-++.+...|.    +|+.+.|+.....     +++|+
T Consensus        96 ~G~IaEm~TGEGKTL~a~lp~~l~al~g~~VhIvT~ndyLA~RD~e~m~~l~~~lGlsv~~i~~~~~~~~r~~~Y~~dI~  175 (908)
T PRK13107         96 SNRIAEMRTGEGKTLTATLPAYLNALTGKGVHVITVNDYLARRDAENNRPLFEFLGLTVGINVAGLGQQEKKAAYNADIT  175 (908)
T ss_pred             CCccccccCCCCchHHHHHHHHHHHhcCCCEEEEeCCHHHHHHHHHHHHHHHHhcCCeEEEecCCCCHHHHHhcCCCCeE
Confidence            45678999999999999877766556788899999999999999988887664    7888777654322     79999


Q ss_pred             EecHHHH
Q 042424          127 VMTTEIL  133 (138)
Q Consensus       127 VtTpe~l  133 (138)
                      ++||..|
T Consensus       176 YgT~~e~  182 (908)
T PRK13107        176 YGTNNEF  182 (908)
T ss_pred             EeCCCcc
Confidence            9999987

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

Probab=98.22  E-value=4.7e-06  Score=76.19  Aligned_cols=81  Identities=19%  Similarity=0.186  Sum_probs=63.7

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCCcCCCCCCEEEecH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVTLSPNASCLVMTT  130 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~~~~~~~IiVtTp  130 (138)
                      ..+.+|+..||+|||..|...|.+.++.  -+|+||++-.++|++|-+..|.+.+.  .......+...+.+++|.|+|.
T Consensus       185 ~~raLlvMATGTGKTrTAiaii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P~~~~~n~i~~~~~~~s~~i~lsTy  264 (875)
T COG4096         185 QNRALLVMATGTGKTRTAIAIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLPFGTKMNKIEDKKGDTSSEIYLSTY  264 (875)
T ss_pred             CceEEEEEecCCCcceeHHHHHHHHHhcchhheeeEEechHHHHHHHHHHHHHhCCCccceeeeecccCCcceeEEEeeh
Confidence            3557799999999999998777777665  48999999999999999999988543  3333333445555789999999


Q ss_pred             HHHHH
Q 042424          131 EILRG  135 (138)
Q Consensus       131 e~l~~  135 (138)
                      +.+-.
T Consensus       265 qt~~~  269 (875)
T COG4096         265 QTMTG  269 (875)
T ss_pred             HHHHh
Confidence            88754

>PF13245 AAA_19: Part of AAA domain

Probab=98.19  E-value=6.3e-06  Score=54.86  Aligned_cols=45  Identities=22%  Similarity=0.273  Sum_probs=39.0

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHc----CCcEEEEechHHHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRD----KQRVIYTSSLKALSNQKYREL  103 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~----~~rviyv~P~kaLv~Q~~~~l  103 (138)
                      +|.+|.|+|||..+...+...+..    ++++++++|+++.+++..+.+
T Consensus        14 vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen   14 VVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCHHHHHHHHHHH
Confidence            469999999998887777776654    789999999999999988887

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.15  E-value=5.8e-06  Score=76.51  Aligned_cols=78  Identities=15%  Similarity=0.066  Sum_probs=66.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC-----CCCEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP-----NASCL  126 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~-----~~~Ii  126 (138)
                      ...+....||+|||++|.+++.-+...|+.+.+++|+.-|+.|.++.+...|.    +|+.++++.....     .++|+
T Consensus        96 ~G~iaEM~TGEGKTLvA~l~a~l~al~G~~VhvvT~ndyLA~RD~e~m~~l~~~lGl~v~~i~~~~~~~err~~Y~~dI~  175 (913)
T PRK13103         96 EGKIAEMRTGEGKTLVGTLAVYLNALSGKGVHVVTVNDYLARRDANWMRPLYEFLGLSVGIVTPFQPPEEKRAAYAADIT  175 (913)
T ss_pred             cCccccccCCCCChHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHHHhcccCCEEEEECCCCCHHHHHHHhcCCEE
Confidence            45668889999999999988876667799999999999999999999998875    7888888765432     79999


Q ss_pred             EecHHHH
Q 042424          127 VMTTEIL  133 (138)
Q Consensus       127 VtTpe~l  133 (138)
                      ++|...|
T Consensus       176 YGT~~e~  182 (913)
T PRK13103        176 YGTNNEF  182 (913)
T ss_pred             EEccccc
Confidence            9998775

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

Probab=98.15  E-value=4.9e-06  Score=74.75  Aligned_cols=51  Identities=24%  Similarity=0.224  Sum_probs=43.2

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHH--cCCcEEEEechHHHHHHHHHHHHHh
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFR--DKQRVIYTSSLKALSNQKYRELHKE  106 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~--~~~rviyv~P~kaLv~Q~~~~l~~~  106 (138)
                      ...++.+|||+|||++++++++..+.  .+.++|+.+||++|.+|.+++|...
T Consensus        17 ~~lliEA~TGtGKTlAYLlpal~~~~~~~~~rvlIstpT~~Lq~Ql~~~l~~l   69 (636)
T TIGR03117        17 RIGMLEASTGVGKTLAMIMAALTMLKERPDQKIAIAVPTLALMGQLWSELERL   69 (636)
T ss_pred             CeEEEEcCCCCcHHHHHHHHHHHHHHhccCceEEEECCcHHHHHHHHHHHHHH
Confidence            45669999999999999987765544  3799999999999999999987753

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.

>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=98.13  E-value=3.4e-05  Score=60.85  Aligned_cols=78  Identities=26%  Similarity=0.268  Sum_probs=54.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC-----CcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCC-------cC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK-----QRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDV-------TL  119 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~-----~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~-------~~  119 (138)
                      ++.+|+-..|.|||+.++..+......+     +++|+|+|. ++..|+.++|.+.+.    .+..+.|+.       ..
T Consensus        26 ~g~lL~de~GlGKT~~~i~~~~~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~~~~~~~~~v~~~~~~~~~~~~~~~~  104 (299)
T PF00176_consen   26 RGGLLADEMGLGKTITAIALISYLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEKWFDPDSLRVIIYDGDSERRRLSKNQ  104 (299)
T ss_dssp             -EEEE---TTSSHHHHHHHHHHHHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHHHSGT-TS-EEEESSSCHHHHTTSSS
T ss_pred             CCEEEEECCCCCchhhhhhhhhhhhhccccccccceeEeecc-chhhhhhhhhccccccccccccccccccccccccccc
Confidence            5667888999999999886665443332     249999999 899999999999773    566666665       22


Q ss_pred             CCCCCEEEecHHHHH
Q 042424          120 SPNASCLVMTTEILR  134 (138)
Q Consensus       120 ~~~~~IiVtTpe~l~  134 (138)
                      ..+.+++|+|++.+.
T Consensus       105 ~~~~~vvi~ty~~~~  119 (299)
T PF00176_consen  105 LPKYDVVITTYETLR  119 (299)
T ss_dssp             CCCSSEEEEEHHHHH
T ss_pred             cccceeeeccccccc
Confidence            337889999999887

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.

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

Probab=98.09  E-value=1.1e-05  Score=74.33  Aligned_cols=46  Identities=17%  Similarity=0.145  Sum_probs=39.3

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYR  101 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~  101 (138)
                      ...++.||||+|||+.+++++......++++++.+||++|.+|...
T Consensus       265 ~~~~~eA~TG~GKT~ayLlp~~~~~~~~~~vvi~t~t~~Lq~Ql~~  310 (850)
T TIGR01407       265 EKSLIEAPTGTGKTLGYLLPALYYAITEKPVVISTNTKVLQSQLLE  310 (850)
T ss_pred             CcEEEECCCCCchhHHHHHHHHHHhcCCCeEEEEeCcHHHHHHHHH
Confidence            5566999999999999998776554467899999999999999865

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.

>KOG0953 consensus Mitochondrial RNA helicase SUV3, DEAD-box superfamily [RNA processing and modification]

Probab=98.02  E-value=4.8e-06  Score=73.67  Aligned_cols=88  Identities=19%  Similarity=0.305  Sum_probs=65.5

Q ss_pred             ccccCCCCccCCCCCCCce--EECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCC
Q 042424           41 EVAVPSCYTLTTDETTHGT--LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDV  117 (138)
Q Consensus        41 ~~~~p~~y~~~~~~~~~~~--l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~  117 (138)
                      ....|..|.|.....++.+  -++||.||||.-|+    +.+...++.+|.-|.+.|+.+.++++++ .+ .+.++||+.
T Consensus       175 DLt~P~~WyP~AR~~~RkIi~H~GPTNSGKTy~AL----qrl~~aksGvycGPLrLLA~EV~~r~na-~gipCdL~TGeE  249 (700)
T KOG0953|consen  175 DLTNPANWYPEARKIRRKIIMHVGPTNSGKTYRAL----QRLKSAKSGVYCGPLRLLAHEVYDRLNA-LGIPCDLLTGEE  249 (700)
T ss_pred             ccCCCcccCchhHhhhheEEEEeCCCCCchhHHHH----HHHhhhccceecchHHHHHHHHHHHhhh-cCCCccccccce
Confidence            3445777776655445544  79999999996544    4445568999999999999999999988 55 889999975


Q ss_pred             cCCC-----CCCEEEecHHHH
Q 042424          118 TLSP-----NASCLVMTTEIL  133 (138)
Q Consensus       118 ~~~~-----~~~IiVtTpe~l  133 (138)
                      ....     .++.+-||.|+.
T Consensus       250 ~~~~~~~~~~a~hvScTVEM~  270 (700)
T KOG0953|consen  250 RRFVLDNGNPAQHVSCTVEMV  270 (700)
T ss_pred             eeecCCCCCcccceEEEEEEe
Confidence            4322     367888887764

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=97.98  E-value=1e-05  Score=74.15  Aligned_cols=77  Identities=18%  Similarity=0.151  Sum_probs=64.6

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC-----CCCEEE
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP-----NASCLV  127 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~-----~~~IiV  127 (138)
                      ..+....||+|||++|.+++..+...|+.+-+++|+--|+.|.++.+...|.    +|+.++|+.+...     .++|+-
T Consensus        95 G~iaEm~TGEGKTLvA~l~a~l~al~G~~v~vvT~neyLA~Rd~e~~~~~~~~LGl~vg~i~~~~~~~~r~~~y~~dI~Y  174 (796)
T PRK12906         95 GNIAEMKTGEGKTLTATLPVYLNALTGKGVHVVTVNEYLSSRDATEMGELYRWLGLTVGLNLNSMSPDEKRAAYNCDITY  174 (796)
T ss_pred             CCcccccCCCCCcHHHHHHHHHHHHcCCCeEEEeccHHHHHhhHHHHHHHHHhcCCeEEEeCCCCCHHHHHHHhcCCCee
Confidence            4478899999999999988877777899999999999999999999988765    8899988765432     788888


Q ss_pred             ecHHHH
Q 042424          128 MTTEIL  133 (138)
Q Consensus       128 tTpe~l  133 (138)
                      +|...|
T Consensus       175 ~t~~e~  180 (796)
T PRK12906        175 STNSEL  180 (796)
T ss_pred             cCCccc
Confidence            886544

>KOG4284 consensus DEAD box protein [Transcription]

Probab=97.98  E-value=3.6e-06  Score=75.80  Aligned_cols=81  Identities=10%  Similarity=0.087  Sum_probs=64.3

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCCcCCC------C
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDVTLSP------N  122 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~~~~~------~  122 (138)
                      +.++.+-.|.|||+++-.+..+.|..   .-.+++|+|||.|+-|+...+.+...     .+.++.|+.....      .
T Consensus        64 DliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~PTREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rlk~  143 (980)
T KOG4284|consen   64 DLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTPTREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRLKQ  143 (980)
T ss_pred             ceEEEecCCCCceEEEEeeeehhcCcccCcceeEEEecchhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhhhh
Confidence            56799999999999987555555542   46789999999999999999988532     6777778765432      7


Q ss_pred             CCEEEecHHHHHHhh
Q 042424          123 ASCLVMTTEILRGML  137 (138)
Q Consensus       123 ~~IiVtTpe~l~~lL  137 (138)
                      ++|+|.||.++..|+
T Consensus       144 ~rIvIGtPGRi~qL~  158 (980)
T KOG4284|consen  144 TRIVIGTPGRIAQLV  158 (980)
T ss_pred             ceEEecCchHHHHHH
Confidence            889999999987653

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=97.97  E-value=8.1e-06  Score=70.44  Aligned_cols=84  Identities=14%  Similarity=0.068  Sum_probs=62.2

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHH-Hc--------CCcEEEEechHHHHHHHHHHHHHh-cC---ceEEEecCCcC--
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAF-RD--------KQRVIYTSSLKALSNQKYRELHKE-FK---DVGLMTGDVTL--  119 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l-~~--------~~rviyv~P~kaLv~Q~~~~l~~~-f~---~v~~~tGd~~~--  119 (138)
                      ....+-.+-||+|||+++++.-+.++ .+        +-+++++.|++.|+-|.--+..+. |.   .|+++.|....  
T Consensus       257 G~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptreLalqie~e~~kysyng~ksvc~ygggnR~eq  336 (629)
T KOG0336|consen  257 GIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTRELALQIEGEVKKYSYNGLKSVCVYGGGNRNEQ  336 (629)
T ss_pred             CcceEEEEecCCCcCHHHhccceeeeeccchhhhccCCCceEEEeccHHHHHHHHhHHhHhhhcCcceEEEecCCCchhH
Confidence            35666888999999999986433222 11        568999999999999998776662 22   68888775432  


Q ss_pred             ----CCCCCEEEecHHHHHHhhC
Q 042424          120 ----SPNASCLVMTTEILRGMLY  138 (138)
Q Consensus       120 ----~~~~~IiVtTpe~l~~lL~  138 (138)
                          ....+||++||.+|..+.|
T Consensus       337 ie~lkrgveiiiatPgrlndL~~  359 (629)
T KOG0336|consen  337 IEDLKRGVEIIIATPGRLNDLQM  359 (629)
T ss_pred             HHHHhcCceEEeeCCchHhhhhh
Confidence                2378999999999988754

>KOG0329 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=97.95  E-value=1.4e-05  Score=65.48  Aligned_cols=80  Identities=19%  Similarity=0.162  Sum_probs=64.1

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHc--C-CcEEEEechHHHHHHHHHHHHHhcC------ceEEEecCCcCCC------
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRD--K-QRVIYTSSLKALSNQKYRELHKEFK------DVGLMTGDVTLSP------  121 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~--~-~rviyv~P~kaLv~Q~~~~l~~~f~------~v~~~tGd~~~~~------  121 (138)
                      ..+..|-.|-|||.++.++-++.+.-  | -.+++++.|++|+-|+.+++.+ |+      .|.+.-|...+..      
T Consensus        81 dvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtrelafqi~~ey~r-fskymP~vkvaVFfGG~~Ikkdee~lk  159 (387)
T KOG0329|consen   81 DVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTRELAFQISKEYER-FSKYMPSVKVSVFFGGLFIKKDEELLK  159 (387)
T ss_pred             hhheecccCCCceeeeehhhhhhcCCCCCeEEEEEEeccHHHHHHHHHHHHH-HHhhCCCceEEEEEcceeccccHHHHh
Confidence            44577889999999999998888764  4 4689999999999999888766 54      5778888776543      


Q ss_pred             -CCCEEEecHHHHHHhh
Q 042424          122 -NASCLVMTTEILRGML  137 (138)
Q Consensus       122 -~~~IiVtTpe~l~~lL  137 (138)
                       ..+|+|+||.++..+.
T Consensus       160 ~~PhivVgTPGrilALv  176 (387)
T KOG0329|consen  160 NCPHIVVGTPGRILALV  176 (387)
T ss_pred             CCCeEEEcCcHHHHHHH
Confidence             5679999999998763

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=97.94  E-value=2.2e-05  Score=64.04  Aligned_cols=51  Identities=25%  Similarity=0.257  Sum_probs=41.7

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHH-cCC-----cEEEEechHHHHHHHHHHHHHh
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFR-DKQ-----RVIYTSSLKALSNQKYRELHKE  106 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~-~~~-----rviyv~P~kaLv~Q~~~~l~~~  106 (138)
                      .+.++.+|||+|||+.++.+++..+. .+.     +++|.++|.++.+|...++++.
T Consensus        28 ~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00488       28 KIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            56779999999999999976654433 343     8999999999999998888764

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=97.94  E-value=2.2e-05  Score=64.04  Aligned_cols=51  Identities=25%  Similarity=0.257  Sum_probs=41.7

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHH-cCC-----cEEEEechHHHHHHHHHHHHHh
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFR-DKQ-----RVIYTSSLKALSNQKYRELHKE  106 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~-~~~-----rviyv~P~kaLv~Q~~~~l~~~  106 (138)
                      .+.++.+|||+|||+.++.+++..+. .+.     +++|.++|.++.+|...++++.
T Consensus        28 ~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00489       28 KIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            56779999999999999976654433 343     8999999999999998888764

>KOG0950 consensus DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only]

Probab=97.84  E-value=3.3e-05  Score=71.55  Aligned_cols=84  Identities=19%  Similarity=0.184  Sum_probs=64.3

Q ss_pred             CCCCceEECcCCCchHHHHHHHH-HHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC---CCCCE
Q 042424           54 ETTHGTLTNPVYNGKTAVAEYAI-AMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS---PNASC  125 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~~ai-~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~---~~~~I  125 (138)
                      ...|.+.++||++|||++++.-| ...+...+.+++++|+.+.+.++...++..+.    .|.-+.|.....   ..-.|
T Consensus       239 e~~nliys~Pts~gktlvaeilml~~~l~~rr~~llilp~vsiv~Ek~~~l~~~~~~~G~~ve~y~g~~~p~~~~k~~sv  318 (1008)
T KOG0950|consen  239 ERKNLIYSLPTSAGKTLVAEILMLREVLCRRRNVLLILPYVSIVQEKISALSPFSIDLGFPVEEYAGRFPPEKRRKRESV  318 (1008)
T ss_pred             cccceEEeCCCccchHHHHHHHHHHHHHHHhhceeEecceeehhHHHHhhhhhhccccCCcchhhcccCCCCCcccceee
Confidence            34788899999999999998544 44456789999999999999999999888433    333344543322   26789


Q ss_pred             EEecHHHHHHhh
Q 042424          126 LVMTTEILRGML  137 (138)
Q Consensus       126 iVtTpe~l~~lL  137 (138)
                      .|||.|+-++++
T Consensus       319 ~i~tiEkansli  330 (1008)
T KOG0950|consen  319 AIATIEKANSLI  330 (1008)
T ss_pred             eeeehHhhHhHH
Confidence            999999988765

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=97.80  E-value=4e-05  Score=69.78  Aligned_cols=77  Identities=16%  Similarity=0.094  Sum_probs=63.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC-----CCCEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP-----NASCL  126 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~-----~~~Ii  126 (138)
                      ...+....||.|||+++.+++......|+.+.++.|+--|+.|-++.+...|.    +|+.++++.+...     +++|+
T Consensus        92 ~G~VaEM~TGEGKTLvA~l~a~l~AL~G~~VhvvT~NdyLA~RDae~m~~ly~~LGLsvg~i~~~~~~~err~aY~~DIt  171 (764)
T PRK12326         92 AGDVIEMATGEGKTLAGAIAAAGYALQGRRVHVITVNDYLARRDAEWMGPLYEALGLTVGWITEESTPEERRAAYACDVT  171 (764)
T ss_pred             CCCcccccCCCCHHHHHHHHHHHHHHcCCCeEEEcCCHHHHHHHHHHHHHHHHhcCCEEEEECCCCCHHHHHHHHcCCCE
Confidence            34567889999999999877776667799999999999999999999988775    7888888765432     78888


Q ss_pred             EecHHH
Q 042424          127 VMTTEI  132 (138)
Q Consensus       127 VtTpe~  132 (138)
                      -+|...
T Consensus       172 YgTn~e  177 (764)
T PRK12326        172 YASVNE  177 (764)
T ss_pred             EcCCcc
Confidence            887654

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

Probab=97.77  E-value=0.0001  Score=67.96  Aligned_cols=60  Identities=20%  Similarity=0.216  Sum_probs=44.7

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHH-HHHHH---hcC-ceEEEecC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKY-RELHK---EFK-DVGLMTGD  116 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~-~~l~~---~f~-~v~~~tGd  116 (138)
                      ...++.|+||+|||++++++++... ++.++|+.+||++|.+|.. +++..   .++ ++..+.|.
T Consensus       265 ~~~~~eA~tGtGKT~ayllp~l~~~-~~~~vvI~t~T~~Lq~Ql~~~~i~~l~~~~~~~~~~~kg~  329 (820)
T PRK07246        265 PASFIEAQTGIGKTYGYLLPLLAQS-DQRQIIVSVPTKILQDQIMAEEVKAIQEVFHIDCHSLKGP  329 (820)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHhc-CCCcEEEEeCcHHHHHHHHHHHHHHHHHhcCCcEEEEECC
Confidence            4566999999999999998866532 5789999999999999995 44443   333 45555543

>KOG0326 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=97.66  E-value=4.3e-05  Score=64.28  Aligned_cols=82  Identities=16%  Similarity=0.042  Sum_probs=63.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhc---C-ceEEEecCCcCCC-------
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEF---K-DVGLMTGDVTLSP-------  121 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f---~-~v~~~tGd~~~~~-------  121 (138)
                      ++.+..+-.|.|||-++...++..+..   .-.+++++|+++|+-|..+...+.-   + .|.+.+|......       
T Consensus       123 rdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPtrelALQtSqvc~~lskh~~i~vmvttGGT~lrDDI~Rl~~  202 (459)
T KOG0326|consen  123 RDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPTRELALQTSQVCKELSKHLGIKVMVTTGGTSLRDDIMRLNQ  202 (459)
T ss_pred             hhhhhhccCCCCCccceechhhhhcCccccceeEEEEeecchhhHHHHHHHHHHhcccCeEEEEecCCcccccceeeecC
Confidence            556678889999999888888877654   3568999999999999887666532   2 5666678775432       


Q ss_pred             CCCEEEecHHHHHHhh
Q 042424          122 NASCLVMTTEILRGML  137 (138)
Q Consensus       122 ~~~IiVtTpe~l~~lL  137 (138)
                      .-+++|+||.++.++.
T Consensus       203 ~VH~~vgTPGRIlDL~  218 (459)
T KOG0326|consen  203 TVHLVVGTPGRILDLA  218 (459)
T ss_pred             ceEEEEcCChhHHHHH
Confidence            6789999999988763

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

Probab=97.65  E-value=9.8e-05  Score=55.32  Aligned_cols=48  Identities=19%  Similarity=0.216  Sum_probs=38.0

Q ss_pred             ceEECcCCCchHHHHH-HHHHHHHHcCCcEEEEechHHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .+|...+|+|||.-.+ -.+.+++.++.|+|++.|||.+++++++.|+.
T Consensus         7 ~~~d~hpGaGKTr~vlp~~~~~~i~~~~rvLvL~PTRvva~em~~aL~~   55 (148)
T PF07652_consen    7 TVLDLHPGAGKTRRVLPEIVREAIKRRLRVLVLAPTRVVAEEMYEALKG   55 (148)
T ss_dssp             EEEE--TTSSTTTTHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHTTT
T ss_pred             eEEecCCCCCCcccccHHHHHHHHHccCeEEEecccHHHHHHHHHHHhc
Confidence            3588999999999655 56667888999999999999999999999876

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 ....

>KOG0352 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=97.61  E-value=0.00011  Score=63.92  Aligned_cols=75  Identities=21%  Similarity=0.216  Sum_probs=54.2

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEE------------ecCCc-CCCC
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLM------------TGDVT-LSPN  122 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~------------tGd~~-~~~~  122 (138)
                      +.-+|.|||+||++++-+..+   -.+.-.|+++|+.||+.++.+.|.+ +. .+.-+            .+|.. ..++
T Consensus        38 DVyVsMPTGaGKSLCyQLPaL---~~~gITIV~SPLiALIkDQiDHL~~-LKVp~~SLNSKlSt~ER~ri~~DL~~ekp~  113 (641)
T KOG0352|consen   38 DVYVSMPTGAGKSLCYQLPAL---VHGGITIVISPLIALIKDQIDHLKR-LKVPCESLNSKLSTVERSRIMGDLAKEKPT  113 (641)
T ss_pred             cEEEeccCCCchhhhhhchHH---HhCCeEEEehHHHHHHHHHHHHHHh-cCCchhHhcchhhHHHHHHHHHHHHhcCCc
Confidence            334999999999999976553   2356889999999999999999887 43 22222            13332 3447


Q ss_pred             CCEEEecHHHHHH
Q 042424          123 ASCLVMTTEILRG  135 (138)
Q Consensus       123 ~~IiVtTpe~l~~  135 (138)
                      ..++-.|||+...
T Consensus       114 ~K~LYITPE~AAt  126 (641)
T KOG0352|consen  114 IKMLYITPEGAAT  126 (641)
T ss_pred             eeEEEEchhhhhh
Confidence            8899999998643

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

Probab=97.60  E-value=0.00022  Score=66.56  Aligned_cols=53  Identities=21%  Similarity=0.215  Sum_probs=41.9

Q ss_pred             CCceEECcCCCchHHHHHHHHH-HHHHcCCcEEEEechHHHHHHHHH----HHHHhcC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIA-MAFRDKQRVIYTSSLKALSNQKYR----ELHKEFK  108 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~-~~l~~~~rviyv~P~kaLv~Q~~~----~l~~~f~  108 (138)
                      ...++.||||.|||+.++++.. .+...++++|+-.+|++|-+|...    .+++.++
T Consensus       277 ~~~~iEA~TGtGKTlaYLlpa~~~a~~~~~~vvIsT~T~~LQ~Ql~~kDiP~L~~~~~  334 (928)
T PRK08074        277 EHALIEAGTGTGKSLAYLLPAAYFAKKKEEPVVISTYTIQLQQQLLEKDIPLLQKIFP  334 (928)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHhhccCCeEEEEcCCHHHHHHHHHhhHHHHHHHcC
Confidence            5566999999999999986554 444468999999999999999875    3455444

>KOG0332 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=97.57  E-value=0.00018  Score=61.42  Aligned_cols=82  Identities=12%  Similarity=0.101  Sum_probs=60.3

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC--ce--EE-EecC-CcCC--CCCC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK--DV--GL-MTGD-VTLS--PNAS  124 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~--~v--~~-~tGd-~~~~--~~~~  124 (138)
                      +|.+-.+-.|+|||.++.++|+....-   .-.++.++|++.|+.|+.+.+.+.-.  .+  .. +-|. ....  -..+
T Consensus       130 ~nlIaQsqsGtGKTaaFvL~MLsrvd~~~~~PQ~iCLaPtrELA~Q~~eVv~eMGKf~~ita~yair~sk~~rG~~i~eq  209 (477)
T KOG0332|consen  130 QNLIAQSQSGTGKTAAFVLTMLSRVDPDVVVPQCICLAPTRELAPQTGEVVEEMGKFTELTASYAIRGSKAKRGNKLTEQ  209 (477)
T ss_pred             hhhhhhhcCCCchhHHHHHHHHHhcCccccCCCceeeCchHHHHHHHHHHHHHhcCceeeeEEEEecCcccccCCcchhh
Confidence            566778889999999999999877653   45788889999999999999998432  22  11 1222 1111  1789


Q ss_pred             EEEecHHHHHHhh
Q 042424          125 CLVMTTEILRGML  137 (138)
Q Consensus       125 IiVtTpe~l~~lL  137 (138)
                      |+|.||..+..++
T Consensus       210 IviGTPGtv~Dlm  222 (477)
T KOG0332|consen  210 IVIGTPGTVLDLM  222 (477)
T ss_pred             eeeCCCccHHHHH
Confidence            9999999887764

>KOG0327 consensus Translation initiation factor 4F, helicase subunit (eIF-4A) and related helicases [Translation, ribosomal structure and biogenesis]

Probab=97.54  E-value=8.4e-05  Score=63.08  Aligned_cols=82  Identities=16%  Similarity=0.083  Sum_probs=62.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcC-------CC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTL-------SP  121 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~-------~~  121 (138)
                      .+....+.+|+|||.++..++++.+..   ...++.++|++.|+.|..+.....+.    +|-.+.|....       ..
T Consensus        64 ~dv~~qaqsgTgKt~af~i~iLq~iD~~~ke~qalilaPtreLa~qi~~v~~~lg~~~~~~v~~~igg~~~~~~~~~i~~  143 (397)
T KOG0327|consen   64 HDVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAPTRELAQQIQKVVRALGDHMDVSVHACIGGTNVRREDQALLK  143 (397)
T ss_pred             CceeEeeeccccchhhhHHHHHhhcCcchHHHHHHHhcchHHHHHHHHHHHHhhhcccceeeeeecCcccchhhhhhhhc
Confidence            567799999999999988888877543   35689999999999999977777443    34444443322       12


Q ss_pred             -CCCEEEecHHHHHHhh
Q 042424          122 -NASCLVMTTEILRGML  137 (138)
Q Consensus       122 -~~~IiVtTpe~l~~lL  137 (138)
                       ...|+|.||.+...+|
T Consensus       144 ~~~hivvGTpgrV~dml  160 (397)
T KOG0327|consen  144 DKPHIVVGTPGRVFDML  160 (397)
T ss_pred             cCceeecCCchhHHHhh
Confidence             4689999999888776

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=97.52  E-value=0.00069  Score=63.59  Aligned_cols=78  Identities=22%  Similarity=0.268  Sum_probs=60.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC--CcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcC-------CC--CC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK--QRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTL-------SP--NA  123 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~--~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~-------~~--~~  123 (138)
                      .+.+|.=..|-|||.-|.+.+...+..|  +++++|+|. +|..|+..++.++|+ ...++.++...       ++  ..
T Consensus       170 ~R~LLADEvGLGKTIeAglil~~l~~~g~~~rvLIVvP~-sL~~QW~~El~~kF~l~~~i~~~~~~~~~~~~~~~pf~~~  248 (956)
T PRK04914        170 PRVLLADEVGLGKTIEAGMIIHQQLLTGRAERVLILVPE-TLQHQWLVEMLRRFNLRFSLFDEERYAEAQHDADNPFETE  248 (956)
T ss_pred             CCEEEEeCCcCcHHHHHHHHHHHHHHcCCCCcEEEEcCH-HHHHHHHHHHHHHhCCCeEEEcCcchhhhcccccCccccC
Confidence            4667888999999999987777666554  699999998 899999999998887 55555443211       21  57


Q ss_pred             CEEEecHHHHH
Q 042424          124 SCLVMTTEILR  134 (138)
Q Consensus       124 ~IiVtTpe~l~  134 (138)
                      +++|++.+.+.
T Consensus       249 ~~vI~S~~~l~  259 (956)
T PRK04914        249 QLVICSLDFLR  259 (956)
T ss_pred             cEEEEEHHHhh
Confidence            89999998664

>PF12340 DUF3638: Protein of unknown function (DUF3638); InterPro: IPR022099 This domain family is found in eukaryotes, and is approximately 230 amino acids in length

Probab=97.51  E-value=0.0008  Score=53.74  Aligned_cols=81  Identities=21%  Similarity=0.245  Sum_probs=60.3

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC---ceEEEe----cCCcCC--------
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK---DVGLMT----GDVTLS--------  120 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~---~v~~~t----Gd~~~~--------  120 (138)
                      .|.+...-.|.|||-|..-.+.-++.+|.+.+.++=-++|.+|.++.++.+++   +-.+++    -+...+        
T Consensus        42 ~n~v~QlnMGeGKTsVI~Pmla~~LAdg~~LvrviVpk~Ll~q~~~~L~~~lg~l~~r~i~~lpFsR~~~~~~~~~~~~~  121 (229)
T PF12340_consen   42 KNSVMQLNMGEGKTSVIVPMLALALADGSRLVRVIVPKALLEQMRQMLRSRLGGLLNRRIYHLPFSRSTPLTPETLEKIR  121 (229)
T ss_pred             CCeEeeecccCCccchHHHHHHHHHcCCCcEEEEEcCHHHHHHHHHHHHHHHHHHhCCeeEEecccCCCCCCHHHHHHHH
Confidence            57789999999999999866666778888877766677999999999999887   212221    111111        


Q ss_pred             -------CCCCEEEecHHHHHHh
Q 042424          121 -------PNASCLVMTTEILRGM  136 (138)
Q Consensus       121 -------~~~~IiVtTpe~l~~l  136 (138)
                             .+..|+|+|||.+.++
T Consensus       122 ~l~~~~~~~~gill~~PEhilSf  144 (229)
T PF12340_consen  122 QLLEECMRSGGILLATPEHILSF  144 (229)
T ss_pred             HHHHHHHHcCCEEEeChHHHHHH
Confidence                   1667999999998875

There are two conserved sequence motifs: LLE and NMG.

>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]

Probab=97.50  E-value=4.9e-05  Score=67.07  Aligned_cols=76  Identities=18%  Similarity=0.172  Sum_probs=62.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCCcCCC--CCCEEEe
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDVTLSP--NASCLVM  128 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~~~~~--~~~IiVt  128 (138)
                      ++.+|..|.|+|||++..-|+.   .-++++|+++..---++|+.+.|.. |.     .++..|.|.+..+  ++.|+|+
T Consensus       321 RSGiIVLPCGAGKtLVGvTAa~---tikK~clvLcts~VSVeQWkqQfk~-wsti~d~~i~rFTsd~Ke~~~~~~gvvvs  396 (776)
T KOG1123|consen  321 RSGIIVLPCGAGKTLVGVTAAC---TIKKSCLVLCTSAVSVEQWKQQFKQ-WSTIQDDQICRFTSDAKERFPSGAGVVVT  396 (776)
T ss_pred             cCceEEEecCCCCceeeeeeee---eecccEEEEecCccCHHHHHHHHHh-hcccCccceEEeeccccccCCCCCcEEEE
Confidence            5678999999999999875552   2378999999998899999988877 43     6899999987644  8889999


Q ss_pred             cHHHHHH
Q 042424          129 TTEILRG  135 (138)
Q Consensus       129 Tpe~l~~  135 (138)
                      |+-++.+
T Consensus       397 TYsMva~  403 (776)
T KOG1123|consen  397 TYSMVAY  403 (776)
T ss_pred             eeehhhh
Confidence            9877643

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

Probab=97.43  E-value=0.00028  Score=53.20  Aligned_cols=48  Identities=21%  Similarity=0.225  Sum_probs=38.3

Q ss_pred             ceEECcCCCchHHHHHHHHHHH--------HHcCCcEEEEechHHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMA--------FRDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~--------l~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .+|.||.|+|||.+...++...        ...++++++++|+.+-+++..+.|.+
T Consensus        20 ~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen   20 TLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             EEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            5699999999997766555554        23489999999999999999999988

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

Probab=97.43  E-value=0.00029  Score=62.94  Aligned_cols=76  Identities=13%  Similarity=0.152  Sum_probs=57.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcCC-----------CCC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTLS-----------PNA  123 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~~-----------~~~  123 (138)
                      .+.++..|||+||++|+-.+.+-  . .+-.|+|+|..||-.++.+.++. .+ .+..+.+....+           ..-
T Consensus        33 ~d~lvvmPTGgGKSlCyQiPAll--~-~G~TLVVSPLiSLM~DQV~~l~~-~Gi~A~~lnS~l~~~e~~~v~~~l~~g~~  108 (590)
T COG0514          33 KDTLVVMPTGGGKSLCYQIPALL--L-EGLTLVVSPLISLMKDQVDQLEA-AGIRAAYLNSTLSREERQQVLNQLKSGQL  108 (590)
T ss_pred             CcEEEEccCCCCcchHhhhHHHh--c-CCCEEEECchHHHHHHHHHHHHH-cCceeehhhcccCHHHHHHHHHHHhcCce
Confidence            67889999999999998654431  2 45899999999999999999988 54 444444432221           256


Q ss_pred             CEEEecHHHHHH
Q 042424          124 SCLVMTTEILRG  135 (138)
Q Consensus       124 ~IiVtTpe~l~~  135 (138)
                      +++.-+||++.+
T Consensus       109 klLyisPErl~~  120 (590)
T COG0514         109 KLLYISPERLMS  120 (590)
T ss_pred             eEEEECchhhcC
Confidence            899999998864

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=97.42  E-value=0.00061  Score=65.53  Aligned_cols=80  Identities=20%  Similarity=0.132  Sum_probs=50.4

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcC--CcEEEEec----hHHHHHHHHHHHHHhcC-ceEEEe-cCCcCCCCCCEEEe
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDK--QRVIYTSS----LKALSNQKYRELHKEFK-DVGLMT-GDVTLSPNASCLVM  128 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~--~rviyv~P----~kaLv~Q~~~~l~~~f~-~v~~~t-Gd~~~~~~~~IiVt  128 (138)
                      -.+++|+||||||...=..+. .+..|  .+++.+-|    .++|+.+.++++...++ .||.-. .+.....+.+|+|+
T Consensus        91 VviI~GeTGSGKTTqlPq~ll-e~g~g~~g~I~~TQPRRlAArsLA~RVA~El~~~lG~~VGY~vrf~~~~s~~t~I~v~  169 (1294)
T PRK11131         91 VVIVAGETGSGKTTQLPKICL-ELGRGVKGLIGHTQPRRLAARTVANRIAEELETELGGCVGYKVRFNDQVSDNTMVKLM  169 (1294)
T ss_pred             eEEEECCCCCCHHHHHHHHHH-HcCCCCCCceeeCCCcHHHHHHHHHHHHHHHhhhhcceeceeecCccccCCCCCEEEE
Confidence            345889999999995322222 12223  34555557    46888888888776555 455422 12233447899999


Q ss_pred             cHHHHHHhh
Q 042424          129 TTEILRGML  137 (138)
Q Consensus       129 Tpe~l~~lL  137 (138)
                      ||.+|...+
T Consensus       170 TpG~LL~~l  178 (1294)
T PRK11131        170 TDGILLAEI  178 (1294)
T ss_pred             ChHHHHHHH
Confidence            999998754

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

Probab=97.40  E-value=0.00036  Score=62.09  Aligned_cols=51  Identities=27%  Similarity=0.215  Sum_probs=42.9

Q ss_pred             CCceEECcCCCchHHHHHH-HHHHHHHcCCcEEEEechHHHHHHHHHHHHHh
Q 042424           56 THGTLTNPVYNGKTAVAEY-AIAMAFRDKQRVIYTSSLKALSNQKYRELHKE  106 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~-ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~  106 (138)
                      ...++.+|||.|||+..+. ++..+...++++++..+|++|-+|..++....
T Consensus        35 ~~~~iEapTGtGKTl~yL~~al~~~~~~~~~viist~t~~lq~q~~~~~~~~   86 (654)
T COG1199          35 EGLLIEAPTGTGKTLAYLLPALAYAREEGKKVIISTRTKALQEQLLEEDLPI   86 (654)
T ss_pred             CcEEEECCCCccHHHHHHHHHHHHHHHcCCcEEEECCCHHHHHHHHHhhcch
Confidence            3477999999999999985 55555556899999999999999999887764

>KOG0328 consensus Predicted ATP-dependent RNA helicase FAL1, involved in rRNA maturation, DEAD-box superfamily [Translation, ribosomal structure and biogenesis]

Probab=97.36  E-value=0.0001  Score=61.24  Aligned_cols=82  Identities=13%  Similarity=0.057  Sum_probs=63.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcC-------CC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTL-------SP  121 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~-------~~  121 (138)
                      ++.+..+-.|.|||..+-..+++.+.-   ...+++++||++|+.|..+.+...-+    .+-.+.|..+.       +-
T Consensus        65 rdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~lilsPTRELa~Qi~~vi~alg~~mnvq~hacigg~n~gedikkld~  144 (400)
T KOG0328|consen   65 RDVIAQAQSGTGKTATFSISVLQSLDISVRETQALILSPTRELAVQIQKVILALGDYMNVQCHACIGGKNLGEDIKKLDY  144 (400)
T ss_pred             cceEEEecCCCCceEEEEeeeeeecccccceeeEEEecChHHHHHHHHHHHHHhcccccceEEEEecCCccchhhhhhcc
Confidence            567799999999998877777776653   45799999999999999999988322    34444554432       33


Q ss_pred             CCCEEEecHHHHHHhh
Q 042424          122 NASCLVMTTEILRGML  137 (138)
Q Consensus       122 ~~~IiVtTpe~l~~lL  137 (138)
                      ..++++.||.+...|+
T Consensus       145 G~hvVsGtPGrv~dmi  160 (400)
T KOG0328|consen  145 GQHVVSGTPGRVLDMI  160 (400)
T ss_pred             cceEeeCCCchHHHHH
Confidence            7889999999988775

>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=97.34  E-value=0.00063  Score=53.76  Aligned_cols=53  Identities=13%  Similarity=0.103  Sum_probs=44.5

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcC----CcEEEEechHHHHHHHHHHHHHhc
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDK----QRVIYTSSLKALSNQKYRELHKEF  107 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~----~rviyv~P~kaLv~Q~~~~l~~~f  107 (138)
                      .++.+|.|..|||||.+...-+.+.+..+    .+++++..|++.+++...++.+.+
T Consensus        13 ~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~aa~e~~~ri~~~l   69 (315)
T PF00580_consen   13 EGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNAAAQEMRERIRELL   69 (315)
T ss_dssp             SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHHHHHHHHHHHHHhc
Confidence            35677999999999999987777777654    789999999999999999998854

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 ....

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=97.30  E-value=0.00047  Score=62.43  Aligned_cols=51  Identities=25%  Similarity=0.247  Sum_probs=44.1

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHH-cC--CcEEEEechHHHHHHHHHHHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFR-DK--QRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~-~~--~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      ..+.++.+|||.|||++.+.+.+..+. .+  .+++|.+.|.+=..|..+++++
T Consensus        29 ~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~sRThsQl~q~i~Elk~   82 (705)
T TIGR00604        29 GDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRK   82 (705)
T ss_pred             CCceEEeCCCCCCccHHHHHHHHHHHHhccccccEEEEcccchHHHHHHHHHHh
Confidence            357789999999999999977766655 34  7999999999999999999988

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).

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

Probab=97.30  E-value=0.00046  Score=61.21  Aligned_cols=50  Identities=28%  Similarity=0.288  Sum_probs=41.7

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      +...|-+-||||||+.....|.+   -++-.++++|.|.|+.|.|.+|++.|.
T Consensus        33 ~~QtLLGvTGSGKTfT~AnVI~~---~~rPtLV~AhNKTLAaQLy~Efk~fFP   82 (663)
T COG0556          33 KHQTLLGVTGSGKTFTMANVIAK---VQRPTLVLAHNKTLAAQLYSEFKEFFP   82 (663)
T ss_pred             eeeEEeeeccCCchhHHHHHHHH---hCCCeEEEecchhHHHHHHHHHHHhCc
Confidence            45669999999999665555533   278899999999999999999999886

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=97.30  E-value=0.0009  Score=60.75  Aligned_cols=61  Identities=21%  Similarity=0.166  Sum_probs=46.0

Q ss_pred             CCceEECcCCCchHHHHHH-HHHHHHHcCCcEEEEechHHHHHHHHHH----HHHhcC---ceEEEecC
Q 042424           56 THGTLTNPVYNGKTAVAEY-AIAMAFRDKQRVIYTSSLKALSNQKYRE----LHKEFK---DVGLMTGD  116 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~-ai~~~l~~~~rviyv~P~kaLv~Q~~~~----l~~~f~---~v~~~tGd  116 (138)
                      ...++-||||.|||+.+++ ++..+...++++|+-..|++|=+|....    +++.++   ++.++.|-
T Consensus        50 ~~lviEAgTGtGKTlaYLlPai~~A~~~~k~vVIST~T~~LQeQL~~kDlP~l~~~l~~~~~~~llKGr  118 (697)
T PRK11747         50 RILVIEAGTGVGKTLSYLLAGIPIARAEKKKLVISTATVALQEQLVSKDLPLLLKISGLDFKFTLAKGR  118 (697)
T ss_pred             ceEEEECCCCcchhHHHHHHHHHHHHHcCCeEEEEcCCHHHHHHHHhhhhhHHHHHcCCCceEEEEcCc
Confidence            4466999999999999986 5555666799999999999999999632    344443   45666553

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=97.14  E-value=0.0012  Score=63.49  Aligned_cols=81  Identities=16%  Similarity=0.075  Sum_probs=54.3

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC--CcEEEEechHHHHHHHHHHHHHhcC-ceEEEec-----CCcCCCCCCEEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK--QRVIYTSSLKALSNQKYRELHKEFK-DVGLMTG-----DVTLSPNASCLV  127 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~--~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tG-----d~~~~~~~~IiV  127 (138)
                      .-.+|+|+||||||...=..++.. ..+  .+++.+-|.+--+...++++.+.++ .+|...|     +...+.+..|++
T Consensus        83 ~vvii~g~TGSGKTTqlPq~lle~-~~~~~~~I~~tQPRRlAA~svA~RvA~elg~~lG~~VGY~vR~~~~~s~~T~I~~  161 (1283)
T TIGR01967        83 QVVIIAGETGSGKTTQLPKICLEL-GRGSHGLIGHTQPRRLAARTVAQRIAEELGTPLGEKVGYKVRFHDQVSSNTLVKL  161 (1283)
T ss_pred             ceEEEeCCCCCCcHHHHHHHHHHc-CCCCCceEecCCccHHHHHHHHHHHHHHhCCCcceEEeeEEcCCcccCCCceeee
Confidence            345699999999999653333322 122  4566777888877777777777666 3333333     334455788999


Q ss_pred             ecHHHHHHhh
Q 042424          128 MTTEILRGML  137 (138)
Q Consensus       128 tTpe~l~~lL  137 (138)
                      +|+.+|...+
T Consensus       162 ~TdGiLLr~l  171 (1283)
T TIGR01967       162 MTDGILLAET  171 (1283)
T ss_pred             ccccHHHHHh
Confidence            9999998654

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.

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

Probab=97.13  E-value=0.0019  Score=60.77  Aligned_cols=49  Identities=12%  Similarity=0.036  Sum_probs=40.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc-C-CcEEEEechHHHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD-K-QRVIYTSSLKALSNQKYRELH  104 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~-~-~rviyv~P~kaLv~Q~~~~l~  104 (138)
                      .+..+..+||+|||.+++..|...... | .+.|++||+.|+-+...+.|+
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~~~~~~~~fii~vp~~aI~egv~~~l~  110 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELHQKYGLFKFIIVVPTPAIKEGTRNFIQ  110 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHHcCCcEEEEEeCCHHHHHHHHHHhh
Confidence            355599999999999999888776554 4 679999999999988876665

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=97.07  E-value=0.0023  Score=60.58  Aligned_cols=79  Identities=11%  Similarity=0.048  Sum_probs=58.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHH-c--CCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCCcC----------C
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFR-D--KQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVTL----------S  120 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~-~--~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~~----------~  120 (138)
                      .+.+|+=..|.|||+.++..+..... .  .+.+|+|+|. +|+.|+.++|.+.+.  .+..++|+...          .
T Consensus       189 ~gGILADEMGLGKTlQaIalL~~L~~~~~~~gp~LIVvP~-SlL~nW~~Ei~kw~p~l~v~~~~G~~~eR~~~~~~~~~~  267 (1033)
T PLN03142        189 INGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPK-STLGNWMNEIRRFCPVLRAVKFHGNPEERAHQREELLVA  267 (1033)
T ss_pred             CCEEEEeCCCccHHHHHHHHHHHHHHhcCCCCCEEEEeCh-HHHHHHHHHHHHHCCCCceEEEeCCHHHHHHHHHHHhcc
Confidence            56788888999999988655443322 2  3678999996 788999999998655  66777776421          1


Q ss_pred             CCCCEEEecHHHHHH
Q 042424          121 PNASCLVMTTEILRG  135 (138)
Q Consensus       121 ~~~~IiVtTpe~l~~  135 (138)
                      .+.+|+|+|++.+..
T Consensus       268 ~~~dVvITSYe~l~~  282 (1033)
T PLN03142        268 GKFDVCVTSFEMAIK  282 (1033)
T ss_pred             cCCCcceecHHHHHH
Confidence            267899999998754

>KOG0353 consensus ATP-dependent DNA helicase [General function prediction only]

Probab=97.05  E-value=0.0011  Score=57.30  Aligned_cols=75  Identities=13%  Similarity=0.185  Sum_probs=55.7

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCc-------------CCC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVT-------------LSP  121 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~-------------~~~  121 (138)
                      ....+..|||.||+++.-+..+   ..++-+++++|..+|.+++.-.++. ++ +..++.....             .+.
T Consensus       110 ed~~lil~tgggkslcyqlpal---~adg~alvi~plislmedqil~lkq-lgi~as~lnansske~~k~v~~~i~nkds  185 (695)
T KOG0353|consen  110 EDAFLILPTGGGKSLCYQLPAL---CADGFALVICPLISLMEDQILQLKQ-LGIDASMLNANSSKEEAKRVEAAITNKDS  185 (695)
T ss_pred             CceEEEEeCCCccchhhhhhHH---hcCCceEeechhHHHHHHHHHHHHH-hCcchhhccCcccHHHHHHHHHHHcCCCc
Confidence            5667999999999999876653   4478899999999999999988887 65 4334332221             122


Q ss_pred             CCCEEEecHHHHH
Q 042424          122 NASCLVMTTEILR  134 (138)
Q Consensus       122 ~~~IiVtTpe~l~  134 (138)
                      ...+|-.|||++.
T Consensus       186 e~kliyvtpekia  198 (695)
T KOG0353|consen  186 EFKLIYVTPEKIA  198 (695)
T ss_pred             eeEEEEecHHHHH
Confidence            5568999999875

>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=97.05  E-value=0.0016  Score=48.32  Aligned_cols=46  Identities=13%  Similarity=0.067  Sum_probs=34.6

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELH  104 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~  104 (138)
                      .+|.+|+|+|||.++...+...++.|.+++|+... .-.++..+.+.
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~s~e-~~~~~~~~~~~   47 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTLE-ESPEELIENAE   47 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEEECC-CCHHHHHHHHH
Confidence            35899999999999987777777889999999754 33455554443

A related protein is found in archaea.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.82  E-value=0.003  Score=49.70  Aligned_cols=47  Identities=15%  Similarity=0.107  Sum_probs=36.2

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .+|.+|+|+|||..+...+...+.+|.+++|++- ..-.+|..+.+..
T Consensus        24 ~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs~-ee~~~~i~~~~~~   70 (237)
T TIGR03877        24 VLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVAL-EEHPVQVRRNMAQ   70 (237)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEEe-eCCHHHHHHHHHH
Confidence            4599999999999999777777788999999984 3455555555544

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.

>TIGR00376 DNA helicase, putative

Probab=96.81  E-value=0.0032  Score=56.73  Aligned_cols=50  Identities=18%  Similarity=0.100  Sum_probs=44.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      ...+|.+|.|+|||.+....+.+++..|.++++++|+..-+++..+.+.+
T Consensus       174 ~~~lI~GpPGTGKT~t~~~ii~~~~~~g~~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       174 DLFLIHGPPGTGKTRTLVELIRQLVKRGLRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEEcCcHHHHHHHHHHHHh
Confidence            34569999999999998877878778899999999999999999999987

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.

>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=96.78  E-value=0.005  Score=50.14  Aligned_cols=78  Identities=21%  Similarity=0.185  Sum_probs=60.0

Q ss_pred             CCceEECcCCCchHHHHHH-HHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC-----CCCE
Q 042424           56 THGTLTNPVYNGKTAVAEY-AIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP-----NASC  125 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~-ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~-----~~~I  125 (138)
                      .+.++..-||-|||+++.+ |+..+ -.|+.|=++....-|+..-++.+...|.    +|+..+++...+.     +++|
T Consensus        91 ~G~laEm~TGEGKTli~~l~a~~~A-L~G~~V~vvT~NdyLA~RD~~~~~~~y~~LGlsv~~~~~~~~~~~r~~~Y~~dI  169 (266)
T PF07517_consen   91 KGRLAEMKTGEGKTLIAALPAALNA-LQGKGVHVVTSNDYLAKRDAEEMRPFYEFLGLSVGIITSDMSSEERREAYAADI  169 (266)
T ss_dssp             TTSEEEESTTSHHHHHHHHHHHHHH-TTSS-EEEEESSHHHHHHHHHHHHHHHHHTT--EEEEETTTEHHHHHHHHHSSE
T ss_pred             cceeEEecCCCCcHHHHHHHHHHHH-HhcCCcEEEeccHHHhhccHHHHHHHHHHhhhccccCccccCHHHHHHHHhCcc
Confidence            4568999999999999964 55444 4588898889999999999988887664    7888887665332     6889


Q ss_pred             EEecHHHHH
Q 042424          126 LVMTTEILR  134 (138)
Q Consensus       126 iVtTpe~l~  134 (138)
                      +-+|...|.
T Consensus       170 ~Y~t~~~~~  178 (266)
T PF07517_consen  170 VYGTNSEFG  178 (266)
T ss_dssp             EEEEHHHHH
T ss_pred             cccccchhh
Confidence            999988775

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 ....

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

Probab=96.75  E-value=0.0034  Score=59.07  Aligned_cols=81  Identities=17%  Similarity=0.227  Sum_probs=59.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHHHHHHHHHHHHHhcCceEEE---ecCCc-----C-CCCCC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKALSNQKYRELHKEFKDVGLM---TGDVT-----L-SPNAS  124 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~---tGd~~-----~-~~~~~  124 (138)
                      .+++|.=-||||||+..+++....+..  ..+++||+-.+.|-.|..++|+. |+.+...   ..+..     . +....
T Consensus       274 ~~G~IWHtqGSGKTlTm~~~A~~l~~~~~~~~v~fvvDR~dLd~Q~~~~f~~-~~~~~~~~~~~~s~~~Lk~~l~~~~~~  352 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFKLARLLLELPKNPKVLFVVDRKDLDDQTSDEFQS-FGKVAFNDPKAESTSELKELLEDGKGK  352 (962)
T ss_pred             CceEEEeecCCchHHHHHHHHHHHHhccCCCeEEEEechHHHHHHHHHHHHH-HHHhhhhcccccCHHHHHHHHhcCCCc
Confidence            346678889999999998877776653  68899999999999999999998 5522111   11111     0 11568


Q ss_pred             EEEecHHHHHHhh
Q 042424          125 CLVMTTEILRGML  137 (138)
Q Consensus       125 IiVtTpe~l~~lL  137 (138)
                      |||||-++|...+
T Consensus       353 ii~TTIQKf~~~~  365 (962)
T COG0610         353 IIVTTIQKFNKAV  365 (962)
T ss_pred             EEEEEecccchhh
Confidence            9999999987653

>PRK08727 hypothetical protein; Validated

Probab=96.74  E-value=0.0072  Score=47.56  Aligned_cols=45  Identities=27%  Similarity=0.212  Sum_probs=30.8

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYREL  103 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l  103 (138)
                      ..++||+|+|||..+-.....+..+|.+++|+. ...+.....+.+
T Consensus        44 l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~-~~~~~~~~~~~~   88 (233)
T PRK08727         44 LYLSGPAGTGKTHLALALCAAAEQAGRSSAYLP-LQAAAGRLRDAL   88 (233)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEe-HHHhhhhHHHHH
Confidence            459999999999887655555556688888875 444444433333

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

Probab=96.70  E-value=0.0038  Score=47.50  Aligned_cols=46  Identities=22%  Similarity=0.198  Sum_probs=32.7

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYR  101 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~  101 (138)
                      ..+.++.+|+|.|||..|...+..++.+|.+++|+ ....|+++...
T Consensus        47 ~~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~-~~~~L~~~l~~   92 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFI-TASDLLDELKQ   92 (178)
T ss_dssp             --EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEE-EHHHHHHHHHC
T ss_pred             CeEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEe-ecCceeccccc
Confidence            35677999999999999877766777777777775 56677776543

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.

>PF12846 AAA_10: AAA-like domain

Probab=96.66  E-value=0.003  Score=49.50  Aligned_cols=40  Identities=18%  Similarity=0.205  Sum_probs=32.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKAL   95 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaL   95 (138)
                      ++.+++|+||+|||......+.+.+..|.+++++=|.-..
T Consensus         2 ~h~~i~G~tGsGKT~~~~~l~~~~~~~g~~~~i~D~~g~~   41 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLKNLLEQLIRRGPRVVIFDPKGDY   41 (304)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHcCCCEEEEcCCchH
Confidence            5778999999999998887777777889888888665433

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

Probab=96.65  E-value=0.0027  Score=49.08  Aligned_cols=47  Identities=17%  Similarity=0.253  Sum_probs=33.3

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHc-CCcEEEEechHHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRD-KQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~-~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .+|.+|+|+|||..+...+...+.+ |.+++|++-. .-.++..+.+..
T Consensus        22 ~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~e-e~~~~l~~~~~s   69 (226)
T PF06745_consen   22 VLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSFE-EPPEELIENMKS   69 (226)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEESS-S-HHHHHHHHHT
T ss_pred             EEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEec-CCHHHHHHHHHH
Confidence            4599999999999999877777788 9999999843 233455555543

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 ....

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=96.55  E-value=0.0061  Score=56.68  Aligned_cols=75  Identities=16%  Similarity=0.126  Sum_probs=58.2

Q ss_pred             CCceEECcCCCchHHHHHHHH-HHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC-----CCCE
Q 042424           56 THGTLTNPVYNGKTAVAEYAI-AMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP-----NASC  125 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai-~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~-----~~~I  125 (138)
                      ...+....||.|||+++.+++ +.++ .|+.|-+|.+..-|+.+-++.+...|.    +||...++.....     .++|
T Consensus        90 ~G~IaEm~TGEGKTL~a~l~ayl~aL-~G~~VhVvT~NdyLA~RD~e~m~pvy~~LGLsvg~i~~~~~~~err~aY~~DI  168 (870)
T CHL00122         90 DGKIAEMKTGEGKTLVATLPAYLNAL-TGKGVHIVTVNDYLAKRDQEWMGQIYRFLGLTVGLIQEGMSSEERKKNYLKDI  168 (870)
T ss_pred             CCccccccCCCCchHHHHHHHHHHHh-cCCceEEEeCCHHHHHHHHHHHHHHHHHcCCceeeeCCCCChHHHHHhcCCCC
Confidence            567789999999999997655 4444 589999999999999998888777654    7888776654332     6788


Q ss_pred             EEecHH
Q 042424          126 LVMTTE  131 (138)
Q Consensus       126 iVtTpe  131 (138)
                      +-+|.-
T Consensus       169 tYgTn~  174 (870)
T CHL00122        169 TYVTNS  174 (870)
T ss_pred             EecCCc
Confidence            888764

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

Probab=96.52  E-value=0.0057  Score=50.83  Aligned_cols=49  Identities=22%  Similarity=0.278  Sum_probs=42.0

Q ss_pred             eEECcCCCchHHHHHHHHHHH--HHcCCcEEEEechHHHHHHHHHHHHHhc
Q 042424           59 TLTNPVYNGKTAVAEYAIAMA--FRDKQRVIYTSSLKALSNQKYRELHKEF  107 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~--l~~~~rviyv~P~kaLv~Q~~~~l~~~f  107 (138)
                      +|.+..|+|||++++..+...  ...+.+++|++...+|.+...+.+.+..
T Consensus         5 ~I~G~aGTGKTvla~~l~~~l~~~~~~~~~~~l~~n~~l~~~l~~~l~~~~   55 (352)
T PF09848_consen    5 LITGGAGTGKTVLALNLAKELQNSEEGKKVLYLCGNHPLRNKLREQLAKKY   55 (352)
T ss_pred             EEEecCCcCHHHHHHHHHHHhhccccCCceEEEEecchHHHHHHHHHhhhc
Confidence            589999999999998777665  4568999999999999998888887655

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

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=96.51  E-value=0.0072  Score=56.51  Aligned_cols=78  Identities=17%  Similarity=0.101  Sum_probs=60.4

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC-----CCCEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP-----NASCL  126 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~-----~~~Ii  126 (138)
                      ...+....||-|||++|.+++.-.-..|+.+-+|.+.-=|+..=++.+...|.    +||...++.....     .++|+
T Consensus        99 ~G~IAEM~TGEGKTL~atlpaylnAL~GkgVhVVTvNdYLA~RDae~m~~vy~~LGLtvg~i~~~~~~~err~aY~~DIt  178 (939)
T PRK12902         99 EGQIAEMKTGEGKTLVATLPSYLNALTGKGVHVVTVNDYLARRDAEWMGQVHRFLGLSVGLIQQDMSPEERKKNYACDIT  178 (939)
T ss_pred             CCceeeecCCCChhHHHHHHHHHHhhcCCCeEEEeCCHHHHHhHHHHHHHHHHHhCCeEEEECCCCChHHHHHhcCCCeE
Confidence            45678899999999999765554434588899999999999988877776554    8888877654432     89999


Q ss_pred             EecHHHH
Q 042424          127 VMTTEIL  133 (138)
Q Consensus       127 VtTpe~l  133 (138)
                      -+|+..|
T Consensus       179 YgTn~e~  185 (939)
T PRK12902        179 YATNSEL  185 (939)
T ss_pred             EecCCcc
Confidence            9998765

>PRK04328 hypothetical protein; Provisional

Probab=96.37  E-value=0.0088  Score=47.58  Aligned_cols=47  Identities=15%  Similarity=0.154  Sum_probs=34.9

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .+|.+|+|+|||..+...+...+.+|.+++|+. +..-.++..+.+..
T Consensus        26 ili~G~pGsGKT~l~~~fl~~~~~~ge~~lyis-~ee~~~~i~~~~~~   72 (249)
T PRK04328         26 VLLSGGPGTGKSIFSQQFLWNGLQMGEPGVYVA-LEEHPVQVRRNMRQ   72 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEE-eeCCHHHHHHHHHH
Confidence            449999999999999987887788899999987 33344444444433

>PRK08181 transposase; Validated

Probab=96.29  E-value=0.011  Score=48.07  Aligned_cols=43  Identities=21%  Similarity=0.190  Sum_probs=32.4

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQK   99 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~   99 (138)
                      .+.+++||+|+|||..+......++.+|.+++|+. ...|+++.
T Consensus       107 ~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~-~~~L~~~l  149 (269)
T PRK08181        107 ANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTR-TTDLVQKL  149 (269)
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHHHcCCceeeee-HHHHHHHH
Confidence            56779999999999988755556666788887764 45677655

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.28  E-value=0.011  Score=41.87  Aligned_cols=40  Identities=18%  Similarity=0.184  Sum_probs=31.1

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQ   98 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q   98 (138)
                      +|++|+|+|||.++...+.....++.+++|+..-..+...
T Consensus         3 ~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~e~~~~~~   42 (165)
T cd01120           3 LVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEEL   42 (165)
T ss_pred             eEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCcchHHH
Confidence            5899999999999876666665678889998876555443

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.

>PRK06526 transposase; Provisional

Probab=96.28  E-value=0.0066  Score=48.82  Aligned_cols=44  Identities=18%  Similarity=0.144  Sum_probs=32.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKY  100 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~  100 (138)
                      .|.+++||+|+|||..+......+...|.+++|+.. ..|+++..
T Consensus        99 ~nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f~t~-~~l~~~l~  142 (254)
T PRK06526         99 ENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATA-AQWVARLA  142 (254)
T ss_pred             ceEEEEeCCCCchHHHHHHHHHHHHHCCCchhhhhH-HHHHHHHH
Confidence            577899999999999987666666677888877544 34665553

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=96.28  E-value=0.0068  Score=48.55  Aligned_cols=33  Identities=15%  Similarity=0.191  Sum_probs=28.3

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      +|++|+|+|||..+...+.+.+.+|.+++|+.-
T Consensus        40 lI~G~pGtGKT~l~~qf~~~~a~~Ge~vlyis~   72 (259)
T TIGR03878        40 NITGVSDTGKSLMVEQFAVTQASRGNPVLFVTV   72 (259)
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEEe
Confidence            499999999999999767666677999999884

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=96.24  E-value=0.012  Score=46.45  Aligned_cols=46  Identities=11%  Similarity=0.096  Sum_probs=34.1

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELH  104 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~  104 (138)
                      .++.+|+|+|||..+...+...+.+|.+++|+.... -..|..+.+.
T Consensus        27 ~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~~e~-~~~~~~~~~~   72 (230)
T PRK08533         27 ILIEGDESTGKSILSQRLAYGFLQNGYSVSYVSTQL-TTTEFIKQMM   72 (230)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEeCCC-CHHHHHHHHH
Confidence            459999999999998877776667889999998543 3344444443

>PRK05973 replicative DNA helicase; Provisional

Probab=96.24  E-value=0.0072  Score=48.37  Aligned_cols=47  Identities=13%  Similarity=0.033  Sum_probs=34.9

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .+|.|++|+|||..++..+..+..+|.+++|++--.. .+|..+++..
T Consensus        67 ~LIaG~PG~GKT~lalqfa~~~a~~Ge~vlyfSlEes-~~~i~~R~~s  113 (237)
T PRK05973         67 VLLGARPGHGKTLLGLELAVEAMKSGRTGVFFTLEYT-EQDVRDRLRA  113 (237)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEEEeCC-HHHHHHHHHH
Confidence            3599999999999998666666677999999875543 3555555544

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=96.23  E-value=0.011  Score=45.07  Aligned_cols=33  Identities=24%  Similarity=0.350  Sum_probs=28.2

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      +++|+|+|||.++...+.+....|.+++|+.-.
T Consensus        17 i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~~e   49 (209)
T TIGR02237        17 IYGPPGSGKTNICMILAVNAARQGKKVVYIDTE   49 (209)
T ss_pred             EECCCCCCHHHHHHHHHHHHHhCCCeEEEEECC
Confidence            999999999999987666666778899998775

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

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

Probab=96.19  E-value=0.016  Score=44.48  Aligned_cols=45  Identities=22%  Similarity=0.267  Sum_probs=32.8

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEechHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLKALSNQKYREL  103 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~kaLv~Q~~~~l  103 (138)
                      .+|.+|.|+|||.+... +..++. .|.++++++||...+.+..+..
T Consensus        21 ~~l~G~aGtGKT~~l~~-~~~~~~~~g~~v~~~apT~~Aa~~L~~~~   66 (196)
T PF13604_consen   21 SVLQGPAGTGKTTLLKA-LAEALEAAGKRVIGLAPTNKAAKELREKT   66 (196)
T ss_dssp             EEEEESTTSTHHHHHHH-HHHHHHHTT--EEEEESSHHHHHHHHHHH
T ss_pred             EEEEECCCCCHHHHHHH-HHHHHHhCCCeEEEECCcHHHHHHHHHhh
Confidence            35899999999987544 444444 5899999999988888766663

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=96.17  E-value=0.005  Score=41.60  Aligned_cols=39  Identities=21%  Similarity=0.088  Sum_probs=26.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKA   94 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~ka   94 (138)
                      .+.++.+|+|+|||.++...+......+..++++.+...
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~~~~   41 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDI   41 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEECCEEc
Confidence            345699999999998876554433222336888887754

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.

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=96.09  E-value=0.016  Score=52.49  Aligned_cols=54  Identities=28%  Similarity=0.311  Sum_probs=43.0

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-c-eEEE
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-D-VGLM  113 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~-v~~~  113 (138)
                      +.++.+-||||||++....+..   .++.+|+|+|.+.++.|.+++|+..|. + |-.+
T Consensus        31 ~~~l~Gvtgs~kt~~~a~~~~~---~~~p~Lvi~~n~~~A~ql~~el~~f~p~~~V~~f   86 (655)
T TIGR00631        31 HQTLLGVTGSGKTFTMANVIAQ---VNRPTLVIAHNKTLAAQLYNEFKEFFPENAVEYF   86 (655)
T ss_pred             cEEEECCCCcHHHHHHHHHHHH---hCCCEEEEECCHHHHHHHHHHHHHhCCCCeEEEE
Confidence            4569999999999876543322   378899999999999999999999776 3 5544

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=96.08  E-value=0.0064  Score=47.74  Aligned_cols=40  Identities=20%  Similarity=0.164  Sum_probs=27.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC--CcEEEEechHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK--QRVIYTSSLKAL   95 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~--~rviyv~P~kaL   95 (138)
                      ...++.+|.|+|||++|..+.++.+.+|  .+++|+-|....
T Consensus        20 ~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~   61 (205)
T PF02562_consen   20 DLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEA   61 (205)
T ss_dssp             SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--T
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCC
Confidence            3455999999999999997777777765  689999888753

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

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=96.06  E-value=0.029  Score=50.69  Aligned_cols=60  Identities=22%  Similarity=0.181  Sum_probs=45.9

Q ss_pred             CccCCCCCCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechH--HHHHHHHHHHHHhcC
Q 042424           48 YTLTTDETTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLK--ALSNQKYRELHKEFK  108 (138)
Q Consensus        48 y~~~~~~~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~k--aLv~Q~~~~l~~~f~  108 (138)
                      |.++....++.++.++||+|||......+.+.++.|..++++=|--  .|....+...+. ++
T Consensus       169 ~l~~~~~~~H~lv~G~TGsGKT~l~~~l~~q~i~~g~~viv~DpKgD~~l~~~~~~~~~~-~G  230 (634)
T TIGR03743       169 YLPLGHRVGHTLVLGTTGVGKTRLAELLITQDIRRGDVVIVIDPKGDADLKRRMRAEAKR-AG  230 (634)
T ss_pred             EeecCCCCCcEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCCchHHHHHHHHHHHH-hC
Confidence            3344344588999999999999998888888888888888888874  377766666555 44

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.

>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=96.03  E-value=0.024  Score=38.74  Aligned_cols=39  Identities=23%  Similarity=0.241  Sum_probs=28.7

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKA   94 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~ka   94 (138)
                      ...++.+|+|+|||.++...+......+..++++.....
T Consensus        20 ~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~~~~   58 (151)
T cd00009          20 KNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDL   58 (151)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEehhhh
Confidence            456699999999998887666655455677777766543

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.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=96.03  E-value=0.011  Score=45.93  Aligned_cols=34  Identities=21%  Similarity=0.092  Sum_probs=28.0

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHc-CCcEEEEec
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRD-KQRVIYTSS   91 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~-~~rviyv~P   91 (138)
                      .+|+|++|+|||.++...+.+...+ |.+++|+.-
T Consensus        16 ~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s~   50 (242)
T cd00984          16 IIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSL   50 (242)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEeC
Confidence            3599999999999998666666665 999999983

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.

>PRK12377 putative replication protein; Provisional

Probab=96.00  E-value=0.023  Score=45.62  Aligned_cols=45  Identities=13%  Similarity=0.070  Sum_probs=31.7

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYR  101 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~  101 (138)
                      .+.++++|+|+|||..+......++.+|..++|+ +...|..+...
T Consensus       102 ~~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~i-~~~~l~~~l~~  146 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVV-TVPDVMSRLHE  146 (248)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEE-EHHHHHHHHHH
Confidence            4567999999999998865555555567777665 45566665543

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

Probab=95.99  E-value=0.042  Score=51.30  Aligned_cols=82  Identities=17%  Similarity=0.110  Sum_probs=61.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEechHHHHHHHHHHHHHhcC-----ceEE-EecCCcCCCCCCEEEe
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLKALSNQKYRELHKEFK-----DVGL-MTGDVTLSPNASCLVM  128 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~-~tGd~~~~~~~~IiVt  128 (138)
                      .-.+|++|||||||.--=..++.+-. .++++..+=|.+--+.-.++++.+.++     .||. +-.|.....+..|-++
T Consensus        66 ~vvii~getGsGKTTqlP~~lle~g~~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~VGY~iRfe~~~s~~Trik~m  145 (845)
T COG1643          66 QVVIIVGETGSGKTTQLPQFLLEEGLGIAGKIGCTQPRRLAARSVAERVAEELGEKLGETVGYSIRFESKVSPRTRIKVM  145 (845)
T ss_pred             CEEEEeCCCCCChHHHHHHHHHhhhcccCCeEEecCchHHHHHHHHHHHHHHhCCCcCceeeEEEEeeccCCCCceeEEe
Confidence            44569999999999876555555432 357889999998777777888877776     3543 3355666778899999


Q ss_pred             cHHHHHHhh
Q 042424          129 TTEILRGML  137 (138)
Q Consensus       129 Tpe~l~~lL  137 (138)
                      |..+|..++
T Consensus       146 TdGiLlrei  154 (845)
T COG1643         146 TDGILLREI  154 (845)
T ss_pred             ccHHHHHHH
Confidence            999998765

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=95.99  E-value=0.012  Score=45.42  Aligned_cols=47  Identities=11%  Similarity=0.087  Sum_probs=35.7

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .++.+++|+|||..+...+...+.+|.+++|+.--. -.+|..+.+..
T Consensus        19 ~li~G~~G~GKt~~~~~~~~~~~~~g~~~~y~s~e~-~~~~l~~~~~~   65 (224)
T TIGR03880        19 IVVIGEYGTGKTTFSLQFLYQGLKNGEKAMYISLEE-REERILGYAKS   65 (224)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCC-CHHHHHHHHHH
Confidence            349999999999999877777778899999987654 34555555544

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.

>KOG0351 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=95.98  E-value=0.0047  Score=58.02  Aligned_cols=76  Identities=17%  Similarity=0.119  Sum_probs=56.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcC-------------CC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTL-------------SP  121 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~-------------~~  121 (138)
                      ....+..|||+||++|+-+..   +..++-.|+|+|..+|...+...|.. .+ ....++++...             +.
T Consensus       280 kd~fvlmpTG~GKSLCYQlPA---~l~~gitvVISPL~SLm~DQv~~L~~-~~I~a~~L~s~q~~~~~~~i~q~l~~~~~  355 (941)
T KOG0351|consen  280 KDCFVLMPTGGGKSLCYQLPA---LLLGGVTVVISPLISLMQDQVTHLSK-KGIPACFLSSIQTAAERLAILQKLANGNP  355 (941)
T ss_pred             CceEEEeecCCceeeEeeccc---cccCCceEEeccHHHHHHHHHHhhhh-cCcceeeccccccHHHHHHHHHHHhCCCC
Confidence            566799999999999984433   23467889999999999999988844 32 44555555443             12


Q ss_pred             CCCEEEecHHHHHH
Q 042424          122 NASCLVMTTEILRG  135 (138)
Q Consensus       122 ~~~IiVtTpe~l~~  135 (138)
                      ..+|+-.|||++..
T Consensus       356 ~ikilYvtPE~v~~  369 (941)
T KOG0351|consen  356 IIKILYVTPEKVVA  369 (941)
T ss_pred             eEEEEEeCHHHhhc
Confidence            56799999998753

>TIGR02012 tigrfam_recA protein RecA

Probab=95.94  E-value=0.017  Score=48.17  Aligned_cols=40  Identities=28%  Similarity=0.255  Sum_probs=33.5

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHH
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQK   99 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~   99 (138)
                      |.+|.|+|||..++.++..+.+.|.+++|+-.-.++-.+.
T Consensus        60 I~G~~GsGKTtLaL~~~~~~~~~g~~v~yId~E~~~~~~~   99 (321)
T TIGR02012        60 IYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVY   99 (321)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHcCCcEEEEcccchhHHHH
Confidence            9999999999999988888888899999987666555443

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.

>PRK04296 thymidine kinase; Provisional

Probab=95.93  E-value=0.013  Score=44.66  Aligned_cols=33  Identities=9%  Similarity=-0.028  Sum_probs=27.7

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      ++++|.|+|||..++-.+.++..+|.+++++-|
T Consensus         6 litG~~GsGKTT~~l~~~~~~~~~g~~v~i~k~   38 (190)
T PRK04296          6 FIYGAMNSGKSTELLQRAYNYEERGMKVLVFKP   38 (190)
T ss_pred             EEECCCCCHHHHHHHHHHHHHHHcCCeEEEEec
Confidence            489999999999888777776677899998866

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=95.92  E-value=0.014  Score=45.53  Aligned_cols=47  Identities=9%  Similarity=0.135  Sum_probs=34.5

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .++.+|+|+|||..+...+...+.+|.+++|+.=-.+. ++..+.+..
T Consensus        28 ~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~~e~~~-~~~~~~~~~   74 (234)
T PRK06067         28 ILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITTENTS-KSYLKQMES   74 (234)
T ss_pred             EEEECCCCCChHHHHHHHHHHHHhCCCEEEEEEcCCCH-HHHHHHHHH
Confidence            34999999999999987777777789999998864332 344444433

>PRK06835 DNA replication protein DnaC; Validated

Probab=95.90  E-value=0.014  Score=48.78  Aligned_cols=43  Identities=16%  Similarity=0.127  Sum_probs=31.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQK   99 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~   99 (138)
                      .+.++.||||+|||..+......++.+|.+++|+. ...|..+.
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t-~~~l~~~l  226 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRT-ADELIEIL  226 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEE-HHHHHHHH
Confidence            56679999999999987755555566788887764 45565554

>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]

Probab=95.89  E-value=0.018  Score=52.59  Aligned_cols=50  Identities=18%  Similarity=0.185  Sum_probs=43.1

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHc-CCcEEEEechHHHHHHHHHHHHHhcC
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRD-KQRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~-~~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      .+|.+|.|.|||+++.-.+.+..++ +..+++++|...-++|.++.+.+ .+
T Consensus       428 sLIQGPPGTGKTvtsa~IVyhl~~~~~~~VLvcApSNiAVDqLaeKIh~-tg  478 (935)
T KOG1802|consen  428 SLIQGPPGTGKTVTSATIVYHLARQHAGPVLVCAPSNIAVDQLAEKIHK-TG  478 (935)
T ss_pred             eeeecCCCCCceehhHHHHHHHHHhcCCceEEEcccchhHHHHHHHHHh-cC
Confidence            3499999999999998777766654 78999999999999999999988 44

>PRK09183 transposase/IS protein; Provisional

Probab=95.82  E-value=0.029  Score=45.04  Aligned_cols=42  Identities=29%  Similarity=0.140  Sum_probs=30.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQ   98 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q   98 (138)
                      .+.++.+|+|+|||..+......+...|.+++|+. ...|..+
T Consensus       103 ~~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~~-~~~l~~~  144 (259)
T PRK09183        103 ENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTT-AADLLLQ  144 (259)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEe-HHHHHHH
Confidence            46679999999999998754555556788888764 3445543

>cd01394 radB RadB

Probab=95.75  E-value=0.017  Score=44.28  Aligned_cols=32  Identities=22%  Similarity=0.245  Sum_probs=27.1

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      .|+++.|+|||..+...+......|.+++|+.
T Consensus        23 ~i~G~~GsGKT~l~~~~a~~~~~~g~~v~yi~   54 (218)
T cd01394          23 QVYGPPGTGKTNIAIQLAVETAGQGKKVAYID   54 (218)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            39999999999999877766667788999983

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK09354 recA recombinase A; Provisional

Probab=95.75  E-value=0.02  Score=48.31  Aligned_cols=41  Identities=27%  Similarity=0.231  Sum_probs=35.1

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHH
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKY  100 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~  100 (138)
                      |.+|.|+|||..++.++..+...|.+++|+-.-.++-.+.+
T Consensus        65 I~G~~GsGKTtLal~~~~~~~~~G~~~~yId~E~s~~~~~a  105 (349)
T PRK09354         65 IYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYA  105 (349)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHcCCcEEEECCccchHHHHH
Confidence            99999999999999988888888999999987777665433

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=95.74  E-value=0.022  Score=47.68  Aligned_cols=41  Identities=29%  Similarity=0.228  Sum_probs=34.0

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHH
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKY  100 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~  100 (138)
                      +.+|.|+|||..++..+..+...|.+++|+-.-.++-.+.+
T Consensus        60 I~Gp~GsGKTtLal~~~~~~~~~g~~~vyId~E~~~~~~~a  100 (325)
T cd00983          60 IYGPESSGKTTLALHAIAEAQKLGGTVAFIDAEHALDPVYA  100 (325)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHcCCCEEEECccccHHHHHH
Confidence            99999999999999888888788999999987665554433

RecA couples ATP hydrolysis to DNA strand exchange.

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=95.73  E-value=0.032  Score=44.81  Aligned_cols=50  Identities=14%  Similarity=-0.000  Sum_probs=36.9

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      ..+.++.||.|.|||.++......++ +.+.-++++++..|+.+....+.+
T Consensus       105 ~~nl~l~G~~G~GKThLa~Ai~~~l~-~~g~sv~f~~~~el~~~Lk~~~~~  154 (254)
T COG1484         105 GENLVLLGPPGVGKTHLAIAIGNELL-KAGISVLFITAPDLLSKLKAAFDE  154 (254)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHHH-HcCCeEEEEEHHHHHHHHHHHHhc
Confidence            35778999999999998875555555 444555567888898888776664

>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=95.73  E-value=0.026  Score=43.61  Aligned_cols=49  Identities=16%  Similarity=0.248  Sum_probs=35.0

Q ss_pred             eEECcCCCchHHHHH-HHHHHHHHcCCcEEEEe--chHHHHHHHHHHHHHhcC
Q 042424           59 TLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTS--SLKALSNQKYRELHKEFK  108 (138)
Q Consensus        59 ~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~--P~kaLv~Q~~~~l~~~f~  108 (138)
                      ++.+|||+|||.... +|.....+ ++++.+++  .+|.=+.++.+.+.+.++
T Consensus         5 ~lvGptGvGKTTt~aKLAa~~~~~-~~~v~lis~D~~R~ga~eQL~~~a~~l~   56 (196)
T PF00448_consen    5 ALVGPTGVGKTTTIAKLAARLKLK-GKKVALISADTYRIGAVEQLKTYAEILG   56 (196)
T ss_dssp             EEEESTTSSHHHHHHHHHHHHHHT-T--EEEEEESTSSTHHHHHHHHHHHHHT
T ss_pred             EEECCCCCchHhHHHHHHHHHhhc-cccceeecCCCCCccHHHHHHHHHHHhc
Confidence            489999999999887 55554444 77765554  357888888888888775

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 ....

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=95.71  E-value=0.019  Score=44.40  Aligned_cols=35  Identities=26%  Similarity=0.245  Sum_probs=28.2

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      ..++.+|+|+|||..+...+...+.+|.+++|+.-
T Consensus        22 ~~~i~G~~G~GKT~l~~~~~~~~~~~g~~~~~is~   56 (229)
T TIGR03881        22 FVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVTT   56 (229)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEEc
Confidence            34599999999999998655566677889999874

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.

>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=95.67  E-value=0.035  Score=41.00  Aligned_cols=47  Identities=17%  Similarity=0.168  Sum_probs=30.6

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEe--chHHHHHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS--SLKALSNQKYRELHK  105 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~--P~kaLv~Q~~~~l~~  105 (138)
                      ++.+|+|+|||.++..........|.+++++.  +.+.-..+....+.+
T Consensus         4 ~~~G~~G~GKTt~~~~la~~~~~~g~~v~~i~~D~~~~~~~~~l~~~~~   52 (173)
T cd03115           4 LLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADTYRPAAIEQLRVLGE   52 (173)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEcCCCChHHHHHHHHhcc
Confidence            48999999999998754444445577877765  555444444444433

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.

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=95.67  E-value=0.019  Score=52.00  Aligned_cols=51  Identities=25%  Similarity=0.273  Sum_probs=41.2

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechH--HHHHHHHHHHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLK--ALSNQKYRELHK  105 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~k--aLv~Q~~~~l~~  105 (138)
                      .++.++.++||+|||....+.+.+.++.|..++++=|-.  .|....+...+.
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            478889999999999999999999998899999998885  455555544444

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.66  E-value=0.025  Score=49.24  Aligned_cols=47  Identities=21%  Similarity=0.140  Sum_probs=37.2

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .+|.+|+|+|||..++..+...+++|.+++|++ +.+-.+|..++...
T Consensus       266 ~li~G~~G~GKt~l~~~f~~~~~~~ge~~~y~s-~eEs~~~i~~~~~~  312 (484)
T TIGR02655       266 ILATGATGTGKTLLVSKFLENACANKERAILFA-YEESRAQLLRNAYS  312 (484)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEE-eeCCHHHHHHHHHH
Confidence            449999999999999988888888899999987 44555666666544

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.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.64  E-value=0.041  Score=44.63  Aligned_cols=50  Identities=14%  Similarity=0.137  Sum_probs=34.9

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEe--chHHHHHHHHHHHHHhcC
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS--SLKALSNQKYRELHKEFK  108 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~--P~kaLv~Q~~~~l~~~f~  108 (138)
                      ++++|+|+|||..+..........|++++++.  ++++-+.++.+.|.+..+
T Consensus        76 ~l~G~~G~GKTTt~akLA~~l~~~g~~V~li~~D~~r~~a~~ql~~~~~~~~  127 (272)
T TIGR00064        76 LFVGVNGVGKTTTIAKLANKLKKQGKSVLLAAGDTFRAAAIEQLEEWAKRLG  127 (272)
T ss_pred             EEECCCCCcHHHHHHHHHHHHHhcCCEEEEEeCCCCCHHHHHHHHHHHHhCC
Confidence            48899999999988633333345677877665  466666677777777554

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.

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=95.64  E-value=0.022  Score=45.15  Aligned_cols=49  Identities=20%  Similarity=0.196  Sum_probs=37.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      ...++.++.|+|||..+...+...++.|.+++|++-- ...++..+.+..
T Consensus        24 ~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs~~-e~~~~l~~~~~~   72 (260)
T COG0467          24 SVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTE-ESPEELLENARS   72 (260)
T ss_pred             cEEEEEcCCCCcHHHHHHHHHHHHHhcCCcEEEEEec-CCHHHHHHHHHH
Confidence            3456999999999999998888877889999998754 344455555544

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=95.58  E-value=0.035  Score=41.40  Aligned_cols=47  Identities=28%  Similarity=0.261  Sum_probs=30.2

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH----------cCCcEEEEechHHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR----------DKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~----------~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .++.||+|+|||.++...+.+...          ++.+++|+..-.. ..+..+++..
T Consensus        35 ~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~   91 (193)
T PF13481_consen   35 TLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRA   91 (193)
T ss_dssp             EEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS--HHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHH
Confidence            459999999999999865555544          4578999876655 4455555554

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=95.58  E-value=0.022  Score=43.94  Aligned_cols=34  Identities=24%  Similarity=0.326  Sum_probs=28.1

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      .+++|+|+|||.++...+...+..+.+++|+.=-
T Consensus        27 ~i~G~~GsGKT~l~~~la~~~~~~~~~v~yi~~e   60 (225)
T PRK09361         27 QIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE   60 (225)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            4999999999999986666666778899988654

>PRK05642 DNA replication initiation factor; Validated

Probab=95.58  E-value=0.021  Score=44.96  Aligned_cols=41  Identities=12%  Similarity=-0.003  Sum_probs=27.8

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQ   98 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q   98 (138)
                      +..++||+|+|||..+..+..+...++.+++|+.- ..+...
T Consensus        47 ~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~~-~~~~~~   87 (234)
T PRK05642         47 LIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPL-AELLDR   87 (234)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEeeH-HHHHhh
Confidence            44699999999999854333333445788888664 455543

>KOG1803 consensus DNA helicase [Replication, recombination and repair]

Probab=95.50  E-value=0.021  Score=51.37  Aligned_cols=47  Identities=19%  Similarity=0.202  Sum_probs=41.8

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELH  104 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~  104 (138)
                      .++.+|.|.|||..-...|.+++.+|+++++.+|+..-++...+++.
T Consensus       204 ~~I~GPPGTGKT~TlvEiI~qlvk~~k~VLVcaPSn~AVdNiverl~  250 (649)
T KOG1803|consen  204 LIIHGPPGTGKTRTLVEIISQLVKQKKRVLVCAPSNVAVDNIVERLT  250 (649)
T ss_pred             eEeeCCCCCCceeeHHHHHHHHHHcCCeEEEEcCchHHHHHHHHHhc
Confidence            34999999999999988999999999999999999988888877644

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=95.49  E-value=0.025  Score=43.23  Aligned_cols=41  Identities=24%  Similarity=0.185  Sum_probs=29.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSN   97 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~   97 (138)
                      .+.++.||+|+|||.++.....++...+..++|+ ....+..
T Consensus        39 ~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i-~~~~~~~   79 (226)
T TIGR03420        39 RFLYLWGESGSGKSHLLQAACAAAEERGKSAIYL-PLAELAQ   79 (226)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEE-eHHHHHH
Confidence            4566999999999999876666655556666664 4545544

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.

>PRK06921 hypothetical protein; Provisional

Probab=95.48  E-value=0.049  Score=43.98  Aligned_cols=44  Identities=18%  Similarity=0.027  Sum_probs=30.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc-CCcEEEEechHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD-KQRVIYTSSLKALSNQKY  100 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~-~~rviyv~P~kaLv~Q~~  100 (138)
                      .+.++.+|+|+|||..+......++.+ |..++|+.. ..+..+..
T Consensus       118 ~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~~-~~l~~~l~  162 (266)
T PRK06921        118 NSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPF-VEGFGDLK  162 (266)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEEH-HHHHHHHH
Confidence            456799999999999876444444455 777777664 45555443

>PRK08084 DNA replication initiation factor; Provisional

Probab=95.43  E-value=0.025  Score=44.50  Aligned_cols=37  Identities=19%  Similarity=-0.021  Sum_probs=27.1

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLK   93 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~k   93 (138)
                      +.+++||+|+|||..+......+...|.+++|+.-..
T Consensus        47 ~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~~~   83 (235)
T PRK08084         47 YIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPLDK   83 (235)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEHHH
Confidence            4569999999999987654544445678888875543

>PRK07952 DNA replication protein DnaC; Validated

Probab=95.40  E-value=0.053  Score=43.46  Aligned_cols=42  Identities=10%  Similarity=0.050  Sum_probs=29.3

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQK   99 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~   99 (138)
                      ..++++++|+|||..+...+.+....|.+++|+ +...|....
T Consensus       101 ~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~i-t~~~l~~~l  142 (244)
T PRK07952        101 SFIFSGKPGTGKNHLAAAICNELLLRGKSVLII-TVADIMSAM  142 (244)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEE-EHHHHHHHH
Confidence            456999999999998875555555567777666 455555433

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=95.36  E-value=0.031  Score=42.33  Aligned_cols=44  Identities=20%  Similarity=0.234  Sum_probs=33.9

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      +|.+++|||||..|+..+..   .+.+++|++-.+++-.+..+++.+
T Consensus         3 li~G~~~sGKS~~a~~~~~~---~~~~~~y~at~~~~d~em~~rI~~   46 (169)
T cd00544           3 LVTGGARSGKSRFAERLAAE---LGGPVTYIATAEAFDDEMAERIAR   46 (169)
T ss_pred             EEECCCCCCHHHHHHHHHHh---cCCCeEEEEccCcCCHHHHHHHHH
Confidence            58999999999988754432   578999999998887666665433

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.

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=95.33  E-value=0.027  Score=44.53  Aligned_cols=35  Identities=23%  Similarity=-0.066  Sum_probs=27.2

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHc-CCcEEEEec
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRD-KQRVIYTSS   91 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~-~~rviyv~P   91 (138)
                      -.+|.+|+|+|||..+...+.++... |.+++|+.-
T Consensus        32 ~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~vl~iS~   67 (271)
T cd01122          32 LIILTAGTGVGKTTFLREYALDLITQHGVRVGTISL   67 (271)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHhcCceEEEEEc
Confidence            34599999999999887555555555 889999874

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.28  E-value=0.027  Score=49.03  Aligned_cols=46  Identities=7%  Similarity=0.021  Sum_probs=33.0

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHc-CCcEEEEechHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRD-KQRVIYTSSLKALSNQKYRELH  104 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~-~~rviyv~P~kaLv~Q~~~~l~  104 (138)
                      .+|++|+|+|||..+...+.+.+.+ |.+++|+.=- .-.++..+...
T Consensus        24 ~Li~G~pGsGKT~la~qfl~~g~~~~ge~~lyvs~e-E~~~~l~~~~~   70 (484)
T TIGR02655        24 TLVSGTSGTGKTLFSIQFLYNGIIHFDEPGVFVTFE-ESPQDIIKNAR   70 (484)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEEe-cCHHHHHHHHH
Confidence            4599999999999999766666565 8999999843 33344444333

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.

>PRK06893 DNA replication initiation factor; Validated

Probab=95.25  E-value=0.031  Score=43.79  Aligned_cols=35  Identities=11%  Similarity=0.052  Sum_probs=27.2

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      ..++||+|+|||..+......+..++.+++|+.-.
T Consensus        42 l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~~   76 (229)
T PRK06893         42 FYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPLS   76 (229)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeHH
Confidence            35999999999998876666666678888887653

>COG3451 VirB4 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]

Probab=95.22  E-value=0.027  Score=52.19  Aligned_cols=38  Identities=18%  Similarity=0.295  Sum_probs=31.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC-CcEEEEechH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK-QRVIYTSSLK   93 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~-~rviyv~P~k   93 (138)
                      ++.+|+||||+|||+...+.++++.+.+ .+++++=+-+
T Consensus       437 ghT~I~G~tGaGKTvLl~~llaq~~k~~~~~iv~fDk~~  475 (796)
T COG3451         437 GHTLIIGPTGAGKTVLLSFLLAQALKYGNPQIVAFDKDN  475 (796)
T ss_pred             CCeEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEcCCC
Confidence            5888999999999999999998888876 7777766543

>COG4889 Predicted helicase [General function prediction only]

Probab=95.19  E-value=0.051  Score=51.38  Aligned_cols=50  Identities=22%  Similarity=0.213  Sum_probs=39.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhc
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEF  107 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f  107 (138)
                      .+.-|....|.|||+.++-.. .++. ..+++|++|..+|..|..++|...-
T Consensus       181 ~RGkLIMAcGTGKTfTsLkis-Eala-~~~iL~LvPSIsLLsQTlrew~~~~  230 (1518)
T COG4889         181 DRGKLIMACGTGKTFTSLKIS-EALA-AARILFLVPSISLLSQTLREWTAQK  230 (1518)
T ss_pred             cCCcEEEecCCCccchHHHHH-HHHh-hhheEeecchHHHHHHHHHHHhhcc
Confidence            455577888999999887433 3333 3899999999999999999998754

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=95.16  E-value=0.026  Score=51.09  Aligned_cols=54  Identities=15%  Similarity=0.102  Sum_probs=45.9

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc-C---CcEEEEechHHHHHHHHHHHHHhcC
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD-K---QRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~-~---~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      .++.+|.|..|||||.+...-+.+.+.. |   .+++.+.-|+.-++++.+++.+.++
T Consensus        15 ~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v~p~~IL~lTFT~kAA~em~~Rl~~~l~   72 (672)
T PRK10919         15 TGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQTLG   72 (672)
T ss_pred             CCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHHhC
Confidence            3667799999999999998888887764 3   6899999999999999999987554

>PRK08116 hypothetical protein; Validated

Probab=95.15  E-value=0.075  Score=42.91  Aligned_cols=43  Identities=23%  Similarity=0.157  Sum_probs=29.6

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYR  101 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~  101 (138)
                      .++.|++|+|||..+.......+.++..++|+ +...|.++...
T Consensus       117 l~l~G~~GtGKThLa~aia~~l~~~~~~v~~~-~~~~ll~~i~~  159 (268)
T PRK08116        117 LLLWGSVGTGKTYLAACIANELIEKGVPVIFV-NFPQLLNRIKS  159 (268)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE-EHHHHHHHHHH
Confidence            66999999999998875444444556666665 45566665543

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.00  E-value=0.087  Score=42.76  Aligned_cols=52  Identities=15%  Similarity=0.181  Sum_probs=32.0

Q ss_pred             CceEECcCCCchHHHHH-HHHHHHHHcC-CcEEEEe--chHHHHHHHHHHHHHhcC
Q 042424           57 HGTLTNPVYNGKTAVAE-YAIAMAFRDK-QRVIYTS--SLKALSNQKYRELHKEFK  108 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~-~ai~~~l~~~-~rviyv~--P~kaLv~Q~~~~l~~~f~  108 (138)
                      ..++++|||+|||..+. ++...+.+.| .++.++.  ++++-+.++...|.+.++
T Consensus       196 vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D~~r~~a~eql~~~~~~~~  251 (282)
T TIGR03499       196 VIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDTYRIGAVEQLKTYAKILG  251 (282)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECCccchhHHHHHHHHHHHhC
Confidence            34499999999999886 4443333334 5554443  335555566666666554

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=94.97  E-value=0.048  Score=42.10  Aligned_cols=37  Identities=14%  Similarity=0.044  Sum_probs=27.4

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      .+.++++|+|+|||..+.....++...+..++|+.-.
T Consensus        43 ~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~~~   79 (227)
T PRK08903         43 RFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDAA   79 (227)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEehH
Confidence            3456999999999998875555555667777777654

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.97  E-value=0.083  Score=48.01  Aligned_cols=77  Identities=10%  Similarity=0.075  Sum_probs=53.6

Q ss_pred             ECcCCCchHHHHHHHHHHHHHcC-CcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCC-----------cCCCCC
Q 042424           61 TNPVYNGKTAVAEYAIAMAFRDK-QRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDV-----------TLSPNA  123 (138)
Q Consensus        61 ~aPTGsGKTlva~~ai~~~l~~~-~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~-----------~~~~~~  123 (138)
                      -..||||||++..-.|+++..+| +..+|.|....+++..-..|.+-..     +-.+..+|.           ..+.+.
T Consensus         3 ~matgsgkt~~ma~lil~~y~kgyr~flffvnq~nilekt~~nftd~~s~kylf~e~i~~~d~~i~ikkvn~fsehnd~i   82 (812)
T COG3421           3 EMATGSGKTLVMAGLILECYKKGYRNFLFFVNQANILEKTKLNFTDSVSSKYLFSENININDENIEIKKVNNFSEHNDAI   82 (812)
T ss_pred             ccccCCChhhHHHHHHHHHHHhchhhEEEEecchhHHHHHHhhcccchhhhHhhhhhhhcCCceeeeeeecccCccCCce
Confidence            35799999999988888888888 5689999988888877666654221     111111221           123367


Q ss_pred             CEEEecHHHHHHhh
Q 042424          124 SCLVMTTEILRGML  137 (138)
Q Consensus       124 ~IiVtTpe~l~~lL  137 (138)
                      .|..+|.+.|.+.+
T Consensus        83 ei~fttiq~l~~d~   96 (812)
T COG3421          83 EIYFTTIQGLFSDF   96 (812)
T ss_pred             EEEEeehHHHHHHH
Confidence            89999999998754

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=94.94  E-value=0.048  Score=37.85  Aligned_cols=52  Identities=15%  Similarity=0.164  Sum_probs=28.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc-----CCcEEEE-echHHHHHHHHHHHHHhc
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD-----KQRVIYT-SSLKALSNQKYRELHKEF  107 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~-----~~rviyv-~P~kaLv~Q~~~~l~~~f  107 (138)
                      +..++.||+|+|||.++...+......     ...++++ +|...-....++.+.+.+
T Consensus         5 ~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l   62 (131)
T PF13401_consen    5 RILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEAL   62 (131)
T ss_dssp             --EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHH
T ss_pred             cccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHh
Confidence            345699999999999987666554332     3444443 333332444555554444

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.91  E-value=0.09  Score=45.66  Aligned_cols=50  Identities=12%  Similarity=0.133  Sum_probs=33.9

Q ss_pred             ceEECcCCCchHHHHH-HHHHHHHHcCCcEEEEe--chHHHHHHHHHHHHHhc
Q 042424           58 GTLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTS--SLKALSNQKYRELHKEF  107 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~--P~kaLv~Q~~~~l~~~f  107 (138)
                      .++++|+|+|||..+. +|....+..|.++.++.  ++++.+.++.+.+.+..
T Consensus       226 i~lvGptGvGKTTtaaKLA~~~~~~~G~~V~Lit~Dt~R~aA~eQLk~yAe~l  278 (432)
T PRK12724        226 VFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTTDNYRIAAIEQLKRYADTM  278 (432)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEecccchhhhHHHHHHHHHHhc
Confidence            3499999999999997 44444455677665443  44677777666665544

>PRK11054 helD DNA helicase IV; Provisional

Probab=94.89  E-value=0.084  Score=48.14  Aligned_cols=54  Identities=7%  Similarity=0.050  Sum_probs=45.2

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc----CCcEEEEechHHHHHHHHHHHHHhcC
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD----KQRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~----~~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      ..+.+|.|..|||||.+...-+.+.+..    ..++++++.++..++++.+++.+.++
T Consensus       209 ~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~lg  266 (684)
T PRK11054        209 EDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRERLG  266 (684)
T ss_pred             CCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHhcC
Confidence            3567799999999999988777666654    46899999999999999999988665

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=94.85  E-value=0.069  Score=46.51  Aligned_cols=47  Identities=19%  Similarity=0.111  Sum_probs=36.2

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .+|.+|+|+|||..+...+..++..|.+++|++-.. -.+|..+.+..
T Consensus       276 ~li~G~~G~GKT~l~~~~~~~~~~~g~~~~yis~e~-~~~~i~~~~~~  322 (509)
T PRK09302        276 ILVSGATGTGKTLLASKFAEAACRRGERCLLFAFEE-SRAQLIRNARS  322 (509)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEEecC-CHHHHHHHHHH
Confidence            348999999999999977777788899999997543 35555555543

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=94.79  E-value=0.051  Score=41.64  Aligned_cols=36  Identities=19%  Similarity=0.142  Sum_probs=28.4

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcC------CcEEEEechHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDK------QRVIYTSSLKA   94 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~------~rviyv~P~ka   94 (138)
                      .|.+|+|+|||.++...+...+..+      .+++|+..-..
T Consensus        23 ~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~~   64 (226)
T cd01393          23 EIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGA   64 (226)
T ss_pred             EEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCCC
Confidence            3999999999999987666665555      78899877543

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.

>TIGR01075 uvrD DNA helicase II

Probab=94.78  E-value=0.075  Score=48.28  Aligned_cols=54  Identities=11%  Similarity=0.036  Sum_probs=45.8

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc-C---CcEEEEechHHHHHHHHHHHHHhcC
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD-K---QRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~-~---~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      .++.+|.|..|||||.+...-+.+.+.. |   .+++.+.-|+..+.++.+++.+.++
T Consensus        17 ~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkAA~em~~Rl~~~~~   74 (715)
T TIGR01075        17 PGNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKAAAEMRHRIGALLG   74 (715)
T ss_pred             CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHHHHHHHHHHHHHhc
Confidence            3567899999999999998888887764 3   6899999999999999999988553

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

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.70  E-value=0.11  Score=44.72  Aligned_cols=52  Identities=19%  Similarity=0.201  Sum_probs=32.7

Q ss_pred             CceEECcCCCchHHHHH-HHHHHH-HHcCCcEEEEe--chHHHHHHHHHHHHHhcC
Q 042424           57 HGTLTNPVYNGKTAVAE-YAIAMA-FRDKQRVIYTS--SLKALSNQKYRELHKEFK  108 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~-~ai~~~-l~~~~rviyv~--P~kaLv~Q~~~~l~~~f~  108 (138)
                      ..++.+|||+|||..+. +|...+ +..|.++.++.  |+++-+.++.+.|.+.++
T Consensus       223 ~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~~r~~a~eqL~~~a~~~~  278 (424)
T PRK05703        223 VVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTYRIGAVEQLKTYAKIMG  278 (424)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCccHHHHHHHHHHHHHHhC
Confidence            45599999999998886 555444 34466665554  345545556666655443

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=94.67  E-value=0.09  Score=45.57  Aligned_cols=41  Identities=20%  Similarity=0.260  Sum_probs=28.7

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQ   98 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q   98 (138)
                      +..+.||+|+|||..+..........+.+++|+.. ..+.++
T Consensus       143 pl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~-~~f~~~  183 (445)
T PRK12422        143 PIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRS-ELFTEH  183 (445)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeH-HHHHHH
Confidence            35699999999999876444444446889998865 334433

>TIGR02746 TraC-F-type type-IV secretion system protein TraC

Probab=94.65  E-value=0.05  Score=49.60  Aligned_cols=39  Identities=10%  Similarity=-0.014  Sum_probs=31.7

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLK   93 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~k   93 (138)
                      +.|.+|.|+||||||+..-..+.+.+..|.+++++=|-.
T Consensus       430 n~n~~I~G~tGsGKS~~~~~l~~~~~~~g~~v~iiD~~~  468 (797)
T TIGR02746       430 NYNIAVVGGSGAGKSFFMQELIVDNLSRGGKVWVIDVGR  468 (797)
T ss_pred             ccceEEEcCCCCCHHHHHHHHHHHHHhCCCEEEEEeCCC
Confidence            357889999999999998776677777788888887753

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.

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=94.61  E-value=0.11  Score=44.67  Aligned_cols=43  Identities=19%  Similarity=0.164  Sum_probs=28.5

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKALSNQKY  100 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~kaLv~Q~~  100 (138)
                      +.+++||+|+|||..+......+..+  +.+++|+.. ..+.++..
T Consensus       150 ~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~-~~~~~~~~  194 (450)
T PRK00149        150 PLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTS-EKFTNDFV  194 (450)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEH-HHHHHHHH
Confidence            35699999999999876544444444  567777744 44554443

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

Probab=94.60  E-value=0.079  Score=49.20  Aligned_cols=49  Identities=18%  Similarity=0.223  Sum_probs=40.9

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEechHHHHHHHHHHHHHh
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLKALSNQKYRELHKE  106 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~kaLv~Q~~~~l~~~  106 (138)
                      .+|-+|.|+|||..-.-.+.+.+. .+.++++|+-.++|+.+.+.+|++.
T Consensus        52 ~vVRSpMGTGKTtaLi~wLk~~l~~~~~~VLvVShRrSL~~sL~~rf~~~  101 (824)
T PF02399_consen   52 LVVRSPMGTGKTTALIRWLKDALKNPDKSVLVVSHRRSLTKSLAERFKKA  101 (824)
T ss_pred             EEEECCCCCCcHHHHHHHHHHhccCCCCeEEEEEhHHHHHHHHHHHHhhc
Confidence            349999999999866666666553 4799999999999999999999874

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

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=94.59  E-value=0.041  Score=45.94  Aligned_cols=34  Identities=18%  Similarity=0.168  Sum_probs=24.8

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      ..+.++++|||||||... .++...+....|++.+
T Consensus       160 ~~nili~G~tgSGKTTll-~aL~~~ip~~~ri~ti  193 (332)
T PRK13900        160 KKNIIISGGTSTGKTTFT-NAALREIPAIERLITV  193 (332)
T ss_pred             CCcEEEECCCCCCHHHHH-HHHHhhCCCCCeEEEe
Confidence            467889999999999875 4555555556676655

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=94.52  E-value=0.13  Score=42.79  Aligned_cols=49  Identities=12%  Similarity=0.102  Sum_probs=32.5

Q ss_pred             eEECcCCCchHHHHH-HHHHHHHHcCCcEEEEe--chHHHHHHHHHHHHHhcC
Q 042424           59 TLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTS--SLKALSNQKYRELHKEFK  108 (138)
Q Consensus        59 ~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~--P~kaLv~Q~~~~l~~~f~  108 (138)
                      .+++|+|+|||..+. +|.. ...+|++++++.  ++++-+-++...|.+..+
T Consensus       118 ~lvGpnGsGKTTt~~kLA~~-l~~~g~~V~Li~~D~~r~~a~eql~~~a~~~~  169 (318)
T PRK10416        118 LVVGVNGVGKTTTIGKLAHK-YKAQGKKVLLAAGDTFRAAAIEQLQVWGERVG  169 (318)
T ss_pred             EEECCCCCcHHHHHHHHHHH-HHhcCCeEEEEecCccchhhHHHHHHHHHHcC
Confidence            489999999999886 4433 234577777664  346666566666666443

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=94.51  E-value=0.038  Score=49.27  Aligned_cols=41  Identities=15%  Similarity=0.090  Sum_probs=29.8

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKAL   95 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaL   95 (138)
                      ..+.++.|+||||||.+....+.+...+|.++|++=|.=..
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            46888999999999976545455545568888887776443

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).

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=94.51  E-value=0.15  Score=46.95  Aligned_cols=77  Identities=18%  Similarity=0.198  Sum_probs=55.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHH-----HHc-----CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC-
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMA-----FRD-----KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS-  120 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~-----l~~-----~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~-  120 (138)
                      ...+|.-.-|-|||+.-.-.|.+.     .+.     ..+.++|+|- +|+.|++.++.++..    +|.+++|+...+ 
T Consensus       346 ~GGILaddmGLGKTlsmislil~qK~~~~~~~~~~~~a~~TLII~Pa-Sli~qW~~Ev~~rl~~n~LsV~~~HG~n~r~i  424 (901)
T KOG4439|consen  346 SGGILADDMGLGKTLSMISLILHQKAARKAREKKGESASKTLIICPA-SLIHQWEAEVARRLEQNALSVYLYHGPNKREI  424 (901)
T ss_pred             CCcccccccccccchHHHHHHHHHHHHHHhhcccccccCCeEEeCcH-HHHHHHHHHHHHHHhhcceEEEEecCCccccC
Confidence            346688889999999544333222     111     1248999997 799999999999886    688889986432 


Q ss_pred             -----CCCCEEEecHHHH
Q 042424          121 -----PNASCLVMTTEIL  133 (138)
Q Consensus       121 -----~~~~IiVtTpe~l  133 (138)
                           .+.+|||||+...
T Consensus       425 ~~~~L~~YDvViTTY~lv  442 (901)
T KOG4439|consen  425 SAKELRKYDVVITTYNLV  442 (901)
T ss_pred             CHHHHhhcceEEEeeecc
Confidence                 1889999998654

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=94.50  E-value=0.11  Score=44.74  Aligned_cols=53  Identities=21%  Similarity=0.275  Sum_probs=39.8

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechH-------HHHHHHHHHHHHhcCceE
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLK-------ALSNQKYRELHKEFKDVG  111 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~k-------aLv~Q~~~~l~~~f~~v~  111 (138)
                      ..|.||+|+|||...-.+...++..  +.+++|+..-.       ++-+...++|++.| ++.
T Consensus       116 lfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~se~f~~~~v~a~~~~~~~~Fk~~y-~~d  177 (408)
T COG0593         116 LFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTNDFVKALRDNEMEKFKEKY-SLD  177 (408)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhhCCCceEEeccHHHHHHHHHHHHHhhhHHHHHHhh-ccC
Confidence            4599999999999765555555555  45889988865       77777788888888 543

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=94.49  E-value=0.12  Score=43.61  Aligned_cols=42  Identities=21%  Similarity=0.181  Sum_probs=27.6

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKALSNQKY  100 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~kaLv~Q~~  100 (138)
                      .++.||+|+|||..+.........+  +.+++|+.. ..+.++..
T Consensus       139 l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~-~~~~~~~~  182 (405)
T TIGR00362       139 LFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSS-EKFTNDFV  182 (405)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEH-HHHHHHHH
Confidence            4699999999999885444443333  678888754 34444433

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).

>PRK08939 primosomal protein DnaI; Reviewed

Probab=94.46  E-value=0.12  Score=42.62  Aligned_cols=44  Identities=7%  Similarity=-0.111  Sum_probs=30.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKY  100 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~  100 (138)
                      .+..+.||+|.|||.++......+..+|.+++|+. .-.|+.+..
T Consensus       157 ~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~-~~~l~~~lk  200 (306)
T PRK08939        157 KGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLH-FPEFIRELK  200 (306)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEE-HHHHHHHHH
Confidence            35569999999999988755555556677776653 234555543

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.46  E-value=0.12  Score=43.97  Aligned_cols=53  Identities=21%  Similarity=0.147  Sum_probs=32.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHH-HHcC-CcEEEEe--chHHHHHHHHHHHHHhcC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMA-FRDK-QRVIYTS--SLKALSNQKYRELHKEFK  108 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~-l~~~-~rviyv~--P~kaLv~Q~~~~l~~~f~  108 (138)
                      ...++.+|||+|||..+.....+. .+.| .++.++.  .++.=+.++.+.|.+.++
T Consensus       138 ~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~g  194 (374)
T PRK14722        138 GVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILG  194 (374)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcC
Confidence            345699999999999986433333 3445 4554443  224445666666666554

>TIGR03744 traC_PFL_4706 conjugative transfer ATPase, PFL_4706 family

Probab=94.44  E-value=0.057  Score=50.50  Aligned_cols=40  Identities=15%  Similarity=0.200  Sum_probs=32.6

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc-CCcEEEEechHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD-KQRVIYTSSLKA   94 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~-~~rviyv~P~ka   94 (138)
                      +.|.+|.||||||||+..-..+.+.+.. +.+++++=|=.+
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            5788999999999999988777777764 788888777554

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.

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=94.43  E-value=0.059  Score=46.96  Aligned_cols=47  Identities=11%  Similarity=0.112  Sum_probs=33.9

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHc-CCcEEEEechHHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRD-KQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~-~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .+|.+++|+|||..+...+.+.+.+ |.+++|+.=. .-.+|..+.+..
T Consensus        34 ~li~G~pGsGKT~l~~qf~~~~~~~~ge~~lyis~e-e~~~~i~~~~~~   81 (509)
T PRK09302         34 TLVSGTAGTGKTLFALQFLVNGIKRFDEPGVFVTFE-ESPEDIIRNVAS   81 (509)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHhcCCCEEEEEcc-CCHHHHHHHHHH
Confidence            3499999999999998666666666 8899888533 344555555544

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=94.42  E-value=0.035  Score=46.71  Aligned_cols=40  Identities=23%  Similarity=0.258  Sum_probs=27.6

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKAL   95 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaL   95 (138)
                      ..|.++++|||||||... .++...+....+++.+=...+|
T Consensus       162 ~~nilI~G~tGSGKTTll-~aLl~~i~~~~rivtiEd~~El  201 (344)
T PRK13851        162 RLTMLLCGPTGSGKTTMS-KTLISAIPPQERLITIEDTLEL  201 (344)
T ss_pred             CCeEEEECCCCccHHHHH-HHHHcccCCCCCEEEECCCccc
Confidence            467889999999999865 4455545455676665555544

>cd01131 PilT Pilus retraction ATPase PilT

Probab=94.42  E-value=0.07  Score=40.88  Aligned_cols=32  Identities=13%  Similarity=0.196  Sum_probs=20.4

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH-c-CCcEEEEe
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR-D-KQRVIYTS   90 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~-~-~~rviyv~   90 (138)
                      .++++|||||||..... +...+. . +.+++.+-
T Consensus         4 ilI~GptGSGKTTll~~-ll~~~~~~~~~~i~t~e   37 (198)
T cd01131           4 VLVTGPTGSGKSTTLAA-MIDYINKNKTHHILTIE   37 (198)
T ss_pred             EEEECCCCCCHHHHHHH-HHHHhhhcCCcEEEEEc
Confidence            35999999999998643 343443 2 44555443

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.

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=94.39  E-value=0.029  Score=47.58  Aligned_cols=18  Identities=33%  Similarity=0.412  Sum_probs=15.8

Q ss_pred             CCceEECcCCCchHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAE   73 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~   73 (138)
                      -|.++.+|||||||+.|-
T Consensus        98 SNILLiGPTGsGKTlLAq  115 (408)
T COG1219          98 SNILLIGPTGSGKTLLAQ  115 (408)
T ss_pred             ccEEEECCCCCcHHHHHH
Confidence            577799999999999874

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=94.36  E-value=0.052  Score=51.71  Aligned_cols=56  Identities=23%  Similarity=0.282  Sum_probs=42.9

Q ss_pred             EECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecC
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGD  116 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd  116 (138)
                      =-|.||||||++= .-|+++|..   |-|..+..-.|+|.-|.-+.++++++    +..++.|+
T Consensus       436 NMASTGcGKT~aN-ARImyaLsd~~~g~RfsiALGLRTLTLQTGda~r~rL~L~~ddLAVlIGs  498 (1110)
T TIGR02562       436 NMASTGCGKTLAN-ARAMYALRDDKQGARFAIALGLRSLTLQTGHALKTRLNLSDDDLAVLIGG  498 (1110)
T ss_pred             EecCCCcchHHHH-HHHHHHhCCCCCCceEEEEccccceeccchHHHHHhcCCCccceEEEECH
Confidence            4577999999864 344455654   56999999999999999999999886    45665543

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.

>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=94.29  E-value=0.041  Score=43.65  Aligned_cols=38  Identities=16%  Similarity=0.231  Sum_probs=25.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC-CcEEEEechHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK-QRVIYTSSLKA   94 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~-~rviyv~P~ka   94 (138)
                      ++.+++||||||||... .+++..+... .+++.+-...+
T Consensus       128 ~~ili~G~tGSGKTT~l-~all~~i~~~~~~iv~iEd~~E  166 (270)
T PF00437_consen  128 GNILISGPTGSGKTTLL-NALLEEIPPEDERIVTIEDPPE  166 (270)
T ss_dssp             EEEEEEESTTSSHHHHH-HHHHHHCHTTTSEEEEEESSS-
T ss_pred             eEEEEECCCccccchHH-HHHhhhccccccceEEeccccc
Confidence            56779999999999876 4444555444 67776654433

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 ....

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=94.28  E-value=0.06  Score=49.04  Aligned_cols=54  Identities=11%  Similarity=0.034  Sum_probs=45.8

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc-C---CcEEEEechHHHHHHHHHHHHHhcC
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD-K---QRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~-~---~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      .++.+|.|..|||||.+...-+.+.+.. |   .+++.+.-|+..++++.+++.+..+
T Consensus        22 ~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~~~   79 (721)
T PRK11773         22 LGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQLLG   79 (721)
T ss_pred             CCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHHhc
Confidence            4677899999999999998888877763 3   6899999999999999999988554

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=94.28  E-value=0.063  Score=45.72  Aligned_cols=45  Identities=16%  Similarity=0.101  Sum_probs=34.6

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQK   99 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~   99 (138)
                      .++.++.++||||||.+....+.+.+..+.++|++=|.-.+....
T Consensus        42 ~~h~~i~g~tGsGKt~~i~~l~~~~~~~~~~~vi~D~kg~~~~~~   86 (410)
T cd01127          42 EAHTMIIGTTGTGKTTQIRELLASIRARGDRAIIYDPNGGFVSKF   86 (410)
T ss_pred             hccEEEEcCCCCCHHHHHHHHHHHHHhcCCCEEEEeCCcchhHhh
Confidence            467889999999999875555556566788999998887765443

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.

>PRK10536 hypothetical protein; Provisional

Probab=94.27  E-value=0.062  Score=43.80  Aligned_cols=39  Identities=26%  Similarity=0.141  Sum_probs=27.4

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC--CcEEEEechHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK--QRVIYTSSLKA   94 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~--~rviyv~P~ka   94 (138)
                      ...++.+|+|+|||+++..+..+++..+  .+++++=|...
T Consensus        75 ~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI~RP~v~  115 (262)
T PRK10536         75 QLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRPVLQ  115 (262)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEEeCCCCC
Confidence            3455999999999999987666655433  45666656543

>PRK10867 signal recognition particle protein; Provisional

Probab=94.13  E-value=0.16  Score=44.00  Aligned_cols=50  Identities=14%  Similarity=0.189  Sum_probs=33.8

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHc-CCcEEEEe--chHHHHHHHHHHHHHhcC
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRD-KQRVIYTS--SLKALSNQKYRELHKEFK  108 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~-~~rviyv~--P~kaLv~Q~~~~l~~~f~  108 (138)
                      ++++|+|+|||.++.....+...+ |.+++++.  ++++-+.++.+.|.+..+
T Consensus       104 ~~vG~~GsGKTTtaakLA~~l~~~~G~kV~lV~~D~~R~aa~eQL~~~a~~~g  156 (433)
T PRK10867        104 MMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLVAADVYRPAAIEQLKTLGEQIG  156 (433)
T ss_pred             EEECCCCCcHHHHHHHHHHHHHHhcCCcEEEEEccccchHHHHHHHHHHhhcC
Confidence            499999999999887333333344 77776654  457777667777766443

>PRK14974 cell division protein FtsY; Provisional

Probab=94.07  E-value=0.18  Score=42.35  Aligned_cols=50  Identities=12%  Similarity=0.088  Sum_probs=32.4

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEec--hHHHHHHHHHHHHHhcC
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS--LKALSNQKYRELHKEFK  108 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P--~kaLv~Q~~~~l~~~f~  108 (138)
                      ++++|+|+|||..+.........+|.+++++..  +|+=+.++.+.+.+.++
T Consensus       144 ~~~G~~GvGKTTtiakLA~~l~~~g~~V~li~~Dt~R~~a~eqL~~~a~~lg  195 (336)
T PRK14974        144 VFVGVNGTGKTTTIAKLAYYLKKNGFSVVIAAGDTFRAGAIEQLEEHAERLG  195 (336)
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHHcCCeEEEecCCcCcHHHHHHHHHHHHHcC
Confidence            499999999999876444443445777776653  34545455556666554

>TIGR00959 ffh signal recognition particle protein

Probab=94.02  E-value=0.18  Score=43.68  Aligned_cols=51  Identities=12%  Similarity=0.149  Sum_probs=33.4

Q ss_pred             ceEECcCCCchHHHHH-HHHHHHHHcCCcEEEEe--chHHHHHHHHHHHHHhcC
Q 042424           58 GTLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTS--SLKALSNQKYRELHKEFK  108 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~--P~kaLv~Q~~~~l~~~f~  108 (138)
                      .++++|+|+|||.++. +|..-+.+.|.+++++.  ++++-+.++.+.+.+..+
T Consensus       102 i~~vG~~GsGKTTtaakLA~~l~~~~g~kV~lV~~D~~R~~a~~QL~~~a~~~g  155 (428)
T TIGR00959       102 ILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLVACDLYRPAAIEQLKVLGQQVG  155 (428)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHhCCCeEEEEeccccchHHHHHHHHHHHhcC
Confidence            3499999999999987 44432224577776554  346666666666666443

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.

>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=93.98  E-value=0.11  Score=44.09  Aligned_cols=47  Identities=17%  Similarity=0.173  Sum_probs=32.7

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYR  101 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~  101 (138)
                      .++.++.+.||||||.+....+.+.+.+|.++|+.=|.-......++
T Consensus        15 ~~~~li~G~~GsGKT~~i~~ll~~~~~~g~~~iI~D~kg~~~~~f~~   61 (386)
T PF10412_consen   15 NRHILIIGATGSGKTQAIRHLLDQIRARGDRAIIYDPKGEFTERFYR   61 (386)
T ss_dssp             GG-EEEEE-TTSSHHHHHHHHHHHHHHTT-EEEEEEETTHHHHHH--
T ss_pred             hCcEEEECCCCCCHHHHHHHHHHHHHHcCCEEEEEECCchHHHHhcC
Confidence            36788999999999986666666666778899888888776555444

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.

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=93.94  E-value=0.098  Score=40.35  Aligned_cols=37  Identities=14%  Similarity=0.178  Sum_probs=30.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHH-HcCCcEEEEech
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAF-RDKQRVIYTSSL   92 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l-~~~~rviyv~P~   92 (138)
                      ++.+|.|-||||||...-..+.+.+ ..+.+++++=|.
T Consensus        24 ~H~~I~G~TGsGKS~~~~~ll~~l~~~~~~~~ii~D~~   61 (229)
T PF01935_consen   24 RHIAIFGTTGSGKSNTVKVLLEELLKKKGAKVIIFDPH   61 (229)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEEcCC
Confidence            6778999999999998877777776 567777777665

It contains several conserved aspartates and histidines that could be metal ligands.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=93.85  E-value=0.19  Score=43.58  Aligned_cols=52  Identities=13%  Similarity=0.098  Sum_probs=33.7

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec--hHHHHHHHHHHHHHhcC
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS--LKALSNQKYRELHKEFK  108 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P--~kaLv~Q~~~~l~~~f~  108 (138)
                      ..++++++|+|||.++.....+....|.+++++.-  +++-+.++.+.+.+..+
T Consensus        97 vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~~D~~R~aa~eQL~~la~~~g  150 (437)
T PRK00771         97 TIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAADTYRPAAYDQLKQLAEKIG  150 (437)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEecCCCCCHHHHHHHHHHHHHcC
Confidence            34599999999999987444444445777766543  35555566666665443

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=93.85  E-value=0.081  Score=44.18  Aligned_cols=34  Identities=18%  Similarity=0.230  Sum_probs=22.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHH---cCCcEEEEe
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFR---DKQRVIYTS   90 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~---~~~rviyv~   90 (138)
                      .|.+++++||||||... .++...+.   .+.|++.+=
T Consensus       145 ~nilI~G~tGSGKTTll-~aL~~~i~~~~~~~rivtiE  181 (323)
T PRK13833        145 LNIVISGGTGSGKTTLA-NAVIAEIVASAPEDRLVILE  181 (323)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHHHhcCCCCceEEEec
Confidence            57789999999999876 44544442   245555443

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=93.84  E-value=0.14  Score=46.26  Aligned_cols=41  Identities=27%  Similarity=0.141  Sum_probs=26.7

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH--cCCcEEEEechHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR--DKQRVIYTSSLKALSNQK   99 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~--~~~rviyv~P~kaLv~Q~   99 (138)
                      .+|++++|+|||..+-.....+..  .+.+++|+.- ..++++.
T Consensus       317 L~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yita-eef~~el  359 (617)
T PRK14086        317 LFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSS-EEFTNEF  359 (617)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeH-HHHHHHH
Confidence            569999999999876533333333  3677877754 4455444

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=93.76  E-value=0.091  Score=47.06  Aligned_cols=54  Identities=15%  Similarity=0.110  Sum_probs=45.3

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc-C---CcEEEEechHHHHHHHHHHHHHhcC
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD-K---QRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~-~---~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      .++.+|.|..|||||.+...-+.+.+.+ +   .+++.|..++..+.++-+++.+.++
T Consensus        14 ~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~~Aa~em~~Rl~~~l~   71 (664)
T TIGR01074        14 TGPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTNKAAREMKERVAKTLG   71 (664)
T ss_pred             CCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHhC
Confidence            3567899999999999998888887753 3   6789999999999999999988654

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

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=93.75  E-value=0.076  Score=46.85  Aligned_cols=25  Identities=28%  Similarity=0.295  Sum_probs=18.8

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcC
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDK   83 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~   83 (138)
                      .++++|||||||.. +|+++..+++.
T Consensus       261 iLvTGPTGSGKTTT-LY~~L~~ln~~  285 (500)
T COG2804         261 ILVTGPTGSGKTTT-LYAALSELNTP  285 (500)
T ss_pred             EEEeCCCCCCHHHH-HHHHHHHhcCC
Confidence            44999999999975 56666666653

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=93.75  E-value=0.25  Score=41.10  Aligned_cols=89  Identities=20%  Similarity=0.160  Sum_probs=61.9

Q ss_pred             cccccCCCCccCCCCCCCceEECcCCCchHHHHHHHHHHHHHcCC-cEEEEechHHHHHHHHHHHHHhcC---ceEEE--
Q 042424           40 HEVAVPSCYTLTTDETTHGTLTNPVYNGKTAVAEYAIAMAFRDKQ-RVIYTSSLKALSNQKYRELHKEFK---DVGLM--  113 (138)
Q Consensus        40 ~~~~~p~~y~~~~~~~~~~~l~aPTGsGKTlva~~ai~~~l~~~~-rviyv~P~kaLv~Q~~~~l~~~f~---~v~~~--  113 (138)
                      |+..+|.+++      ...++.=-||.||--...-.|++.+.+|+ |.|+++-.-.|-.+..++|++.-.   .+-.+  
T Consensus        53 h~~~Lp~~~R------~Gf~lGDGtGvGKGR~iAgiI~~n~l~Gr~r~vwvS~s~dL~~Da~RDl~DIG~~~i~v~~l~~  126 (303)
T PF13872_consen   53 HEQILPGGSR------AGFFLGDGTGVGKGRQIAGIILENWLRGRKRAVWVSVSNDLKYDAERDLRDIGADNIPVHPLNK  126 (303)
T ss_pred             HHhhcccccC------cEEEeccCCCcCccchhHHHHHHHHHcCCCceEEEECChhhhhHHHHHHHHhCCCcccceechh
Confidence            4445666653      22336666999999988888888877764 699999999999999999998432   12111  


Q ss_pred             --ecCCcCCCCCCEEEecHHHHHH
Q 042424          114 --TGDVTLSPNASCLVMTTEILRG  135 (138)
Q Consensus       114 --tGd~~~~~~~~IiVtTpe~l~~  135 (138)
                        .|+. ...+..||.+|+-.|..
T Consensus       127 ~~~~~~-~~~~~GvlF~TYs~L~~  149 (303)
T PF13872_consen  127 FKYGDI-IRLKEGVLFSTYSTLIS  149 (303)
T ss_pred             hccCcC-CCCCCCccchhHHHHHh
Confidence              1221 22366799999988764

>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=93.72  E-value=0.19  Score=34.50  Aligned_cols=34  Identities=21%  Similarity=0.145  Sum_probs=23.7

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKAL   95 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaL   95 (138)
                      ++.+|.|+|||.++...+...   +..++.+......
T Consensus         2 ll~G~~G~GKT~l~~~la~~l---~~~~~~i~~~~~~   35 (132)
T PF00004_consen    2 LLHGPPGTGKTTLARALAQYL---GFPFIEIDGSELI   35 (132)
T ss_dssp             EEESSTTSSHHHHHHHHHHHT---TSEEEEEETTHHH
T ss_pred             EEECcCCCCeeHHHHHHHhhc---ccccccccccccc
Confidence            589999999998886555432   5566666655544

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 ....

>TIGR00929 VirB4_CagE type IV secretion/conjugal transfer ATPase, VirB4 family

Probab=93.68  E-value=0.09  Score=47.71  Aligned_cols=49  Identities=14%  Similarity=0.198  Sum_probs=37.7

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCC-cEEEEechHHHHHHHHHHHHHhcC
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQ-RVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~-rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      +.|.+|.|+||+|||+..-+.+.+.+..|. +++++=|-.+     ++.+.+.++
T Consensus       434 ~~n~~I~G~tGsGKS~~~~~l~~~~~~~~~~~v~iiD~~~~-----~~~~~~~~g  483 (785)
T TIGR00929       434 LGHTLIFGPTGSGKTTLLNFLLAQMQKYGGMTIFAFDKDRG-----MEIFIRAFG  483 (785)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhhccCCCeEEEEeCCCC-----hHHhhhccC
Confidence            578889999999999988777777766666 8888888765     444555554

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).

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=93.68  E-value=0.22  Score=43.89  Aligned_cols=50  Identities=22%  Similarity=0.248  Sum_probs=34.2

Q ss_pred             eEECcCCCchHHHHH-HHHHHHHHcCC-cEEEEe--chHHHHHHHHHHHHHhcC
Q 042424           59 TLTNPVYNGKTAVAE-YAIAMAFRDKQ-RVIYTS--SLKALSNQKYRELHKEFK  108 (138)
Q Consensus        59 ~l~aPTGsGKTlva~-~ai~~~l~~~~-rviyv~--P~kaLv~Q~~~~l~~~f~  108 (138)
                      .+.+|||+|||..+. ++......+|. ++.++.  +++.=+.++.+.|.+.++
T Consensus       260 ~LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI~~Dt~RigA~EQLr~~AeilG  313 (484)
T PRK06995        260 ALMGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIGGHEQLRIYGKILG  313 (484)
T ss_pred             EEECCCCccHHHHHHHHHHHHHHhcCCCeEEEEeCCccchhHHHHHHHHHHHhC
Confidence            499999999999886 55444445554 554332  446667788888877665

>TIGR03783 Bac_Flav_CT_G Bacteroides conjugation system ATPase, TraG family

Probab=93.58  E-value=0.15  Score=47.49  Aligned_cols=44  Identities=9%  Similarity=0.224  Sum_probs=34.9

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec---hHHHHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS---LKALSNQ   98 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P---~kaLv~Q   98 (138)
                      ++|..|.|+||+|||......+.+.+..|.+++++=+   ++.|++-
T Consensus       438 n~N~~I~G~sGsGKS~l~~~l~~~~~~~g~~vviiD~g~sy~~l~~~  484 (829)
T TIGR03783       438 NRNKFILGPSGSGKSFFTNHLVRQYYEQGTHILLVDTGNSYQGLCEL  484 (829)
T ss_pred             cCceEEECCCCCCHHHHHHHHHHHHHhcCCEEEEECCCccHHHHHHH
Confidence            4788999999999999998888887788888877755   4555443

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.

>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=93.56  E-value=0.11  Score=36.74  Aligned_cols=21  Identities=33%  Similarity=0.321  Sum_probs=16.7

Q ss_pred             ceEECcCCCchHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAM   78 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~   78 (138)
                      .+|.+|+|+|||.++......
T Consensus         2 vlL~G~~G~GKt~l~~~la~~   22 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAAL   22 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            469999999999998755443

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.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=93.54  E-value=0.12  Score=42.49  Aligned_cols=40  Identities=20%  Similarity=0.268  Sum_probs=26.4

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKAL   95 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaL   95 (138)
                      ..+.++++|||||||.... ++...+..   +.|++.+=-..+|
T Consensus       132 ~~~ilI~G~tGSGKTTll~-al~~~i~~~~~~~ri~tiEd~~El  174 (299)
T TIGR02782       132 RKNILVVGGTGSGKTTLAN-ALLAEIAKNDPTDRVVIIEDTREL  174 (299)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHhhccCCCceEEEECCchhh
Confidence            3677899999999998764 34444432   4666665554444

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.

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=93.50  E-value=0.23  Score=45.00  Aligned_cols=54  Identities=28%  Similarity=0.302  Sum_probs=41.9

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC--ceEEE
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK--DVGLM  113 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~  113 (138)
                      +.++.+.+||||+++....+ .  ..++.+|+|+|....+.|.+++|+..|+  .|..+
T Consensus        34 ~~ll~Gl~gs~ka~lia~l~-~--~~~r~vLIVt~~~~~A~~l~~dL~~~~~~~~v~~f   89 (652)
T PRK05298         34 HQTLLGVTGSGKTFTMANVI-A--RLQRPTLVLAHNKTLAAQLYSEFKEFFPENAVEYF   89 (652)
T ss_pred             cEEEEcCCCcHHHHHHHHHH-H--HhCCCEEEEECCHHHHHHHHHHHHHhcCCCeEEEe
Confidence            45699999999998754322 1  2378999999999999999999999776  35544

>PRK13873 conjugal transfer ATPase TrbE; Provisional

Probab=93.48  E-value=0.1  Score=48.13  Aligned_cols=48  Identities=15%  Similarity=0.066  Sum_probs=34.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEechHHHHHHHHHHHHHhcC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      +|.+|.||||||||+..-+.+.+.++ .|.+++++=+-++     ++.+.+.++
T Consensus       442 gn~~I~G~tGsGKS~l~~~l~~~~~~~~g~~v~i~D~~~s-----~~~l~~alG  490 (811)
T PRK13873        442 GHTLVVGPTGAGKSVLLALMALQFRRYPGAQVFAFDFGGS-----IRAATLAMG  490 (811)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhhhcCCCeEEEEeCCCC-----HHHHHHhcC
Confidence            58899999999999998776666665 4777777766442     344444454

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=93.45  E-value=0.14  Score=37.42  Aligned_cols=34  Identities=24%  Similarity=0.214  Sum_probs=26.6

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      .+++|.+||||..+...+....++|.++.++...
T Consensus         4 ~VvG~~~sGKTTl~~~Li~~l~~~g~~v~~ik~~   37 (140)
T PF03205_consen    4 QVVGPKNSGKTTLIRKLINELKRRGYRVAVIKHT   37 (140)
T ss_dssp             EEEESTTSSHHHHHHHHHHHHHHTT--EEEEEE-
T ss_pred             EEECCCCCCHHHHHHHHHHHHhHcCCceEEEEEc
Confidence            4899999999999998888887788888776554

>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=93.44  E-value=0.14  Score=40.53  Aligned_cols=34  Identities=26%  Similarity=0.075  Sum_probs=28.2

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHc-CCcEEEEech
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRD-KQRVIYTSSL   92 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~-~~rviyv~P~   92 (138)
                      +|.|++|.|||..++..+.++..+ +..++|++.-
T Consensus        23 vi~a~pg~GKT~~~l~ia~~~a~~~~~~vly~SlE   57 (259)
T PF03796_consen   23 VIAARPGVGKTAFALQIALNAALNGGYPVLYFSLE   57 (259)
T ss_dssp             EEEESTTSSHHHHHHHHHHHHHHTTSSEEEEEESS
T ss_pred             EEEecccCCchHHHHHHHHHHHHhcCCeEEEEcCC
Confidence            499999999999999777766665 6899998864

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 ....

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=93.42  E-value=0.11  Score=39.90  Aligned_cols=34  Identities=12%  Similarity=0.150  Sum_probs=25.5

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHc------CCcEEEEech
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRD------KQRVIYTSSL   92 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~------~~rviyv~P~   92 (138)
                      .|++|.|+|||..+...+...+..      +.+++|+.--
T Consensus        23 ~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e   62 (235)
T cd01123          23 EIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTE   62 (235)
T ss_pred             EEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCC
Confidence            399999999999998655554333      3788888753

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 .

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=93.42  E-value=0.11  Score=40.67  Aligned_cols=20  Identities=25%  Similarity=0.217  Sum_probs=16.0

Q ss_pred             CceEECcCCCchHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai   76 (138)
                      ..+++||.|+|||.++....
T Consensus        45 ~~~l~G~~G~GKTtl~~~l~   64 (269)
T TIGR03015        45 FILITGEVGAGKTTLIRNLL   64 (269)
T ss_pred             EEEEEcCCCCCHHHHHHHHH
Confidence            34699999999998876544

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.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.36  E-value=0.21  Score=43.08  Aligned_cols=52  Identities=10%  Similarity=0.100  Sum_probs=33.3

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEe--chHHHHHHHHHHHHHhcC
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS--SLKALSNQKYRELHKEFK  108 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~--P~kaLv~Q~~~~l~~~f~  108 (138)
                      ..++++|+|+|||..+.-...+...+|.++.++.  |+++=+.++.+.+.+..+
T Consensus       208 ii~lvGptGvGKTTt~akLA~~l~~~g~~V~lItaDtyR~gAveQLk~yae~lg  261 (407)
T PRK12726        208 IISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFITTDTFRSGAVEQFQGYADKLD  261 (407)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCccCccHHHHHHHHhhcCC
Confidence            3459999999999888643344556677765544  445545555555655443

>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=93.34  E-value=0.094  Score=44.20  Aligned_cols=38  Identities=16%  Similarity=0.289  Sum_probs=24.6

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKALS   96 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~kaLv   96 (138)
                      +|.+||||||+-...-.|--.+.+  -..|+||+|.+-.+
T Consensus        91 ~VYGPTG~GKSqLlRNLis~~lI~P~PETVfFItP~~~mI  130 (369)
T PF02456_consen   91 VVYGPTGSGKSQLLRNLISCQLIQPPPETVFFITPQKDMI  130 (369)
T ss_pred             EEECCCCCCHHHHHHHhhhcCcccCCCCceEEECCCCCCC
Confidence            399999999996433222111121  57899999986543

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

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=93.31  E-value=0.28  Score=42.68  Aligned_cols=52  Identities=17%  Similarity=0.098  Sum_probs=31.9

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEe--chHHHHHHHHHHHHHhcC
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS--SLKALSNQKYRELHKEFK  108 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~--P~kaLv~Q~~~~l~~~f~  108 (138)
                      ...+.+|||+|||..+.........+|.++.++.  +.++-+-++.+.+.+..+
T Consensus       243 vI~LVGptGvGKTTTiaKLA~~L~~~GkkVglI~aDt~RiaAvEQLk~yae~lg  296 (436)
T PRK11889        243 TIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITTDHSRIGTVQQLQDYVKTIG  296 (436)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEEecCCcchHHHHHHHHHhhhcC
Confidence            3459999999999988633333345576765544  345444444555555443

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=93.28  E-value=0.16  Score=37.75  Aligned_cols=33  Identities=21%  Similarity=0.220  Sum_probs=23.8

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      .+++++|||||.++...+.....+|.++.++-+
T Consensus         3 ~i~G~~gsGKTtl~~~l~~~l~~~G~~V~viK~   35 (155)
T TIGR00176         3 QIVGPKNSGKTTLIERLVKALKARGYRVATIKH   35 (155)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhcCCeEEEEec
Confidence            388999999999887655544345667766654

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.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.26  E-value=0.25  Score=42.22  Aligned_cols=52  Identities=12%  Similarity=0.085  Sum_probs=34.3

Q ss_pred             CceEECcCCCchHHHHH-HHHHHHHH---cCCcEEE--EechHHHHHHHHHHHHHhcC
Q 042424           57 HGTLTNPVYNGKTAVAE-YAIAMAFR---DKQRVIY--TSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~-~ai~~~l~---~~~rviy--v~P~kaLv~Q~~~~l~~~f~  108 (138)
                      ..++.+|||+|||..+. +|....+.   +|.++.+  +=++++-+.++.+.+.+.++
T Consensus       176 vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lg  233 (388)
T PRK12723        176 VFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMG  233 (388)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCC
Confidence            34599999999999986 44333332   3455533  33557777777888877665

>PRK13891 conjugal transfer protein TrbE; Provisional

Probab=93.25  E-value=0.13  Score=48.00  Aligned_cols=39  Identities=15%  Similarity=0.020  Sum_probs=30.0

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEechH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLK   93 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~k   93 (138)
                      .++.+|.||||||||+..-+.+.+..+ .+.+++++=|-+
T Consensus       488 ~gh~~I~G~tGsGKS~l~~~L~~~~~k~~~~~v~i~D~~~  527 (852)
T PRK13891        488 LGHTFMFGPTGAGKSTHLGIIAAQLRRYAGMSIYAFDKGM  527 (852)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhcCCCEEEEEcCCc
Confidence            467889999999999998776666655 467777766654

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=93.20  E-value=0.19  Score=47.21  Aligned_cols=77  Identities=17%  Similarity=0.143  Sum_probs=53.3

Q ss_pred             CCceEECcCCCchHHHHHHHHH-HHHHcCCcEEEEechHHHHHHHHHHHHHhc---C-ceEEEecCCcCCC-----CCCE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIA-MAFRDKQRVIYTSSLKALSNQKYRELHKEF---K-DVGLMTGDVTLSP-----NASC  125 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~-~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f---~-~v~~~tGd~~~~~-----~~~I  125 (138)
                      ...+.-..||-|||++|.+++. .+| .|+.|-+|...-=|+..=++.+...|   + +||+...+...+.     .++|
T Consensus        92 ~G~IAEMkTGEGKTLvAtLpayLnAL-~GkgVhVVTvNdYLA~RDae~mg~vy~fLGLsvG~i~~~~~~~~rr~aY~~DI  170 (925)
T PRK12903         92 LGSVAEMKTGEGKTITSIAPVYLNAL-TGKGVIVSTVNEYLAERDAEEMGKVFNFLGLSVGINKANMDPNLKREAYACDI  170 (925)
T ss_pred             cCCeeeecCCCCccHHHHHHHHHHHh-cCCceEEEecchhhhhhhHHHHHHHHHHhCCceeeeCCCCChHHHHHhccCCC
Confidence            3456889999999999987554 444 47777666666668876666655544   4 8888776554322     7888


Q ss_pred             EEecHHHH
Q 042424          126 LVMTTEIL  133 (138)
Q Consensus       126 iVtTpe~l  133 (138)
                      +-+|.-.|
T Consensus       171 tYgTn~E~  178 (925)
T PRK12903        171 TYSVHSEL  178 (925)
T ss_pred             eeecCccc
Confidence            88887553

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=93.18  E-value=0.29  Score=42.44  Aligned_cols=40  Identities=18%  Similarity=0.073  Sum_probs=27.4

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHH---cCCcEEEEechHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFR---DKQRVIYTSSLKALSNQ   98 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~---~~~rviyv~P~kaLv~Q   98 (138)
                      +..+.|++|+|||..+ .|+.+.+.   .+.+++|+... .+.++
T Consensus       143 pl~i~G~~G~GKTHLl-~Ai~~~l~~~~~~~~v~yv~~~-~f~~~  185 (450)
T PRK14087        143 PLFIYGESGMGKTHLL-KAAKNYIESNFSDLKVSYMSGD-EFARK  185 (450)
T ss_pred             ceEEECCCCCcHHHHH-HHHHHHHHHhCCCCeEEEEEHH-HHHHH
Confidence            3559999999999776 55555543   36788887663 34433

>PRK11823 DNA repair protein RadA; Provisional

Probab=93.14  E-value=0.23  Score=42.96  Aligned_cols=45  Identities=16%  Similarity=0.047  Sum_probs=32.2

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYREL  103 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l  103 (138)
                      .++.+++|+|||..++..+.....++.+++|+.-..+ .+|...+.
T Consensus        83 ~lI~G~pG~GKTtL~lq~a~~~a~~g~~vlYvs~Ees-~~qi~~ra  127 (446)
T PRK11823         83 VLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVSGEES-ASQIKLRA  127 (446)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEcccc-HHHHHHHH
Confidence            3499999999999998666555566889999985433 34544433

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=93.13  E-value=0.11  Score=46.12  Aligned_cols=26  Identities=23%  Similarity=0.234  Sum_probs=19.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD   82 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~   82 (138)
                      +..++++|||||||... ++++..+..
T Consensus       317 Glilv~G~tGSGKTTtl-~a~l~~~~~  342 (564)
T TIGR02538       317 GMVLVTGPTGSGKTVSL-YTALNILNT  342 (564)
T ss_pred             CeEEEECCCCCCHHHHH-HHHHHhhCC
Confidence            34569999999999875 556566653

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.

>PRK13764 ATPase; Provisional

Probab=93.11  E-value=0.13  Score=46.38  Aligned_cols=31  Identities=19%  Similarity=0.243  Sum_probs=21.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVI   87 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rvi   87 (138)
                      .+.++++|||||||... .++...+....+.+
T Consensus       258 ~~ILIsG~TGSGKTTll-~AL~~~i~~~~riV  288 (602)
T PRK13764        258 EGILIAGAPGAGKSTFA-QALAEFYADMGKIV  288 (602)
T ss_pred             CEEEEECCCCCCHHHHH-HHHHHHHhhCCCEE
Confidence            56779999999999876 44555555444444

>PRK13700 conjugal transfer protein TraD; Provisional

Probab=93.06  E-value=0.17  Score=46.65  Aligned_cols=82  Identities=15%  Similarity=0.157  Sum_probs=53.3

Q ss_pred             CCCCCCCC-----CcchhhhhcCC--CCCCcccccccCCCCccCCCCCCCceEECcCCCchHHHHHHHHHHHHHcCCcEE
Q 042424           15 ADSHVRGT-----PKEESTKKQRN--PTRSCVHEVAVPSCYTLTTDETTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVI   87 (138)
Q Consensus        15 ~~~~~~~~-----p~~~~~~~~~~--~~~~~~~~~~~p~~y~~~~~~~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rvi   87 (138)
                      +|...+|.     |++..+..+..  .++.+..-+-+|.+.     ..++.++.+-||+|||.+....+.+...+|.|+|
T Consensus       143 ~d~~irG~~l~~~~~~l~k~lk~~~~~s~i~I~gvPip~~~-----E~~H~li~GttGSGKS~~i~~LL~~ir~RGdrAI  217 (732)
T PRK13700        143 ENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDS-----EIQNFCLHGTVGAGKSEVIRRLANYARQRGDMVV  217 (732)
T ss_pred             hhhhcCcceecCCHHHHHHHHHhcCCCCCeeEccccCCcch-----hhcceEEeCCCCCCHHHHHHHHHHHHHHcCCeEE
Confidence            45555664     44444443332  344444444444443     2367889999999999977666666666799999


Q ss_pred             EEechHHHHHHHHH
Q 042424           88 YTSSLKALSNQKYR  101 (138)
Q Consensus        88 yv~P~kaLv~Q~~~  101 (138)
                      +.=|.=+.+...|+
T Consensus       218 IyD~~GeFv~~FY~  231 (732)
T PRK13700        218 IYDRSGEFVKSYYD  231 (732)
T ss_pred             EEeCCCchHHHhcC
Confidence            98888777765554

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=92.97  E-value=0.13  Score=38.77  Aligned_cols=33  Identities=18%  Similarity=0.222  Sum_probs=21.4

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      .+.++++|||||||.... ++...+....+++.+
T Consensus        26 ~~i~I~G~tGSGKTTll~-aL~~~i~~~~~~i~i   58 (186)
T cd01130          26 KNILISGGTGSGKTTLLN-ALLAFIPPDERIITI   58 (186)
T ss_pred             CEEEEECCCCCCHHHHHH-HHHhhcCCCCCEEEE
Confidence            456799999999998653 344444444555544

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.

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=92.96  E-value=0.3  Score=44.51  Aligned_cols=48  Identities=17%  Similarity=0.133  Sum_probs=38.1

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHc------CCcEEEEechHHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRD------KQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~------~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .++.+..|||||.+|+.-++..+..      ++.++++.|.+-+.+=..+.|=+
T Consensus       229 lVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~vFleYis~VLPe  282 (747)
T COG3973         229 LVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNRVFLEYISRVLPE  282 (747)
T ss_pred             EEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEcCcHHHHHHHHHhchh
Confidence            4499999999999999877777653      45599999999887766665554

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=92.94  E-value=0.32  Score=41.96  Aligned_cols=42  Identities=21%  Similarity=0.146  Sum_probs=27.1

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKALSNQK   99 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~kaLv~Q~   99 (138)
                      +.+++||+|+|||..+-.........  +.+++|+... .+.++.
T Consensus       132 ~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~~-~f~~~~  175 (440)
T PRK14088        132 PLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSE-KFLNDL  175 (440)
T ss_pred             eEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHH-HHHHHH
Confidence            45699999999998875333333332  5688887653 344444

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=92.93  E-value=0.14  Score=46.56  Aligned_cols=55  Identities=13%  Similarity=0.058  Sum_probs=45.5

Q ss_pred             CCCCceEECcCCCchHHHHHHHHHHHHHc-C---CcEEEEechHHHHHHHHHHHHHhcC
Q 042424           54 ETTHGTLTNPVYNGKTAVAEYAIAMAFRD-K---QRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~~ai~~~l~~-~---~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      ..++.+|.|..|||||.+...-+.+.+.. +   .+++.+.=|+.-+.++.+++.+.++
T Consensus        16 ~~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i~P~~IL~lTFT~kAA~em~~Rl~~~~~   74 (726)
T TIGR01073        16 TEGPLLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTNKAAREMKERVEKLLG   74 (726)
T ss_pred             CCCCEEEEeCCCCCHHHHHHHHHHHHHHcCCCCHHHeeeeeccHHHHHHHHHHHHHHhc
Confidence            34677899999999999998888888764 3   6899999999999999988887543

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

>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=92.91  E-value=0.18  Score=42.16  Aligned_cols=44  Identities=27%  Similarity=0.266  Sum_probs=33.2

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHH
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYREL  103 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l  103 (138)
                      +.+|.|+|||..++.++..+.+.+..++|+-+-.+|-...++.+
T Consensus        58 i~G~~ssGKttLaL~~ia~~q~~g~~~a~ID~e~~ld~~~a~~l  101 (322)
T PF00154_consen   58 IYGPESSGKTTLALHAIAEAQKQGGICAFIDAEHALDPEYAESL  101 (322)
T ss_dssp             EEESTTSSHHHHHHHHHHHHHHTT-EEEEEESSS---HHHHHHT
T ss_pred             EeCCCCCchhhhHHHHHHhhhcccceeEEecCcccchhhHHHhc
Confidence            99999999999999999888777888888888777765555443

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 ....

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=92.85  E-value=0.17  Score=41.12  Aligned_cols=35  Identities=11%  Similarity=0.088  Sum_probs=25.9

Q ss_pred             eEECcCCCchHHHHHHHHHHHHH------cCCcEEEEechH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFR------DKQRVIYTSSLK   93 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~------~~~rviyv~P~k   93 (138)
                      .+++|.|+|||.++...+..+..      .+.+++|+.---
T Consensus        99 ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~  139 (310)
T TIGR02236        99 EVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTEN  139 (310)
T ss_pred             EEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCC
Confidence            39999999999999866655432      134899998444

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.

>PRK10436 hypothetical protein; Provisional

Probab=92.84  E-value=0.11  Score=45.28  Aligned_cols=31  Identities=19%  Similarity=0.241  Sum_probs=20.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc-CCcEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD-KQRVI   87 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~-~~rvi   87 (138)
                      +..++++|||||||... ++++..+.+ +.+++
T Consensus       219 GliLvtGpTGSGKTTtL-~a~l~~~~~~~~~i~  250 (462)
T PRK10436        219 GLILVTGPTGSGKTVTL-YSALQTLNTAQINIC  250 (462)
T ss_pred             CeEEEECCCCCChHHHH-HHHHHhhCCCCCEEE
Confidence            34559999999999865 555555544 34443

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=92.84  E-value=0.13  Score=41.53  Aligned_cols=33  Identities=18%  Similarity=0.177  Sum_probs=21.3

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc-CCcEEEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD-KQRVIYT   89 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~-~~rviyv   89 (138)
                      +..++++|||||||.... +++..+.. +.+++.+
T Consensus        81 GlilisG~tGSGKTT~l~-all~~i~~~~~~iiti  114 (264)
T cd01129          81 GIILVTGPTGSGKTTTLY-SALSELNTPEKNIITV  114 (264)
T ss_pred             CEEEEECCCCCcHHHHHH-HHHhhhCCCCCeEEEE
Confidence            345699999999998764 34444443 4555554

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.

>PRK13721 conjugal transfer ATP-binding protein TraC; Provisional

Probab=92.78  E-value=0.14  Score=47.45  Aligned_cols=39  Identities=10%  Similarity=-0.009  Sum_probs=30.0

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLK   93 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~k   93 (138)
                      +.|.+|.|+||||||+..-..+.+.+..|.+++++=|-.
T Consensus       449 N~N~~I~G~sGsGKS~l~k~l~~~~~~~g~~viiiD~~~  487 (844)
T PRK13721        449 NYNMAVCGTSGAGKTGLIQPLIRSVLDSGGFAVVFDMGD  487 (844)
T ss_pred             cccEEEEcCCCCCHHHHHHHHHHhhhccCCEEEEEeCCC
Confidence            468899999999999988766666556677777766653

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=92.76  E-value=1  Score=38.01  Aligned_cols=56  Identities=13%  Similarity=0.152  Sum_probs=42.4

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEec--hHHHHHHHHHHHHHhcCceEEEec
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS--LKALSNQKYRELHKEFKDVGLMTG  115 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P--~kaLv~Q~~~~l~~~f~~v~~~tG  115 (138)
                      ++++-.|+|||...--...+...+|+++++.+-  +||=+-++.+.|-++.+ |.++.+
T Consensus       143 l~vGVNG~GKTTTIaKLA~~l~~~g~~VllaA~DTFRAaAiEQL~~w~er~g-v~vI~~  200 (340)
T COG0552         143 LFVGVNGVGKTTTIAKLAKYLKQQGKSVLLAAGDTFRAAAIEQLEVWGERLG-VPVISG  200 (340)
T ss_pred             EEEecCCCchHhHHHHHHHHHHHCCCeEEEEecchHHHHHHHHHHHHHHHhC-CeEEcc
Confidence            399999999999876544555567888877763  59999999999999764 444443

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=92.74  E-value=0.21  Score=46.38  Aligned_cols=42  Identities=26%  Similarity=0.207  Sum_probs=34.6

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKY  100 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~  100 (138)
                      .+.+|.|+|||..++..+..+...|.+++|+-.--++..+.+
T Consensus        64 eI~G~~GsGKTtLal~~~~~a~~~G~~v~yId~E~t~~~~~A  105 (790)
T PRK09519         64 EIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYA  105 (790)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCccchhHHHH
Confidence            399999999999999878777778899999988777764433

>TIGR00665 DnaB replicative DNA helicase

Probab=92.69  E-value=0.18  Score=42.90  Aligned_cols=34  Identities=26%  Similarity=0.171  Sum_probs=26.0

Q ss_pred             eEECcCCCchHHHHHHHHHHH-HHcCCcEEEEech
Q 042424           59 TLTNPVYNGKTAVAEYAIAMA-FRDKQRVIYTSSL   92 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~-l~~~~rviyv~P~   92 (138)
                      +|.|++|+|||..++..+.+. ...|..++|++.-
T Consensus       199 vi~g~pg~GKT~~~l~~a~~~a~~~g~~vl~~SlE  233 (434)
T TIGR00665       199 ILAARPSMGKTAFALNIAENAAIKEGKPVAFFSLE  233 (434)
T ss_pred             EEEeCCCCChHHHHHHHHHHHHHhCCCeEEEEeCc
Confidence            499999999999998555554 4468888888654

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=92.64  E-value=0.37  Score=41.85  Aligned_cols=49  Identities=12%  Similarity=0.078  Sum_probs=33.7

Q ss_pred             eEECcCCCchHHHHH-HHHHHHHHcCCcEEEEe--chHHHHHHHHHHHHHhcC
Q 042424           59 TLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTS--SLKALSNQKYRELHKEFK  108 (138)
Q Consensus        59 ~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~--P~kaLv~Q~~~~l~~~f~  108 (138)
                      .+++|+|+|||..+. +|.. ...+|.+++++.  ++++-+-++.+.+.+..+
T Consensus       104 ~lvG~~GvGKTTtaaKLA~~-l~~~G~kV~lV~~D~~R~aA~eQLk~~a~~~~  155 (429)
T TIGR01425       104 MFVGLQGSGKTTTCTKLAYY-YQRKGFKPCLVCADTFRAGAFDQLKQNATKAR  155 (429)
T ss_pred             EEECCCCCCHHHHHHHHHHH-HHHCCCCEEEEcCcccchhHHHHHHHHhhccC
Confidence            499999999998876 5543 335577876665  357666666666666543

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.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=92.56  E-value=0.16  Score=42.36  Aligned_cols=38  Identities=13%  Similarity=0.095  Sum_probs=24.7

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKA   94 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~ka   94 (138)
                      +..++++|||||||.... ++...+..  +.+++.+--..+
T Consensus       123 g~ili~G~tGSGKTT~l~-al~~~i~~~~~~~i~tiEdp~E  162 (343)
T TIGR01420       123 GLILVTGPTGSGKSTTLA-SMIDYINKNAAGHIITIEDPIE  162 (343)
T ss_pred             cEEEEECCCCCCHHHHHH-HHHHhhCcCCCCEEEEEcCChh
Confidence            456699999999998764 44444442  456666544333

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.

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=92.48  E-value=0.2  Score=37.87  Aligned_cols=43  Identities=19%  Similarity=0.271  Sum_probs=31.5

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYREL  103 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l  103 (138)
                      .++.+|+|||||..|+..+.   ..+.+++|++..+..-++..+++
T Consensus         4 ili~G~~~sGKS~~a~~l~~---~~~~~~~~iat~~~~~~e~~~ri   46 (170)
T PRK05800          4 ILVTGGARSGKSRFAERLAA---QSGLQVLYIATAQPFDDEMAARI   46 (170)
T ss_pred             EEEECCCCccHHHHHHHHHH---HcCCCcEeCcCCCCChHHHHHHH
Confidence            45999999999998874443   23567889888777666665555

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=92.34  E-value=0.19  Score=42.41  Aligned_cols=24  Identities=21%  Similarity=0.145  Sum_probs=17.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAF   80 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l   80 (138)
                      +..++++|||||||... .++...+
T Consensus       135 glilI~GpTGSGKTTtL-~aLl~~i  158 (358)
T TIGR02524       135 GIVFITGATGSGKSTLL-AAIIREL  158 (358)
T ss_pred             CEEEEECCCCCCHHHHH-HHHHHHH
Confidence            44569999999999865 4555554

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.

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=92.34  E-value=0.21  Score=42.41  Aligned_cols=32  Identities=22%  Similarity=0.252  Sum_probs=25.7

Q ss_pred             eEECcCCCchHHHHHHHHHHH-HHcCCcEEEEe
Q 042424           59 TLTNPVYNGKTAVAEYAIAMA-FRDKQRVIYTS   90 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~-l~~~~rviyv~   90 (138)
                      +|.|++|+|||..++..+.+. +.+|.+++|++
T Consensus       198 viag~pg~GKT~~al~ia~~~a~~~g~~v~~fS  230 (421)
T TIGR03600       198 VIGARPSMGKTTLALNIAENVALREGKPVLFFS  230 (421)
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEE
Confidence            499999999999998555444 46788998887

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.

>TIGR00416 sms DNA repair protein RadA

Probab=92.28  E-value=0.23  Score=43.23  Aligned_cols=43  Identities=14%  Similarity=0.117  Sum_probs=32.3

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRE  102 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~  102 (138)
                      +|.+++|+|||..++..+.....++.+++|+.--.+ .+|...+
T Consensus        98 lI~G~pGsGKTTL~lq~a~~~a~~g~kvlYvs~EEs-~~qi~~r  140 (454)
T TIGR00416        98 LIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGEES-LQQIKMR  140 (454)
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEECcCC-HHHHHHH
Confidence            499999999999998766666566789999986543 3454443

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)).

>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=92.26  E-value=0.14  Score=35.19  Aligned_cols=19  Identities=21%  Similarity=0.342  Sum_probs=15.5

Q ss_pred             eEECcCCCchHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIA   77 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~   77 (138)
                      +|+||+|||||.++-....
T Consensus         3 ~I~G~~gsGKST~a~~La~   21 (121)
T PF13207_consen    3 IISGPPGSGKSTLAKELAE   21 (121)
T ss_dssp             EEEESTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            5899999999998865443

...

>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=92.22  E-value=0.14  Score=38.92  Aligned_cols=33  Identities=21%  Similarity=0.114  Sum_probs=19.8

Q ss_pred             eEECcCCCchHHHHHHH-HHHHHHcCCcEEEEec
Q 042424           59 TLTNPVYNGKTAVAEYA-IAMAFRDKQRVIYTSS   91 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~a-i~~~l~~~~rviyv~P   91 (138)
                      +++|..|||||+.+... +..++++|++++.=+|
T Consensus         4 ~~~G~pGsGKS~~av~~~i~~~l~~gr~V~tni~   37 (193)
T PF05707_consen    4 LITGKPGSGKSYYAVSYVIIPALKKGRPVYTNIP   37 (193)
T ss_dssp             EEE--TTSSHHHHHHHHHHH-GGGS---EEE--T
T ss_pred             EEEcCCCCcHhHHHHHHHHHHHHhCCCEEEEccC
Confidence            48999999999998755 7777777777666444

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.

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=92.21  E-value=0.23  Score=48.01  Aligned_cols=61  Identities=13%  Similarity=0.127  Sum_probs=46.3

Q ss_pred             CccCCCCCCCceEECcCCCchHHHHHHHHHHHHHcC---CcEEEEechHHHHHHHHHHHHHhcC
Q 042424           48 YTLTTDETTHGTLTNPVYNGKTAVAEYAIAMAFRDK---QRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        48 y~~~~~~~~~~~l~aPTGsGKTlva~~ai~~~l~~~---~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      ++++.....+.+|+|.-|||||.+..--+.+.+..|   .++++|.=|++-+.++-.++++.+.
T Consensus         7 ~~ai~~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~~~~~il~~tFt~~aa~e~~~ri~~~l~   70 (1232)
T TIGR02785         7 WQAIYTRGQNILVSASAGSGKTAVLVERIIKKILRGVDIDRLLVVTFTNAAAREMKERIEEALQ   70 (1232)
T ss_pred             HHHHhCCCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCHhhEEEEeccHHHHHHHHHHHHHHHH
Confidence            344444456788999999999999876555555544   4699999999999998888887553

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.

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=92.21  E-value=0.18  Score=43.12  Aligned_cols=56  Identities=20%  Similarity=0.083  Sum_probs=40.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcCceEEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLM  113 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~  113 (138)
                      .+.++.||||||||.......  .+..+..+|++=|--.|....+..+++...+|-++
T Consensus        45 ~h~lvig~tgSGKt~~~viP~--ll~~~~s~iV~D~KgEl~~~t~~~r~~~G~~V~vl  100 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPN--LLNYPGSMIVTDPKGELYEKTAGYRKKRGYKVYVL  100 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhH--HHhccCCEEEEECCCcHHHHHHHHHHHCCCEEEEe
Confidence            367899999999998765432  24455688999999999887777666643355554

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

>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional

Probab=92.15  E-value=0.11  Score=43.13  Aligned_cols=15  Identities=20%  Similarity=0.246  Sum_probs=13.4

Q ss_pred             eEECcCCCchHHHHH
Q 042424           59 TLTNPVYNGKTAVAE   73 (138)
Q Consensus        59 ~l~aPTGsGKTlva~   73 (138)
                      +|++|||||||-.|+
T Consensus         8 ~I~GpTasGKS~LAl   22 (300)
T PRK14729          8 FIFGPTAVGKSNILF   22 (300)
T ss_pred             EEECCCccCHHHHHH
Confidence            499999999998876

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=91.99  E-value=0.14  Score=44.95  Aligned_cols=31  Identities=23%  Similarity=0.330  Sum_probs=20.4

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHc-CCcEEEE
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRD-KQRVIYT   89 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~-~~rviyv   89 (138)
                      .++++|||||||... ++++..+.. +.+++.+
T Consensus       245 ilitGptGSGKTTtL-~a~L~~l~~~~~~iiTi  276 (486)
T TIGR02533       245 ILVTGPTGSGKTTTL-YAALSRLNTPERNILTV  276 (486)
T ss_pred             EEEEcCCCCCHHHHH-HHHHhccCCCCCcEEEE
Confidence            459999999999876 444454543 4455444

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.

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=91.91  E-value=0.22  Score=39.91  Aligned_cols=49  Identities=14%  Similarity=0.209  Sum_probs=34.1

Q ss_pred             EECcCCCchHHHHHHHHHHHH-H-----cCCcEEEEechHHHHHHHHHHHHHhcC
Q 042424           60 LTNPVYNGKTAVAEYAIAMAF-R-----DKQRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l-~-----~~~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      +++|.|+|||-+++.....+. .     .+.+++|+--.-...-+...++.+.|+
T Consensus        43 i~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~~i~~~~~   97 (256)
T PF08423_consen   43 IVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQQIAERFG   97 (256)
T ss_dssp             EEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHHHHHHHTT
T ss_pred             EEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHHHHhhccc
Confidence            999999999999985444432 2     157899997666666666666666553

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain

Probab=91.88  E-value=0.42  Score=30.51  Aligned_cols=32  Identities=25%  Similarity=0.211  Sum_probs=22.8

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      ++++..|+|||.++...+....+.|.+++++-
T Consensus         3 ~~~g~~G~Gktt~~~~l~~~l~~~g~~v~~~~   34 (99)
T cd01983           3 VVTGKGGVGKTTLAANLAAALAKRGKRVLLID   34 (99)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCeEEEEC
Confidence            36777799999998755444434577877765

Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=91.83  E-value=0.26  Score=41.91  Aligned_cols=33  Identities=15%  Similarity=0.248  Sum_probs=21.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYT   89 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv   89 (138)
                      +..++++|||||||... .++...+..   +.+++.+
T Consensus       150 GlilI~G~TGSGKTT~l-~al~~~i~~~~~~~~Ivti  185 (372)
T TIGR02525       150 GLGLICGETGSGKSTLA-ASIYQHCGETYPDRKIVTY  185 (372)
T ss_pred             CEEEEECCCCCCHHHHH-HHHHHHHHhcCCCceEEEE
Confidence            45669999999999875 455555432   3455444

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).

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=91.83  E-value=0.45  Score=41.10  Aligned_cols=56  Identities=18%  Similarity=0.203  Sum_probs=37.2

Q ss_pred             CceEECcCCCchHHHHH-HHHHHHHHc-CCcE-EEEe-chHHHHHHHHHHHHHhcC-ceEE
Q 042424           57 HGTLTNPVYNGKTAVAE-YAIAMAFRD-KQRV-IYTS-SLKALSNQKYRELHKEFK-DVGL  112 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~-~ai~~~l~~-~~rv-iyv~-P~kaLv~Q~~~~l~~~f~-~v~~  112 (138)
                      -.++.||||.|||..-. +|....+.. ++++ |+.. .+|.=+.++.+.+.+.++ .+.+
T Consensus       205 vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA~EQLk~Ya~im~vp~~v  265 (407)
T COG1419         205 VIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQLKTYADIMGVPLEV  265 (407)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhHHHHHHHHHHHhCCceEE
Confidence            34599999999998765 666555333 3443 3333 457778888888888776 4433

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=91.76  E-value=0.28  Score=41.61  Aligned_cols=35  Identities=17%  Similarity=0.135  Sum_probs=27.8

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLK   93 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~k   93 (138)
                      ++.+++|+|||..++..+......+.+++|+.-..
T Consensus        86 LI~G~pG~GKStLllq~a~~~a~~g~~VlYvs~EE  120 (372)
T cd01121          86 LIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSGEE  120 (372)
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEECCc
Confidence            49999999999999866655556678999987643

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.

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=91.75  E-value=0.27  Score=40.40  Aligned_cols=47  Identities=21%  Similarity=0.306  Sum_probs=40.4

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHh
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKE  106 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~  106 (138)
                      +.+|-|||||.+++.++..+...|.+++|+--.-+|--+..+.+...
T Consensus        65 iyG~~gsGKT~lal~~~~~aq~~g~~a~fIDtE~~l~p~r~~~l~~~  111 (279)
T COG0468          65 IYGPESSGKTTLALQLVANAQKPGGKAAFIDTEHALDPERAKQLGVD  111 (279)
T ss_pred             EecCCCcchhhHHHHHHHHhhcCCCeEEEEeCCCCCCHHHHHHHHHh
Confidence            99999999999999999999888999999988777776666666654

>PRK08506 replicative DNA helicase; Provisional

Probab=91.74  E-value=0.28  Score=42.80  Aligned_cols=44  Identities=16%  Similarity=0.096  Sum_probs=32.2

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYREL  103 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l  103 (138)
                      +|.|.+|.|||..++..+.++..+|.+++|++.- -=.+|...++
T Consensus       196 vIaarpg~GKT~fal~ia~~~~~~g~~V~~fSlE-Ms~~ql~~Rl  239 (472)
T PRK08506        196 IIAARPSMGKTTLCLNMALKALNQDKGVAFFSLE-MPAEQLMLRM  239 (472)
T ss_pred             EEEcCCCCChHHHHHHHHHHHHhcCCcEEEEeCc-CCHHHHHHHH
Confidence            4999999999999987777777778888888654 2334444444

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=91.69  E-value=0.17  Score=41.43  Aligned_cols=34  Identities=15%  Similarity=0.218  Sum_probs=21.8

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      ..+.++++|||||||.... ++...+....+++.+
T Consensus       144 ~~~ili~G~tGsGKTTll~-al~~~~~~~~~iv~i  177 (308)
T TIGR02788       144 RKNIIISGGTGSGKTTFLK-SLVDEIPKDERIITI  177 (308)
T ss_pred             CCEEEEECCCCCCHHHHHH-HHHccCCccccEEEE
Confidence            3577799999999998753 333333334455544

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.

>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=91.67  E-value=0.25  Score=37.34  Aligned_cols=40  Identities=23%  Similarity=0.200  Sum_probs=24.9

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEechHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLKALSN   97 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~kaLv~   97 (138)
                      +.++.+|||+|||.++... .+.+. .+.+-++.+-...+..
T Consensus         5 ~~ll~GpsGvGKT~la~~l-a~~l~~~~~~~~~~~d~s~~~~   45 (171)
T PF07724_consen    5 NFLLAGPSGVGKTELAKAL-AELLFVGSERPLIRIDMSEYSE   45 (171)
T ss_dssp             EEEEESSTTSSHHHHHHHH-HHHHT-SSCCEEEEEEGGGHCS
T ss_pred             EEEEECCCCCCHHHHHHHH-HHHhccCCccchHHHhhhcccc
Confidence            4569999999999877532 23344 4455555555444443

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 ....

>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=91.62  E-value=0.37  Score=36.34  Aligned_cols=17  Identities=29%  Similarity=0.384  Sum_probs=14.3

Q ss_pred             eEECcCCCchHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~a   75 (138)
                      .++|++|||||..+...
T Consensus         3 ~i~G~sgsGKttla~~l   19 (179)
T cd02028           3 GIAGPSGSGKTTFAKKL   19 (179)
T ss_pred             EEECCCCCCHHHHHHHH
Confidence            48999999999998633

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PRK05595 replicative DNA helicase; Provisional

Probab=91.61  E-value=0.29  Score=42.12  Aligned_cols=34  Identities=24%  Similarity=0.133  Sum_probs=26.7

Q ss_pred             eEECcCCCchHHHHHHHHHH-HHHcCCcEEEEech
Q 042424           59 TLTNPVYNGKTAVAEYAIAM-AFRDKQRVIYTSSL   92 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~-~l~~~~rviyv~P~   92 (138)
                      +|.|.+|.|||..++..+.+ ++++|.+++|++.-
T Consensus       205 viaarpg~GKT~~al~ia~~~a~~~g~~vl~fSlE  239 (444)
T PRK05595        205 LIAARPSMGKTTFALNIAEYAALREGKSVAIFSLE  239 (444)
T ss_pred             EEEecCCCChHHHHHHHHHHHHHHcCCcEEEEecC
Confidence            48999999999999854443 55678899888664

>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=91.47  E-value=0.19  Score=34.32  Aligned_cols=20  Identities=20%  Similarity=0.157  Sum_probs=15.7

Q ss_pred             eEECcCCCchHHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAM   78 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~   78 (138)
                      .|+|++|||||.++.....+
T Consensus         2 ~i~G~~GsGKtTia~~L~~~   21 (129)
T PF13238_consen    2 GISGIPGSGKTTIAKELAER   21 (129)
T ss_dssp             EEEESTTSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            48999999999999644433

...

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

Probab=91.43  E-value=0.39  Score=46.20  Aligned_cols=57  Identities=19%  Similarity=0.181  Sum_probs=47.6

Q ss_pred             HHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCCcCC-----------CCCCEEEecH
Q 042424           74 YAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVTLS-----------PNASCLVMTT  130 (138)
Q Consensus        74 ~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~~~-----------~~~~IiVtTp  130 (138)
                      -||++-+.+|+++.||.|..+-++++.+++++...  +|++.+|....+           .+.+|+|||.
T Consensus       794 eAI~REl~RgGQvfYv~NrV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TT  863 (1139)
T COG1197         794 EAILRELLRGGQVFYVHNRVESIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTT  863 (1139)
T ss_pred             HHHHHHHhcCCEEEEEecchhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEee
Confidence            46666667799999999999999999999999765  789989877542           3899999995

>PRK13768 GTPase; Provisional

Probab=91.38  E-value=0.34  Score=38.63  Aligned_cols=31  Identities=13%  Similarity=0.013  Sum_probs=22.0

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      ++.+|.|+|||..+..........|.+++++
T Consensus         6 ~v~G~~G~GKTt~~~~~~~~l~~~g~~v~~i   36 (253)
T PRK13768          6 FFLGTAGSGKTTLTKALSDWLEEQGYDVAIV   36 (253)
T ss_pred             EEECCCCccHHHHHHHHHHHHHhcCCceEEE
Confidence            4899999999998864333333457777665

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=91.37  E-value=0.34  Score=39.89  Aligned_cols=41  Identities=22%  Similarity=0.195  Sum_probs=29.2

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALS   96 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv   96 (138)
                      .+.+|.|+.|+|||..-..++..|+.+|--++||---..++
T Consensus        24 ~r~vL~G~~GsGKS~~L~q~~~~A~~~~wiVl~vp~a~~~~   64 (309)
T PF10236_consen   24 NRYVLTGERGSGKSVLLAQAVHYARENGWIVLYVPSAQDWV   64 (309)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhCCEEEEEcCCHHHHh
Confidence            45569999999999998899988877644444443334443

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=91.37  E-value=0.41  Score=40.34  Aligned_cols=41  Identities=24%  Similarity=0.267  Sum_probs=27.9

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHc--CCcEEE-------E-echHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIY-------T-SSLKALSNQK   99 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~--~~rviy-------v-~P~kaLv~Q~   99 (138)
                      .++++|||||||.. +.+|...+++  ...+|-       + -..++|++|.
T Consensus       128 ILVTGpTGSGKSTT-lAamId~iN~~~~~HIlTIEDPIE~vh~skkslI~QR  178 (353)
T COG2805         128 ILVTGPTGSGKSTT-LAAMIDYINKHKAKHILTIEDPIEYVHESKKSLINQR  178 (353)
T ss_pred             EEEeCCCCCcHHHH-HHHHHHHHhccCCcceEEecCchHhhhcchHhhhhHH
Confidence            34999999999865 4567777765  334432       2 3458888886

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=91.36  E-value=0.32  Score=39.85  Aligned_cols=34  Identities=12%  Similarity=0.132  Sum_probs=25.6

Q ss_pred             EECcCCCchHHHHHHHHHHHHHc------CCcEEEEechH
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRD------KQRVIYTSSLK   93 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~------~~rviyv~P~k   93 (138)
                      |++|+|+|||..+...+..+...      +.+++|+.---
T Consensus       107 i~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~  146 (317)
T PRK04301        107 FYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEG  146 (317)
T ss_pred             EECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCC
Confidence            99999999999998666655432      35788887543

>PHA02542 41 41 helicase; Provisional

Probab=91.24  E-value=0.33  Score=42.49  Aligned_cols=32  Identities=25%  Similarity=0.148  Sum_probs=26.1

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      ++.|++|.|||.+++..+.++...|.+++|++
T Consensus       194 iIaarPgmGKTtfalniA~~~a~~g~~Vl~fS  225 (473)
T PHA02542        194 VLLAGVNVGKSLGLCSLAADYLQQGYNVLYIS  225 (473)
T ss_pred             EEEcCCCccHHHHHHHHHHHHHhcCCcEEEEe
Confidence            48999999999999865555556788888876

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=91.10  E-value=0.24  Score=41.19  Aligned_cols=40  Identities=18%  Similarity=0.187  Sum_probs=24.5

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHH---HcCCcEEEEechHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAF---RDKQRVIYTSSLKAL   95 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l---~~~~rviyv~P~kaL   95 (138)
                      ..+.++++|||||||.... ++...+   ....|++.+=.+.+|
T Consensus       148 ~~~ilI~G~tGSGKTTll~-aL~~~~~~~~~~~rivtIEd~~El  190 (319)
T PRK13894        148 HRNILVIGGTGSGKTTLVN-AIINEMVIQDPTERVFIIEDTGEI  190 (319)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHhhhhcCCCceEEEEcCCCcc
Confidence            3677899999999996653 343332   224555554444433

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=91.05  E-value=0.35  Score=40.09  Aligned_cols=48  Identities=17%  Similarity=0.282  Sum_probs=31.2

Q ss_pred             EECcCCCchHHHHHHHHHHH-HH-----cCCcEEEEechHHHHHHHHHHHHHhc
Q 042424           60 LTNPVYNGKTAVAEYAIAMA-FR-----DKQRVIYTSSLKALSNQKYRELHKEF  107 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~-l~-----~~~rviyv~P~kaLv~Q~~~~l~~~f  107 (138)
                      +++|.|+|||.+++..+..+ +.     .+.+++|+.---++--+...++.+.|
T Consensus       101 I~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~~~a~~~  154 (313)
T TIGR02238       101 VFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRAIAERF  154 (313)
T ss_pred             EECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHHHHHHHc
Confidence            99999999999997544333 22     25789999865554434444444434

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.

>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=90.99  E-value=0.7  Score=36.05  Aligned_cols=33  Identities=36%  Similarity=0.329  Sum_probs=23.2

Q ss_pred             eEECcCCCchHHHHHHHHHHHHH---cCCcEEEEech
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFR---DKQRVIYTSSL   92 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~---~~~rviyv~P~   92 (138)
                      .|.+|+|+|||.. +.|+...+.   .+.+++|+...
T Consensus        38 ~l~G~~G~GKTHL-L~Ai~~~~~~~~~~~~v~y~~~~   73 (219)
T PF00308_consen   38 FLYGPSGLGKTHL-LQAIANEAQKQHPGKRVVYLSAE   73 (219)
T ss_dssp             EEEESTTSSHHHH-HHHHHHHHHHHCTTS-EEEEEHH
T ss_pred             EEECCCCCCHHHH-HHHHHHHHHhccccccceeecHH
Confidence            5999999999995 455555543   26788888653

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.

>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=90.98  E-value=0.44  Score=36.08  Aligned_cols=26  Identities=12%  Similarity=0.075  Sum_probs=18.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFR   81 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~   81 (138)
                      .+.++.+.||||||.+....+...+.
T Consensus        39 ~h~li~G~tgsGKS~~l~~ll~~l~~   64 (205)
T PF01580_consen   39 PHLLIAGATGSGKSTLLRTLLLSLAL   64 (205)
T ss_dssp             -SEEEE--TTSSHHHHHHHHHHHHHT
T ss_pred             ceEEEEcCCCCCccHHHHHHHHHHHH
Confidence            57889999999999987655555554

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.

>PF05729 NACHT: NACHT domain

Probab=90.90  E-value=0.48  Score=33.59  Aligned_cols=40  Identities=13%  Similarity=0.111  Sum_probs=25.3

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcC-----CcEEEEechHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDK-----QRVIYTSSLKALSNQ   98 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~-----~rviyv~P~kaLv~Q   98 (138)
                      +|.|+.|+|||.++...+......+     ..+++....+.+..+
T Consensus         4 ~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   48 (166)
T PF05729_consen    4 WISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDS   48 (166)
T ss_pred             EEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhc
Confidence            5999999999998865554443332     135555555555443

>PRK05748 replicative DNA helicase; Provisional

Probab=90.83  E-value=0.35  Score=41.54  Aligned_cols=46  Identities=15%  Similarity=-0.051  Sum_probs=31.0

Q ss_pred             ceEECcCCCchHHHHHHHHHHH-HHcCCcEEEEechHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMA-FRDKQRVIYTSSLKALSNQKYRELH  104 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~-l~~~~rviyv~P~kaLv~Q~~~~l~  104 (138)
                      .+|.|++|.|||..++..+.+. .+.|..++|++.- --.+|..+++.
T Consensus       206 ivIaarpg~GKT~~al~ia~~~a~~~g~~v~~fSlE-ms~~~l~~R~l  252 (448)
T PRK05748        206 IIVAARPSVGKTAFALNIAQNVATKTDKNVAIFSLE-MGAESLVMRML  252 (448)
T ss_pred             EEEEeCCCCCchHHHHHHHHHHHHhCCCeEEEEeCC-CCHHHHHHHHH
Confidence            3499999999999998655554 3558888877543 23344444443

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]

Probab=90.75  E-value=1.2  Score=41.78  Aligned_cols=79  Identities=15%  Similarity=0.110  Sum_probs=56.6

Q ss_pred             CCceEECcCCCchHHHHH--HHHHHHHHc-CCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCCcCC----------
Q 042424           56 THGTLTNPVYNGKTAVAE--YAIAMAFRD-KQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVTLS----------  120 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~--~ai~~~l~~-~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~~~----------  120 (138)
                      -|.++.=--|-|||+-..  ++.+...+. .+.-++++|.-.|. .+.++|++...  ++.++.||....          
T Consensus       187 ingILaDEMGLGKTlQtIs~l~yl~~~~~~~GPfLVi~P~StL~-NW~~Ef~rf~P~l~~~~~~Gdk~eR~~~~r~~~~~  265 (971)
T KOG0385|consen  187 INGILADEMGLGKTLQTISLLGYLKGRKGIPGPFLVIAPKSTLD-NWMNEFKRFTPSLNVVVYHGDKEERAALRRDIMLP  265 (971)
T ss_pred             cccEeehhcccchHHHHHHHHHHHHHhcCCCCCeEEEeeHhhHH-HHHHHHHHhCCCcceEEEeCCHHHHHHHHHHhhcc
Confidence            367788889999998664  343333222 47789999997664 57788888443  678888986432          


Q ss_pred             CCCCEEEecHHHHHH
Q 042424          121 PNASCLVMTTEILRG  135 (138)
Q Consensus       121 ~~~~IiVtTpe~l~~  135 (138)
                      ...+|+|||+|+...
T Consensus       266 ~~fdV~iTsYEi~i~  280 (971)
T KOG0385|consen  266 GRFDVCITSYEIAIK  280 (971)
T ss_pred             CCCceEeehHHHHHh
Confidence            178999999998753

>cd02034 CooC The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH)

Probab=90.69  E-value=0.59  Score=33.08  Aligned_cols=32  Identities=19%  Similarity=0.081  Sum_probs=22.4

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      .++++..|+|||.++........+++.+++++
T Consensus         2 i~~~GkgG~GKTt~a~~la~~l~~~g~~V~~i   33 (116)
T cd02034           2 IAITGKGGVGKTTIAALLARYLAEKGKPVLAI   33 (116)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            35899999999999875544443456776544

CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=90.69  E-value=0.7  Score=41.46  Aligned_cols=50  Identities=16%  Similarity=0.171  Sum_probs=29.3

Q ss_pred             CCceEECcCCCchHHHHH-HHHHHHHHc-CCcEEEEe--chHHHHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAE-YAIAMAFRD-KQRVIYTS--SLKALSNQKYRELHK  105 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~-~ai~~~l~~-~~rviyv~--P~kaLv~Q~~~~l~~  105 (138)
                      +..++++|||+|||..+. ++....... ++++.++.  +++.-+.++.+.+.+
T Consensus       351 ~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtDtyRigA~EQLk~ya~  404 (559)
T PRK12727        351 GVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHSYGR  404 (559)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEecccccccHHHHHHHhhc
Confidence            344599999999998885 444333333 45565543  345545454444444

>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=90.68  E-value=0.4  Score=38.57  Aligned_cols=35  Identities=14%  Similarity=0.215  Sum_probs=22.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC-CcEEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK-QRVIYTSS   91 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~-~rviyv~P   91 (138)
                      -+.++.|++|||||......+.. +.+. ..+++++|
T Consensus        14 fr~viIG~sGSGKT~li~~lL~~-~~~~f~~I~l~t~   49 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTTLIKSLLYY-LRHKFDHIFLITP   49 (241)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHh-hcccCCEEEEEec
Confidence            36679999999999877655543 3333 34444445

This is thought to be an ATPase involved in viral DNA packaging [].

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=90.60  E-value=0.86  Score=38.19  Aligned_cols=50  Identities=8%  Similarity=0.140  Sum_probs=37.7

Q ss_pred             ceEECcCCCchHHHHH-HHHHHHHH--cCCcEEEEechHH-HHHHHHHHHHHhc
Q 042424           58 GTLTNPVYNGKTAVAE-YAIAMAFR--DKQRVIYTSSLKA-LSNQKYRELHKEF  107 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~-~ai~~~l~--~~~rviyv~P~ka-Lv~Q~~~~l~~~f  107 (138)
                      .++.+..|||||.++. ..+..++.  .+.+++++-++.. |-+-.+.++.+.+
T Consensus         4 ~i~~GgrgSGKS~~~~~~~~~~~~~~~~~~~~~~~r~~~~sl~~sv~~~l~~~i   57 (396)
T TIGR01547         4 IIAKGGRRSGKTFAIALKLVEKLAINKKQQNILAARKVQNSIRDSVFKDIENLL   57 (396)
T ss_pred             EEEeCCCCcccHHHHHHHHHHHHHhcCCCcEEEEEehhhhHHHHHHHHHHHHHH
Confidence            3588999999999986 45555566  5788999999855 6666777777543

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.

>cd03114 ArgK-like The function of this protein family is unkown

Probab=90.46  E-value=0.52  Score=34.59  Aligned_cols=30  Identities=20%  Similarity=0.159  Sum_probs=19.4

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIY   88 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviy   88 (138)
                      .++++.|+|||..+..........|.++++
T Consensus         3 ~~~G~~GsGKTt~~~~l~~~~~~~g~~v~i   32 (148)
T cd03114           3 GITGVPGAGKSTLIDALITALRARGKRVAV   32 (148)
T ss_pred             EEECCCCCcHHHHHHHHHHHHHHCCCEEEE
Confidence            478999999999876444333334554433

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.

>COG0378 HypB Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]

Probab=90.40  E-value=0.43  Score=37.56  Aligned_cols=57  Identities=21%  Similarity=0.299  Sum_probs=34.5

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCCc
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVT  118 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~  118 (138)
                      +.+|.|||||.+.+..+.. +++..++.++.- --+.++-++.+++..+  -+++.||+..
T Consensus        18 v~Gp~GSGKTaLie~~~~~-L~~~~~~aVI~~-Di~t~~Da~~l~~~~g~~i~~v~TG~~C   76 (202)
T COG0378          18 VGGPPGSGKTALIEKTLRA-LKDEYKIAVITG-DIYTKEDADRLRKLPGEPIIGVETGKGC   76 (202)
T ss_pred             ecCCCCcCHHHHHHHHHHH-HHhhCCeEEEec-eeechhhHHHHHhCCCCeeEEeccCCcc
Confidence            8999999999887766654 344444444332 2233344555555344  4678888544

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=90.33  E-value=0.26  Score=41.23  Aligned_cols=53  Identities=9%  Similarity=-0.066  Sum_probs=38.0

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEE
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLM  113 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~  113 (138)
                      .++.||||||||......  ..+..+..+|++=|--++.+.....+++ .+ .|-++
T Consensus         2 ~lv~g~tGsGKt~~~viP--~ll~~~~s~vv~D~Kge~~~~t~~~r~~-~G~~V~v~   55 (384)
T cd01126           2 VLVFAPTRSGKGVGFVIP--NLLTWPGSVVVLDPKGENFELTSEHRRA-LGRKVFVF   55 (384)
T ss_pred             eeEecCCCCCCccEEEcc--chhcCCCCEEEEccchhHHHHHHHHHHH-cCCeEEEE
Confidence            469999999999865422  2234468899999999998877766655 44 55555

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.

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]

Probab=90.33  E-value=1.7  Score=40.69  Aligned_cols=80  Identities=16%  Similarity=0.154  Sum_probs=55.5

Q ss_pred             CCCceEECcCCCchHHHH--HHHHHHHH-HcCCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCCc-----------
Q 042424           55 TTHGTLTNPVYNGKTAVA--EYAIAMAF-RDKQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVT-----------  118 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva--~~ai~~~l-~~~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~-----------  118 (138)
                      ....+|.=.-|-|||.-.  +++.++.- +--+.+|+|+|. +|+.|+.++|+..|.  .|.+++|...           
T Consensus       224 ~~GGILgDeMGLGKTIQiisFLaaL~~S~k~~~paLIVCP~-Tii~qW~~E~~~w~p~~rv~ilh~t~s~~r~~~~~~~~  302 (923)
T KOG0387|consen  224 RAGGILGDEMGLGKTIQIISFLAALHHSGKLTKPALIVCPA-TIIHQWMKEFQTWWPPFRVFILHGTGSGARYDASHSSH  302 (923)
T ss_pred             cCCCeecccccCccchhHHHHHHHHhhcccccCceEEEccH-HHHHHHHHHHHHhCcceEEEEEecCCcccccccchhhh
Confidence            345678788999999643  33333221 113789999998 688999999999776  6777765322           


Q ss_pred             ---------CCCCCCEEEecHHHHHH
Q 042424          119 ---------LSPNASCLVMTTEILRG  135 (138)
Q Consensus       119 ---------~~~~~~IiVtTpe~l~~  135 (138)
                               ...+..|+|||++.|.-
T Consensus       303 ~~~~~L~r~~~~~~~ilitty~~~r~  328 (923)
T KOG0387|consen  303 KKDKLLIRKVATDGGILITTYDGFRI  328 (923)
T ss_pred             hhhhhheeeecccCcEEEEehhhhcc
Confidence                     01277899999998754

>PHA00729 NTP-binding motif containing protein

Probab=90.31  E-value=0.9  Score=36.25  Aligned_cols=48  Identities=15%  Similarity=0.056  Sum_probs=31.1

Q ss_pred             CceEECcCCCchHHHHHHHHHHHH-------------HcCCcEEEEechHHHHHHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAF-------------RDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l-------------~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      +.+++|++|+|||.+|........             ..+ +-.+++...+|.++....+.+
T Consensus        19 nIlItG~pGvGKT~LA~aLa~~l~~~l~~l~~~~~~~d~~-~~~~fid~~~Ll~~L~~a~~~   79 (226)
T PHA00729         19 SAVIFGKQGSGKTTYALKVARDVFWKLNNLSTKDDAWQYV-QNSYFFELPDALEKIQDAIDN   79 (226)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhhcccccchhhHHhcC-CcEEEEEHHHHHHHHHHHHhc
Confidence            667999999999998864333321             223 345556777777777655443

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=90.24  E-value=0.71  Score=43.68  Aligned_cols=56  Identities=20%  Similarity=0.200  Sum_probs=45.6

Q ss_pred             HHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCCcCC-----------CCCCEEEecH
Q 042424           75 AIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVTLS-----------PNASCLVMTT  130 (138)
Q Consensus        75 ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~~~-----------~~~~IiVtTp  130 (138)
                      ++...+.+++++++++|++.=++..++.|++.+.  .|+.++|+....           .+.+|+|||.
T Consensus       652 ~i~~el~~g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~  720 (926)
T TIGR00580       652 AIRRELLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTT  720 (926)
T ss_pred             HHHHHHHcCCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECC
Confidence            4555566789999999999999999999998664  789999987542           2789999996

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.

>PRK13830 conjugal transfer protein TrbE; Provisional

Probab=90.21  E-value=0.3  Score=45.34  Aligned_cols=37  Identities=16%  Similarity=0.179  Sum_probs=26.3

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEec
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSS   91 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P   91 (138)
                      .++.+|++|||+|||....+.+.+.++ .+.+++++=+
T Consensus       456 ~g~~~i~G~tGsGKS~l~~~l~~~~~~~~~~~v~~~D~  493 (818)
T PRK13830        456 VGHTLIFGPTGSGKSTLLALIAAQFRRYAGAQIFAFDK  493 (818)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcccccCCCEEEEECC
Confidence            367889999999999988755555444 3556655544

>PRK05541 adenylylsulfate kinase; Provisional

Probab=90.17  E-value=0.59  Score=34.52  Aligned_cols=31  Identities=26%  Similarity=0.183  Sum_probs=20.0

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      +++++.|||||.++.......-..+..++++
T Consensus        11 ~i~G~~GsGKst~a~~l~~~l~~~~~~~~~~   41 (176)
T PRK05541         11 WITGLAGSGKTTIAKALYERLKLKYSNVIYL   41 (176)
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHHcCCcEEEE
Confidence            4999999999999854433322234444444

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=90.15  E-value=0.48  Score=35.70  Aligned_cols=16  Identities=38%  Similarity=0.347  Sum_probs=13.8

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      .|+||+|||||.++..
T Consensus         3 gi~G~~GsGKSTl~~~   18 (198)
T cd02023           3 GIAGGSGSGKTTVAEE   18 (198)
T ss_pred             EEECCCCCCHHHHHHH
Confidence            4899999999998853

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>PF13476 AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V_A 3QG5_B 3QF7_A 3THO_A

Probab=90.00  E-value=0.32  Score=35.71  Aligned_cols=22  Identities=27%  Similarity=0.381  Sum_probs=16.5

Q ss_pred             ceEECcCCCchHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAF   80 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l   80 (138)
                      .+++||+|+|||.+. -||..++
T Consensus        22 ~vi~G~Ng~GKStil-~ai~~~L   43 (202)
T PF13476_consen   22 NVIYGPNGSGKSTIL-EAIRYAL   43 (202)
T ss_dssp             EEEEESTTSSHHHHH-HHHHHHH
T ss_pred             EEEECCCCCCHHHHH-HHHHHHH
Confidence            459999999999887 3444444

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=89.97  E-value=0.79  Score=44.16  Aligned_cols=54  Identities=13%  Similarity=0.119  Sum_probs=44.9

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcC-----CcEEEEechHHHHHHHHHHHHHhcC
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDK-----QRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~-----~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      ..+.+|.|-.|||||.+-..-+++.+..+     .++++|.-|++=+.++..++.+.+.
T Consensus        16 ~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~~v~~ILvvTFT~aAa~Emk~RI~~~L~   74 (1139)
T COG1074          16 GQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRDRLK   74 (1139)
T ss_pred             CCcEEEEEcCCCCchhHHHHHHHHHHhhcCCCChhHeeeeeccHHHHHHHHHHHHHHHH
Confidence            45778999999999999876666666552     4799999999999999999988765

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]

Probab=89.92  E-value=0.54  Score=43.90  Aligned_cols=77  Identities=18%  Similarity=0.123  Sum_probs=53.6

Q ss_pred             CCceEECcCCCchHHHH--HHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCCcCC-----------
Q 042424           56 THGTLTNPVYNGKTAVA--EYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVTLS-----------  120 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva--~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~~~-----------  120 (138)
                      -+++|.=--|-|||.-+  ++|.+..+...+.=++|||.-.| +.+.++|++.+.  .|-.+.|.+...           
T Consensus       419 l~gILADEMGLGKTiQvIaFlayLkq~g~~gpHLVVvPsSTl-eNWlrEf~kwCPsl~Ve~YyGSq~ER~~lR~~i~~~~  497 (941)
T KOG0389|consen  419 LNGILADEMGLGKTIQVIAFLAYLKQIGNPGPHLVVVPSSTL-ENWLREFAKWCPSLKVEPYYGSQDERRELRERIKKNK  497 (941)
T ss_pred             ccceehhhccCcchhHHHHHHHHHHHcCCCCCcEEEecchhH-HHHHHHHHHhCCceEEEeccCcHHHHHHHHHHHhccC
Confidence            35677777999999644  45554433334667899999555 668899999666  566677765321           


Q ss_pred             CCCCEEEecHHHH
Q 042424          121 PNASCLVMTTEIL  133 (138)
Q Consensus       121 ~~~~IiVtTpe~l  133 (138)
                      .+.+|+|||+..+
T Consensus       498 ~~ydVllTTY~la  510 (941)
T KOG0389|consen  498 DDYDVLLTTYNLA  510 (941)
T ss_pred             CCccEEEEEeecc
Confidence            2789999998654

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

Probab=89.84  E-value=0.78  Score=41.98  Aligned_cols=57  Identities=23%  Similarity=0.295  Sum_probs=44.2

Q ss_pred             HHHHHHHcCCcEEEEechHH--------HHHHHHHHHHHhcC--ceEEEecCCcCCC-----------CCCEEEecHH
Q 042424           75 AIAMAFRDKQRVIYTSSLKA--------LSNQKYRELHKEFK--DVGLMTGDVTLSP-----------NASCLVMTTE  131 (138)
Q Consensus        75 ai~~~l~~~~rviyv~P~ka--------Lv~Q~~~~l~~~f~--~v~~~tGd~~~~~-----------~~~IiVtTpe  131 (138)
                      .|...+.+|.++.+|+|..+        -+.+.+.+++..|.  .||+++|-.+.+.           ..+|+|+|..
T Consensus       465 ~i~~ei~~GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaTTV  542 (677)
T COG1200         465 RIREEIAKGRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTV  542 (677)
T ss_pred             HHHHHHHcCCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcCCCcEEEEeeE
Confidence            55566678999999999964        56678888887676  6999999776432           6789999964

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=89.82  E-value=1.2  Score=36.99  Aligned_cols=34  Identities=18%  Similarity=0.105  Sum_probs=24.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc--CCcEEEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYT   89 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv   89 (138)
                      .+.+|+||+|+|||.+....+.+.-..  +..++|+
T Consensus        56 ~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~i   91 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYI   91 (394)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEE
Confidence            456799999999999887766654333  3556666

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=89.80  E-value=0.8  Score=37.16  Aligned_cols=18  Identities=39%  Similarity=0.313  Sum_probs=15.5

Q ss_pred             CceEECcCCCchHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~   74 (138)
                      +.++.+|+|+|||.+|..
T Consensus        60 ~vll~G~pGTGKT~lA~~   77 (284)
T TIGR02880        60 HMSFTGNPGTGKTTVALR   77 (284)
T ss_pred             eEEEEcCCCCCHHHHHHH
Confidence            567999999999999853

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.

>PTZ00301 uridine kinase; Provisional

Probab=89.71  E-value=0.62  Score=36.39  Aligned_cols=16  Identities=13%  Similarity=0.291  Sum_probs=13.9

Q ss_pred             EECcCCCchHHHHHHH
Q 042424           60 LTNPVYNGKTAVAEYA   75 (138)
Q Consensus        60 l~aPTGsGKTlva~~a   75 (138)
                      |+||+|||||.+|...
T Consensus         8 IaG~SgSGKTTla~~l   23 (210)
T PTZ00301          8 ISGASGSGKSSLSTNI   23 (210)
T ss_pred             EECCCcCCHHHHHHHH
Confidence            9999999999998533

>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=89.52  E-value=0.35  Score=33.97  Aligned_cols=16  Identities=31%  Similarity=0.449  Sum_probs=13.8

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      +++||.|||||.++..
T Consensus         3 i~~G~pgsGKSt~a~~   18 (143)
T PF13671_consen    3 ILCGPPGSGKSTLAKR   18 (143)
T ss_dssp             EEEESTTSSHHHHHHH
T ss_pred             EEECCCCCCHHHHHHH
Confidence            5899999999998753

...

>PF13173 AAA_14: AAA domain

Probab=89.52  E-value=0.5  Score=33.31  Aligned_cols=32  Identities=22%  Similarity=0.255  Sum_probs=23.6

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      .+|.||-|+|||.+....+.... ...+++|+.
T Consensus         5 ~~l~G~R~vGKTtll~~~~~~~~-~~~~~~yi~   36 (128)
T PF13173_consen    5 IILTGPRGVGKTTLLKQLAKDLL-PPENILYIN   36 (128)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhc-ccccceeec
Confidence            45999999999998876665543 456777763

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=89.49  E-value=0.63  Score=36.39  Aligned_cols=14  Identities=29%  Similarity=0.427  Sum_probs=12.9

Q ss_pred             EECcCCCchHHHHH
Q 042424           60 LTNPVYNGKTAVAE   73 (138)
Q Consensus        60 l~aPTGsGKTlva~   73 (138)
                      |+||+|||||..+.
T Consensus         4 I~G~sGSGKTTla~   17 (220)
T cd02025           4 IAGSVAVGKSTTAR   17 (220)
T ss_pred             eeCCCCCCHHHHHH
Confidence            88999999999985

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=89.45  E-value=0.64  Score=39.19  Aligned_cols=48  Identities=15%  Similarity=0.205  Sum_probs=31.0

Q ss_pred             EECcCCCchHHHHHHHHHHH-HH--c---CCcEEEEechHHHHHHHHHHHHHhc
Q 042424           60 LTNPVYNGKTAVAEYAIAMA-FR--D---KQRVIYTSSLKALSNQKYRELHKEF  107 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~-l~--~---~~rviyv~P~kaLv~Q~~~~l~~~f  107 (138)
                      |++|.|+|||.++...+..+ +.  .   +.+++|+----++--+...++.+.|
T Consensus       131 I~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~ia~~~  184 (344)
T PLN03187        131 AFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVPIAERF  184 (344)
T ss_pred             EecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHHHHHHc
Confidence            99999999999998444333 31  1   3689999875544444444444434

>PRK14494 putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein protein; Provisional

Probab=89.43  E-value=0.61  Score=37.16  Aligned_cols=32  Identities=19%  Similarity=0.082  Sum_probs=23.9

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      +++++|+|||.++...+.+...+|.++.++=+
T Consensus         6 ivG~~gsGKTtl~~~l~~~L~~~G~~V~viK~   37 (229)
T PRK14494          6 VIGFKDSGKTTLIEKILKNLKERGYRVATAKH   37 (229)
T ss_pred             EECCCCChHHHHHHHHHHHHHhCCCeEEEEEe
Confidence            88999999999987655554345778777744

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=89.41  E-value=0.21  Score=43.98  Aligned_cols=18  Identities=33%  Similarity=0.422  Sum_probs=15.7

Q ss_pred             CCceEECcCCCchHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAE   73 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~   73 (138)
                      -|.++.+|||||||+++-
T Consensus       227 SNvLllGPtGsGKTllaq  244 (564)
T KOG0745|consen  227 SNVLLLGPTGSGKTLLAQ  244 (564)
T ss_pred             ccEEEECCCCCchhHHHH
Confidence            577899999999999873

>PRK08760 replicative DNA helicase; Provisional

Probab=89.40  E-value=0.56  Score=41.01  Aligned_cols=45  Identities=24%  Similarity=0.107  Sum_probs=30.4

Q ss_pred             eEECcCCCchHHHHHHHHHHH-HHcCCcEEEEechHHHHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMA-FRDKQRVIYTSSLKALSNQKYRELH  104 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~-l~~~~rviyv~P~kaLv~Q~~~~l~  104 (138)
                      +|.|.+|.|||..++..+..+ .+.|.+++|++.--+ .+|...++.
T Consensus       233 vIaarPg~GKTafal~iA~~~a~~~g~~V~~fSlEMs-~~ql~~Rl~  278 (476)
T PRK08760        233 ILAARPAMGKTTFALNIAEYAAIKSKKGVAVFSMEMS-ASQLAMRLI  278 (476)
T ss_pred             EEEeCCCCChhHHHHHHHHHHHHhcCCceEEEeccCC-HHHHHHHHH
Confidence            489999999999998555544 455788888765432 244444443

>COG0324 MiaA tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]

Probab=89.35  E-value=0.27  Score=40.93  Aligned_cols=15  Identities=40%  Similarity=0.585  Sum_probs=13.0

Q ss_pred             eEECcCCCchHHHHH
Q 042424           59 TLTNPVYNGKTAVAE   73 (138)
Q Consensus        59 ~l~aPTGsGKTlva~   73 (138)
                      +|++||++|||-.|.
T Consensus         7 ~I~GPTAsGKT~lai   21 (308)
T COG0324           7 VIAGPTASGKTALAI   21 (308)
T ss_pred             EEECCCCcCHHHHHH
Confidence            599999999997665

>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed

Probab=89.20  E-value=0.34  Score=40.10  Aligned_cols=16  Identities=38%  Similarity=0.480  Sum_probs=14.0

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      +|++|||||||.+|.-
T Consensus         8 ~i~GptgsGKt~la~~   23 (307)
T PRK00091          8 VIVGPTASGKTALAIE   23 (307)
T ss_pred             EEECCCCcCHHHHHHH
Confidence            4999999999998863

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=89.18  E-value=2.2  Score=38.44  Aligned_cols=78  Identities=18%  Similarity=0.170  Sum_probs=53.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC---ceEEEecCCcCCC-----CCCEEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK---DVGLMTGDVTLSP-----NASCLV  127 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~---~v~~~tGd~~~~~-----~~~IiV  127 (138)
                      ...++.---|-|||.-+...++.- -++...++++|+.|| .|+.+++...-.   .|-++.|......     +.+++.
T Consensus       205 ~GGiLADEMGMGKTIQtIaLllae-~~ra~tLVvaP~VAl-mQW~nEI~~~T~gslkv~~YhG~~R~~nikel~~YDvVL  282 (791)
T KOG1002|consen  205 AGGILADEMGMGKTIQTIALLLAE-VDRAPTLVVAPTVAL-MQWKNEIERHTSGSLKVYIYHGAKRDKNIKELMNYDVVL  282 (791)
T ss_pred             ccceehhhhccchHHHHHHHHHhc-cccCCeeEEccHHHH-HHHHHHHHHhccCceEEEEEecccccCCHHHhhcCcEEE
Confidence            455666678999997665333221 246789999999998 477777766333   5777788543221     889999


Q ss_pred             ecHHHHHH
Q 042424          128 MTTEILRG  135 (138)
Q Consensus       128 tTpe~l~~  135 (138)
                      +|+..+.+
T Consensus       283 Tty~vvEs  290 (791)
T KOG1002|consen  283 TTYAVVES  290 (791)
T ss_pred             EecHHHHH
Confidence            99987765

>CHL00181 cbbX CbbX; Provisional

Probab=89.18  E-value=1  Score=36.72  Aligned_cols=23  Identities=30%  Similarity=0.252  Sum_probs=17.9

Q ss_pred             CceEECcCCCchHHHHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMA   79 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~   79 (138)
                      +.++.+|+|+|||.+|......+
T Consensus        61 ~ill~G~pGtGKT~lAr~la~~~   83 (287)
T CHL00181         61 HMSFTGSPGTGKTTVALKMADIL   83 (287)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Confidence            45799999999999997544433

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=89.14  E-value=0.44  Score=37.80  Aligned_cols=22  Identities=27%  Similarity=0.141  Sum_probs=17.8

Q ss_pred             CCceEECcCCCchHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIA   77 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~   77 (138)
                      .+.++.+|+|+|||.+|.....
T Consensus        43 ~~vll~GppGtGKTtlA~~ia~   64 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVARILGK   64 (261)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHH
Confidence            4667999999999999965443

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>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=89.14  E-value=0.33  Score=39.33  Aligned_cols=22  Identities=23%  Similarity=0.240  Sum_probs=17.4

Q ss_pred             CCCceEECcCCCchHHHHHHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai   76 (138)
                      ..+.+++||+|+|||.+....+
T Consensus        33 ~~pvLl~G~~GtGKT~li~~~l   54 (272)
T PF12775_consen   33 GRPVLLVGPSGTGKTSLIQNFL   54 (272)
T ss_dssp             TEEEEEESSTTSSHHHHHHHHH
T ss_pred             CCcEEEECCCCCchhHHHHhhh
Confidence            4667899999999998765544

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=89.05  E-value=0.43  Score=34.92  Aligned_cols=47  Identities=11%  Similarity=0.047  Sum_probs=31.0

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCc---EEE-----EechHHHHHHHHHHHHHh
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQR---VIY-----TSSLKALSNQKYRELHKE  106 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~r---viy-----v~P~kaLv~Q~~~~l~~~  106 (138)
                      +-+|||.|||.++.+...+...+|.+   +-.     =.|...-+.+.-+++++.
T Consensus        58 fHG~tGtGKn~v~~liA~~ly~~G~~S~~V~~f~~~~hFP~~~~v~~Yk~~L~~~  112 (127)
T PF06309_consen   58 FHGWTGTGKNFVSRLIAEHLYKSGMKSPFVHQFIATHHFPHNSNVDEYKEQLKSW  112 (127)
T ss_pred             eecCCCCcHHHHHHHHHHHHHhcccCCCceeeecccccCCCchHHHHHHHHHHHH
Confidence            78999999999998777665565433   222     234556666666666653

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=88.95  E-value=0.64  Score=39.37  Aligned_cols=27  Identities=19%  Similarity=0.255  Sum_probs=22.2

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD   82 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~   82 (138)
                      .|.++.+|||+|||.++.+.+.+....
T Consensus        43 ~n~~iyG~~GTGKT~~~~~v~~~l~~~   69 (366)
T COG1474          43 SNIIIYGPTGTGKTATVKFVMEELEES   69 (366)
T ss_pred             ccEEEECCCCCCHhHHHHHHHHHHHhh
Confidence            457799999999999998888776544

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=88.92  E-value=0.71  Score=36.05  Aligned_cols=32  Identities=38%  Similarity=0.546  Sum_probs=23.7

Q ss_pred             eEECcCCCchHHHHH-HHHHHHH-----------HcCCcEEEEe
Q 042424           59 TLTNPVYNGKTAVAE-YAIAMAF-----------RDKQRVIYTS   90 (138)
Q Consensus        59 ~l~aPTGsGKTlva~-~ai~~~l-----------~~~~rviyv~   90 (138)
                      ++.+|.|+|||..++ +|+.-+.           ..+.+++|+.
T Consensus         5 ll~g~~G~GKS~lal~la~~va~G~~~~g~~~~~~~~~~Vlyi~   48 (239)
T cd01125           5 ALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLS   48 (239)
T ss_pred             EEEcCCCCCHHHHHHHHHHHHhcCccccCCccccCCCceEEEEE
Confidence            599999999999997 4443321           1357899998

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=88.86  E-value=0.73  Score=36.78  Aligned_cols=31  Identities=23%  Similarity=0.176  Sum_probs=21.4

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      .+.++.+|+|+|||.++..... .+  |...+.+
T Consensus        22 ~~vLL~G~~GtGKT~lA~~la~-~l--g~~~~~i   52 (262)
T TIGR02640        22 YPVHLRGPAGTGKTTLAMHVAR-KR--DRPVMLI   52 (262)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHH-Hh--CCCEEEE
Confidence            5667999999999999864322 22  5555554

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).

>PF13500 AAA_26: AAA domain; PDB: 3OF5_A 2IOJ_A 4A0G_B 4A0R_A 4A0H_B 4A0F_B 3FMI_C 3FPA_D 3FMF_C 3FGN_A

Probab=88.72  E-value=0.95  Score=34.14  Aligned_cols=33  Identities=21%  Similarity=0.058  Sum_probs=24.6

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      ...-|++|||.+++..+....++|.++-|+=|.
T Consensus         6 ~~t~t~vGKT~vslgL~~~l~~~g~~v~~~KPi   38 (199)
T PF13500_consen    6 TGTDTGVGKTVVSLGLARALRRRGIKVGYFKPI   38 (199)
T ss_dssp             EESSSSSSHHHHHHHHHHHHHHTTSEEEEEEEE
T ss_pred             EeCCCCCCHHHHHHHHHHHHHhCCCceEEEeee
Confidence            556689999999986665555668888777665

...

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]

Probab=88.64  E-value=1.3  Score=43.23  Aligned_cols=79  Identities=23%  Similarity=0.220  Sum_probs=57.9

Q ss_pred             CCceEECcCCCchHHHHH--HHHHHHHHc------CCc-EEEEechHHHHHHHHHHHHHhcC--ceEEEecCCcCC----
Q 042424           56 THGTLTNPVYNGKTAVAE--YAIAMAFRD------KQR-VIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVTLS----  120 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~--~ai~~~l~~------~~r-viyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~~~----  120 (138)
                      -++++|=.-|-|||+-..  .|--++.++      ... .++|+|. +|+.-+..+|.+.|.  +|-.+.|.-...    
T Consensus       995 LHGILcDDMGLGKTLQticilAsd~y~r~s~~~e~~~~PSLIVCPs-TLtGHW~~E~~kf~pfL~v~~yvg~p~~r~~lR 1073 (1549)
T KOG0392|consen  995 LHGILCDDMGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCPS-TLTGHWKSEVKKFFPFLKVLQYVGPPAERRELR 1073 (1549)
T ss_pred             ccceeeccccccHHHHHHHHHHHHHHhhcccchhhccCCeEEECCc-hhhhHHHHHHHHhcchhhhhhhcCChHHHHHHH
Confidence            478899999999999765  333333332      222 7999998 689999999999766  666666653322    


Q ss_pred             ---CCCCEEEecHHHHHH
Q 042424          121 ---PNASCLVMTTEILRG  135 (138)
Q Consensus       121 ---~~~~IiVtTpe~l~~  135 (138)
                         .+++|||+.++.+.+
T Consensus      1074 ~q~~~~~iiVtSYDv~Rn 1091 (1549)
T KOG0392|consen 1074 DQYKNANIIVTSYDVVRN 1091 (1549)
T ss_pred             hhccccceEEeeHHHHHH
Confidence               278999999999885

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=88.52  E-value=1.3  Score=42.46  Aligned_cols=53  Identities=13%  Similarity=0.149  Sum_probs=43.4

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC---CcEEEEechHHHHHHHHHHHHHhcC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK---QRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~---~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      .+.+|.|+-|||||.+-..-+...+..|   .+++.|.-|+.=+.++..++.+.+.
T Consensus        11 ~~~~~~a~agsgkt~~l~~~~~~~~~~~~~~~~i~~~t~t~~aa~em~~Ri~~~L~   66 (1141)
T TIGR02784        11 TSAWVSANAGSGKTHVLTQRVIRLLLNGVPPSKILCLTYTKAAAAEMQNRVFDRLG   66 (1141)
T ss_pred             CCEEEEEECCCCHHHHHHHHHHHHHHcCCCCCeEEEEecCHHHHHHHHHHHHHHHH
Confidence            5667999999999998876666666543   7899999999999999888887664

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.

>PF01656 CbiA: CobQ/CobB/MinD/ParA nucleotide binding domain; InterPro: IPR002586 This entry consists of various cobyrinic acid a,c-diamide synthases

Probab=88.52  E-value=1  Score=33.06  Aligned_cols=32  Identities=19%  Similarity=0.163  Sum_probs=21.1

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      +.+.--|+|||.++.........+|++++++=
T Consensus         3 v~~~kGG~GKTt~a~~la~~la~~g~~VlliD   34 (195)
T PF01656_consen    3 VTSGKGGVGKTTIAANLAQALARKGKKVLLID   34 (195)
T ss_dssp             EEESSTTSSHHHHHHHHHHHHHHTTS-EEEEE
T ss_pred             EEcCCCCccHHHHHHHHHhccccccccccccc
Confidence            36677899999999743333334688887763

These include CbiA and CbiP from Salmonella typhimurium []., and CobQ from Rhodobacter capsulatus []. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria [].; PDB: 3K9G_A 3K9H_B 3EZ9_B 3EZF_A 3EZ2_B 3EZ6_A 3EZ7_A 1G3Q_A 1G3R_A 1DTS_A ....

>PRK13898 type IV secretion system ATPase VirB4; Provisional

Probab=88.50  E-value=0.44  Score=43.99  Aligned_cols=39  Identities=21%  Similarity=0.336  Sum_probs=29.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKA   94 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~ka   94 (138)
                      ++.++.||||+|||...-+.+.+....+.+++++=|-.+
T Consensus       447 ~~~~i~G~tGsGKS~l~~~l~~~~~~~~~~i~~~D~~~~  485 (800)
T PRK13898        447 GHTLIIGPTGAGKTVLMNFLCAQAMKFSPRMFFFDKDRG  485 (800)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhhcccCCCeEEEeCCCcC
Confidence            678899999999999886655555455778888877554

>COG4240 Predicted kinase [General function prediction only]

Probab=88.48  E-value=0.69  Score=37.80  Aligned_cols=31  Identities=16%  Similarity=0.291  Sum_probs=22.9

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcC-CcEEEEe
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDK-QRVIYTS   90 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~-~rviyv~   90 (138)
                      +++|-|||||..+........++| .++++++
T Consensus        55 isGpQGSGKStls~~i~~~L~~kg~ert~~lS   86 (300)
T COG4240          55 ISGPQGSGKSTLSALIVRLLAAKGLERTATLS   86 (300)
T ss_pred             eecCCCCchhhHHHHHHHHHHHhcccceEEee
Confidence            999999999999876555444555 5776654

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=88.47  E-value=1.1  Score=41.30  Aligned_cols=42  Identities=17%  Similarity=0.105  Sum_probs=31.0

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEechHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLKALSNQKY  100 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~kaLv~Q~~  100 (138)
                      .+|.++.|+|||.+.-.. ..++. .|.++++++||-.-+....
T Consensus       371 ~il~G~aGTGKTtll~~i-~~~~~~~g~~V~~~ApTg~Aa~~L~  413 (744)
T TIGR02768       371 AVVVGRAGTGKSTMLKAA-REAWEAAGYRVIGAALSGKAAEGLQ  413 (744)
T ss_pred             EEEEecCCCCHHHHHHHH-HHHHHhCCCeEEEEeCcHHHHHHHH
Confidence            459999999999876543 33444 5899999999966555443

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.

>TIGR00347 bioD dethiobiotin synthase

Probab=88.42  E-value=0.88  Score=33.20  Aligned_cols=30  Identities=20%  Similarity=0.019  Sum_probs=22.6

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      ..+-||+|||.++...+....++|.++.|+
T Consensus         3 ~~t~~~~GKT~va~~L~~~l~~~g~~V~~~   32 (166)
T TIGR00347         3 TGTDTGVGKTVASSALAAKLKKAGYSVGYY   32 (166)
T ss_pred             ecCCCCccHHHHHHHHHHHHHHCCCcEEEE
Confidence            456789999999986555544568888886

Dethiobiotin synthase is involved in biotin biosynthesis and catalyses the reaction (CO2 + 7,8-diaminononanoate + ATP = dethiobiotin + phosphate + ADP). The enzyme binds ATP (see motif in first 12 residues of the SEED alignment) and requires magnesium as a co-factor.

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=88.40  E-value=0.48  Score=34.47  Aligned_cols=16  Identities=25%  Similarity=0.302  Sum_probs=13.5

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      ++++|+|||||.++..
T Consensus         2 ~l~G~~GsGKSTla~~   17 (163)
T TIGR01313         2 VLMGVAGSGKSTIASA   17 (163)
T ss_pred             EEECCCCCCHHHHHHH
Confidence            5899999999988753

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=88.39  E-value=1.4  Score=40.97  Aligned_cols=50  Identities=18%  Similarity=0.209  Sum_probs=31.4

Q ss_pred             eEECcCCCchHHHHH-HHHHHHHHcCC-cEEEEe--chHHHHHHHHHHHHHhcC
Q 042424           59 TLTNPVYNGKTAVAE-YAIAMAFRDKQ-RVIYTS--SLKALSNQKYRELHKEFK  108 (138)
Q Consensus        59 ~l~aPTGsGKTlva~-~ai~~~l~~~~-rviyv~--P~kaLv~Q~~~~l~~~f~  108 (138)
                      .+.+|||+|||..+. ++......+|+ ++.++.  +++.=+.++.+.+.+.++
T Consensus       189 ~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~Dt~RigA~eQL~~~a~~~g  242 (767)
T PRK14723        189 ALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTDSFRIGALEQLRIYGRILG  242 (767)
T ss_pred             EEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecCcccchHHHHHHHHHHHhCC
Confidence            399999999988775 55444345554 554433  235445566667777554

>cd02035 ArsA ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell

Probab=88.31  E-value=0.89  Score=35.13  Aligned_cols=32  Identities=22%  Similarity=0.190  Sum_probs=23.6

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      ++++..|.|||.++........+.|.|++++.
T Consensus         3 ~~~g~~g~Gkt~~~~~la~~~a~~g~~~~l~~   34 (217)
T cd02035           3 FFTGKGGVGKTTIAAATAVRLAEEGKKVLLVS   34 (217)
T ss_pred             EEeCCCCchHHHHHHHHHHHHHHCCCcEEEEE
Confidence            47899999999998744444446788877763

This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces resistance to the toxic agents. The pump is composed of two subunits, the catalytic ArsA subunit and the membrane subunit ArsB, which are encoded by arsA and arsB genes respectively. Arsenic efflux in bacteria is catalyzed by either ArsB alone or by ArsAB complex. The ATP-coupled pump, however, is more efficient. ArsA is composed of two homologous halves, A1 and A2, connected by a short linker sequence.

>PRK10689 transcription-repair coupling factor; Provisional

Probab=88.31  E-value=1.4  Score=42.66  Aligned_cols=58  Identities=17%  Similarity=0.079  Sum_probs=46.3

Q ss_pred             HHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCCcCCC-----------CCCEEEecHH
Q 042424           74 YAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVTLSP-----------NASCLVMTTE  131 (138)
Q Consensus        74 ~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~~~~-----------~~~IiVtTpe  131 (138)
                      .++...+.++.++++++|++.-++..++.+++.+.  .|..++|+...+.           +.+|+|||.-
T Consensus       800 ~~il~el~r~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdI  870 (1147)
T PRK10689        800 EAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTI  870 (1147)
T ss_pred             HHHHHHHhcCCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECch
Confidence            45555566788999999999999999999998764  7888999875432           7889999963

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=88.28  E-value=0.44  Score=34.39  Aligned_cols=18  Identities=22%  Similarity=0.368  Sum_probs=14.2

Q ss_pred             eEECcCCCchHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai   76 (138)
                      +|++|||||||.++...+
T Consensus         3 ~i~GpsGsGKstl~~~L~   20 (137)
T cd00071           3 VLSGPSGVGKSTLLKRLL   20 (137)
T ss_pred             EEECCCCCCHHHHHHHHH
Confidence            589999999998765433

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=88.26  E-value=0.96  Score=34.11  Aligned_cols=29  Identities=24%  Similarity=0.009  Sum_probs=24.2

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEE
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIY   88 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviy   88 (138)
                      +..++|.|||.+|.--..++..+|.++++
T Consensus         7 vy~g~G~Gkt~~a~g~~~ra~~~g~~v~~   35 (159)
T cd00561           7 VYTGNGKGKTTAALGLALRALGHGYRVGV   35 (159)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHCCCeEEE
Confidence            77888999999998666667788888887

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.

>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]

Probab=88.21  E-value=3.1  Score=39.51  Aligned_cols=82  Identities=20%  Similarity=0.109  Sum_probs=51.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHHH-HHcC--CcEEEEechHHHHHHHHHHHHHhc----C-ceEEEe-cCCcCCCCCCEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMA-FRDK--QRVIYTSSLKALSNQKYRELHKEF----K-DVGLMT-GDVTLSPNASCL  126 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~-l~~~--~rviyv~P~kaLv~Q~~~~l~~~f----~-~v~~~t-Gd~~~~~~~~Ii  126 (138)
                      .-.++++-||+|||.=.-..|+.. +..|  .+++..-|.|--|-..+++....-    + .||--. .+.....+..++
T Consensus       189 qVvvIsGeTGcGKTTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsvAeRVa~ER~~~~g~~VGYqvrl~~~~s~~t~L~  268 (924)
T KOG0920|consen  189 QVVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISVAERVAKERGESLGEEVGYQVRLESKRSRETRLL  268 (924)
T ss_pred             ceEEEeCCCCCCchhhhhHHHHHHHHhcCCCCeEEecCCchHHHHHHHHHHHHHhccccCCeeeEEEeeecccCCceeEE
Confidence            445699999999998876555444 4443  568888898655555555554322    2 343222 122223368899


Q ss_pred             EecHHHHHHhh
Q 042424          127 VMTTEILRGML  137 (138)
Q Consensus       127 VtTpe~l~~lL  137 (138)
                      .||...|+..|
T Consensus       269 fcTtGvLLr~L  279 (924)
T KOG0920|consen  269 FCTTGVLLRRL  279 (924)
T ss_pred             EecHHHHHHHh
Confidence            99999988765

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=88.19  E-value=0.64  Score=43.75  Aligned_cols=43  Identities=12%  Similarity=0.029  Sum_probs=32.5

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHc--C-CcEEEEechHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRD--K-QRVIYTSSLKALSNQKY  100 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~--~-~rviyv~P~kaLv~Q~~  100 (138)
                      |.-|..-||.|||++++-.|.. |++  | -+.|+|||+.|+-+-++
T Consensus        76 NiDI~METGTGKTy~Ylrtmfe-Lhk~YG~~KFIivVPs~AIkeGv~  121 (985)
T COG3587          76 NIDILMETGTGKTYTYLRTMFE-LHKKYGLFKFIIVVPSLAIKEGVF  121 (985)
T ss_pred             eeeEEEecCCCceeeHHHHHHH-HHHHhCceeEEEEeccHHHHhhhH
Confidence            4448899999999999755543 333  5 68999999999876643

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=88.18  E-value=1  Score=35.13  Aligned_cols=36  Identities=14%  Similarity=-0.096  Sum_probs=28.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      ++..+..++|-|||.+|+--..+++.+|.+++++==
T Consensus        23 g~v~v~~g~GkGKtt~a~g~a~ra~g~G~~V~ivQF   58 (191)
T PRK05986         23 GLLIVHTGNGKGKSTAAFGMALRAVGHGKKVGVVQF   58 (191)
T ss_pred             CeEEEECCCCCChHHHHHHHHHHHHHCCCeEEEEEE
Confidence            455699999999999998666677778887766543

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=88.11  E-value=1  Score=41.89  Aligned_cols=48  Identities=19%  Similarity=0.138  Sum_probs=39.0

Q ss_pred             EECcCCCchHHHHHHHHHHHHHc--C-----CcEEEEechHHHHHHHHHHHHHhcC
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRD--K-----QRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~--~-----~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      +.=--|+|||+...-.|...+++  +     .+.|+|+|- +|++-++++|.+...
T Consensus       268 mAd~~GlGKTlq~IsflwtlLrq~P~~~~~~~k~lVV~P~-sLv~nWkkEF~KWl~  322 (776)
T KOG0390|consen  268 MADEPGLGKTLQCISFIWTLLRQFPQAKPLINKPLVVAPS-SLVNNWKKEFGKWLG  322 (776)
T ss_pred             eeCCCCcchHHHHHHHHHHHHHhCcCccccccccEEEccH-HHHHHHHHHHHHhcc
Confidence            44447999999988777777765  5     789999997 799999999999665

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

Probab=88.10  E-value=0.68  Score=38.79  Aligned_cols=52  Identities=19%  Similarity=0.165  Sum_probs=34.1

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHH--HHHHHHhcC
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQK--YRELHKEFK  108 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~--~~~l~~~f~  108 (138)
                      +..|.+|-|+|||.+....+......++.+++++||-.-|...  -..+...|+
T Consensus        24 ~~fv~G~~GtGKs~l~~~i~~~~~~~~~~~~~~a~tg~AA~~i~~G~T~hs~f~   77 (364)
T PF05970_consen   24 NFFVTGPAGTGKSFLIKAIIDYLRSRGKKVLVTAPTGIAAFNIPGGRTIHSFFG   77 (364)
T ss_pred             EEEEEcCCCCChhHHHHHHHHHhccccceEEEecchHHHHHhccCCcchHHhcC
Confidence            3459999999999886544443333477889999985544444  344555454

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

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=88.05  E-value=0.66  Score=37.41  Aligned_cols=23  Identities=26%  Similarity=0.183  Sum_probs=17.9

Q ss_pred             CceEECcCCCchHHHHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMA   79 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~   79 (138)
                      +.++.||.|+|||.++.......
T Consensus        38 ~lll~Gp~GtGKT~la~~~~~~l   60 (337)
T PRK12402         38 HLLVQGPPGSGKTAAVRALAREL   60 (337)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            45699999999999886555443

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=87.94  E-value=0.83  Score=37.42  Aligned_cols=38  Identities=24%  Similarity=0.267  Sum_probs=27.1

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALS   96 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv   96 (138)
                      ..++++-|||||+..- ++...+..+..++++.|-..+.
T Consensus        54 ~~vtGevGsGKTv~~R-al~~s~~~d~~~~v~i~~~~~s   91 (269)
T COG3267          54 LAVTGEVGSGKTVLRR-ALLASLNEDQVAVVVIDKPTLS   91 (269)
T ss_pred             EEEEecCCCchhHHHH-HHHHhcCCCceEEEEecCcchh
Confidence            4599999999999998 6666656666666555544333

>PRK13853 type IV secretion system protein VirB4; Provisional

Probab=87.73  E-value=0.51  Score=43.58  Aligned_cols=37  Identities=19%  Similarity=0.298  Sum_probs=24.4

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHH----cCCcEEEEech
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFR----DKQRVIYTSSL   92 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~----~~~rviyv~P~   92 (138)
                      ++.+|.||||||||...-+.+.+..+    .+.+++++=+-
T Consensus       427 g~~~I~G~tGsGKS~l~~~l~~~~~~~~~~~~~~v~i~D~~  467 (789)
T PRK13853        427 GMTAIFGPIGRGKTTLMTFILAMLEQSMVDRAGAVVFFDKD  467 (789)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhCccccCCCCceEEEeCCC
Confidence            67889999999999987644432212    25566665443

>PLN02165 adenylate isopentenyltransferase

Probab=87.61  E-value=0.42  Score=40.24  Aligned_cols=16  Identities=13%  Similarity=0.173  Sum_probs=14.0

Q ss_pred             ceEECcCCCchHHHHH
Q 042424           58 GTLTNPVYNGKTAVAE   73 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~   73 (138)
                      .+|.+|||||||.++.
T Consensus        46 ivIiGPTGSGKStLA~   61 (334)
T PLN02165         46 VVIMGATGSGKSRLSV   61 (334)
T ss_pred             EEEECCCCCcHHHHHH
Confidence            3599999999999886

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=87.54  E-value=0.82  Score=34.54  Aligned_cols=15  Identities=33%  Similarity=0.530  Sum_probs=13.4

Q ss_pred             EECcCCCchHHHHHH
Q 042424           60 LTNPVYNGKTAVAEY   74 (138)
Q Consensus        60 l~aPTGsGKTlva~~   74 (138)
                      |+||+|||||.+|..
T Consensus         4 I~G~sgSGKTTla~~   18 (194)
T PF00485_consen    4 IAGPSGSGKTTLAKR   18 (194)
T ss_dssp             EEESTTSSHHHHHHH
T ss_pred             EECCCCCCHHHHHHH
Confidence            899999999998853

7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms []. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2ZSE_A 2ZS7_A 3AF0_A 3AVP_A 2ZS9_A 2ZS8_A 3AEZ_A 2ZSB_A 2ZSD_A 2GEV_A ....

>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=87.45  E-value=1  Score=37.04  Aligned_cols=39  Identities=26%  Similarity=0.189  Sum_probs=26.7

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEe--chHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS--SLKALSN   97 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~--P~kaLv~   97 (138)
                      ++++.-|.|||.+|.....++-++|+|+++++  |..+|.+
T Consensus         5 ~~~GKGGVGKTT~aaA~A~~~A~~G~rtLlvS~Dpa~~L~d   45 (305)
T PF02374_consen    5 FFGGKGGVGKTTVAAALALALARRGKRTLLVSTDPAHSLSD   45 (305)
T ss_dssp             EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEESSTTTHHHH
T ss_pred             EEecCCCCCcHHHHHHHHHHHhhCCCCeeEeecCCCccHHH
Confidence            48899999999999743334446789988874  5555543

...

>PRK00889 adenylylsulfate kinase; Provisional

Probab=87.33  E-value=1.2  Score=32.75  Aligned_cols=32  Identities=19%  Similarity=-0.060  Sum_probs=21.1

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      ..+.++.|||||.++.......-..|..++++
T Consensus         7 i~~~G~~GsGKST~a~~la~~l~~~g~~v~~i   38 (175)
T PRK00889          7 VWFTGLSGAGKTTIARALAEKLREAGYPVEVL   38 (175)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            34999999999999864443332345555554

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=87.30  E-value=0.29  Score=44.77  Aligned_cols=20  Identities=30%  Similarity=0.232  Sum_probs=15.9

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      ...++++|.|+|||++|-..
T Consensus       546 sGvLL~GPPGCGKTLlAKAV  565 (802)
T KOG0733|consen  546 SGVLLCGPPGCGKTLLAKAV  565 (802)
T ss_pred             CceEEeCCCCccHHHHHHHH
Confidence            44569999999999987543

>PRK07667 uridine kinase; Provisional

Probab=87.18  E-value=1.2  Score=33.90  Aligned_cols=14  Identities=21%  Similarity=0.290  Sum_probs=13.1

Q ss_pred             EECcCCCchHHHHH
Q 042424           60 LTNPVYNGKTAVAE   73 (138)
Q Consensus        60 l~aPTGsGKTlva~   73 (138)
                      ++|+.|||||.++.
T Consensus        22 I~G~~gsGKStla~   35 (193)
T PRK07667         22 IDGLSRSGKTTFVA   35 (193)
T ss_pred             EECCCCCCHHHHHH
Confidence            99999999999885

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=87.16  E-value=0.72  Score=29.60  Aligned_cols=16  Identities=25%  Similarity=0.337  Sum_probs=13.6

Q ss_pred             CceEECcCCCchHHHH
Q 042424           57 HGTLTNPVYNGKTAVA   72 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva   72 (138)
                      ..++++|+|||||.+.
T Consensus        25 ~tli~G~nGsGKSTll   40 (62)
T PF13555_consen   25 VTLITGPNGSGKSTLL   40 (62)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3669999999999765

>PRK05480 uridine/cytidine kinase; Provisional

Probab=87.15  E-value=1  Score=34.19  Aligned_cols=15  Identities=33%  Similarity=0.355  Sum_probs=13.3

Q ss_pred             eEECcCCCchHHHHH
Q 042424           59 TLTNPVYNGKTAVAE   73 (138)
Q Consensus        59 ~l~aPTGsGKTlva~   73 (138)
                      .|+||+|||||..+.
T Consensus        10 ~I~G~sGsGKTTl~~   24 (209)
T PRK05480         10 GIAGGSGSGKTTVAS   24 (209)
T ss_pred             EEECCCCCCHHHHHH
Confidence            399999999998884

>TIGR00750 lao LAO/AO transport system ATPase

Probab=87.09  E-value=1.2  Score=36.30  Aligned_cols=32  Identities=19%  Similarity=0.020  Sum_probs=21.2

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      ..+++|+|+|||............+|.++.++
T Consensus        37 i~i~G~~G~GKttl~~~l~~~~~~~~~~v~~i   68 (300)
T TIGR00750        37 VGITGTPGAGKSTLLEALGMELRRRGLKVAVI   68 (300)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            34999999999997764443333456666543

Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however.

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=87.02  E-value=1.1  Score=32.58  Aligned_cols=24  Identities=21%  Similarity=0.116  Sum_probs=14.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMA   79 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~   79 (138)
                      +..+|.|+.|+|||.+....+.+.
T Consensus        25 ~~~ll~G~~G~GKT~ll~~~~~~~   48 (185)
T PF13191_consen   25 RNLLLTGESGSGKTSLLRALLDRL   48 (185)
T ss_dssp             --EEE-B-TTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHH
Confidence            455699999999998865444333

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=87.00  E-value=2.2  Score=34.95  Aligned_cols=23  Identities=26%  Similarity=0.325  Sum_probs=18.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAM   78 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~   78 (138)
                      .+.+|+||+|+|||.++...+.+
T Consensus        41 ~~i~I~G~~GtGKT~l~~~~~~~   63 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVTKYVMKE   63 (365)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHH
Confidence            45669999999999888655544

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>PRK06696 uridine kinase; Validated

Probab=86.96  E-value=1.2  Score=34.41  Aligned_cols=28  Identities=25%  Similarity=0.278  Sum_probs=18.7

Q ss_pred             EECcCCCchHHHHHHHHHHHHHc-CCcEEE
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRD-KQRVIY   88 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~-~~rviy   88 (138)
                      |+|++|||||.+|... ...+.. |..++.
T Consensus        27 I~G~sgsGKSTlA~~L-~~~l~~~g~~v~~   55 (223)
T PRK06696         27 IDGITASGKTTFADEL-AEEIKKRGRPVIR   55 (223)
T ss_pred             EECCCCCCHHHHHHHH-HHHHHHcCCeEEE
Confidence            9999999999988533 334443 444443

>PF03237 Terminase_6: Terminase-like family; InterPro: IPR004921 The terminase is a component of the molecular motor that translocates genomic DNA into empty capsids during DNA packaging []

Probab=86.94  E-value=1.3  Score=35.14  Aligned_cols=40  Identities=15%  Similarity=0.145  Sum_probs=23.6

Q ss_pred             eEECcCCCchHHHHH-HHHHHHHHcCC-cEEEEechHHHHHH
Q 042424           59 TLTNPVYNGKTAVAE-YAIAMAFRDKQ-RVIYTSSLKALSNQ   98 (138)
Q Consensus        59 ~l~aPTGsGKTlva~-~ai~~~l~~~~-rviyv~P~kaLv~Q   98 (138)
                      ++.++-|+|||.+.. .++.+++.... +.++++++..-+.+
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~~~~vi~~~~~~~~~~   42 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPPGRRVIIASTYRQARD   42 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS--EEEEEESSHHHHH
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCCCcEEEEecCHHHHHH
Confidence            367899999999976 56666666542 55555566444444

The large subunit heterodimerises with the small terminase protein, which is docked on the capsid portal protein. The latter forms a ring through which genomic DNA is translocated into the capsid. The terminase protein may have or induce an endonuclease activity to cleave DNA after encapsidation. This entry represents a family of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2O0K_A 3CPE_A 2O0J_A 2O0H_A 3C6H_A 3C6A_A.

>TIGR00174 miaA tRNA isopentenyltransferase (miaA)

Probab=86.63  E-value=0.63  Score=38.31  Aligned_cols=17  Identities=24%  Similarity=0.262  Sum_probs=14.3

Q ss_pred             eEECcCCCchHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~a   75 (138)
                      +|++|||+|||.++.-.
T Consensus         3 ~i~G~t~~GKs~la~~l   19 (287)
T TIGR00174         3 FIMGPTAVGKSQLAIQL   19 (287)
T ss_pred             EEECCCCCCHHHHHHHH
Confidence            58999999999988633

Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine.

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=86.59  E-value=0.76  Score=38.52  Aligned_cols=40  Identities=15%  Similarity=0.185  Sum_probs=25.2

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKAL   95 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaL   95 (138)
                      ..+.+++++||||||.... ++...+....+++++=-..+|
T Consensus       178 ~~~ili~G~tGsGKTTll~-al~~~i~~~~riv~iEd~~El  217 (340)
T TIGR03819       178 RLAFLISGGTGSGKTTLLS-ALLALVAPDERIVLVEDAAEL  217 (340)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHccCCCCCcEEEECCccee
Confidence            3678899999999997653 233333445566665444444

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.

>PRK06762 hypothetical protein; Provisional

Probab=86.58  E-value=1.2  Score=32.43  Aligned_cols=17  Identities=24%  Similarity=0.278  Sum_probs=14.2

Q ss_pred             eEECcCCCchHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~a   75 (138)
                      +++|+.|||||.+|...
T Consensus         6 ~i~G~~GsGKST~A~~L   22 (166)
T PRK06762          6 IIRGNSGSGKTTIAKQL   22 (166)
T ss_pred             EEECCCCCCHHHHHHHH
Confidence            49999999999988533

>PRK00300 gmk guanylate kinase; Provisional

Probab=86.54  E-value=0.66  Score=34.93  Aligned_cols=18  Identities=22%  Similarity=0.285  Sum_probs=14.4

Q ss_pred             ceEECcCCCchHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~a   75 (138)
                      .++.+|+|||||.++...
T Consensus         8 i~i~G~sGsGKstl~~~l   25 (205)
T PRK00300          8 IVLSGPSGAGKSTLVKAL   25 (205)
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            359999999999877543

>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=86.54  E-value=0.85  Score=37.72  Aligned_cols=34  Identities=15%  Similarity=0.146  Sum_probs=22.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      .+.+++++||||||.. +.|+...+-...|++.+=
T Consensus       144 ~siii~G~t~sGKTt~-lnall~~Ip~~~rivtIE  177 (312)
T COG0630         144 KSIIICGGTASGKTTL-LNALLDFIPPEERIVTIE  177 (312)
T ss_pred             CcEEEECCCCCCHHHH-HHHHHHhCCchhcEEEEe
Confidence            5677999999999975 344444444444444443

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=86.53  E-value=1.5  Score=31.93  Aligned_cols=31  Identities=23%  Similarity=0.154  Sum_probs=19.9

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      +++++.|||||..+..........+..++++
T Consensus         3 ~i~G~~GsGKSTla~~L~~~l~~~g~~~~~i   33 (149)
T cd02027           3 WLTGLSGSGKSTIARALEEKLFQRGRPVYVL   33 (149)
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHHcCCCEEEE
Confidence            4899999999998864333322335455544

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=86.51  E-value=0.27  Score=45.59  Aligned_cols=38  Identities=24%  Similarity=0.200  Sum_probs=29.1

Q ss_pred             CCcccccccCCCCccCCCCC-CCceEECcCCCchHHHHH
Q 042424           36 RSCVHEVAVPSCYTLTTDET-THGTLTNPVYNGKTAVAE   73 (138)
Q Consensus        36 ~~~~~~~~~p~~y~~~~~~~-~~~~l~aPTGsGKTlva~   73 (138)
                      .+..++.-+|..|+.+..-. +..+|++|.|+|||+.|-
T Consensus       324 ~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAK  362 (774)
T KOG0731|consen  324 MEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAK  362 (774)
T ss_pred             HHHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHH
Confidence            35667778899898665443 456699999999999764

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=86.43  E-value=1.3  Score=34.69  Aligned_cols=31  Identities=19%  Similarity=0.053  Sum_probs=20.5

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      +++|+.|||||.+|.....+.-..+..++++
T Consensus         3 vl~G~pGSGKST~a~~La~~l~~~~~~v~~i   33 (249)
T TIGR03574         3 ILTGLPGVGKSTFSKELAKKLSEKNIDVIIL   33 (249)
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHHcCCceEEE
Confidence            5899999999999864333322235555555

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]

Probab=86.42  E-value=2.3  Score=38.88  Aligned_cols=79  Identities=16%  Similarity=0.148  Sum_probs=49.0

Q ss_pred             CceEECcCCCchHHHHHHHHHHH-HHcCCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEe-cCCcCCCCCCEEEec
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMA-FRDKQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMT-GDVTLSPNASCLVMT  129 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~-l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~t-Gd~~~~~~~~IiVtT  129 (138)
                      -.+|.+.||||||.=.=..+..+ +...+++.+.=|.|--+--.+++..+.++     .||.-. =|.....+..|..+|
T Consensus        68 vlIviGeTGsGKSTQipQyL~eaG~~~~g~I~~TQPRRVAavslA~RVAeE~~~~lG~~VGY~IRFed~ts~~TrikymT  147 (674)
T KOG0922|consen   68 VLIVIGETGSGKSTQIPQYLAEAGFASSGKIACTQPRRVAAVSLAKRVAEEMGCQLGEEVGYTIRFEDSTSKDTRIKYMT  147 (674)
T ss_pred             EEEEEcCCCCCccccHhHHHHhcccccCCcEEeecCchHHHHHHHHHHHHHhCCCcCceeeeEEEecccCCCceeEEEec
Confidence            35599999999997654444333 33345588888987666666666666554     454321 111222366778888


Q ss_pred             HHHHHH
Q 042424          130 TEILRG  135 (138)
Q Consensus       130 pe~l~~  135 (138)
                      -..|+.
T Consensus       148 DG~LLR  153 (674)
T KOG0922|consen  148 DGMLLR  153 (674)
T ss_pred             chHHHH
Confidence            777654

>PRK07004 replicative DNA helicase; Provisional

Probab=86.33  E-value=1  Score=39.15  Aligned_cols=33  Identities=21%  Similarity=-0.007  Sum_probs=24.7

Q ss_pred             eEECcCCCchHHHHHHHHHH-HHHcCCcEEEEec
Q 042424           59 TLTNPVYNGKTAVAEYAIAM-AFRDKQRVIYTSS   91 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~-~l~~~~rviyv~P   91 (138)
                      +|.|.+|.|||..++..+.+ ++..|..++|++.
T Consensus       217 viaarpg~GKT~~al~ia~~~a~~~~~~v~~fSl  250 (460)
T PRK07004        217 IVAGRPSMGKTAFSMNIGEYVAVEYGLPVAVFSM  250 (460)
T ss_pred             EEEeCCCCCccHHHHHHHHHHHHHcCCeEEEEeC
Confidence            48999999999999844443 4556888877754

>PRK09165 replicative DNA helicase; Provisional

Probab=86.19  E-value=1.1  Score=39.24  Aligned_cols=45  Identities=22%  Similarity=0.010  Sum_probs=28.3

Q ss_pred             ceEECcCCCchHHHHHHHHHHHH-H--------------cCCcEEEEechHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAF-R--------------DKQRVIYTSSLKALSNQKYREL  103 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l-~--------------~~~rviyv~P~kaLv~Q~~~~l  103 (138)
                      .+|.|++|.|||..++..+.+.. .              +|.+++|++--. =.+|...++
T Consensus       220 ivIaarpg~GKT~~al~ia~~~a~~~~~~~~~~~~~~~~~g~~vl~fSlEM-s~~ql~~R~  279 (497)
T PRK09165        220 IILAGRPSMGKTALATNIAFNAAKAYRREAQPDGSKKAVNGGVVGFFSLEM-SAEQLATRI  279 (497)
T ss_pred             EEEEeCCCCChHHHHHHHHHHHHHhhcccccccccccccCCCeEEEEeCcC-CHHHHHHHH
Confidence            34999999999999974444332 2              256777775432 334555444

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

Probab=86.18  E-value=4.2  Score=27.40  Aligned_cols=66  Identities=17%  Similarity=0.113  Sum_probs=43.5

Q ss_pred             CchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCC-----------CCCCEEEecHH
Q 042424           66 NGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLS-----------PNASCLVMTTE  131 (138)
Q Consensus        66 sGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~-----------~~~~IiVtTpe  131 (138)
                      .+|-......+......+.++|+.++++.-+++.++.|.+....+..++|+...+           .+..|+++|..
T Consensus        11 ~~k~~~i~~~i~~~~~~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~   87 (131)
T cd00079          11 DEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDV   87 (131)
T ss_pred             HHHHHHHHHHHHhcccCCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcCh
Confidence            3554433333333323478999999999999999999987333788888875421           14568887754

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=86.16  E-value=1.4  Score=42.14  Aligned_cols=76  Identities=13%  Similarity=0.052  Sum_probs=45.5

Q ss_pred             CCceEECcCCCchHHHHHH-HHHHHHHcCCcEEEEechHHHHHHHHHHHHHh---cC-ceEEEecCCcCCC-----CCCE
Q 042424           56 THGTLTNPVYNGKTAVAEY-AIAMAFRDKQRVIYTSSLKALSNQKYRELHKE---FK-DVGLMTGDVTLSP-----NASC  125 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~-ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~---f~-~v~~~tGd~~~~~-----~~~I  125 (138)
                      ...+.-..||-|||++|-+ +.+.||. |+.|-+|.-.-=|+..=++.+...   ++ +||.+..+.....     .++|
T Consensus       152 ~G~IAEM~TGEGKTLvatlp~yLnAL~-G~gVHvVTvNDYLA~RDaewm~p~y~flGLtVg~i~~~~~~~~Rr~aY~~DI  230 (1025)
T PRK12900        152 SGKISEMATGEGKTLVSTLPTFLNALT-GRGVHVVTVNDYLAQRDKEWMNPVFEFHGLSVGVILNTMRPEERREQYLCDI  230 (1025)
T ss_pred             cCCccccCCCCCcchHhHHHHHHHHHc-CCCcEEEeechHhhhhhHHHHHHHHHHhCCeeeeeCCCCCHHHHHHhCCCcc
Confidence            3456778899999999975 4555554 444433333333665544444443   44 7887755443321     7788


Q ss_pred             EEecHHH
Q 042424          126 LVMTTEI  132 (138)
Q Consensus       126 iVtTpe~  132 (138)
                      .-+|.--
T Consensus       231 tYgTn~E  237 (1025)
T PRK12900        231 TYGTNNE  237 (1025)
T ss_pred             eecCCCc
Confidence            8777643

>PRK05636 replicative DNA helicase; Provisional

Probab=86.11  E-value=1.2  Score=39.32  Aligned_cols=47  Identities=13%  Similarity=0.123  Sum_probs=30.4

Q ss_pred             cCCCCccCCCC-----CCCc-eEECcCCCchHHHHHHHHHH-HHHcCCcEEEEe
Q 042424           44 VPSCYTLTTDE-----TTHG-TLTNPVYNGKTAVAEYAIAM-AFRDKQRVIYTS   90 (138)
Q Consensus        44 ~p~~y~~~~~~-----~~~~-~l~aPTGsGKTlva~~ai~~-~l~~~~rviyv~   90 (138)
                      +|.||..+...     .+.. +|.|.+|.|||..++..+.. ++++|..++|++
T Consensus       248 i~TG~~~LD~~t~Gl~~G~Liiiaarpg~GKT~~al~~a~~~a~~~g~~v~~fS  301 (505)
T PRK05636        248 IPTGFKDLDDLTNGLRGGQMIIVAARPGVGKSTLALDFMRSASIKHNKASVIFS  301 (505)
T ss_pred             eecChHHHhhhcCCCCCCceEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEE
Confidence            56666544321     1333 48999999999999854444 345677887773

>PRK07261 topology modulation protein; Provisional

Probab=85.98  E-value=0.48  Score=35.41  Aligned_cols=17  Identities=18%  Similarity=0.118  Sum_probs=14.6

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .+|+|++|||||..+..
T Consensus         3 i~i~G~~GsGKSTla~~   19 (171)
T PRK07261          3 IAIIGYSGSGKSTLARK   19 (171)
T ss_pred             EEEEcCCCCCHHHHHHH
Confidence            45899999999999864

>TIGR02773 addB_Gpos ATP-dependent nuclease subunit B

Probab=85.98  E-value=2.1  Score=41.21  Aligned_cols=49  Identities=12%  Similarity=0.131  Sum_probs=38.2

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      .|.|+.|||||.+...-|.+.+..   +.+.++++|... .-++-+++.+.++
T Consensus         5 fi~G~aGSGKT~~l~~ri~~~l~~~~~~~~~illVPeq~-TF~~e~rl~~~~~   56 (1158)
T TIGR02773         5 FIYGRAGTGKSTFCIDEIKQKIKENPLGKPIILIVPDQM-TFQMEQALLNDIE   56 (1158)
T ss_pred             EEEeCCCCChHHHHHHHHHHHHhhCCCCCcEEEEcCCcc-cHHHHHHHHHhcc
Confidence            488999999999999888888754   679999999874 5556666665443

DNA repair is accomplished by several different systems in prokaryotes. Recombinational repair of double-stranded DNA breaks involves the RecBCD pathway in some lineages, and AddAB (also called RexAB) in other. The AddA protein is conserved between the firmicutes and the alphaproteobacteria, while the partner protein is not. Nevertheless, the partner is designated AddB in both systems. This model describes the AddB protein as found Bacillus subtilis and related species. Although the RexB protein of Streptococcus and Lactococcus is considered to be orthologous, functionally equivalent, and merely named differently, all members of this protein family have a P-loop nucleotide binding motif GxxGxGK[ST] at the N-terminus, unlike RexB proteins, and a CxxCxxxxxC motif at the C-terminus, both of which may be relevant to function.

>PRK00090 bioD dithiobiotin synthetase; Reviewed

Probab=85.97  E-value=1.5  Score=33.53  Aligned_cols=33  Identities=15%  Similarity=-0.044  Sum_probs=23.6

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      ...-|++|||.++...+....++|.++.|.=|.
T Consensus         5 ~~t~t~~GKT~vs~~L~~~l~~~g~~v~~~KPv   37 (222)
T PRK00090          5 TGTDTDVGKTVVTAALAQALREAGYSVAGYKPV   37 (222)
T ss_pred             EeCCCCcCHHHHHHHHHHHHHHcCCceEEEeeE
Confidence            456789999999976555544567777776653

>KOG2749 consensus mRNA cleavage and polyadenylation factor IA/II complex, subunit CLP1 [RNA processing and modification]

Probab=85.96  E-value=1.1  Score=38.49  Aligned_cols=34  Identities=15%  Similarity=0.334  Sum_probs=26.4

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      .+.++.+||.+|||.++...+-.+++.|++-+|+
T Consensus       104 Prv~vVGp~d~GKsTl~r~L~nyavk~gr~Plfv  137 (415)
T KOG2749|consen  104 PRVMVVGPTDVGKSTLCRILLNYAVKQGRRPLFV  137 (415)
T ss_pred             CEEEEECCCccchHHHHHHHHHHHHHcCCcceEE
Confidence            3456999999999999987777777776665443

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=85.94  E-value=0.79  Score=39.45  Aligned_cols=18  Identities=33%  Similarity=0.412  Sum_probs=16.1

Q ss_pred             CCceEECcCCCchHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAE   73 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~   73 (138)
                      .+.++.+|||+|||.+|.
T Consensus       109 ~~iLl~Gp~GtGKT~lAr  126 (412)
T PRK05342        109 SNILLIGPTGSGKTLLAQ  126 (412)
T ss_pred             ceEEEEcCCCCCHHHHHH
Confidence            567899999999999985

>PRK08118 topology modulation protein; Reviewed

Probab=85.92  E-value=0.51  Score=35.26  Aligned_cols=17  Identities=24%  Similarity=0.194  Sum_probs=14.4

Q ss_pred             CceEECcCCCchHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAE   73 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~   73 (138)
                      +.+|++|.|||||.+|-
T Consensus         3 rI~I~G~~GsGKSTlak   19 (167)
T PRK08118          3 KIILIGSGGSGKSTLAR   19 (167)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            34699999999999875

>KOG0349 consensus Putative DEAD-box RNA helicase DDX1 [RNA processing and modification]

Probab=85.85  E-value=0.47  Score=41.97  Aligned_cols=54  Identities=19%  Similarity=0.261  Sum_probs=38.6

Q ss_pred             CCcEEEEechHHHHHHHHHHHHHhcC------ceE--E-EecCCcC------CCCCCEEEecHHHHHHhh
Q 042424           83 KQRVIYTSSLKALSNQKYRELHKEFK------DVG--L-MTGDVTL------SPNASCLVMTTEILRGML  137 (138)
Q Consensus        83 ~~rviyv~P~kaLv~Q~~~~l~~~f~------~v~--~-~tGd~~~------~~~~~IiVtTpe~l~~lL  137 (138)
                      .-.++++-|.++|++|.++.+.+ |.      .+.  + +.|....      ....+|+|.||.+++.++
T Consensus       286 ap~avivepsrelaEqt~N~i~~-Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g~~ivvGtpgRl~~~i  354 (725)
T KOG0349|consen  286 APEAVIVEPSRELAEQTHNQIEE-FKMHTSNPEVRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPI  354 (725)
T ss_pred             CcceeEecCcHHHHHHHHhhHHH-HHhhcCChhhhhhhhhhhHHhHHHHHHhhcCceeeecCchhhhhhh
Confidence            35789999999999999997666 43      233  3 3333221      226789999999998775

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=85.80  E-value=1.5  Score=33.50  Aligned_cols=31  Identities=19%  Similarity=0.020  Sum_probs=25.7

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      .+..++|-|||.+|+-...+++.+|.+++++
T Consensus         9 ~v~~g~GkGKtt~a~g~a~ra~~~g~~v~iv   39 (173)
T TIGR00708         9 IVHTGNGKGKTTAAFGMALRALGHGKKVGVI   39 (173)
T ss_pred             EEECCCCCChHHHHHHHHHHHHHCCCeEEEE
Confidence            3888999999999986666777888888766

Alternate name: corrinoid adenosyltransferase.

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=85.68  E-value=0.98  Score=37.72  Aligned_cols=73  Identities=21%  Similarity=0.257  Sum_probs=41.8

Q ss_pred             CCCCcchhhhhcCCCC-----------CCcc---cccccCCCCccCCCCCCCceEECcCCCchHHHHHHHHHHHHHcC-C
Q 042424           20 RGTPKEESTKKQRNPT-----------RSCV---HEVAVPSCYTLTTDETTHGTLTNPVYNGKTAVAEYAIAMAFRDK-Q   84 (138)
Q Consensus        20 ~~~p~~~~~~~~~~~~-----------~~~~---~~~~~p~~y~~~~~~~~~~~l~aPTGsGKTlva~~ai~~~l~~~-~   84 (138)
                      -.+|.+++....+.+.           ..|.   .....|..|.--  ..+|.+..+|+|.|||.+|-     ++... +
T Consensus       104 l~~~~~~~~e~~~~it~ddViGqEeAK~kcrli~~yLenPe~Fg~W--APknVLFyGppGTGKTm~Ak-----alane~k  176 (368)
T COG1223         104 LETPREEDREIISDITLDDVIGQEEAKRKCRLIMEYLENPERFGDW--APKNVLFYGPPGTGKTMMAK-----ALANEAK  176 (368)
T ss_pred             ecCcchhhhhhhccccHhhhhchHHHHHHHHHHHHHhhChHHhccc--CcceeEEECCCCccHHHHHH-----HHhcccC
Confidence            4567777776555443           2232   233455543322  13788899999999997653     33332 3


Q ss_pred             cEEEEechHHHHHHH
Q 042424           85 RVIYTSSLKALSNQK   99 (138)
Q Consensus        85 rviyv~P~kaLv~Q~   99 (138)
                      --++.+--..|+-++
T Consensus       177 vp~l~vkat~liGeh  191 (368)
T COG1223         177 VPLLLVKATELIGEH  191 (368)
T ss_pred             CceEEechHHHHHHH
Confidence            345556656665444

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=85.61  E-value=1.3  Score=40.01  Aligned_cols=56  Identities=14%  Similarity=-0.083  Sum_probs=40.4

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEE
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLM  113 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~  113 (138)
                      ..+.++.||||||||......-+  +..+..+|++=|--++........++ ++ .|-++
T Consensus       158 ~~hvLviapTgSGKg~g~VIPnL--L~~~~S~VV~DpKGEl~~~Ta~~R~~-~G~~V~vf  214 (606)
T PRK13897        158 FQHALLFAPTGSGKGVGFVIPNL--LFWEDSVVVHDIKLENYELTSGWREK-QGQKVFVW  214 (606)
T ss_pred             CceEEEEcCCCCCcceEEehhhH--HhCCCCEEEEeCcHHHHHHHHHHHHH-CCCeEEEE
Confidence            36788999999999987654332  23467888888888888777755544 66 56655

>PRK00131 aroK shikimate kinase; Reviewed

Probab=85.50  E-value=1.1  Score=32.34  Aligned_cols=18  Identities=17%  Similarity=0.185  Sum_probs=15.1

Q ss_pred             CceEECcCCCchHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~   74 (138)
                      ..++++|.|||||.++..
T Consensus         6 ~i~l~G~~GsGKstla~~   23 (175)
T PRK00131          6 NIVLIGFMGAGKSTIGRL   23 (175)
T ss_pred             eEEEEcCCCCCHHHHHHH
Confidence            455999999999999863

>PRK03846 adenylylsulfate kinase; Provisional

Probab=85.45  E-value=1.7  Score=32.97  Aligned_cols=31  Identities=16%  Similarity=-0.047  Sum_probs=19.8

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      .++++.|||||.++..........|..++++
T Consensus        28 ~i~G~~GsGKSTla~~l~~~l~~~~~~~~~l   58 (198)
T PRK03846         28 WFTGLSGSGKSTVAGALEEALHELGVSTYLL   58 (198)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhCCCCEEEE
Confidence            3999999999987753333222345555555

>PRK08233 hypothetical protein; Provisional

Probab=85.41  E-value=0.85  Score=33.34  Aligned_cols=15  Identities=27%  Similarity=0.308  Sum_probs=13.1

Q ss_pred             EECcCCCchHHHHHH
Q 042424           60 LTNPVYNGKTAVAEY   74 (138)
Q Consensus        60 l~aPTGsGKTlva~~   74 (138)
                      +.+++|||||..+..
T Consensus         8 I~G~~GsGKtTla~~   22 (182)
T PRK08233          8 IAAVSGGGKTTLTER   22 (182)
T ss_pred             EECCCCCCHHHHHHH
Confidence            889999999998853

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=85.41  E-value=0.57  Score=40.47  Aligned_cols=18  Identities=33%  Similarity=0.412  Sum_probs=16.0

Q ss_pred             CCceEECcCCCchHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAE   73 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~   73 (138)
                      .+.++.+|||+|||.+|.
T Consensus       117 ~~iLL~GP~GsGKT~lAr  134 (413)
T TIGR00382       117 SNILLIGPTGSGKTLLAQ  134 (413)
T ss_pred             ceEEEECCCCcCHHHHHH
Confidence            567799999999999985

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.

>PF01745 IPT: Isopentenyl transferase; InterPro: IPR002648 Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid []

Probab=85.35  E-value=1.4  Score=35.45  Aligned_cols=16  Identities=38%  Similarity=0.418  Sum_probs=12.6

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      ++.+|||+|||-.|..
T Consensus         5 ~i~GpT~tGKt~~ai~   20 (233)
T PF01745_consen    5 LIVGPTGTGKTALAIA   20 (233)
T ss_dssp             EEE-STTSSHHHHHHH
T ss_pred             EEECCCCCChhHHHHH
Confidence            5899999999987753

; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.

>PTZ00035 Rad51 protein; Provisional

Probab=85.31  E-value=1.5  Score=36.69  Aligned_cols=33  Identities=18%  Similarity=0.223  Sum_probs=23.4

Q ss_pred             EECcCCCchHHHHHHHHHHHHH------cCCcEEEEech
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFR------DKQRVIYTSSL   92 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~------~~~rviyv~P~   92 (138)
                      |++|.|+|||..+...+.....      .+.+++|+---
T Consensus       123 I~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE  161 (337)
T PTZ00035        123 LFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTE  161 (337)
T ss_pred             EECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEcc
Confidence            9999999999999744433321      35688887643

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=85.27  E-value=2.4  Score=39.27  Aligned_cols=50  Identities=16%  Similarity=0.194  Sum_probs=40.3

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEechHHHHHHHHHHHHHhc
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLKALSNQKYRELHKEF  107 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~kaLv~Q~~~~l~~~f  107 (138)
                      .++.+|=|.|||.+...++...+. .|.+++|++|...-+.+.++++++.+
T Consensus       190 tV~taPRqrGKS~iVgi~l~~La~f~Gi~IlvTAH~~~ts~evF~rv~~~l  240 (752)
T PHA03333        190 TAATVPRRCGKTTIMAIILAAMISFLEIDIVVQAQRKTMCLTLYNRVETVV  240 (752)
T ss_pred             eEEEeccCCCcHHHHHHHHHHHHHhcCCeEEEECCChhhHHHHHHHHHHHH
Confidence            458999999999998755554444 58999999999999999888876654

>PRK06851 hypothetical protein; Provisional

Probab=85.24  E-value=1.4  Score=37.49  Aligned_cols=37  Identities=16%  Similarity=0.119  Sum_probs=28.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcE-EEEech
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRV-IYTSSL   92 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rv-iyv~P~   92 (138)
                      +..+|.+++|+|||.+....+..+..+|.++ +|=+|.
T Consensus       215 ~~~~i~G~pG~GKstl~~~i~~~a~~~G~~v~~~hC~~  252 (367)
T PRK06851        215 NRYFLKGRPGTGKSTMLKKIAKAAEERGFDVEVYHCGF  252 (367)
T ss_pred             eEEEEeCCCCCcHHHHHHHHHHHHHhCCCeEEEEeCCC
Confidence            3455999999999999987777777788766 444444

>TIGR03263 guanyl_kin guanylate kinase

Probab=85.22  E-value=0.79  Score=33.72  Aligned_cols=17  Identities=18%  Similarity=0.329  Sum_probs=13.9

Q ss_pred             eEECcCCCchHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~a   75 (138)
                      ++.+|+|||||.++...
T Consensus         5 ~l~G~~GsGKsTl~~~L   21 (180)
T TIGR03263         5 VISGPSGVGKSTLVKAL   21 (180)
T ss_pred             EEECCCCCCHHHHHHHH
Confidence            59999999999876533

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.

>KOG1131 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 5'-3' helicase subunit RAD3 [Transcription; Replication, recombination and repair]

Probab=85.10  E-value=2.6  Score=38.14  Aligned_cols=53  Identities=25%  Similarity=0.266  Sum_probs=39.0

Q ss_pred             CCCCceEECcCCCchHHHHH-HHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHh
Q 042424           54 ETTHGTLTNPVYNGKTAVAE-YAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKE  106 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~-~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~  106 (138)
                      ..++.++-.|+|.|||+.-+ +.+...+..   -.+.||.+-|..=++....+++..
T Consensus        34 akGh~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRTvpEieK~l~El~~l   90 (755)
T KOG1131|consen   34 AKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEELKRL   90 (755)
T ss_pred             cCCcEEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCcchHHHHHHHHHHHH
Confidence            34788999999999998765 344444443   478999998887777777777654

>PF02283 CobU: Cobinamide kinase / cobinamide phosphate guanyltransferase; InterPro: IPR003203 This family is composed of a group of bifunctional cobalbumin biosynthesis enzymes which display cobinamide kinase and cobinamide phosphate guanyltransferase activity

Probab=85.04  E-value=2.4  Score=31.97  Aligned_cols=44  Identities=16%  Similarity=0.243  Sum_probs=33.6

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      ++++...||||-.|+..+   ...+.+.+|++-.++.=.++.+++.+
T Consensus         2 lv~GG~rSGKS~~Ae~la---~~~~~~~~YiAT~~~~D~em~~RI~~   45 (167)
T PF02283_consen    2 LVTGGARSGKSSFAERLA---LSFGGPVTYIATARPFDEEMRERIAR   45 (167)
T ss_dssp             EEEESTTSSHHHHHHHHH---TS--SCEEEEESSHHHHHHHHHHHHH
T ss_pred             EEeCCCCcchHHHHHHHH---HhcCCCcEEEeCCCCCCHHHHHHHHH
Confidence            588999999998887443   23468999999999997777777765

The crystal structure of the enzyme reveals the molecule to be a trimer with a propeller-like shape [].; GO: 0000166 nucleotide binding, 0043752 adenosylcobinamide kinase activity, 0051188 cofactor biosynthetic process; PDB: 1CBU_C 1C9K_B.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=84.99  E-value=2.4  Score=38.98  Aligned_cols=43  Identities=16%  Similarity=-0.048  Sum_probs=30.3

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHH-cC--CcEEEEechHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFR-DK--QRVIYTSSLKALSNQKY  100 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~-~~--~rviyv~P~kaLv~Q~~  100 (138)
                      -.+|+++.|+|||.+....+ .++. .+  .+++.++||-.-+....
T Consensus       340 ~~iitGgpGTGKTt~l~~i~-~~~~~~~~~~~v~l~ApTg~AA~~L~  385 (720)
T TIGR01448       340 VVILTGGPGTGKTTITRAII-ELAEELGGLLPVGLAAPTGRAAKRLG  385 (720)
T ss_pred             eEEEECCCCCCHHHHHHHHH-HHHHHcCCCceEEEEeCchHHHHHHH
Confidence            35699999999998875333 3343 35  68889999966665443

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.

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=84.94  E-value=1.2  Score=36.74  Aligned_cols=14  Identities=29%  Similarity=0.427  Sum_probs=13.0

Q ss_pred             EECcCCCchHHHHH
Q 042424           60 LTNPVYNGKTAVAE   73 (138)
Q Consensus        60 l~aPTGsGKTlva~   73 (138)
                      |.||+|||||..+.
T Consensus        67 IaG~~GSGKSTlar   80 (290)
T TIGR00554        67 IAGSVAVGKSTTAR   80 (290)
T ss_pred             EECCCCCCHHHHHH
Confidence            99999999999884

Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model.

>PHA00350 putative assembly protein

Probab=84.93  E-value=1.2  Score=38.39  Aligned_cols=29  Identities=28%  Similarity=0.291  Sum_probs=23.8

Q ss_pred             eEECcCCCchHHHHH-HHHHHHHHcCCcEE
Q 042424           59 TLTNPVYNGKTAVAE-YAIAMAFRDKQRVI   87 (138)
Q Consensus        59 ~l~aPTGsGKTlva~-~ai~~~l~~~~rvi   87 (138)
                      ++.+..|||||+.+. +.|..++++|++++
T Consensus         5 l~tG~pGSGKT~~aV~~~i~palk~GR~V~   34 (399)
T PHA00350          5 AIVGRPGSYKSYEAVVYHIIPALKDGRKVI   34 (399)
T ss_pred             EEecCCCCchhHHHHHHHHHHHHHCCCEEE
Confidence            489999999999997 57888888886543

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=84.84  E-value=3.6  Score=36.11  Aligned_cols=46  Identities=9%  Similarity=-0.065  Sum_probs=29.8

Q ss_pred             CCCCceEECcCCCchHHHHH-HHHHHHHHcCCcEEEEechHHHHHHHHHHH
Q 042424           54 ETTHGTLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTSSLKALSNQKYREL  103 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l  103 (138)
                      .+.|.++.+|+|.|||.++. ++...++..|   -|+ -.-.|..+.....
T Consensus       208 ~~~Nli~lGp~GTGKThla~~l~~~~a~~sG---~f~-T~a~Lf~~L~~~~  254 (449)
T TIGR02688       208 PNYNLIELGPKGTGKSYIYNNLSPYVILISG---GTI-TVAKLFYNISTRQ  254 (449)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHhHHHHHHcC---CcC-cHHHHHHHHHHHH
Confidence            34788999999999998875 4555456666   222 2334555555433

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>PF06414 Zeta_toxin: Zeta toxin; InterPro: IPR010488 This entry represents a domain originally identified in bacterial zeta toxin proteins, where it comprises the whole protein []

Probab=84.83  E-value=1.1  Score=34.05  Aligned_cols=19  Identities=16%  Similarity=0.256  Sum_probs=14.6

Q ss_pred             eEECcCCCchHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIA   77 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~   77 (138)
                      ++.|+.|||||.++...+.
T Consensus        19 i~aG~~GsGKSt~~~~~~~   37 (199)
T PF06414_consen   19 IIAGQPGSGKSTLARQLLE   37 (199)
T ss_dssp             EEES-TTSTTHHHHHHHHH
T ss_pred             EEeCCCCCCHHHHHHHhhh
Confidence            3899999999998876554

It has subsequently been found in a number of other proteins, such as polynucleotide kinase and 2',3'-cyclic-nucleotide 3'-phosphodiesterase. It appears to function as a kinase domain [, ].; GO: 0005524 ATP binding, 0016301 kinase activity; PDB: 2P5T_H 1GVN_B 3Q8X_D.

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=84.74  E-value=1  Score=33.35  Aligned_cols=18  Identities=33%  Similarity=0.202  Sum_probs=14.8

Q ss_pred             ceEECcCCCchHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~a   75 (138)
                      .+|.+|.|||||.++...
T Consensus         2 I~i~G~pGsGKst~a~~L   19 (194)
T cd01428           2 ILLLGPPGSGKGTQAERL   19 (194)
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            469999999999888543

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=84.67  E-value=2.3  Score=26.93  Aligned_cols=16  Identities=31%  Similarity=0.364  Sum_probs=13.5

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      .++++.|||||.++..
T Consensus         3 ~i~G~~gsGKst~~~~   18 (69)
T cd02019           3 AITGGSGSGKSTVAKK   18 (69)
T ss_pred             EEECCCCCCHHHHHHH
Confidence            4899999999988753

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=84.65  E-value=3.1  Score=37.43  Aligned_cols=48  Identities=15%  Similarity=0.138  Sum_probs=31.6

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHH--c---CCcEEEEechHHHHHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFR--D---KQRVIYTSSLKALSNQKYRELH  104 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~--~---~~rviyv~P~kaLv~Q~~~~l~  104 (138)
                      -.+|+++.|+|||.+....+.....  .   +.++++++||---+....+.+.
T Consensus       162 ~~vitGgpGTGKTt~v~~ll~~l~~~~~~~~~~~I~l~APTGkAA~rL~e~~~  214 (586)
T TIGR01447       162 FSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPTGKAAARLAESLR  214 (586)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHhccccCCCcEEEECCcHHHHHHHHHHHH
Confidence            3459999999999987533332222  1   1579999999655555555443

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.

>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]

Probab=84.60  E-value=0.68  Score=43.33  Aligned_cols=21  Identities=29%  Similarity=0.525  Sum_probs=15.5

Q ss_pred             eEECcCCCchHHHHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAF   80 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l   80 (138)
                      +|+||||||||.+.. ||..||
T Consensus        29 lI~G~nGsGKSSIld-AI~~AL   49 (908)
T COG0419          29 LIVGPNGAGKSSILD-AITFAL   49 (908)
T ss_pred             EEECCCCCcHHHHHH-HHHHHH
Confidence            499999999997753 444444

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=84.57  E-value=2.1  Score=32.19  Aligned_cols=30  Identities=27%  Similarity=0.175  Sum_probs=20.6

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      +++-.|||||.+|...-.+....|.++.++
T Consensus         7 ltGlsGsGKtTlA~~L~~~L~~~g~~~~~L   36 (156)
T PF01583_consen    7 LTGLSGSGKTTLARALERRLFARGIKVYLL   36 (156)
T ss_dssp             EESSTTSSHHHHHHHHHHHHHHTTS-EEEE
T ss_pred             EECCCCCCHHHHHHHHHHHHHHcCCcEEEe
Confidence            899999999988765444433456666665

Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....

>PHA02244 ATPase-like protein

Probab=84.57  E-value=1.7  Score=37.32  Aligned_cols=20  Identities=25%  Similarity=0.149  Sum_probs=16.6

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      .+.+|.+|||+|||.++...
T Consensus       120 ~PVLL~GppGtGKTtLA~aL  139 (383)
T PHA02244        120 IPVFLKGGAGSGKNHIAEQI  139 (383)
T ss_pred             CCEEEECCCCCCHHHHHHHH
Confidence            56779999999999887643

>PF02492 cobW: CobW/HypB/UreG, nucleotide-binding domain; InterPro: IPR003495 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt

Probab=84.49  E-value=1.7  Score=32.43  Aligned_cols=35  Identities=20%  Similarity=0.156  Sum_probs=24.1

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKA   94 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~ka   94 (138)
                      ++++.-|||||......+. ...++.|+.++..--.
T Consensus         4 ii~GfLGsGKTTli~~ll~-~~~~~~~~~vI~ne~g   38 (178)
T PF02492_consen    4 IITGFLGSGKTTLINHLLK-RNRQGERVAVIVNEFG   38 (178)
T ss_dssp             EEEESTTSSHHHHHHHHHH-HHTTTS-EEEEECSTT
T ss_pred             EEEcCCCCCHHHHHHHHHH-HhcCCceeEEEEcccc
Confidence            5899999999987655554 3456788877766433

Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents CobW-like proteins, including P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [], and urease accessory protein UreG, which acts as a chaperone in the activation of urease upon insertion of nickel into the active site [].; PDB: 2WSM_B 1NIJ_A 2HF9_A 2HF8_B.

>PRK08840 replicative DNA helicase; Provisional

Probab=84.37  E-value=1.6  Score=38.06  Aligned_cols=44  Identities=18%  Similarity=0.088  Sum_probs=29.6

Q ss_pred             eEECcCCCchHHHHHHHHHHH-HHcCCcEEEEechHHHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMA-FRDKQRVIYTSSLKALSNQKYREL  103 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~-l~~~~rviyv~P~kaLv~Q~~~~l  103 (138)
                      +|.|.+|.|||..++..+.++ ..+|..++|++.-.+ .+|...++
T Consensus       221 viaarPg~GKTafalnia~~~a~~~~~~v~~fSlEMs-~~ql~~Rl  265 (464)
T PRK08840        221 IVAARPSMGKTTFAMNLCENAAMDQDKPVLIFSLEMP-AEQLMMRM  265 (464)
T ss_pred             EEEeCCCCchHHHHHHHHHHHHHhCCCeEEEEeccCC-HHHHHHHH
Confidence            489999999999997544444 456788888765432 44444444

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=84.36  E-value=1.1  Score=35.55  Aligned_cols=32  Identities=22%  Similarity=0.401  Sum_probs=18.2

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      |.||-|||||..+. ++.+.+...+|-++++..
T Consensus         1 ViGpaGSGKTT~~~-~~~~~~~~~~~~~~~vNL   32 (238)
T PF03029_consen    1 VIGPAGSGKTTFCK-GLSEWLESNGRDVYIVNL   32 (238)
T ss_dssp             -EESTTSSHHHHHH-HHHHHHTTT-S-EEEEE-
T ss_pred             CCCCCCCCHHHHHH-HHHHHHHhccCCceEEEc
Confidence            57999999997553 444445544455555543

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=84.25  E-value=1.3  Score=41.39  Aligned_cols=17  Identities=24%  Similarity=0.190  Sum_probs=14.7

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .+++||||+|||.+|..
T Consensus       601 ~Lf~Gp~G~GKT~lA~a  617 (857)
T PRK10865        601 FLFLGPTGVGKTELCKA  617 (857)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            46999999999999854

>PLN03025 replication factor C subunit; Provisional

Probab=84.24  E-value=1.3  Score=36.22  Aligned_cols=24  Identities=21%  Similarity=0.066  Sum_probs=18.2

Q ss_pred             CCceEECcCCCchHHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMA   79 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~   79 (138)
                      .+.+++||.|+|||..+.......
T Consensus        35 ~~lll~Gp~G~GKTtla~~la~~l   58 (319)
T PLN03025         35 PNLILSGPPGTGKTTSILALAHEL   58 (319)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHH
Confidence            346799999999998886554443

>PRK08006 replicative DNA helicase; Provisional

Probab=84.18  E-value=1.7  Score=38.02  Aligned_cols=59  Identities=17%  Similarity=0.049  Sum_probs=35.5

Q ss_pred             cCCCCccCCC---C--CCC-ceEECcCCCchHHHHHHHHHHH-HHcCCcEEEEechHHHHHHHHHHH
Q 042424           44 VPSCYTLTTD---E--TTH-GTLTNPVYNGKTAVAEYAIAMA-FRDKQRVIYTSSLKALSNQKYREL  103 (138)
Q Consensus        44 ~p~~y~~~~~---~--~~~-~~l~aPTGsGKTlva~~ai~~~-l~~~~rviyv~P~kaLv~Q~~~~l  103 (138)
                      +|.||..+..   +  .+. .+|.|.+|.|||..++..+.++ ..+|..++|++.-. =.+|...++
T Consensus       207 i~TG~~~LD~~~~Gl~~G~LiiIaarPgmGKTafalnia~~~a~~~g~~V~~fSlEM-~~~ql~~Rl  272 (471)
T PRK08006        207 VNTGYDDLNKKTAGLQPSDLIIVAARPSMGKTTFAMNLCENAAMLQDKPVLIFSLEM-PGEQIMMRM  272 (471)
T ss_pred             ccCCCHHHHHhhcCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhcCCeEEEEeccC-CHHHHHHHH
Confidence            5666654322   1  123 3489999999999998544444 45678888876542 233444443

>PRK06904 replicative DNA helicase; Validated

Probab=84.15  E-value=1.7  Score=38.04  Aligned_cols=46  Identities=17%  Similarity=0.051  Sum_probs=30.8

Q ss_pred             eEECcCCCchHHHHHHHHHHH-HHcCCcEEEEechHHHHHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMA-FRDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~-l~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      +|.|.+|.|||..++..+.++ ...|..++|++.- -=.+|...++-.
T Consensus       225 iIaarPg~GKTafalnia~~~a~~~g~~Vl~fSlE-Ms~~ql~~Rlla  271 (472)
T PRK06904        225 IVAARPSMGKTTFAMNLCENAAMASEKPVLVFSLE-MPAEQIMMRMLA  271 (472)
T ss_pred             EEEeCCCCChHHHHHHHHHHHHHhcCCeEEEEecc-CCHHHHHHHHHH
Confidence            489999999999987544444 3457788877554 344555555443

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=84.13  E-value=1  Score=36.86  Aligned_cols=20  Identities=35%  Similarity=0.321  Sum_probs=16.5

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      .+.++++|.|+|||.++...
T Consensus        52 ~~~ll~GppG~GKT~la~~i   71 (328)
T PRK00080         52 DHVLLYGPPGLGKTTLANII   71 (328)
T ss_pred             CcEEEECCCCccHHHHHHHH
Confidence            45679999999999988743

>PRK07773 replicative DNA helicase; Validated

Probab=84.11  E-value=1.5  Score=41.14  Aligned_cols=34  Identities=18%  Similarity=-0.006  Sum_probs=25.2

Q ss_pred             ceEECcCCCchHHHHHHHHHHH-HHcCCcEEEEec
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMA-FRDKQRVIYTSS   91 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~-l~~~~rviyv~P   91 (138)
                      .+|.|++|.|||..++..+.+. .+.+..++|++-
T Consensus       220 ivIagrPg~GKT~fal~ia~~~a~~~~~~V~~fSl  254 (886)
T PRK07773        220 IIVAARPSMGKTTFGLDFARNCAIRHRLAVAIFSL  254 (886)
T ss_pred             EEEEeCCCCCcHHHHHHHHHHHHHhcCCeEEEEec
Confidence            3499999999999998555444 445777877764

>cd00550 ArsA_ATPase Oxyanion-translocating ATPase (ArsA)

Probab=84.09  E-value=1.7  Score=34.58  Aligned_cols=32  Identities=16%  Similarity=0.121  Sum_probs=23.4

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      ++++..|.|||.++......+.+.|+|++++.
T Consensus         4 ~~~gkgG~GKtt~a~~la~~~a~~g~~vLlvd   35 (254)
T cd00550           4 FFGGKGGVGKTTISAATAVRLAEQGKKVLLVS   35 (254)
T ss_pred             EEECCCCchHHHHHHHHHHHHHHCCCCceEEe
Confidence            47888999999999744444446688887763

This ATPase is involved in transport of arsenite, antimonite or other oxyanions across biological membranes in all three kingdoms of life. ArsA contains a highly conserved AAA motif present in the AAA+ ATPase superfamily associated with a variety of cellular activities. To form a functional ATP-driven pump, ArsA interacts with the permease ArsB, which is a channel-forming integral membrane protein. One of the most interesting features of ArsA is the allosteric activation by its transport substrates. A divalent cation, typically Mg2+, is required for its enzymatic activity.

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=84.03  E-value=1.1  Score=33.04  Aligned_cols=16  Identities=25%  Similarity=0.503  Sum_probs=14.1

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      +|.+|.|||||.++-.
T Consensus         5 ~i~G~sGsGKttl~~~   20 (179)
T TIGR02322         5 YVVGPSGAGKDTLLDY   20 (179)
T ss_pred             EEECCCCCCHHHHHHH
Confidence            5999999999999863

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=83.78  E-value=3.8  Score=36.87  Aligned_cols=56  Identities=25%  Similarity=0.345  Sum_probs=40.9

Q ss_pred             HHHHHHHcCCcEEEEechH--------HHHHHHHHHHHHhcC--ceEEEecCCcCC-----------CCCCEEEecH
Q 042424           75 AIAMAFRDKQRVIYTSSLK--------ALSNQKYRELHKEFK--DVGLMTGDVTLS-----------PNASCLVMTT  130 (138)
Q Consensus        75 ai~~~l~~~~rviyv~P~k--------aLv~Q~~~~l~~~f~--~v~~~tGd~~~~-----------~~~~IiVtTp  130 (138)
                      .+...+.++.++++++|+.        .-+++.++.+.+.|.  .|+.++|+.+..           .+.+|+|||.
T Consensus       440 ~i~~~l~~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~  516 (630)
T TIGR00643       440 FIEEEIAKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATT  516 (630)
T ss_pred             HHHHHHHhCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECc
Confidence            3444456688999999975        346677788887665  789999987542           2678999996

>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor

Probab=83.78  E-value=2.3  Score=31.13  Aligned_cols=31  Identities=19%  Similarity=0.076  Sum_probs=20.5

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      ++.||-|||||..+.....+.-..|.+++.+
T Consensus         4 ~ieG~~GsGKtT~~~~L~~~l~~~g~~v~~~   34 (200)
T cd01672           4 VFEGIDGAGKTTLIELLAERLEARGYEVVLT   34 (200)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            4899999999998864333222346666555

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>PRK08356 hypothetical protein; Provisional

Probab=83.74  E-value=0.93  Score=34.33  Aligned_cols=17  Identities=29%  Similarity=0.468  Sum_probs=14.9

Q ss_pred             eEECcCCCchHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~a   75 (138)
                      ++++|.|||||.++.+.
T Consensus         9 ~~~G~~gsGK~t~a~~l   25 (195)
T PRK08356          9 GVVGKIAAGKTTVAKFF   25 (195)
T ss_pred             EEECCCCCCHHHHHHHH
Confidence            48999999999999755

>PRK14530 adenylate kinase; Provisional

Probab=83.71  E-value=1.3  Score=33.97  Aligned_cols=19  Identities=16%  Similarity=-0.022  Sum_probs=15.5

Q ss_pred             CceEECcCCCchHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~a   75 (138)
                      +.+|.+|+|||||.++...
T Consensus         5 ~I~i~G~pGsGKsT~~~~L   23 (215)
T PRK14530          5 RILLLGAPGAGKGTQSSNL   23 (215)
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4569999999999988643

>PRK06321 replicative DNA helicase; Provisional

Probab=83.59  E-value=1.8  Score=37.86  Aligned_cols=33  Identities=27%  Similarity=0.125  Sum_probs=24.3

Q ss_pred             eEECcCCCchHHHHHHHHHHH-HHcCCcEEEEec
Q 042424           59 TLTNPVYNGKTAVAEYAIAMA-FRDKQRVIYTSS   91 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~-l~~~~rviyv~P   91 (138)
                      +|.|.+|.|||..++..+.++ ...|..++|++.
T Consensus       230 iiaarPgmGKTafal~ia~~~a~~~g~~v~~fSL  263 (472)
T PRK06321        230 ILAARPAMGKTALALNIAENFCFQNRLPVGIFSL  263 (472)
T ss_pred             EEEeCCCCChHHHHHHHHHHHHHhcCCeEEEEec
Confidence            489999999999998544443 345778877754

>PRK14737 gmk guanylate kinase; Provisional

Probab=83.59  E-value=0.98  Score=34.42  Aligned_cols=19  Identities=11%  Similarity=0.258  Sum_probs=15.5

Q ss_pred             eEECcCCCchHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIA   77 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~   77 (138)
                      +|++|.|+|||.++-..+.
T Consensus         8 vl~GpsG~GK~tl~~~l~~   26 (186)
T PRK14737          8 IISSVAGGGKSTIIQALLE   26 (186)
T ss_pred             EEECCCCCCHHHHHHHHHh
Confidence            4999999999988765544

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=83.53  E-value=1.3  Score=31.02  Aligned_cols=15  Identities=33%  Similarity=0.607  Sum_probs=13.4

Q ss_pred             eEECcCCCchHHHHH
Q 042424           59 TLTNPVYNGKTAVAE   73 (138)
Q Consensus        59 ~l~aPTGsGKTlva~   73 (138)
                      ++++++|||||.+|.
T Consensus         3 ~i~G~~GsGKst~a~   17 (147)
T cd02020           3 AIDGPAGSGKSTVAK   17 (147)
T ss_pred             EEECCCCCCHHHHHH
Confidence            489999999999886

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=83.53  E-value=5.4  Score=32.57  Aligned_cols=55  Identities=11%  Similarity=0.160  Sum_probs=41.9

Q ss_pred             HHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCCcCC---------------CCCCEEEecH
Q 042424           76 IAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVTLS---------------PNASCLVMTT  130 (138)
Q Consensus        76 i~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~~~---------------~~~~IiVtTp  130 (138)
                      +...+..+++++++++++.-++..++.|++...  .+..++|+....               .+..|+|||.
T Consensus       215 l~~~~~~~~~~lVf~~t~~~~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~  286 (358)
T TIGR01587       215 LLEFIKKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQ  286 (358)
T ss_pred             HHHHhhCCCeEEEEECCHHHHHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECc
Confidence            334445689999999999999999999988554  588888875321               1556999996

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.

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=83.46  E-value=1.1  Score=37.86  Aligned_cols=21  Identities=29%  Similarity=0.200  Sum_probs=16.7

Q ss_pred             CCceEECcCCCchHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai   76 (138)
                      .+.++.+|+|+|||+++....
T Consensus       166 ~gvLL~GppGtGKT~lAkaia  186 (389)
T PRK03992        166 KGVLLYGPPGTGKTLLAKAVA  186 (389)
T ss_pred             CceEEECCCCCChHHHHHHHH
Confidence            456799999999998876443

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=83.39  E-value=4  Score=30.31  Aligned_cols=30  Identities=20%  Similarity=0.207  Sum_probs=20.8

Q ss_pred             eEECcCCCchHHHHHHHHHHHHH-cCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv   89 (138)
                      ++.|+-|||||..+.... +++. .|.+++++
T Consensus         7 vieG~~GsGKsT~~~~L~-~~l~~~g~~v~~~   37 (195)
T TIGR00041         7 VIEGIDGAGKTTQANLLK-KLLQENGYDVLFT   37 (195)
T ss_pred             EEECCCCCCHHHHHHHHH-HHHHHcCCeEEEE
Confidence            499999999998886432 3444 36666554

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.

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=83.23  E-value=3  Score=36.32  Aligned_cols=41  Identities=17%  Similarity=0.077  Sum_probs=27.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQK   99 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~   99 (138)
                      .+.++.+|.|+|||.+|.+...   ..+.....+..+.+=+.+.
T Consensus        49 ~SmIl~GPPG~GKTTlA~liA~---~~~~~f~~~sAv~~gvkdl   89 (436)
T COG2256          49 HSMILWGPPGTGKTTLARLIAG---TTNAAFEALSAVTSGVKDL   89 (436)
T ss_pred             ceeEEECCCCCCHHHHHHHHHH---hhCCceEEeccccccHHHH
Confidence            6788999999999998764332   2245555555555444443

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=83.13  E-value=2.2  Score=35.82  Aligned_cols=30  Identities=17%  Similarity=0.057  Sum_probs=20.0

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      +++|.|+|||......+......|.++.++
T Consensus        61 i~G~~GaGKSTl~~~l~~~l~~~g~~v~vi   90 (332)
T PRK09435         61 ITGVPGVGKSTFIEALGMHLIEQGHKVAVL   90 (332)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            999999999998764444333445555433

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=83.07  E-value=2.2  Score=35.87  Aligned_cols=48  Identities=13%  Similarity=0.237  Sum_probs=31.4

Q ss_pred             EECcCCCchHHHHHHHHHHHHH---c---CCcEEEEechHHHHHHHHHHHHHhc
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFR---D---KQRVIYTSSLKALSNQKYRELHKEF  107 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~---~---~~rviyv~P~kaLv~Q~~~~l~~~f  107 (138)
                      ++++.|+|||..++..+..+..   .   +.+++|+----++--+...++.+.|
T Consensus       128 i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl~qia~~~  181 (342)
T PLN03186        128 IYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRLIQIAERF  181 (342)
T ss_pred             EECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHHHHHHHHc
Confidence            9999999999999744433321   1   3489998766655444444544444

>cd02037 MRP-like MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily

Probab=82.92  E-value=2.2  Score=31.23  Aligned_cols=29  Identities=24%  Similarity=0.125  Sum_probs=20.6

Q ss_pred             EECcCCCchHHHHH-HHHHHHHHcCCcEEEE
Q 042424           60 LTNPVYNGKTAVAE-YAIAMAFRDKQRVIYT   89 (138)
Q Consensus        60 l~aPTGsGKTlva~-~ai~~~l~~~~rviyv   89 (138)
                      .+.--|.|||.++. +|.. .-..|.|++++
T Consensus         5 ~s~kgG~GKTt~a~~LA~~-la~~g~~vllv   34 (169)
T cd02037           5 MSGKGGVGKSTVAVNLALA-LAKLGYKVGLL   34 (169)
T ss_pred             ecCCCcCChhHHHHHHHHH-HHHcCCcEEEE
Confidence            45667899999997 4443 33568888777

Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions as a Na+/H+ antiporter.

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=82.91  E-value=2.3  Score=34.61  Aligned_cols=31  Identities=19%  Similarity=0.193  Sum_probs=23.5

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcC-CcEEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDK-QRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~-~rviyv   89 (138)
                      ++|+--|+|||.++.+.+.+.+.++ .+++.|
T Consensus         4 aI~GKGG~GKTtiaalll~~l~~~~~~~VLvV   35 (255)
T COG3640           4 AITGKGGVGKTTIAALLLKRLLSKGGYNVLVV   35 (255)
T ss_pred             EEecCCCccHHHHHHHHHHHHHhcCCceEEEE
Confidence            5899999999999987555556665 666655

>PTZ00293 thymidine kinase; Provisional

Probab=82.90  E-value=2.4  Score=33.44  Aligned_cols=34  Identities=12%  Similarity=0.205  Sum_probs=27.4

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      ++++|-+||||.-.+..+.+....|++++++-|.
T Consensus         8 vi~GpMfSGKTteLLr~i~~y~~ag~kv~~~kp~   41 (211)
T PTZ00293          8 VIIGPMFSGKTTELMRLVKRFTYSEKKCVVIKYS   41 (211)
T ss_pred             EEECCCCChHHHHHHHHHHHHHHcCCceEEEEec
Confidence            4899999999976666676666678899888885

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=82.85  E-value=1.6  Score=29.99  Aligned_cols=20  Identities=20%  Similarity=0.140  Sum_probs=15.5

Q ss_pred             EECcCCCchHHHHHHHHHHH
Q 042424           60 LTNPVYNGKTAVAEYAIAMA   79 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~   79 (138)
                      +.+|.|.|||..+...+...
T Consensus         3 i~G~~G~GKS~l~~~l~~~l   22 (107)
T PF00910_consen    3 IYGPPGIGKSTLAKELAKDL   22 (107)
T ss_pred             EECCCCCCHHHHHHHHHHHH
Confidence            78999999999997544333

All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=82.83  E-value=2.7  Score=31.22  Aligned_cols=31  Identities=23%  Similarity=0.054  Sum_probs=19.8

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      .++++.|+|||.++..........|..++++
T Consensus        22 ~i~G~~GsGKstla~~l~~~l~~~~~~~~~l   52 (184)
T TIGR00455        22 WLTGLSGSGKSTIANALEKKLESKGYRVYVL   52 (184)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHcCCcEEEE
Confidence            3999999999988754333322334445554

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>TIGR00235 udk uridine kinase

Probab=82.83  E-value=1.1  Score=34.14  Aligned_cols=15  Identities=33%  Similarity=0.322  Sum_probs=13.1

Q ss_pred             eEECcCCCchHHHHH
Q 042424           59 TLTNPVYNGKTAVAE   73 (138)
Q Consensus        59 ~l~aPTGsGKTlva~   73 (138)
                      .|++|+|||||..+.
T Consensus        10 ~I~G~sGsGKSTl~~   24 (207)
T TIGR00235        10 GIGGGSGSGKTTVAR   24 (207)
T ss_pred             EEECCCCCCHHHHHH
Confidence            399999999998774

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional

Probab=82.77  E-value=2.2  Score=34.79  Aligned_cols=30  Identities=20%  Similarity=0.113  Sum_probs=21.5

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      .++++.|||||.++...+....++| ++.++
T Consensus         5 ~i~G~~gSGKTTLi~~Li~~L~~~G-~V~~I   34 (274)
T PRK14493          5 SIVGYKATGKTTLVERLVDRLSGRG-RVGTV   34 (274)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhCC-CEEEE
Confidence            3889999999999876665544456 55444

>COG1192 Soj ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=82.60  E-value=1.7  Score=34.02  Aligned_cols=30  Identities=30%  Similarity=0.254  Sum_probs=20.1

Q ss_pred             EECcCCCchHHHHH-HHHHHHHHcCCcEEEE
Q 042424           60 LTNPVYNGKTAVAE-YAIAMAFRDKQRVIYT   89 (138)
Q Consensus        60 l~aPTGsGKTlva~-~ai~~~l~~~~rviyv   89 (138)
                      ..---|.|||.++. +|..-+...|+|++++
T Consensus         8 ~n~KGGvGKTT~a~nLa~~La~~~~~kVLli   38 (259)
T COG1192           8 ANQKGGVGKTTTAVNLAAALAKRGGKKVLLI   38 (259)
T ss_pred             EecCCCccHHHHHHHHHHHHHHhcCCcEEEE
Confidence            44557899999997 4554443455777665

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=82.53  E-value=2  Score=39.37  Aligned_cols=56  Identities=18%  Similarity=0.051  Sum_probs=38.3

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEE
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLM  113 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~  113 (138)
                      ..+.++.||||||||......-  .+..+..+|++=|--++.+......++ .+ .|-++
T Consensus       139 ~~hvlviApTgSGKgvg~VIPn--LL~~~gS~VV~DpKGE~~~~Ta~~R~~-~G~~V~~F  195 (670)
T PRK13850        139 QPHSLVVAPTRAGKGVGVVIPT--LLTFKGSVIALDVKGELFELTSRARKA-SGDAVFKF  195 (670)
T ss_pred             CceEEEEecCCCCceeeehHhH--HhcCCCCEEEEeCCchHHHHHHHHHHh-CCCEEEEe
Confidence            3577899999999998764322  234467888888888888776654444 66 35443

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=82.51  E-value=0.96  Score=33.93  Aligned_cols=18  Identities=22%  Similarity=0.126  Sum_probs=14.7

Q ss_pred             CceEECcCCCchHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~   74 (138)
                      ..+|.+|.|||||.++-.
T Consensus         4 ~i~l~G~sGsGKsTl~~~   21 (186)
T PRK10078          4 LIWLMGPSGSGKDSLLAA   21 (186)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            346999999999988753

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=82.39  E-value=0.44  Score=34.50  Aligned_cols=37  Identities=27%  Similarity=0.222  Sum_probs=22.3

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQ   98 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q   98 (138)
                      ++.++-|||||...- ++.+++  |..-.+.+||=+|++.
T Consensus        19 ~L~GdLGaGKTtf~r-~l~~~l--g~~~~V~SPTF~l~~~   55 (123)
T PF02367_consen   19 LLSGDLGAGKTTFVR-GLARAL--GIDEEVTSPTFSLVNE   55 (123)
T ss_dssp             EEEESTTSSHHHHHH-HHHHHT--T--S----TTTTSEEE
T ss_pred             EEECCCCCCHHHHHH-HHHHHc--CCCCCcCCCCeEEEEE
Confidence            399999999998765 444444  4444788999887643

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.

>PRK01184 hypothetical protein; Provisional

Probab=82.37  E-value=1.1  Score=33.15  Aligned_cols=16  Identities=13%  Similarity=0.090  Sum_probs=13.8

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      .+++|.|||||.++.+
T Consensus         5 ~l~G~~GsGKsT~a~~   20 (184)
T PRK01184          5 GVVGMPGSGKGEFSKI   20 (184)
T ss_pred             EEECCCCCCHHHHHHH
Confidence            4899999999998763

>PRK06620 hypothetical protein; Validated

Probab=82.36  E-value=0.91  Score=35.37  Aligned_cols=17  Identities=24%  Similarity=0.327  Sum_probs=14.3

Q ss_pred             CceEECcCCCchHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAE   73 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~   73 (138)
                      ..+++||.|+|||..+.
T Consensus        46 ~l~l~Gp~G~GKThLl~   62 (214)
T PRK06620         46 TLLIKGPSSSGKTYLTK   62 (214)
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            35699999999998765

>PRK06749 replicative DNA helicase; Provisional

Probab=82.16  E-value=2.2  Score=36.80  Aligned_cols=34  Identities=26%  Similarity=-0.024  Sum_probs=25.9

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      +|.|.+|.|||..++..+.++..+|..++|++.-
T Consensus       190 iIaarPgmGKTafal~ia~~~a~~g~~v~~fSlE  223 (428)
T PRK06749        190 VLGARPSMGKTAFALNVGLHAAKSGAAVGLFSLE  223 (428)
T ss_pred             EEEeCCCCCchHHHHHHHHHHHhcCCCEEEEEee
Confidence            4899999999999985555555667788777543

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=82.14  E-value=1.5  Score=31.02  Aligned_cols=17  Identities=29%  Similarity=0.225  Sum_probs=14.4

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .+++++.|||||.++..
T Consensus         2 i~l~G~~GsGKstla~~   18 (154)
T cd00464           2 IVLIGMMGAGKTTVGRL   18 (154)
T ss_pred             EEEEcCCCCCHHHHHHH
Confidence            46899999999998853

Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=82.14  E-value=4.4  Score=36.16  Aligned_cols=49  Identities=27%  Similarity=0.304  Sum_probs=39.8

Q ss_pred             CCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCC-----------CCCCEEEecHH
Q 042424           83 KQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLS-----------PNASCLVMTTE  131 (138)
Q Consensus        83 ~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~-----------~~~~IiVtTpe  131 (138)
                      +.++|++++++..+++.++.|.+..-.+..++|+....           .+.+|||||..
T Consensus       257 ~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv  316 (572)
T PRK04537        257 GARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDV  316 (572)
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehh
Confidence            67899999999999999999987433899999986542           26789999953

>KOG0732 consensus AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones]

Probab=82.07  E-value=0.74  Score=44.13  Aligned_cols=76  Identities=18%  Similarity=0.114  Sum_probs=42.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCcchhhh-hc------CCCCCCcccccccCCCCccCCCCCCC-ceEECcCCCchHHHHHHH
Q 042424            4 SQTPGKRKAPKADSHVRGTPKEESTK-KQ------RNPTRSCVHEVAVPSCYTLTTDETTH-GTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~p~~~~~~-~~------~~~~~~~~~~~~~p~~y~~~~~~~~~-~~l~aPTGsGKTlva~~a   75 (138)
                      +|+-+.++.+..|.+..+.-.-..-. ..      .+..+-+.-...+|.-|+.+.....+ .++++|.|+|||+++...
T Consensus       240 ~~~~~~~~~~~~d~dp~~~~~~v~fd~vggl~~~i~~LKEmVl~PLlyPE~f~~~~itpPrgvL~~GppGTGkTl~araL  319 (1080)
T KOG0732|consen  240 LQTAGLRVQKEADSDPLSVDSSVGFDSVGGLENYINQLKEMVLLPLLYPEFFDNFNITPPRGVLFHGPPGTGKTLMARAL  319 (1080)
T ss_pred             cccchhhcccccccCchhhhcccCccccccHHHHHHHHHHHHHhHhhhhhHhhhcccCCCcceeecCCCCCchhHHHHhh
Confidence            45666666666666554432211111 00      00113344455566667655444444 569999999999998755


Q ss_pred             HHHH
Q 042424           76 IAMA   79 (138)
Q Consensus        76 i~~~   79 (138)
                      +..+
T Consensus       320 a~~~  323 (1080)
T KOG0732|consen  320 AAAC  323 (1080)
T ss_pred             hhhh
Confidence            4444

>TIGR01968 minD_bact septum site-determining protein MinD

Probab=82.06  E-value=2.4  Score=32.64  Aligned_cols=29  Identities=21%  Similarity=0.192  Sum_probs=20.4

Q ss_pred             EECcCCCchHHHHH-HHHHHHHHcCCcEEEE
Q 042424           60 LTNPVYNGKTAVAE-YAIAMAFRDKQRVIYT   89 (138)
Q Consensus        60 l~aPTGsGKTlva~-~ai~~~l~~~~rviyv   89 (138)
                      .++-.|.|||.++. +|..- .+.|.|++++
T Consensus         7 ~s~kGGvGKTt~a~~lA~~l-a~~g~~vlli   36 (261)
T TIGR01968         7 TSGKGGVGKTTTTANLGTAL-ARLGKKVVLI   36 (261)
T ss_pred             ecCCCCccHHHHHHHHHHHH-HHcCCeEEEE
Confidence            66778999999987 44432 2457777765

This model describes the bacterial and chloroplast form of MinD, a multifunctional cell division protein that guides correct placement of the septum. The homologous archaeal MinD proteins, with many archaeal genomes having two or more forms, are described by a separate model.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=82.06  E-value=4.2  Score=36.87  Aligned_cols=48  Identities=15%  Similarity=0.151  Sum_probs=32.6

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHH--c--CCcEEEEechHHHHHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFR--D--KQRVIYTSSLKALSNQKYRELH  104 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~--~--~~rviyv~P~kaLv~Q~~~~l~  104 (138)
                      -.+|+++.|+|||.+....+...++  .  ..+++.++||---+....+.+.
T Consensus       169 ~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~  220 (615)
T PRK10875        169 ISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLTESLG  220 (615)
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHH
Confidence            3559999999999887533332222  2  3578889999766666665554

>cd03116 MobB Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes

Probab=82.04  E-value=2.8  Score=31.28  Aligned_cols=31  Identities=23%  Similarity=0.104  Sum_probs=20.6

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      .++++.|||||.+....+...-..|.++-++
T Consensus         5 ~i~G~~gsGKTTli~~L~~~l~~~g~~V~~i   35 (159)
T cd03116           5 GFVGYSGSGKTTLLEKLIPALSARGLRVAVI   35 (159)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHcCCcEEEE
Confidence            3899999999998875554432345555333

In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.

>PLN02840 tRNA dimethylallyltransferase

Probab=82.04  E-value=1.3  Score=38.48  Aligned_cols=15  Identities=27%  Similarity=0.448  Sum_probs=13.6

Q ss_pred             eEECcCCCchHHHHH
Q 042424           59 TLTNPVYNGKTAVAE   73 (138)
Q Consensus        59 ~l~aPTGsGKTlva~   73 (138)
                      +|.+|||||||.++.
T Consensus        25 ~I~GptgsGKTtla~   39 (421)
T PLN02840         25 VISGPTGAGKSRLAL   39 (421)
T ss_pred             EEECCCCCCHHHHHH
Confidence            499999999999886

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=81.95  E-value=1.5  Score=35.19  Aligned_cols=20  Identities=35%  Similarity=0.295  Sum_probs=16.0

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      .+.++++|.|+|||..+...
T Consensus        31 ~~~ll~Gp~G~GKT~la~~i   50 (305)
T TIGR00635        31 DHLLLYGPPGLGKTTLAHII   50 (305)
T ss_pred             CeEEEECCCCCCHHHHHHHH
Confidence            35679999999999887643

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=81.91  E-value=1.7  Score=32.39  Aligned_cols=20  Identities=30%  Similarity=0.345  Sum_probs=15.7

Q ss_pred             CceEECcCCCchHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai   76 (138)
                      ..+|++|+|+||+.++...+
T Consensus         4 ~ivl~Gpsg~GK~~l~~~L~   23 (183)
T PF00625_consen    4 PIVLVGPSGSGKSTLAKRLI   23 (183)
T ss_dssp             EEEEESSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            35699999999997765444

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=81.88  E-value=2.6  Score=40.56  Aligned_cols=76  Identities=16%  Similarity=0.019  Sum_probs=45.2

Q ss_pred             CCceEECcCCCchHHHHHH-HHHHHHHcCCcEEEEechHHHHHHHHHHHHHh---cC-ceEEEec-CCcCCC-----CCC
Q 042424           56 THGTLTNPVYNGKTAVAEY-AIAMAFRDKQRVIYTSSLKALSNQKYRELHKE---FK-DVGLMTG-DVTLSP-----NAS  124 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~-ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~---f~-~v~~~tG-d~~~~~-----~~~  124 (138)
                      ...+.-..||-|||++|-+ +.+.||. |+.+-+|...-=|+..=++.+...   ++ +||.+.. +.....     .++
T Consensus       183 ~G~IAEM~TGEGKTLvAtlp~yLnAL~-GkgVHvVTVNDYLA~RDaewmgply~fLGLsvg~i~~~~~~~~~rr~aY~~D  261 (1112)
T PRK12901        183 QGKIAEMATGEGKTLVATLPVYLNALT-GNGVHVVTVNDYLAKRDSEWMGPLYEFHGLSVDCIDKHQPNSEARRKAYNAD  261 (1112)
T ss_pred             CCceeeecCCCCchhHHHHHHHHHHHc-CCCcEEEEechhhhhccHHHHHHHHHHhCCceeecCCCCCCHHHHHHhCCCc
Confidence            4556788999999999975 5555554 555444444444666555444443   34 7877644 212111     677


Q ss_pred             EEEecHHH
Q 042424          125 CLVMTTEI  132 (138)
Q Consensus       125 IiVtTpe~  132 (138)
                      |.-+|.-.
T Consensus       262 ItYgTn~E  269 (1112)
T PRK12901        262 ITYGTNNE  269 (1112)
T ss_pred             ceecCCCc
Confidence            77777543

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=81.86  E-value=1.5  Score=31.32  Aligned_cols=16  Identities=19%  Similarity=0.221  Sum_probs=13.9

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      +++++.|||||.++-.
T Consensus         3 ~l~G~~GsGKST~a~~   18 (150)
T cd02021           3 VVMGVSGSGKSTVGKA   18 (150)
T ss_pred             EEEcCCCCCHHHHHHH
Confidence            4899999999998864

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=81.73  E-value=1.2  Score=38.52  Aligned_cols=39  Identities=21%  Similarity=0.271  Sum_probs=29.3

Q ss_pred             EECcCCCchHHHHHH-HHHHHHHcC--CcEEEEechHHHHHH
Q 042424           60 LTNPVYNGKTAVAEY-AIAMAFRDK--QRVIYTSSLKALSNQ   98 (138)
Q Consensus        60 l~aPTGsGKTlva~~-ai~~~l~~~--~rviyv~P~kaLv~Q   98 (138)
                      +.++-|+|||+.|+. ++.+.+.++  +++|+.=|+..+.++
T Consensus       250 L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~d  291 (436)
T COG1875         250 LGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGED  291 (436)
T ss_pred             eeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCcccc
Confidence            899999999999985 455555543  678888888777643

>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes

Probab=81.68  E-value=2.7  Score=34.60  Aligned_cols=30  Identities=17%  Similarity=0.150  Sum_probs=18.9

Q ss_pred             eEECcCCCchHHHHHHHHHHHHH-cCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv   89 (138)
                      .++|++|||||.++.. +.+.+. .|.++.++
T Consensus         3 gItG~SGSGKTTv~~~-l~~~l~~~g~~v~vI   33 (277)
T cd02029           3 AVTGSSGAGTTTVKRA-FEHIFAREGIHPAVV   33 (277)
T ss_pred             EEECCCCCCHHHHHHH-HHHHHHhcCCceEEE
Confidence            3899999999999852 222333 24444444

PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=81.65  E-value=2.3  Score=33.06  Aligned_cols=14  Identities=36%  Similarity=0.596  Sum_probs=12.9

Q ss_pred             EECcCCCchHHHHH
Q 042424           60 LTNPVYNGKTAVAE   73 (138)
Q Consensus        60 l~aPTGsGKTlva~   73 (138)
                      |.+|+|||||..+.
T Consensus        38 i~G~~GsGKTTl~~   51 (229)
T PRK09270         38 IAGPPGAGKSTLAE   51 (229)
T ss_pred             EECCCCCCHHHHHH
Confidence            99999999999875

>PRK06547 hypothetical protein; Provisional

Probab=81.56  E-value=1.5  Score=33.00  Aligned_cols=17  Identities=24%  Similarity=0.194  Sum_probs=14.0

Q ss_pred             eEECcCCCchHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~a   75 (138)
                      +|.++.|||||.++...
T Consensus        19 ~i~G~~GsGKTt~a~~l   35 (172)
T PRK06547         19 LIDGRSGSGKTTLAGAL   35 (172)
T ss_pred             EEECCCCCCHHHHHHHH
Confidence            38899999999988543

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=81.48  E-value=2.7  Score=32.07  Aligned_cols=18  Identities=22%  Similarity=0.174  Sum_probs=14.5

Q ss_pred             EECcCCCchHHHHHHHHH
Q 042424           60 LTNPVYNGKTAVAEYAIA   77 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~   77 (138)
                      ++++.|||||......+.
T Consensus        11 ivG~sgsGKTTLi~~li~   28 (173)
T PRK10751         11 IAAWSGTGKTTLLKKLIP   28 (173)
T ss_pred             EECCCCChHHHHHHHHHH
Confidence            999999999988764443

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=81.41  E-value=5.3  Score=36.64  Aligned_cols=41  Identities=27%  Similarity=0.205  Sum_probs=26.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc------CCcEEEEechHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD------KQRVIYTSSLKALS   96 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~------~~rviyv~P~kaLv   96 (138)
                      .|.++.+|.|+|||.++.....+....      ...-+|.+..-+|+
T Consensus       204 ~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~~~~~~l~  250 (731)
T TIGR02639       204 NNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSLDMGSLL  250 (731)
T ss_pred             CceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEEecHHHHh
Confidence            578899999999999987544443222      12334455554554

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=81.38  E-value=2.3  Score=38.33  Aligned_cols=36  Identities=14%  Similarity=0.105  Sum_probs=24.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC--CcEEEEech
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK--QRVIYTSSL   92 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~--~rviyv~P~   92 (138)
                      .+.++++|+|+|||.++.... ..+...  ..++|+...
T Consensus        38 ~~~ll~G~pG~GKT~la~~la-~~l~~~~~~~~~~~~n~   75 (608)
T TIGR00764        38 RNVLLIGEPGVGKSMLAKAMA-ELLPDEELEDILVYPNP   75 (608)
T ss_pred             CCEEEECCCCCCHHHHHHHHH-HHcCchhheeEEEEeCC
Confidence            577799999999999886433 444443  445555444

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=81.35  E-value=1.4  Score=36.67  Aligned_cols=21  Identities=29%  Similarity=0.200  Sum_probs=16.5

Q ss_pred             CCceEECcCCCchHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai   76 (138)
                      ...++.+|.|+|||.++....
T Consensus       157 ~gvLL~GppGtGKT~lakaia  177 (364)
T TIGR01242       157 KGVLLYGPPGTGKTLLAKAVA  177 (364)
T ss_pred             ceEEEECCCCCCHHHHHHHHH
Confidence            446799999999998876443

Many proteins may score above the trusted cutoff because an internal

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=81.29  E-value=2.3  Score=37.08  Aligned_cols=48  Identities=21%  Similarity=0.164  Sum_probs=31.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYREL  103 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l  103 (138)
                      .+.++.+|.|.|||..|-+.+...-.+..+.|-++-+.+-+++...-|
T Consensus       163 pSmIlWGppG~GKTtlArlia~tsk~~SyrfvelSAt~a~t~dvR~if  210 (554)
T KOG2028|consen  163 PSMILWGPPGTGKTTLARLIASTSKKHSYRFVELSATNAKTNDVRDIF  210 (554)
T ss_pred             CceEEecCCCCchHHHHHHHHhhcCCCceEEEEEeccccchHHHHHHH
Confidence            467799999999998886655433223455666677766665554444

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=81.26  E-value=5.1  Score=36.46  Aligned_cols=56  Identities=25%  Similarity=0.376  Sum_probs=40.9

Q ss_pred             HHHHHHHcCCcEEEEechH--------HHHHHHHHHHHHhcC--ceEEEecCCcCC-----------CCCCEEEecH
Q 042424           75 AIAMAFRDKQRVIYTSSLK--------ALSNQKYRELHKEFK--DVGLMTGDVTLS-----------PNASCLVMTT  130 (138)
Q Consensus        75 ai~~~l~~~~rviyv~P~k--------aLv~Q~~~~l~~~f~--~v~~~tGd~~~~-----------~~~~IiVtTp  130 (138)
                      .+...+.+|.++++++|+.        .-+.+.++.|++.|.  .|+.++|+....           .+.+|+|||.
T Consensus       463 ~i~~~~~~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~  539 (681)
T PRK10917        463 RIREEIAKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATT  539 (681)
T ss_pred             HHHHHHHcCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECc
Confidence            3444456789999999953        335677888888775  799999986532           1678999996

>PRK06217 hypothetical protein; Validated

Probab=81.24  E-value=0.98  Score=33.79  Aligned_cols=16  Identities=19%  Similarity=0.194  Sum_probs=14.0

Q ss_pred             ceEECcCCCchHHHHH
Q 042424           58 GTLTNPVYNGKTAVAE   73 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~   73 (138)
                      .+|.+++|||||.++.
T Consensus         4 I~i~G~~GsGKSTla~   19 (183)
T PRK06217          4 IHITGASGSGTTTLGA   19 (183)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            4699999999999885

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=81.18  E-value=2.5  Score=38.46  Aligned_cols=56  Identities=13%  Similarity=0.064  Sum_probs=39.6

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEE
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLM  113 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~  113 (138)
                      ..+.++.||||+|||......  ..+..+..+|++=|--++...... +++.++ +|-++
T Consensus       224 ~~H~Lv~ApTgsGKt~g~VIP--nLL~~~gS~VV~DpKgEl~~~Ta~-~R~~~G~~V~vf  280 (641)
T PRK13822        224 STHGLVFAGSGGFKTTSVVVP--TALKWGGPLVVLDPSTEVAPMVSE-HRRDAGREVIVL  280 (641)
T ss_pred             CceEEEEeCCCCCccceEehh--hhhcCCCCEEEEeCcHHHHHHHHH-HHHHCCCeEEEE
Confidence            367889999999999865433  234557788888898888776554 455566 56555

>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=81.14  E-value=4.7  Score=32.41  Aligned_cols=41  Identities=17%  Similarity=0.197  Sum_probs=31.0

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEec---hHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS---LKALSNQK   99 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P---~kaLv~Q~   99 (138)
                      ++-++.|+|||+.+...+.=.|..|.++.|++-   .+..+.|+
T Consensus        32 lIEGd~~tGKSvLsqr~~YG~L~~g~~v~yvsTe~T~refi~qm   75 (235)
T COG2874          32 LIEGDNGTGKSVLSQRFAYGFLMNGYRVTYVSTELTVREFIKQM   75 (235)
T ss_pred             EEECCCCccHHHHHHHHHHHHHhCCceEEEEEechhHHHHHHHH
Confidence            389999999999987666666778899888864   34444444

>TIGR02767 TraG-Ti Ti-type conjugative transfer system protien TraG

Probab=81.13  E-value=3.1  Score=37.84  Aligned_cols=55  Identities=11%  Similarity=0.007  Sum_probs=39.7

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC--ceEEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK--DVGLM  113 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~  113 (138)
                      .+.++.||||||||+.....  ..+..+..+|++=|--++...... +++.++  .|-++
T Consensus       212 ~H~lv~ApTgsGKgvg~VIP--nLL~~~gS~VV~DpKgE~~~~Ta~-~R~~~Gg~~V~vf  268 (623)
T TIGR02767       212 THMIFFAGSGGFKTTSVVVP--TALKYGGPLVCLDPSTEVAPMVCE-HRRQAGNRKVIVL  268 (623)
T ss_pred             ceEEEEeCCCCCccceeehh--hhhcCCCCEEEEEChHHHHHHHHH-HHHHcCCCcEEEE
Confidence            57889999999999865433  345667889999998888776664 454454  55555

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.

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=81.11  E-value=1.8  Score=39.30  Aligned_cols=57  Identities=16%  Similarity=-0.034  Sum_probs=37.5

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEE
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLM  113 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~  113 (138)
                      ..+.++.||||||||......-  .+..+..+|++=|--++......-.++..+ .|-++
T Consensus       175 ~~HvlviapTgSGKgvg~ViPn--LL~~~~S~VV~D~KGE~~~~Tag~R~~~~G~~V~~f  232 (636)
T PRK13880        175 PEHVLTYAPTRSGKGVGLVVPT--LLSWGHSSVITDLKGELWALTAGWRQKHAKNKVLRF  232 (636)
T ss_pred             CceEEEEecCCCCCceEEEccc--hhhCCCCEEEEeCcHHHHHHHHHHHHHhCCCeEEEE
Confidence            3678899999999998654222  134578888888888887555443334334 45443

>COG3857 AddB ATP-dependent nuclease, subunit B [DNA replication, recombination, and repair]

Probab=81.04  E-value=5.1  Score=38.62  Aligned_cols=48  Identities=23%  Similarity=0.273  Sum_probs=40.0

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhc
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEF  107 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f  107 (138)
                      ++.+-+|+|||....-.+...+.+|++++|++|. ++.-|+-+++-+..
T Consensus         5 ~lyg~~gtgkT~~l~~e~~~~~~~gkpviyIvP~-q~sFe~E~~~L~~~   52 (1108)
T COG3857           5 LLYGRAGTGKTEILTEEIQEELEKGKPVIYIVPS-QMSFEKEKEILERL   52 (1108)
T ss_pred             eehhhccccHHHHHHHHHHHHHHcCCcEEEEccc-chhHHHHHHHHhCc
Confidence            5788899999988888888888899999999998 56677777776644

>PF02463 SMC_N: RecF/RecN/SMC N terminal domain; InterPro: IPR003395 This domain is found at the N terminus of structural maintenance of chromosomes (SMC) proteins, which function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression []

Probab=81.02  E-value=1.1  Score=34.21  Aligned_cols=17  Identities=24%  Similarity=0.403  Sum_probs=14.0

Q ss_pred             CceEECcCCCchHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAE   73 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~   73 (138)
                      -.++++|+|+|||.+..
T Consensus        26 ~~~i~G~NGsGKS~ile   42 (220)
T PF02463_consen   26 LNVIVGPNGSGKSNILE   42 (220)
T ss_dssp             EEEEEESTTSSHHHHHH
T ss_pred             CEEEEcCCCCCHHHHHH
Confidence            34699999999998764

The domain is also found in RecF and RecN proteins, which are involved in DNA metabolism and recombination.; PDB: 3HTK_A 1W1W_C 2WD5_A 3L51_A 1XEW_Y 3KTA_B 3NWC_B 1XEX_A 1GXL_C 1GXK_A ....

>TIGR00609 recB exodeoxyribonuclease V, beta subunit

Probab=80.80  E-value=5.2  Score=38.48  Aligned_cols=53  Identities=8%  Similarity=0.034  Sum_probs=42.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC-----CcEEEEechHHHHHHHHHHHHHhcC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK-----QRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~-----~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      +..+|.|.-|+|||........+.+..+     .++++|.=|++=+.+...++++++.
T Consensus        10 G~~lieAsAGtGKT~ti~~~~lrll~~~~~~~~~~iLvvTFT~aAt~el~~RIr~rL~   67 (1087)
T TIGR00609        10 GTFLIEASAGTGKTFTIAQLYLRLLLEGGPLTVEEILVVTFTNAATEELKTRIRGRIH   67 (1087)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHhcCCCCChhhEEEEehhHHHHHHHHHHHHHHHH
Confidence            5678999999999998765555555433     6799999999999999999988764

All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=80.79  E-value=1.7  Score=32.17  Aligned_cols=19  Identities=21%  Similarity=0.142  Sum_probs=15.3

Q ss_pred             ceEECcCCCchHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai   76 (138)
                      .++++|.|||||.++....
T Consensus         5 i~l~G~~gsGKst~a~~l~   23 (175)
T cd00227           5 IILNGGSSAGKSSIARALQ   23 (175)
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            3599999999999986433

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=80.47  E-value=3.3  Score=33.69  Aligned_cols=44  Identities=18%  Similarity=0.085  Sum_probs=26.9

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec--hH-HHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS--LK-ALSNQKY  100 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P--~k-aLv~Q~~  100 (138)
                      ..++.+|+|+|||..+.........++.++.++.-  .+ +.++|..
T Consensus        77 ~i~~~G~~g~GKTtl~~~l~~~l~~~~~~v~~i~~D~~ri~~~~ql~  123 (270)
T PRK06731         77 TIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITTDHSRIGTVQQLQ  123 (270)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHH
Confidence            45599999999999876444333344566655443  22 4555543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	138
3l9o_A	1108	Crystal Structure Of Mtr4, A Co-Factor Of The Nucle		7e-28
2xgj_A	1010	Structure Of Mtr4, A Dexh Helicase Involved In Nucl		7e-28
4a4z_A	997	Crystal Structure Of The S. Cerevisiae Dexh Helicas		7e-22

>pdb|3L9O|A Chain A, Crystal Structure Of Mtr4, A Co-Factor Of The Nuclear Exosome Length = 1108

Iteration: 1
 Score =  119 bits (297), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 55/72 (76%), Positives = 63/72 (87%)
Query: 67  GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
           GKT VAEYAIA + ++KQRVIYTS +KALSNQKYREL  EF DVGLMTGD+T++P+A CL
Sbjct: 211 GKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCL 270
Query: 127 VMTTEILRGMLY 138
           VMTTEILR MLY
Sbjct: 271 VMTTEILRSMLY 282

>pdb|2XGJ|A Chain A, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna Processing And Surveillance Length = 1010

Iteration: 1
 Score =  119 bits (297), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 55/72 (76%), Positives = 63/72 (87%)
Query: 67  GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCL 126
           GKT VAEYAIA + ++KQRVIYTS +KALSNQKYREL  EF DVGLMTGD+T++P+A CL
Sbjct: 113 GKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCL 172
Query: 127 VMTTEILRGMLY 138
           VMTTEILR MLY
Sbjct: 173 VMTTEILRSMLY 184

>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2 Bound To Amppnp Length = 997

Iteration: 1
 Score = 99.0 bits (245), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 48/74 (64%), Positives = 60/74 (81%), Gaps = 2/74 (2%)
Query: 67  GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDV--GLMTGDVTLSPNAS 124
           GKT VAEYAIAMA R+  + IYTS +KALSNQK+R+  + F DV  GL+TGDV ++P+A+
Sbjct: 66  GKTVVAEYAIAMAHRNMTKTIYTSPIKALSNQKFRDFKETFDDVNIGLITGDVQINPDAN 125
Query: 125 CLVMTTEILRGMLY 138
           CL+MTTEILR MLY
Sbjct: 126 CLIMTTEILRSMLY 139

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	138
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	1e-36
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	1e-35
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	3e-34
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	4e-22
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	4e-16
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	1e-15
3b6e_A	216	Interferon-induced helicase C domain-containing P;	8e-10
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	6e-05

>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 =  131 bits (330), Expect = 1e-36
 Identities = 63/165 (38%), Positives = 82/165 (49%), Gaps = 28/165 (16%)

Query: 2   EESQTPGKRKAPKADSHVRGTPKEESTKKQRNPTRSCVHEVAVPSCYTLTTD-------- 53
           +  +    R+   +         +     +   +    H+VA+P  Y  T          
Sbjct: 20  DSFEQEASREVDASKGLTNSETLQVEQDGKVRLSHQVRHQVALPPNYDYTPIAEHKRVNE 79

Query: 54  -------------------ETTHGTL-TNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLK 93
                              +     L +     GKT VAEYAIA + ++KQRVIYTS +K
Sbjct: 80  ARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIK 139

Query: 94  ALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRGMLY 138
           ALSNQKYREL  EF DVGLMTGD+T++P+A CLVMTTEILR MLY
Sbjct: 140 ALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRSMLY 184

>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 =  128 bits (322), Expect = 1e-35
 Identities = 63/165 (38%), Positives = 82/165 (49%), Gaps = 28/165 (16%)

Query: 2   EESQTPGKRKAPKADSHVRGTPKEESTKKQRNPTRSCVHEVAVPSCYTLTTD-------- 53
           +  +    R+   +         +     +   +    H+VA+P  Y  T          
Sbjct: 118 DSFEQEASREVDASKGLTNSETLQVEQDGKVRLSHQVRHQVALPPNYDYTPIAEHKRVNE 177

Query: 54  -------------------ETTHGTL-TNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLK 93
                              +     L +     GKT VAEYAIA + ++KQRVIYTS +K
Sbjct: 178 ARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIK 237

Query: 94  ALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRGMLY 138
           ALSNQKYREL  EF DVGLMTGD+T++P+A CLVMTTEILR MLY
Sbjct: 238 ALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRSMLY 282

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A Length = 997

 Score =  124 bits (312), Expect = 3e-34
 Identities = 48/95 (50%), Positives = 65/95 (68%), Gaps = 4/95 (4%)

Query: 46  SCYTLTTDETTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHK 105
           + Y L   +     +      GKT VAEYAIAMA R+  + IYTS +KALSNQK+R+  +
Sbjct: 47  AVYHLEQGD--SVFVAAHTSAGKTVVAEYAIAMAHRNMTKTIYTSPIKALSNQKFRDFKE 104

Query: 106 EF--KDVGLMTGDVTLSPNASCLVMTTEILRGMLY 138
            F   ++GL+TGDV ++P+A+CL+MTTEILR MLY
Sbjct: 105 TFDDVNIGLITGDVQINPDANCLIMTTEILRSMLY 139

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 89.8 bits (223), Expect = 4e-22
 Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 10/81 (12%)

Query: 67  GKTAVAEYAI-AMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP 121
           GKT +AE  I +   ++  + IY + L+AL+N+KY    K+++     V + +GD     
Sbjct: 58  GKTLIAEMGIISFLLKNGGKAIYVTPLRALTNEKYLTF-KDWELIGFKVAMTSGDYDTDD 116

Query: 122 ----NASCLVMTTEILRGMLY 138
               N   ++ T E L  +  
Sbjct: 117 AWLKNYDIIITTYEKLDSLWR 137

>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 = 72.5 bits (178), Expect = 4e-16
 Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 9/87 (10%)

Query: 60  LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKD----VGLMTG 115
           L  P   GKT +AE A+        + +Y   L+AL+ +KY    K+++     +G+ TG
Sbjct: 45  LAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGEKYESF-KKWEKIGLRIGISTG 103

Query: 116 DVTLSP----NASCLVMTTEILRGMLY 138
           D         +   +V T+E    ++ 
Sbjct: 104 DYESRDEHLGDCDIIVTTSEKADSLIR 130

>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 = 71.4 bits (175), Expect = 1e-15
 Identities = 22/101 (21%), Positives = 42/101 (41%), Gaps = 10/101 (9%)

Query: 47  CYTLTTDETTHGTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLKALSNQKYRELHK 105
                  E  +  ++ P  +GKT +AE A+         + +Y   LKAL+ +K++E  +
Sbjct: 31  ALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPLKALAEEKFQEF-Q 89

Query: 106 EFKD----VGLMTGDVTLSP----NASCLVMTTEILRGMLY 138
           +++     V + TGD             ++ T E    +L 
Sbjct: 90  DWEKIGLRVAMATGDYDSKDEWLGKYDIIIATAEKFDSLLR 130

>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 = 53.7 bits (129), Expect = 8e-10
 Identities = 20/89 (22%), Positives = 31/89 (34%), Gaps = 17/89 (19%)

Query: 67  GKTAVAEYAIAMAFRD------KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGD 116
           GKT VA Y                +VI   +   L  Q +R+  + F      V  ++GD
Sbjct: 60  GKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLSGD 119

Query: 117 VTLSPNASC-------LVMTTEILRGMLY 138
             L  +          ++ T +IL   L 
Sbjct: 120 TQLKISFPEVVKSCDIIISTAQILENSLL 148

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A Length = 677

 Score = 40.3 bits (93), Expect = 6e-05
 Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 9/71 (12%)

Query: 67  GKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGD-----VTLSP 121
           GKT  A       +   +  +Y   LK L+++ + + +       L+TG+          
Sbjct: 167 GKTYHA----IQKYFSAKSGVYCGPLKLLAHEIFEKSNAAGVPCDLVTGEERVTVQPNGK 222

Query: 122 NASCLVMTTEI 132
            AS +  T E+
Sbjct: 223 QASHVSCTVEM 233

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	138
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.77
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.73
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.69
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.68
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.62
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.61
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.6
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.59
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.58
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.57
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.57
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.57
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.57
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.56
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.56
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.56
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.56
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.55
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.54
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.54
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.54
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.54
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.54
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.53
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.53
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.53
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.52
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.49
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.49
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.49
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.49
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.47
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.47
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.47
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.46
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.46
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.46
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.46
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.45
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.45
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.45
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.44
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.44
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.43
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.43
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.41
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.41
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.4
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.4
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.37
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.36
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.35
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.3
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.27
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.24
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.22
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.18
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.16
3h1t_A	590	Type I site-specific restriction-modification syst	99.14
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.13
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.07
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.0
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	98.99
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	98.96
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	98.94
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	98.92
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	98.92
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	98.89
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	98.86
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	98.84
1yks_A	440	Genome polyprotein [contains: flavivirin protease	98.83
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	98.78
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	98.77
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	98.69
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	98.67
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.64
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	98.63
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.48
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	98.42
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	98.34
3jux_A	822	Protein translocase subunit SECA; protein transloc	97.44
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	97.33
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	97.01
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	96.92
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	96.83
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	96.58
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	96.52
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	96.26
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	96.11
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	95.94
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	95.9
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	95.82
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	95.73
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	95.73
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	95.69
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	95.65
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	95.56
2qgz_A	308	Helicase loader, putative primosome component; str	95.56
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	95.48
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	95.46
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	95.46
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	95.34
3bos_A	242	Putative DNA replication factor; P-loop containing	95.26
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	95.03
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	95.02
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	94.78
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	94.57
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	94.44
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	94.43
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	94.37
3io5_A	333	Recombination and repair protein; storage dimer, i	94.36
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	94.32
2cvh_A	220	DNA repair and recombination protein RADB; filamen	94.28
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	94.12
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	94.1
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	94.05
1u94_A	356	RECA protein, recombinase A; homologous recombinat	94.01
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	93.97
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	93.96
1xp8_A	366	RECA protein, recombinase A; recombination, radior	93.58
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	93.48
2z43_A	324	DNA repair and recombination protein RADA; archaea	93.47
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	93.46
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	93.4
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	93.2
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	93.2
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	93.15
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	93.12
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	93.01
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	93.0
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	92.84
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	92.78
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	92.71
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	92.69
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	92.66
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	92.28
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	92.28
2r6a_A	454	DNAB helicase, replicative helicase; replication,	92.24
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	92.21
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	92.14
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	92.01
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	91.82
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	91.77
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	91.74
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	91.65
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	91.64
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	91.62
2eyu_A	261	Twitching motility protein PILT; pilus retraction	91.29
2chg_A	226	Replication factor C small subunit; DNA-binding pr	91.29
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	91.21
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	91.18
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	90.81
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	90.8
3co5_A	143	Putative two-component system transcriptional RES	90.77
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	90.75
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	90.56
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	90.5
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	90.4
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	90.28
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	90.26
4a74_A	231	DNA repair and recombination protein RADA; hydrola	90.22
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	90.12
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	90.11
2ewv_A	372	Twitching motility protein PILT; pilus retraction	90.06
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	90.02
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	89.95
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	89.83
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	89.79
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	89.76
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	89.75
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	89.73
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	89.72
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	89.66
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	89.62
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	89.59
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	89.58
1p9r_A	418	General secretion pathway protein E; bacterial typ	89.51
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	89.51
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	89.41
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	89.4
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	89.27
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	89.23
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	89.21
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	89.11
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	89.04
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	89.02
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	88.95
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	88.91
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	88.78
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	88.76
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	88.76
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	88.64
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	88.62
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	88.55
2xxa_A	433	Signal recognition particle protein; protein trans	88.52
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	88.49
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	88.49
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	88.4
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	88.37
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	88.31
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	88.3
1byi_A	224	Dethiobiotin synthase; biotin synthesis, cyclo-lig	88.26
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	88.24
3bs4_A	260	Uncharacterized protein PH0321; structural genomic	88.19
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	87.93
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	87.92
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	87.91
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	87.82
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	87.81
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	87.8
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	87.79
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	87.64
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	87.47
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	87.43
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	87.41
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	87.32
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	87.3
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	87.27
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	87.18
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	87.08
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	86.92
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	86.9
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	86.89
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	86.88
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	86.86
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	86.84
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	86.83
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	86.77
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	86.72
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	86.7
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	86.64
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	86.58
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	86.54
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	86.51
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	86.26
2og2_A	359	Putative signal recognition particle receptor; nuc	86.22
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	86.21
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	86.11
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	86.04
1g3q_A	237	MIND ATPase, cell division inhibitor; alpha-beta-a	86.0
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	85.97
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	85.88
1ihu_A	589	Arsenical pump-driving ATPase; aluminum fluoride,	85.76
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	85.71
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	85.64
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	85.53
3of5_A	228	Dethiobiotin synthetase; structural genomics, cent	85.52
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	85.51
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	85.48
1hyq_A	263	MIND, cell division inhibitor (MIND-1); MINC, FTSZ	85.48
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	85.47
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	85.24
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	85.23
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	85.05
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	84.85
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	84.78
3fgn_A	251	Dethiobiotin synthetase; biotin biosynthesis, BIOD	84.78
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	84.75
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	84.72
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	84.65
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	84.63
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	84.52
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	84.51
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	84.51
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	84.5
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	84.41
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	84.28
3zq6_A	324	Putative arsenical pump-driving ATPase; tail-ancho	84.21
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	84.18
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	84.16
3kta_A	182	Chromosome segregation protein SMC; structural mai	84.14
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	84.06
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	83.96
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	83.88
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	83.8
2ph1_A	262	Nucleotide-binding protein; alpha-beta protein, st	83.76
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	83.76
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	83.73
3q9l_A	260	Septum site-determining protein MIND; ATPase, bact	83.71
2woo_A	329	ATPase GET3; tail-anchored, membrane protein, targ	83.53
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	83.52
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	83.46
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	83.45
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	83.38
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	83.33
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	83.32
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	83.31
3qxc_A	242	Dethiobiotin synthetase; DTBS, structural genomics	83.31
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	83.31
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	83.3
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	83.23
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	83.17
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	83.07
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	82.88
3qf7_A	365	RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.	82.68
3ug7_A	349	Arsenical pump-driving ATPase; tail-anchored, memb	82.65
3auy_A	371	DNA double-strand break repair RAD50 ATPase; DNA r	82.61
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	82.52
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	82.39
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	82.3
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	82.25
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	82.23
1via_A	175	Shikimate kinase; structural genomics, transferase	82.18
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	82.13
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	82.08
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	82.05
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	82.03
3kjh_A	254	CO dehydrogenase/acetyl-COA synthase complex, acce	82.02
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	81.99
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	81.93
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	81.89
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	81.88
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	81.75
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	81.69
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	81.67
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	81.55
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	81.53
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	81.47
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	81.47
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	81.45
1yks_A	440	Genome polyprotein [contains: flavivirin protease	81.45
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	81.25
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	81.21
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	81.16
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	81.0
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	80.91
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	80.79
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	80.79
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	80.68
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	80.59
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	80.27
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	80.22
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	80.1
2r44_A	331	Uncharacterized protein; putative ATPase, structur	80.08
2chq_A	319	Replication factor C small subunit; DNA-binding pr	80.07
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	80.01
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	80.01

>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=99.77  E-value=7.2e-19  Score=168.04  Aligned_cols=86  Identities=22%  Similarity=0.283  Sum_probs=76.4

Q ss_pred             CCCCCceEECcCCCchHHHHHHHHHHHHHc-----------CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCC
Q 042424           53 DETTHGTLTNPVYNGKTAVAEYAIAMAFRD-----------KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDV  117 (138)
Q Consensus        53 ~~~~~~~l~aPTGsGKTlva~~ai~~~l~~-----------~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~  117 (138)
                      ..+.|.+++||||||||++|+++|++++.+           +.++||++|+|||++|++++|++.|+    .|+.++||.
T Consensus        93 ~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~kALa~e~~~~l~~~~~~~gi~V~~~tGd~  172 (1724)
T 4f92_B           93 ETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFGKRLATYGITVAELTGDH  172 (1724)
T ss_dssp             TCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSSHHHHHHHHHHHHHHHTTTTCCEEECCSSC
T ss_pred             cCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCHHHHHHHHHHHHHHHHhhCCCEEEEEECCC
Confidence            345789999999999999999999999853           57899999999999999999999886    789999998


Q ss_pred             cCCC----CCCEEEecHHHHHHhhC
Q 042424          118 TLSP----NASCLVMTTEILRGMLY  138 (138)
Q Consensus       118 ~~~~----~~~IiVtTpe~l~~lL~  138 (138)
                      ..+.    +++|+|||||+|++|++
T Consensus       173 ~~~~~~~~~~~IlVtTpEkld~llr  197 (1724)
T 4f92_B          173 QLCKEEISATQIIVCTPEKWDIITR  197 (1724)
T ss_dssp             SSCCTTGGGCSEEEECHHHHHHHTT
T ss_pred             CCCccccCCCCEEEECHHHHHHHHc
Confidence            7654    68999999999998873

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.73  E-value=6.8e-18  Score=154.83  Aligned_cols=83  Identities=66%  Similarity=0.973  Sum_probs=78.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCCCCCCEEEecHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRG  135 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~~~~~IiVtTpe~l~~  135 (138)
                      .+.++++|||||||+++++++..++.+|.+++|++|+++|++|++++|++.|+++++++||...+.+++|+|+|||+|.+
T Consensus       102 ~~vLV~apTGSGKTlva~lai~~~l~~g~rvL~l~PtkaLa~Q~~~~l~~~~~~vglltGd~~~~~~~~IvV~Tpe~L~~  181 (1010)
T 2xgj_A          102 ESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRS  181 (1010)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHHHHHSCEEEECSSCEECTTCSEEEEEHHHHHH
T ss_pred             CCEEEECCCCCChHHHHHHHHHHHhccCCeEEEECChHHHHHHHHHHHHHHhCCEEEEeCCCccCCCCCEEEEcHHHHHH
Confidence            46789999999999999999999998899999999999999999999999899999999999998899999999999998


Q ss_pred             hhC
Q 042424          136 MLY  138 (138)
Q Consensus       136 lL~  138 (138)
                      +||
T Consensus       182 ~L~  184 (1010)
T 2xgj_A          182 MLY  184 (1010)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            874

>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=99.69  E-value=6.1e-17  Score=149.69  Aligned_cols=83  Identities=66%  Similarity=0.973  Sum_probs=79.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCCCCCCEEEecHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEILRG  135 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~~~~~IiVtTpe~l~~  135 (138)
                      .+.++++|||||||+++.++++.++..+.+++|++|+++|++|++++|++.|+.|++++|+...+.+++|+|+||++|.+
T Consensus       200 ~dvLV~ApTGSGKTlva~l~i~~~l~~g~rvlvl~PtraLa~Q~~~~l~~~~~~VglltGd~~~~~~~~IlV~Tpe~L~~  279 (1108)
T 3l9o_A          200 ESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRS  279 (1108)
T ss_dssp             CCEEEECCSSSHHHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHHHHTSSEEEECSSCBCCCSCSEEEEEHHHHHH
T ss_pred             CCEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEcCcHHHHHHHHHHHHHHhCCccEEeCccccCCCCCEEEeChHHHHH
Confidence            57789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhC
Q 042424          136 MLY  138 (138)
Q Consensus       136 lL~  138 (138)
                      +||
T Consensus       280 ~L~  282 (1108)
T 3l9o_A          280 MLY  282 (1108)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            874

>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=99.68  E-value=1.5e-17  Score=158.98  Aligned_cols=85  Identities=25%  Similarity=0.389  Sum_probs=75.6

Q ss_pred             CCCCCceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCCcCCC----
Q 042424           53 DETTHGTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDVTLSP----  121 (138)
Q Consensus        53 ~~~~~~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~~~~~----  121 (138)
                      ..+.|.++++|||||||++++++|++++.+  +.++||++|++||++|++++|++.|+     .|+.++||...+.    
T Consensus       940 ~~~~nvlv~APTGSGKTliaelail~~l~~~~~~kavyi~P~raLa~q~~~~~~~~f~~~~g~~V~~ltGd~~~~~~~~~ 1019 (1724)
T 4f92_B          940 NSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLNKKVVLLTGETSTDLKLLG 1019 (1724)
T ss_dssp             SCCSCEEEECCTTSCCHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHHHTTTSCCCEEECCSCHHHHHHHHH
T ss_pred             cCCCcEEEEeCCCCCchHHHHHHHHHHHHhCCCCEEEEEcChHHHHHHHHHHHHHHhchhcCCEEEEEECCCCcchhhcC
Confidence            455788999999999999999999999864  67999999999999999999998875     6899999876552    


Q ss_pred             CCCEEEecHHHHHHhh
Q 042424          122 NASCLVMTTEILRGML  137 (138)
Q Consensus       122 ~~~IiVtTpe~l~~lL  137 (138)
                      +++|+|||||+|++++
T Consensus      1020 ~~~IiV~TPEkld~ll 1035 (1724)
T 4f92_B         1020 KGNIIISTPEKWDILS 1035 (1724)
T ss_dssp             HCSEEEECHHHHHHHH
T ss_pred             CCCEEEECHHHHHHHH
Confidence            7899999999999876

>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=99.62  E-value=1.3e-15  Score=119.19  Aligned_cols=82  Identities=18%  Similarity=0.148  Sum_probs=68.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHH-------cCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC----
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFR-------DKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS----  120 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~-------~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~----  120 (138)
                      ++.++++|||||||+++.+++++.+.       .+.++||++|+++|+.|+++++++.+.    .++.++|+....    
T Consensus        92 ~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~lil~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  171 (262)
T 3ly5_A           92 RDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQ  171 (262)
T ss_dssp             CCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHH
T ss_pred             CcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEEEEeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHH
Confidence            67889999999999999988887764       378899999999999999999999654    577788876432    


Q ss_pred             ---CCCCEEEecHHHHHHhh
Q 042424          121 ---PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 ---~~~~IiVtTpe~l~~lL  137 (138)
                         .+.+|+|+||++|..++
T Consensus       172 ~~~~~~~Iiv~Tp~~l~~~~  191 (262)
T 3ly5_A          172 KLGNGINIIVATPGRLLDHM  191 (262)
T ss_dssp             HHHHCCSEEEECHHHHHHHH
T ss_pred             HhcCCCCEEEEcHHHHHHHH
Confidence               26899999999998754

>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=99.61  E-value=3.6e-15  Score=113.14  Aligned_cols=83  Identities=11%  Similarity=0.006  Sum_probs=64.7

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHH---------cCCcEEEEechHHHHHHHHHHHHHhcC---ceEEEecCCcCCC-
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFR---------DKQRVIYTSSLKALSNQKYRELHKEFK---DVGLMTGDVTLSP-  121 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~---------~~~rviyv~P~kaLv~Q~~~~l~~~f~---~v~~~tGd~~~~~-  121 (138)
                      .++.++++|||+|||++++++++..+.         .+.+++|++|+++|++|+++++++...   .+..+.|+...+. 
T Consensus        57 ~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~  136 (228)
T 3iuy_A           57 GIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQ  136 (228)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHHC---------CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC------C
T ss_pred             CCCEEEECCCCChHHHHHHHHHHHHHHhccchhhccCCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEECCCChHHH
Confidence            467889999999999999988777653         467899999999999999999998432   5666666654432 


Q ss_pred             ------CCCEEEecHHHHHHhh
Q 042424          122 ------NASCLVMTTEILRGML  137 (138)
Q Consensus       122 ------~~~IiVtTpe~l~~lL  137 (138)
                            +.+|+|+||++|.+++
T Consensus       137 ~~~~~~~~~iiv~Tp~~l~~~~  158 (228)
T 3iuy_A          137 IEDISKGVDIIIATPGRLNDLQ  158 (228)
T ss_dssp             HHHHHSCCSEEEECHHHHHHHH
T ss_pred             HHHhcCCCCEEEECHHHHHHHH
Confidence                  5799999999998764

>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=99.60  E-value=2.9e-15  Score=115.17  Aligned_cols=83  Identities=12%  Similarity=0.055  Sum_probs=67.9

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc--------CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC-
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD--------KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP-  121 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~--------~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~-  121 (138)
                      .++.++++|||+|||++++++++..+..        +.++||++|+++|++|+++.+++.+.    .+..+.|+...+. 
T Consensus        66 g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~  145 (242)
T 3fe2_A           66 GLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQ  145 (242)
T ss_dssp             TCCEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHH
T ss_pred             CCCEEEECCCcCHHHHHHHHHHHHHHHhccccccCCCCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHH
Confidence            3678899999999999999888877652        67899999999999999999988532    6777777654321 


Q ss_pred             ------CCCEEEecHHHHHHhh
Q 042424          122 ------NASCLVMTTEILRGML  137 (138)
Q Consensus       122 ------~~~IiVtTpe~l~~lL  137 (138)
                            +.+|+|+||++|..++
T Consensus       146 ~~~~~~~~~I~v~Tp~~l~~~l  167 (242)
T 3fe2_A          146 IRDLERGVEICIATPGRLIDFL  167 (242)
T ss_dssp             HHHHHHCCSEEEECHHHHHHHH
T ss_pred             HHHhcCCCCEEEECHHHHHHHH
Confidence                  6899999999998765

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.59  E-value=6.8e-15  Score=112.13  Aligned_cols=83  Identities=25%  Similarity=0.207  Sum_probs=67.2

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHH-------cCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC---
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFR-------DKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS---  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~-------~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~---  120 (138)
                      .++.++++|||+|||+++.+++++.+.       .+.+++|++|+++|++|+++++++.+.    .++.+.|+...+   
T Consensus        62 ~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~  141 (236)
T 2pl3_A           62 GKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEA  141 (236)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHH
T ss_pred             CCCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHH
Confidence            367889999999999999888877653       368899999999999999999998553    577777865432   


Q ss_pred             ---CCCCEEEecHHHHHHhh
Q 042424          121 ---PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 ---~~~~IiVtTpe~l~~lL  137 (138)
                         .+.+|+|+||+++..++
T Consensus       142 ~~~~~~~iiv~Tp~~l~~~l  161 (236)
T 2pl3_A          142 ERINNINILVCTPGRLLQHM  161 (236)
T ss_dssp             HHHTTCSEEEECHHHHHHHH
T ss_pred             HhCCCCCEEEECHHHHHHHH
Confidence               26899999999997654

>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=99.58  E-value=3e-15  Score=114.75  Aligned_cols=83  Identities=24%  Similarity=0.218  Sum_probs=66.4

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc----CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCc--------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD----KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVT--------  118 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~----~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~--------  118 (138)
                      .++.++++|||+|||+++++++++.+..    +.+++|++|+++|++|+++++++.+.    .+..+.|+..        
T Consensus        66 ~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  145 (245)
T 3dkp_A           66 GRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPK  145 (245)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHHCSCCSSSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEECCCHHHHHHTTTSTT
T ss_pred             CCCEEEECCCCCcHHHHHHHHHHHHHhhcccCCceEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEecCccHHHHhhhh
Confidence            3678899999999999999888887753    56899999999999999999999654    4455544321        


Q ss_pred             CCCCCCEEEecHHHHHHhh
Q 042424          119 LSPNASCLVMTTEILRGML  137 (138)
Q Consensus       119 ~~~~~~IiVtTpe~l~~lL  137 (138)
                      ...+.+|+|+||+++..++
T Consensus       146 ~~~~~~I~v~Tp~~l~~~l  164 (245)
T 3dkp_A          146 SSKKFDILVTTPNRLIYLL  164 (245)
T ss_dssp             SCCCCCEEEECHHHHHHHH
T ss_pred             hcCCCCEEEECHHHHHHHH
Confidence            1236799999999998765

>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=99.57  E-value=1.2e-14  Score=109.60  Aligned_cols=83  Identities=13%  Similarity=0.039  Sum_probs=64.8

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP------  121 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~------  121 (138)
                      .++.++++|||+|||+++.+++++.+..   +.+++|++|+++|++|+++++++.+.    .+..+.|+.....      
T Consensus        51 ~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~  130 (224)
T 1qde_A           51 GHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR  130 (224)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------CT
T ss_pred             CCCEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEEEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhcCC
Confidence            3678899999999999988888777642   57999999999999999999998543    5677777654321      


Q ss_pred             CCCEEEecHHHHHHhh
Q 042424          122 NASCLVMTTEILRGML  137 (138)
Q Consensus       122 ~~~IiVtTpe~l~~lL  137 (138)
                      +++|+|+||+++..++
T Consensus       131 ~~~iiv~Tp~~l~~~~  146 (224)
T 1qde_A          131 DAQIVVGTPGRVFDNI  146 (224)
T ss_dssp             TCSEEEECHHHHHHHH
T ss_pred             CCCEEEECHHHHHHHH
Confidence            5899999999987654

>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=99.57  E-value=6.8e-15  Score=128.95  Aligned_cols=82  Identities=27%  Similarity=0.432  Sum_probs=72.3

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC----CCCEE
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP----NASCL  126 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~----~~~Ii  126 (138)
                      ..+.++++|||||||+++.+++++.+.++.+++|++|+++|+.|++++|++ |.    .++.++|+...+.    +.+|+
T Consensus        40 ~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~l~i~P~r~La~q~~~~~~~-~~~~g~~v~~~~G~~~~~~~~~~~~~Ii  118 (702)
T 2p6r_A           40 GKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGEKYESFKK-WEKIGLRIGISTGDYESRDEHLGDCDII  118 (702)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHHTT-TTTTTCCEEEECSSCBCCSSCSTTCSEE
T ss_pred             CCcEEEEcCCccHHHHHHHHHHHHHHHhCCcEEEEeCcHHHHHHHHHHHHH-HHhcCCEEEEEeCCCCcchhhccCCCEE
Confidence            468889999999999999999998888889999999999999999999954 43    7899999876543    78999


Q ss_pred             EecHHHHHHhh
Q 042424          127 VMTTEILRGML  137 (138)
Q Consensus       127 VtTpe~l~~lL  137 (138)
                      |+|||+|+.++
T Consensus       119 v~Tpe~l~~~l  129 (702)
T 2p6r_A          119 VTTSEKADSLI  129 (702)
T ss_dssp             EEEHHHHHHHH
T ss_pred             EECHHHHHHHH
Confidence            99999998865

>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=99.57  E-value=1.3e-14  Score=111.73  Aligned_cols=83  Identities=17%  Similarity=0.053  Sum_probs=67.4

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc------------CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCc
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD------------KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVT  118 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~------------~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~  118 (138)
                      .++.++++|||+|||+++++++++.+..            +.++||++|+++|++|+++++++...    .+..+.|+..
T Consensus        60 ~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~  139 (253)
T 1wrb_A           60 HRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGAD  139 (253)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSC
T ss_pred             CCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCCceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCC
Confidence            3678899999999999999888877643            35899999999999999999988543    5666777654


Q ss_pred             CC-------CCCCEEEecHHHHHHhh
Q 042424          119 LS-------PNASCLVMTTEILRGML  137 (138)
Q Consensus       119 ~~-------~~~~IiVtTpe~l~~lL  137 (138)
                      .+       .+.+|+|+||++|..++
T Consensus       140 ~~~~~~~~~~~~~Ivv~Tp~~l~~~l  165 (253)
T 1wrb_A          140 THSQIREVQMGCHLLVATPGRLVDFI  165 (253)
T ss_dssp             SHHHHHHHSSCCSEEEECHHHHHHHH
T ss_pred             HHHHHHHhCCCCCEEEECHHHHHHHH
Confidence            32       26799999999998764

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.57  E-value=5.5e-15  Score=135.41  Aligned_cols=84  Identities=55%  Similarity=0.885  Sum_probs=77.0

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCCcCCCCCCEEEecHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVTLSPNASCLVMTTEI  132 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~~~~~~~IiVtTpe~  132 (138)
                      ..+.++++|||||||+++.+++...+..+.+++|++|+++|++|++++|++.|.  .++.++|+...+.+.+|+|+||++
T Consensus        54 g~~vlv~apTGsGKTlv~~~~i~~~~~~g~~vlvl~PtraLa~Q~~~~l~~~~~~~~v~~l~G~~~~~~~~~IlV~Tpe~  133 (997)
T 4a4z_A           54 GDSVFVAAHTSAGKTVVAEYAIAMAHRNMTKTIYTSPIKALSNQKFRDFKETFDDVNIGLITGDVQINPDANCLIMTTEI  133 (997)
T ss_dssp             TCEEEEECCTTSCSHHHHHHHHHHHHHTTCEEEEEESCGGGHHHHHHHHHTTC--CCEEEECSSCEECTTSSEEEEEHHH
T ss_pred             CCCEEEEECCCCcHHHHHHHHHHHHHhcCCeEEEEeCCHHHHHHHHHHHHHHcCCCeEEEEeCCCccCCCCCEEEECHHH
Confidence            367789999999999999999998888899999999999999999999999885  899999999988899999999999


Q ss_pred             HHHhhC
Q 042424          133 LRGMLY  138 (138)
Q Consensus       133 l~~lL~  138 (138)
                      |.++++
T Consensus       134 L~~~l~  139 (997)
T 4a4z_A          134 LRSMLY  139 (997)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            988763

>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=99.56  E-value=1.4e-14  Score=115.92  Aligned_cols=82  Identities=13%  Similarity=0.034  Sum_probs=66.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCCcCCC----CC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDVTLSP----NA  123 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~~~~~----~~  123 (138)
                      ++.++++|||||||+++++++++.+..   +.++||++|+++|+.|+++.+++...     .+....|+.....    ..
T Consensus       132 ~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  211 (300)
T 3fmo_B          132 QNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISE  211 (300)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTCCCCC
T ss_pred             CeEEEECCCCCCccHHHHHHHHHhhhccCCCceEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhhcCCC
Confidence            678899999999999999888887653   34799999999999999999988542     5666666554332    67


Q ss_pred             CEEEecHHHHHHhh
Q 042424          124 SCLVMTTEILRGML  137 (138)
Q Consensus       124 ~IiVtTpe~l~~lL  137 (138)
                      +|+|+||++|..++
T Consensus       212 ~IlV~TP~~l~~~l  225 (300)
T 3fmo_B          212 QIVIGTPGTVLDWC  225 (300)
T ss_dssp             SEEEECHHHHHHHH
T ss_pred             CEEEECHHHHHHHH
Confidence            89999999998765

>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=99.56  E-value=1.3e-14  Score=107.72  Aligned_cols=83  Identities=20%  Similarity=0.107  Sum_probs=68.5

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHH------cCCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCCcCC------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFR------DKQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVTLS------  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~------~~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~~~------  120 (138)
                      .++.++++|||+|||+++..++.+.+.      .+.+++|++|+++|++|+++++++.+.  .+..+.|+....      
T Consensus        38 ~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  117 (207)
T 2gxq_A           38 GKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEAL  117 (207)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHCTTSCEEEECSSSCSHHHHHHH
T ss_pred             CCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEECCHHHHHHHHHHHHHHhhcceEEEEECCCChHHHHHHh
Confidence            367789999999999999988887764      367899999999999999999999665  677777765432      


Q ss_pred             -CCCCEEEecHHHHHHhh
Q 042424          121 -PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 -~~~~IiVtTpe~l~~lL  137 (138)
                       .+.+|+|+||+++..++
T Consensus       118 ~~~~~i~v~T~~~l~~~~  135 (207)
T 2gxq_A          118 LRGADAVVATPGRALDYL  135 (207)
T ss_dssp             HHCCSEEEECHHHHHHHH
T ss_pred             hCCCCEEEECHHHHHHHH
Confidence             26899999999997754

>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=99.56  E-value=9.5e-15  Score=108.67  Aligned_cols=83  Identities=12%  Similarity=0.040  Sum_probs=67.7

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCCcC-------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDVTL-------  119 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~~~-------  119 (138)
                      .++.++++|||+|||+++.++++..+..   +.+++|++|+++|++|+++.+++.+.     .+..+.|+...       
T Consensus        40 ~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~  119 (206)
T 1vec_A           40 GRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRL  119 (206)
T ss_dssp             TCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHT
T ss_pred             CCCEEEECCCCCchHHHHHHHHHHHhcccCCCeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhc
Confidence            3678899999999999999888876543   56899999999999999999988552     57777776543       


Q ss_pred             CCCCCEEEecHHHHHHhh
Q 042424          120 SPNASCLVMTTEILRGML  137 (138)
Q Consensus       120 ~~~~~IiVtTpe~l~~lL  137 (138)
                      ..+.+|+|+||+++..++
T Consensus       120 ~~~~~i~v~T~~~l~~~~  137 (206)
T 1vec_A          120 DDTVHVVIATPGRILDLI  137 (206)
T ss_dssp             TSCCSEEEECHHHHHHHH
T ss_pred             CCCCCEEEeCHHHHHHHH
Confidence            236899999999997654

>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=99.56  E-value=1.1e-14  Score=111.24  Aligned_cols=83  Identities=11%  Similarity=0.063  Sum_probs=68.1

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCCcCC------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDVTLS------  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~~~~------  120 (138)
                      .++.++++|||+|||+++.+++++.+..   +.+++|++|+++|++|+++++++...     .++.+.|+...+      
T Consensus        61 ~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~  140 (230)
T 2oxc_A           61 GLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL  140 (230)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT
T ss_pred             CCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc
Confidence            3678899999999999998888776532   57999999999999999999998542     577888876432      


Q ss_pred             CCCCEEEecHHHHHHhh
Q 042424          121 PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 ~~~~IiVtTpe~l~~lL  137 (138)
                      .+.+|+|+||+++..++
T Consensus       141 ~~~~Iiv~Tp~~l~~~~  157 (230)
T 2oxc_A          141 KKCHIAVGSPGRIKQLI  157 (230)
T ss_dssp             TSCSEEEECHHHHHHHH
T ss_pred             cCCCEEEECHHHHHHHH
Confidence            26899999999998764

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.55  E-value=1.9e-14  Score=126.14  Aligned_cols=84  Identities=30%  Similarity=0.418  Sum_probs=71.9

Q ss_pred             CCCCceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEechHHHHHHHHHHHHHh--cC-ceEEEecCCcCCC----CCCE
Q 042424           54 ETTHGTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLKALSNQKYRELHKE--FK-DVGLMTGDVTLSP----NASC  125 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~kaLv~Q~~~~l~~~--f~-~v~~~tGd~~~~~----~~~I  125 (138)
                      ...+.++++|||||||+++.+++++.+. ++.+++|++|+++|+.|++++|+..  ++ .|+.++|+...+.    +.+|
T Consensus        45 ~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~il~i~P~r~La~q~~~~~~~~~~~g~~v~~~~G~~~~~~~~~~~~~I  124 (715)
T 2va8_A           45 EGNRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVTPLRALTNEKYLTFKDWELIGFKVAMTSGDYDTDDAWLKNYDI  124 (715)
T ss_dssp             TTCCEEEECCTTSCHHHHHHHHHHHHHHHSCSEEEEECSCHHHHHHHHHHHGGGGGGTCCEEECCSCSSSCCGGGGGCSE
T ss_pred             CCCcEEEEcCCCCcHHHHHHHHHHHHHHHCCCeEEEEeCcHHHHHHHHHHHHHhhcCCCEEEEEeCCCCCchhhcCCCCE
Confidence            3578889999999999999988888776 6899999999999999999999532  23 7899999876654    7899


Q ss_pred             EEecHHHHHHhh
Q 042424          126 LVMTTEILRGML  137 (138)
Q Consensus       126 iVtTpe~l~~lL  137 (138)
                      +||||++|+.++
T Consensus       125 iv~Tpe~l~~~~  136 (715)
T 2va8_A          125 IITTYEKLDSLW  136 (715)
T ss_dssp             EEECHHHHHHHH
T ss_pred             EEEcHHHHHHHH
Confidence            999999998865

>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=99.54  E-value=1.1e-14  Score=128.03  Aligned_cols=84  Identities=26%  Similarity=0.421  Sum_probs=72.0

Q ss_pred             CCCCceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEechHHHHHHHHHHHHHh--cC-ceEEEecCCcCCC----CCCE
Q 042424           54 ETTHGTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLKALSNQKYRELHKE--FK-DVGLMTGDVTLSP----NASC  125 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~kaLv~Q~~~~l~~~--f~-~v~~~tGd~~~~~----~~~I  125 (138)
                      ...+.++++|||||||+++.+++++.+. ++.+++|++|+++|+.|++++|++.  ++ .|+.++||...+.    +.+|
T Consensus        38 ~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~~l~i~P~raLa~q~~~~~~~l~~~g~~v~~~~G~~~~~~~~~~~~~I  117 (720)
T 2zj8_A           38 EGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPLKALAEEKFQEFQDWEKIGLRVAMATGDYDSKDEWLGKYDI  117 (720)
T ss_dssp             GTCEEEEECCGGGCHHHHHHHHHHHHHHHHCSEEEEECSSGGGHHHHHHHTGGGGGGTCCEEEECSCSSCCCGGGGGCSE
T ss_pred             CCCcEEEEcCCccHHHHHHHHHHHHHHHhCCCEEEEEcCcHHHHHHHHHHHHHHHhcCCEEEEecCCCCccccccCCCCE
Confidence            3577889999999999999988887765 6899999999999999999999642  23 7899999876654    7899


Q ss_pred             EEecHHHHHHhh
Q 042424          126 LVMTTEILRGML  137 (138)
Q Consensus       126 iVtTpe~l~~lL  137 (138)
                      +|+||++|+.++
T Consensus       118 iv~Tpe~l~~~~  129 (720)
T 2zj8_A          118 IIATAEKFDSLL  129 (720)
T ss_dssp             EEECHHHHHHHH
T ss_pred             EEECHHHHHHHH
Confidence            999999998764

>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=99.54  E-value=1.9e-14  Score=111.84  Aligned_cols=83  Identities=13%  Similarity=0.077  Sum_probs=67.6

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC-------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS-------  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~-------  120 (138)
                      .++.++++|||+|||+++.+++++.+..   +.+++|++|+++|++|++++|++...    .++.+.|+....       
T Consensus        80 ~~~~lv~a~TGsGKT~~~~~~il~~l~~~~~~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~  159 (249)
T 3ber_A           80 GRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALA  159 (249)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHHHHSCCSSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHHH
T ss_pred             CCCEEEEcCCCCCchhHhHHHHHHHHhcCCCCceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHhc
Confidence            3678899999999999999888777653   45799999999999999999988543    677777765432       


Q ss_pred             CCCCEEEecHHHHHHhh
Q 042424          121 PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 ~~~~IiVtTpe~l~~lL  137 (138)
                      .+++|+|+||++|..++
T Consensus       160 ~~~~I~v~Tp~~l~~~l  176 (249)
T 3ber_A          160 KKPHIIIATPGRLIDHL  176 (249)
T ss_dssp             TCCSEEEECHHHHHHHH
T ss_pred             CCCCEEEECHHHHHHHH
Confidence            37899999999997754

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.54  E-value=9.9e-15  Score=110.28  Aligned_cols=83  Identities=16%  Similarity=0.135  Sum_probs=66.6

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC--------ceEEEecCCcC----
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK--------DVGLMTGDVTL----  119 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~--------~v~~~tGd~~~----  119 (138)
                      .++.++++|||+|||+++.+++++.+..   +.+++|++|+++|++|+++++++...        .+..+.|+...    
T Consensus        41 ~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~  120 (219)
T 1q0u_A           41 GESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKAL  120 (219)
T ss_dssp             TCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTT
T ss_pred             CCCEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcCcHHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHH
Confidence            3677899999999999999888877653   57899999999999999999988542        45666666532    


Q ss_pred             ---CCCCCEEEecHHHHHHhh
Q 042424          120 ---SPNASCLVMTTEILRGML  137 (138)
Q Consensus       120 ---~~~~~IiVtTpe~l~~lL  137 (138)
                         ..+.+|+|+||+++..++
T Consensus       121 ~~~~~~~~Iiv~Tp~~l~~~l  141 (219)
T 1q0u_A          121 EKLNVQPHIVIGTPGRINDFI  141 (219)
T ss_dssp             CCCSSCCSEEEECHHHHHHHH
T ss_pred             HHcCCCCCEEEeCHHHHHHHH
Confidence               126789999999998754

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.54  E-value=1.7e-14  Score=117.91  Aligned_cols=83  Identities=16%  Similarity=0.093  Sum_probs=69.8

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC---ceEEEecCCcCC-----------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK---DVGLMTGDVTLS-----------  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~---~v~~~tGd~~~~-----------  120 (138)
                      .++.++++|||+|||++++.++.+.+..+.+++|++|+++|+.|++++|++...   .++.++|+...+           
T Consensus        36 ~~~~lv~apTGsGKT~~~l~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~l~~  115 (414)
T 3oiy_A           36 GKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEE  115 (414)
T ss_dssp             TCCEECCSCSSSSHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCHHHHHHHHHHHHhcCCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEEECCCChhhHHHHHHHhhc
Confidence            357889999999999988888777777789999999999999999999999533   788888887541           


Q ss_pred             CCCCEEEecHHHHHHhh
Q 042424          121 PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 ~~~~IiVtTpe~l~~lL  137 (138)
                      .+.+|+|+||++|..++
T Consensus       116 ~~~~Iiv~Tp~~l~~~l  132 (414)
T 3oiy_A          116 DDYHILVFSTQFVSKNR  132 (414)
T ss_dssp             TCCSEEEEEHHHHHHCH
T ss_pred             CCCCEEEECHHHHHHHH
Confidence            14899999999997653

>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=99.54  E-value=1.8e-14  Score=110.56  Aligned_cols=83  Identities=14%  Similarity=0.082  Sum_probs=64.5

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHH---cCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFR---DKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP------  121 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~---~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~------  121 (138)
                      .++.++++|||+|||+++.+++++.+.   .+.+++|++|+++|++|+++++++...    .+..+.|+.....      
T Consensus        67 ~~~~li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~  146 (237)
T 3bor_A           67 GYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQ  146 (237)
T ss_dssp             TCCEEECCCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC------------
T ss_pred             CCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHHHHHHHh
Confidence            367889999999999999888887764   367999999999999999999998543    4566666544321      


Q ss_pred             --CCCEEEecHHHHHHhh
Q 042424          122 --NASCLVMTTEILRGML  137 (138)
Q Consensus       122 --~~~IiVtTpe~l~~lL  137 (138)
                        ..+|+|+||+++..++
T Consensus       147 ~~~~~Ilv~Tp~~l~~~l  164 (237)
T 3bor_A          147 AEAPHIVVGTPGRVFDML  164 (237)
T ss_dssp             -CCCSEEEECHHHHHHHH
T ss_pred             cCCCCEEEECHHHHHHHH
Confidence              3799999999988764

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.53  E-value=3.1e-14  Score=118.60  Aligned_cols=83  Identities=18%  Similarity=0.295  Sum_probs=72.0

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc-----CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC----
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD-----KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP----  121 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~-----~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~----  121 (138)
                      ..+.++++|||+|||+++.+++.+.+..     +.++||++|+++|++|++++|++.+.    .++.++|+...+.    
T Consensus        19 ~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~   98 (555)
T 3tbk_A           19 GKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERLGYNIASISGATSDSVSVQH   98 (555)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTCCEEEECTTTGGGSCHHH
T ss_pred             CCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhccCCcEEEEEcCCCcchhhHHH
Confidence            3678899999999999999999888775     78999999999999999999999753    7888999876543    


Q ss_pred             ---CCCEEEecHHHHHHhh
Q 042424          122 ---NASCLVMTTEILRGML  137 (138)
Q Consensus       122 ---~~~IiVtTpe~l~~lL  137 (138)
                         +.+|+|+||++|..++
T Consensus        99 ~~~~~~i~v~T~~~l~~~~  117 (555)
T 3tbk_A           99 IIEDNDIIILTPQILVNNL  117 (555)
T ss_dssp             HHHHCSEEEECHHHHHHHH
T ss_pred             HhcCCCEEEECHHHHHHHH
Confidence               5899999999998764

>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=99.53  E-value=2.7e-14  Score=119.41  Aligned_cols=83  Identities=19%  Similarity=0.318  Sum_probs=69.0

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc-----CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC----
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD-----KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP----  121 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~-----~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~----  121 (138)
                      ..+.++++|||+|||+++.+++.+.+..     +.++||++|+++|+.|++++|++.+.    .++.++|+...+.    
T Consensus        22 ~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  101 (556)
T 4a2p_A           22 GKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEK  101 (556)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEECCCC-----CHHH
T ss_pred             CCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEeCCCCcchhHHH
Confidence            3678899999999999999999888775     78999999999999999999999753    6888888875443    


Q ss_pred             ---CCCEEEecHHHHHHhh
Q 042424          122 ---NASCLVMTTEILRGML  137 (138)
Q Consensus       122 ---~~~IiVtTpe~l~~lL  137 (138)
                         +.+|+|+||++|..++
T Consensus       102 ~~~~~~i~v~T~~~l~~~~  120 (556)
T 4a2p_A          102 VIEDSDIIVVTPQILVNSF  120 (556)
T ss_dssp             HHHHCSEEEECHHHHHHHH
T ss_pred             hhCCCCEEEECHHHHHHHH
Confidence               6899999999998764

>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=99.53  E-value=2.9e-14  Score=107.43  Aligned_cols=83  Identities=17%  Similarity=0.114  Sum_probs=67.7

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhc----C-ceEEEecCCcCC------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEF----K-DVGLMTGDVTLS------  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f----~-~v~~~tGd~~~~------  120 (138)
                      .++.++++|||+|||+++++++...+..   +.+++|++|+++|++|+++++++..    + .++.+.|+...+      
T Consensus        51 ~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~  130 (220)
T 1t6n_A           51 GMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVL  130 (220)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHH
T ss_pred             CCCEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHH
Confidence            3678899999999999999888877654   3589999999999999999998854    2 678888876432      


Q ss_pred             --CCCCEEEecHHHHHHhh
Q 042424          121 --PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 --~~~~IiVtTpe~l~~lL  137 (138)
                        ...+|+|+||+++..++
T Consensus       131 ~~~~~~i~v~T~~~l~~~~  149 (220)
T 1t6n_A          131 KKNCPHIVVGTPGRILALA  149 (220)
T ss_dssp             HHSCCSEEEECHHHHHHHH
T ss_pred             hcCCCCEEEeCHHHHHHHH
Confidence              24699999999998754

>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=99.52  E-value=6.6e-14  Score=111.75  Aligned_cols=82  Identities=17%  Similarity=0.135  Sum_probs=66.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHH---cCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC---CCCCE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFR---DKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS---PNASC  125 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~---~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~---~~~~I  125 (138)
                      ++.++++|||+|||+++.++++..+.   .+.+++|++|+++|++|+++++++...    .+....|+....   .+++|
T Consensus        45 ~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  124 (395)
T 3pey_A           45 RNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNKQINAQV  124 (395)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEESTTSSCTTSCBCCSE
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEECCCHHHHHHHHHHHHHHhcccCeeEEEEecCchhhhccCCCCE
Confidence            67789999999999999988887764   367999999999999999999998543    456666654332   27899


Q ss_pred             EEecHHHHHHhh
Q 042424          126 LVMTTEILRGML  137 (138)
Q Consensus       126 iVtTpe~l~~lL  137 (138)
                      +|+||++|..++
T Consensus       125 iv~T~~~l~~~~  136 (395)
T 3pey_A          125 IVGTPGTVLDLM  136 (395)
T ss_dssp             EEECHHHHHHHH
T ss_pred             EEEcHHHHHHHH
Confidence            999999998764

>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=99.49  E-value=1.3e-13  Score=110.98  Aligned_cols=82  Identities=13%  Similarity=0.027  Sum_probs=66.3

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCCcCC----CCC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDVTLS----PNA  123 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~~~~----~~~  123 (138)
                      ++.++++|||+|||+++++++++.+..   +.+++|++|+++|++|+++.+++...     .++...|+....    ...
T Consensus        65 ~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  144 (412)
T 3fht_A           65 QNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISE  144 (412)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTTCCCCC
T ss_pred             CeEEEECCCCchHHHHHHHHHHHHhhhcCCCCCEEEECCCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhhhcCCC
Confidence            677899999999999999888877654   45899999999999999999888432     566666654432    267


Q ss_pred             CEEEecHHHHHHhh
Q 042424          124 SCLVMTTEILRGML  137 (138)
Q Consensus       124 ~IiVtTpe~l~~lL  137 (138)
                      +|+|+||++|..++
T Consensus       145 ~ivv~T~~~l~~~~  158 (412)
T 3fht_A          145 QIVIGTPGTVLDWC  158 (412)
T ss_dssp             SEEEECHHHHHHHH
T ss_pred             CEEEECchHHHHHH
Confidence            99999999998765

>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=99.49  E-value=6.8e-14  Score=116.36  Aligned_cols=83  Identities=18%  Similarity=0.219  Sum_probs=68.0

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc--------CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcC---
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD--------KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTL---  119 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~--------~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~---  119 (138)
                      .++.++++|||||||+++++++++.+..        +.++||++|+++|+.|+++++++...    .++.+.|+...   
T Consensus        93 g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~  172 (434)
T 2db3_A           93 GRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQ  172 (434)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHH
T ss_pred             CCCEEEECCCCCCchHHHHHHHHHHHHhcccccccCCccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHH
Confidence            3678899999999999999888777642        45899999999999999999998543    56777776643   


Q ss_pred             ----CCCCCEEEecHHHHHHhh
Q 042424          120 ----SPNASCLVMTTEILRGML  137 (138)
Q Consensus       120 ----~~~~~IiVtTpe~l~~lL  137 (138)
                          ..+++|+|+||++|..++
T Consensus       173 ~~~l~~~~~Ivv~Tp~~l~~~l  194 (434)
T 2db3_A          173 NECITRGCHVVIATPGRLLDFV  194 (434)
T ss_dssp             HHHHTTCCSEEEECHHHHHHHH
T ss_pred             HHHhhcCCCEEEEChHHHHHHH
Confidence                237899999999998764

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.49  E-value=7.1e-14  Score=113.19  Aligned_cols=83  Identities=19%  Similarity=0.116  Sum_probs=67.0

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---------------------CCcEEEEechHHHHHHHHHHHHHhcC----c
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---------------------KQRVIYTSSLKALSNQKYRELHKEFK----D  109 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---------------------~~rviyv~P~kaLv~Q~~~~l~~~f~----~  109 (138)
                      .++.++++|||+|||+++++++++.+..                     +.++||++|+++|++|+++++++...    .
T Consensus        52 ~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~  131 (417)
T 2i4i_A           52 KRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVR  131 (417)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCC
T ss_pred             CCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhccccccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcCCce
Confidence            4678899999999999998877766532                     15799999999999999999998543    5


Q ss_pred             eEEEecCCcC-------CCCCCEEEecHHHHHHhh
Q 042424          110 VGLMTGDVTL-------SPNASCLVMTTEILRGML  137 (138)
Q Consensus       110 v~~~tGd~~~-------~~~~~IiVtTpe~l~~lL  137 (138)
                      +..+.|+...       ..+.+|+|+||++|..++
T Consensus       132 ~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l  166 (417)
T 2i4i_A          132 PCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMM  166 (417)
T ss_dssp             EEEECSSSCHHHHHHHHTTCCSEEEECHHHHHHHH
T ss_pred             EEEEECCCCHHHHHHHhhCCCCEEEEChHHHHHHH
Confidence            7777777543       236899999999998764

>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=99.49  E-value=8.7e-14  Score=103.32  Aligned_cols=83  Identities=25%  Similarity=0.259  Sum_probs=64.6

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc------CCcEEEEechHHHHHH-HHHHHHHhcC---ceEEEecCCcCCC---
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD------KQRVIYTSSLKALSNQ-KYRELHKEFK---DVGLMTGDVTLSP---  121 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~------~~rviyv~P~kaLv~Q-~~~~l~~~f~---~v~~~tGd~~~~~---  121 (138)
                      ..+.++.+|||+|||+++.+++.+.+..      +.+++|++|+++|++| ..+.+.+...   .+..++|+.....   
T Consensus        48 ~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~  127 (216)
T 3b6e_A           48 GKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLSGDTQLKISFP  127 (216)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTHHHHHTTTSCEEECCC---CCCCHH
T ss_pred             CCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHHHHHhccCceEEEEeCCcccchhHH
Confidence            3678899999999999999887776643      6799999999999999 6666766433   6788888765443   


Q ss_pred             ----CCCEEEecHHHHHHhh
Q 042424          122 ----NASCLVMTTEILRGML  137 (138)
Q Consensus       122 ----~~~IiVtTpe~l~~lL  137 (138)
                          +.+|+|+||+.|..++
T Consensus       128 ~~~~~~~i~v~T~~~l~~~~  147 (216)
T 3b6e_A          128 EVVKSCDIIISTAQILENSL  147 (216)
T ss_dssp             HHHHHCSEEEEEHHHHHHHH
T ss_pred             hhccCCCEEEECHHHHHHHH
Confidence                4899999999998754

>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=99.47  E-value=8e-14  Score=118.25  Aligned_cols=82  Identities=15%  Similarity=0.101  Sum_probs=65.7

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC-------CcEEEEechHHHHHHHHHHHHHhcC--------ceEEEecCCcC-
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK-------QRVIYTSSLKALSNQKYRELHKEFK--------DVGLMTGDVTL-  119 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~-------~rviyv~P~kaLv~Q~~~~l~~~f~--------~v~~~tGd~~~-  119 (138)
                      ++.++++|||+|||+++++++++.+..+       .++||++|+++|+.|++++|++.+.        .+..+.|+... 
T Consensus       112 ~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lil~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  191 (563)
T 3i5x_A          112 HDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFR  191 (563)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHH
T ss_pred             CeEEEECCCCCCccHHHHHHHHHHHHhccccccCCeeEEEEcCcHHHHHHHHHHHHHHHhhccccCceeEEEEECCcCHH
Confidence            5677999999999999999888887653       3899999999999999999998432        35555665432 


Q ss_pred             -------CCCCCEEEecHHHHHHhh
Q 042424          120 -------SPNASCLVMTTEILRGML  137 (138)
Q Consensus       120 -------~~~~~IiVtTpe~l~~lL  137 (138)
                             ..+.+|+|+||++|..++
T Consensus       192 ~~~~~~~~~~~~Iiv~Tp~~l~~~l  216 (563)
T 3i5x_A          192 AAMNKMNKLRPNIVIATPGRLIDVL  216 (563)
T ss_dssp             HHHHHHHHHCCSEEEECHHHHHHHH
T ss_pred             HHHHHHhcCCCCEEEECcHHHHHHH
Confidence                   127899999999998754

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.47  E-value=2.4e-13  Score=117.76  Aligned_cols=83  Identities=19%  Similarity=0.247  Sum_probs=70.8

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcC-----CcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC----
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDK-----QRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP----  121 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~-----~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~----  121 (138)
                      ..+.++++|||+|||+++.+++.+.+..+     .++|+++|+++|+.|++++|++.+.    .++.++|+...+.    
T Consensus        28 g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~  107 (696)
T 2ykg_A           28 GKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQ  107 (696)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCSSSCHHH
T ss_pred             CCCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHHHHHHHHHHHHHhccCCceEEEEeCCccccccHHH
Confidence            36788999999999999998888777642     7899999999999999999999763    7888888875432    


Q ss_pred             ---CCCEEEecHHHHHHhh
Q 042424          122 ---NASCLVMTTEILRGML  137 (138)
Q Consensus       122 ---~~~IiVtTpe~l~~lL  137 (138)
                         +.+|+|+||++|.+++
T Consensus       108 ~~~~~~Iiv~Tp~~L~~~l  126 (696)
T 2ykg_A          108 IVENNDIIILTPQILVNNL  126 (696)
T ss_dssp             HHHTCSEEEECHHHHHHHH
T ss_pred             hccCCCEEEECHHHHHHHH
Confidence               7899999999998764

>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=99.47  E-value=1.5e-13  Score=110.97  Aligned_cols=82  Identities=17%  Similarity=0.080  Sum_probs=68.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHH---cCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcC-------CC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFR---DKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTL-------SP  121 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~---~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~-------~~  121 (138)
                      ++.++++|||+|||+++.++++..+.   .+.+++|++|+++|++|+++++++.+.    .+..++|+...       ..
T Consensus        59 ~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~  138 (400)
T 1s2m_A           59 RDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNE  138 (400)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTS
T ss_pred             CCEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcCCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHHhcC
Confidence            57789999999999999988887765   356899999999999999999998654    57777777542       24


Q ss_pred             CCCEEEecHHHHHHhh
Q 042424          122 NASCLVMTTEILRGML  137 (138)
Q Consensus       122 ~~~IiVtTpe~l~~lL  137 (138)
                      +.+|+|+||++|..++
T Consensus       139 ~~~Ivv~T~~~l~~~~  154 (400)
T 1s2m_A          139 TVHILVGTPGRVLDLA  154 (400)
T ss_dssp             CCSEEEECHHHHHHHH
T ss_pred             CCCEEEEchHHHHHHH
Confidence            7899999999997654

>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=99.46  E-value=1.3e-13  Score=109.03  Aligned_cols=82  Identities=16%  Similarity=0.097  Sum_probs=67.7

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC------CCC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS------PNA  123 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~------~~~  123 (138)
                      .+.++++|||+|||+++..++...+..  +.++++++|+++|++|+++++++.++    .+..+.|+....      .+.
T Consensus        45 ~~~l~~~~TGsGKT~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~  124 (367)
T 1hv8_A           45 YNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKNA  124 (367)
T ss_dssp             SEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHHTC
T ss_pred             CCEEEECCCCChHHHHHHHHHHHHhcccCCCcEEEEcCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHhhcCCC
Confidence            567799999999999998888776654  78999999999999999999999765    566677765432      178


Q ss_pred             CEEEecHHHHHHhh
Q 042424          124 SCLVMTTEILRGML  137 (138)
Q Consensus       124 ~IiVtTpe~l~~lL  137 (138)
                      +|+|+||++|..++
T Consensus       125 ~iiv~T~~~l~~~~  138 (367)
T 1hv8_A          125 NIVVGTPGRILDHI  138 (367)
T ss_dssp             SEEEECHHHHHHHH
T ss_pred             CEEEecHHHHHHHH
Confidence            99999999998754

>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=99.46  E-value=1.6e-13  Score=114.46  Aligned_cols=82  Identities=13%  Similarity=0.034  Sum_probs=65.3

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC---CcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCCcCC----CCC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK---QRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDVTLS----PNA  123 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~---~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~~~~----~~~  123 (138)
                      ++.++++|||||||+++++++++.+..+   .++||++|+++|+.|+++.+++...     .++...|+....    .+.
T Consensus       132 ~~~l~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  211 (479)
T 3fmp_B          132 QNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISE  211 (479)
T ss_dssp             CEEEEECCSSSSHHHHHHHHHHTTCCTTSCSCCEEEECSSHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTTCCCCC
T ss_pred             CcEEEEcCCCCchhHHHHHHHHHHHhhcCCCCcEEEEeChHHHHHHHHHHHHHHHhhCCCceEEEEeCCccccccccCCC
Confidence            5678999999999999999988776643   3899999999999999988877432     456665554332    267


Q ss_pred             CEEEecHHHHHHhh
Q 042424          124 SCLVMTTEILRGML  137 (138)
Q Consensus       124 ~IiVtTpe~l~~lL  137 (138)
                      +|+|+||++|..++
T Consensus       212 ~Ivv~Tp~~l~~~l  225 (479)
T 3fmp_B          212 QIVIGTPGTVLDWC  225 (479)
T ss_dssp             SEEEECHHHHHHHH
T ss_pred             CEEEECchHHHHHH
Confidence            89999999998765

>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=99.46  E-value=2.5e-13  Score=120.83  Aligned_cols=83  Identities=19%  Similarity=0.318  Sum_probs=69.8

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc-----CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC----
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD-----KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP----  121 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~-----~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~----  121 (138)
                      .++.++++|||+|||+++.+++.+.+..     +.++||++|+++|+.|++++|++.+.    .++.++|+...+.    
T Consensus       263 ~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~  342 (797)
T 4a2q_A          263 GKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEK  342 (797)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECCC-----CHHH
T ss_pred             CCCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHhcccCCceEEEEeCCcchhhhHHH
Confidence            3678899999999999999999888875     78999999999999999999999763    7888999875543    


Q ss_pred             ---CCCEEEecHHHHHHhh
Q 042424          122 ---NASCLVMTTEILRGML  137 (138)
Q Consensus       122 ---~~~IiVtTpe~l~~lL  137 (138)
                         +.+|+|+||++|...+
T Consensus       343 ~~~~~~Ivv~Tp~~l~~~l  361 (797)
T 4a2q_A          343 VIEDSDIIVVTPQILVNSF  361 (797)
T ss_dssp             HHHTCSEEEECHHHHHHHH
T ss_pred             hhCCCCEEEEchHHHHHHH
Confidence               7899999999998764

>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=99.46  E-value=2.5e-13  Score=106.46  Aligned_cols=80  Identities=18%  Similarity=0.144  Sum_probs=65.5

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC------CCCC
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS------PNAS  124 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~------~~~~  124 (138)
                      .++.++++|||+|||+++..++.+   .+.+++|++|+++|++|+++++++...    .+..+.|+...+      .+.+
T Consensus        31 ~~~~lv~~~TGsGKT~~~~~~~~~---~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  107 (337)
T 2z0m_A           31 GKNVVVRAKTGSGKTAAYAIPILE---LGMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVRNAD  107 (337)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHH---HTCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECTTSCHHHHHHHHTTCS
T ss_pred             CCCEEEEcCCCCcHHHHHHHHHHh---hcCCEEEEeCCHHHHHHHHHHHHHHhhhcCCcEEEEECCcchHHHHhhcCCCC
Confidence            367889999999999998877654   489999999999999999999998543    677777765432      2689


Q ss_pred             EEEecHHHHHHhh
Q 042424          125 CLVMTTEILRGML  137 (138)
Q Consensus       125 IiVtTpe~l~~lL  137 (138)
                      |+|+||++|.+++
T Consensus       108 i~v~T~~~l~~~~  120 (337)
T 2z0m_A          108 IVVATPGRLLDLW  120 (337)
T ss_dssp             EEEECHHHHHHHH
T ss_pred             EEEECHHHHHHHH
Confidence            9999999998754

>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=99.45  E-value=1.5e-13  Score=111.42  Aligned_cols=83  Identities=12%  Similarity=0.071  Sum_probs=68.2

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHH---cCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC-------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFR---DKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS-------  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~---~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~-------  120 (138)
                      .++.++++|||+|||+++++++++.+.   .+.++||++|+++|++|++++|++...    .+..+.|+....       
T Consensus        74 ~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~  153 (410)
T 2j0s_A           74 GRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLD  153 (410)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHH
T ss_pred             CCCEEEECCCCCCchHHHHHHHHHHHhhccCCceEEEEcCcHHHHHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHhh
Confidence            367889999999999999988887764   368999999999999999999998443    567777765432       


Q ss_pred             CCCCEEEecHHHHHHhh
Q 042424          121 PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 ~~~~IiVtTpe~l~~lL  137 (138)
                      .+.+|+|+||++|..++
T Consensus       154 ~~~~ivv~Tp~~l~~~l  170 (410)
T 2j0s_A          154 YGQHVVAGTPGRVFDMI  170 (410)
T ss_dssp             HCCSEEEECHHHHHHHH
T ss_pred             cCCCEEEcCHHHHHHHH
Confidence            26799999999998765

>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=99.45  E-value=2e-13  Score=109.48  Aligned_cols=83  Identities=17%  Similarity=0.114  Sum_probs=67.9

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhc----C-ceEEEecCCcCC------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEF----K-DVGLMTGDVTLS------  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f----~-~v~~~tGd~~~~------  120 (138)
                      ..+.++++|||+|||+++++++...+..   +.++||++|+++|++|+++++++..    + .++.+.|+...+      
T Consensus        45 ~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~  124 (391)
T 1xti_A           45 GMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVL  124 (391)
T ss_dssp             TCCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHH
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHH
Confidence            3678899999999999999888877653   5699999999999999999998853    2 678888876432      


Q ss_pred             --CCCCEEEecHHHHHHhh
Q 042424          121 --PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 --~~~~IiVtTpe~l~~lL  137 (138)
                        ...+|+|+||++|..++
T Consensus       125 ~~~~~~iiv~T~~~l~~~~  143 (391)
T 1xti_A          125 KKNCPHIVVGTPGRILALA  143 (391)
T ss_dssp             HHSCCSEEEECHHHHHHHH
T ss_pred             hcCCCCEEEECHHHHHHHH
Confidence              24799999999998754

>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=99.45  E-value=1.7e-13  Score=110.57  Aligned_cols=83  Identities=14%  Similarity=0.077  Sum_probs=67.3

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHH---cCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC-------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFR---DKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS-------  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~---~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~-------  120 (138)
                      .++.++++|||+|||+++.+++++.+.   .+.+++|++|+++|+.|+++++++.+.    .+....|+....       
T Consensus        77 ~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (414)
T 3eiq_A           77 GYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQ  156 (414)
T ss_dssp             TCCEEECCCSCSSSHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHGGGSCCCEEECCCCTTHHHHHHHHT
T ss_pred             CCCEEEECCCCCcccHHHHHHHHHHHhhcCCceeEEEEeChHHHHHHHHHHHHHHhcccCceEEEEECCcchHHHHHHHh
Confidence            357889999999999999988887765   368899999999999999999998543    455556654321       


Q ss_pred             -CCCCEEEecHHHHHHhh
Q 042424          121 -PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 -~~~~IiVtTpe~l~~lL  137 (138)
                       .+.+|+|+||++|..++
T Consensus       157 ~~~~~iiv~T~~~l~~~l  174 (414)
T 3eiq_A          157 MEAPHIIVGTPGRVFDML  174 (414)
T ss_dssp             TTCCSEEEECHHHHHHHH
T ss_pred             cCCCCEEEECHHHHHHHH
Confidence             46799999999988764

>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=99.44  E-value=4.4e-13  Score=105.23  Aligned_cols=80  Identities=13%  Similarity=0.136  Sum_probs=64.2

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC-CcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC----CCCCEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK-QRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS----PNASCL  126 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~-~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~----~~~~Ii  126 (138)
                      .+.++++|||+|||+++..++...+.++ .+++|++|+++|++|++++|++.+.    .+..+.|+....    .+.+|+
T Consensus       129 ~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~  208 (282)
T 1rif_A          129 RRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIGGGASKDDKYKNDAPVV  208 (282)
T ss_dssp             SEEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEECSTTCSSTTCCCTTCSEE
T ss_pred             CCeEEEcCCCCCcHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHHHHHhcccccceEEEEeCCCcchhhhccCCcEE
Confidence            5678999999999999987777776655 4999999999999999999998543    455555554433    478999


Q ss_pred             EecHHHHHH
Q 042424          127 VMTTEILRG  135 (138)
Q Consensus       127 VtTpe~l~~  135 (138)
                      |+||+.+..
T Consensus       209 v~T~~~l~~  217 (282)
T 1rif_A          209 VGTWQTVVK  217 (282)
T ss_dssp             EECHHHHTT
T ss_pred             EEchHHHHh
Confidence            999998754

>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=99.44  E-value=1.3e-13  Score=110.50  Aligned_cols=82  Identities=13%  Similarity=0.043  Sum_probs=67.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC------C
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP------N  122 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~------~  122 (138)
                      ++.++++|||+|||+++.+++++.+..   +.+++|++|+++|++|++++|++.+.    .+..+.|+.....      +
T Consensus        59 ~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~  138 (394)
T 1fuu_A           59 HDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRD  138 (394)
T ss_dssp             CCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHHH
T ss_pred             CCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEcCCHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcCC
Confidence            677899999999999998888777643   67999999999999999999998653    5777777654321      6


Q ss_pred             CCEEEecHHHHHHhh
Q 042424          123 ASCLVMTTEILRGML  137 (138)
Q Consensus       123 ~~IiVtTpe~l~~lL  137 (138)
                      .+|+|+||++|...+
T Consensus       139 ~~i~v~T~~~l~~~~  153 (394)
T 1fuu_A          139 AQIVVGTPGRVFDNI  153 (394)
T ss_dssp             CSEEEECHHHHHHHH
T ss_pred             CCEEEECHHHHHHHH
Confidence            889999999987654

>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=99.43  E-value=1.5e-13  Score=119.17  Aligned_cols=82  Identities=27%  Similarity=0.276  Sum_probs=68.3

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC------CcEEEEechHHHHHHH-HHHHHHhcC---ceEEEecCCcCCC----
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK------QRVIYTSSLKALSNQK-YRELHKEFK---DVGLMTGDVTLSP----  121 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~------~rviyv~P~kaLv~Q~-~~~l~~~f~---~v~~~tGd~~~~~----  121 (138)
                      .+.++++|||+|||+++.+++.+.+..+      .++||++|+++|+.|+ +++|++.+.   .++.++|+...+.    
T Consensus        23 ~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~~~~v~~~~g~~~~~~~~~~  102 (699)
T 4gl2_A           23 KNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLSGDTQLKISFPE  102 (699)
T ss_dssp             CCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHHHTTTSCEEEEC----CCCCHHH
T ss_pred             CCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHHcCcCceEEEEeCCcchhhHHHh
Confidence            5788999999999999999888876542      8999999999999999 999999775   7888999876542    


Q ss_pred             ---CCCEEEecHHHHHHhh
Q 042424          122 ---NASCLVMTTEILRGML  137 (138)
Q Consensus       122 ---~~~IiVtTpe~l~~lL  137 (138)
                         +.+|+|+||++|.+.+
T Consensus       103 ~~~~~~Ilv~Tp~~L~~~l  121 (699)
T 4gl2_A          103 VVKSCDIIISTAQILENSL  121 (699)
T ss_dssp             HHHSCSEEEEEHHHHHHHT
T ss_pred             hhcCCCEEEECHHHHHHHH
Confidence               7899999999998765

>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=99.43  E-value=3.5e-13  Score=108.83  Aligned_cols=81  Identities=20%  Similarity=0.240  Sum_probs=69.5

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC------CCCE
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP------NASC  125 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~------~~~I  125 (138)
                      +.++++|||+|||+++..++...+. .+.++|+++|+++|++|++++|++.++    .+..++|+.....      +.+|
T Consensus        25 ~~ll~~~tG~GKT~~~~~~~~~~~~~~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~i  104 (494)
T 1wp9_A           25 NCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWARAKV  104 (494)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEECSCSCHHHHHHHHHHCSE
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHhcCCCeEEEEECCHHHHHHHHHHHHHHhCcchhheEEeeCCcchhhhhhhccCCCE
Confidence            7889999999999999988777665 588999999999999999999999775    6888888765431      6899


Q ss_pred             EEecHHHHHHhh
Q 042424          126 LVMTTEILRGML  137 (138)
Q Consensus       126 iVtTpe~l~~lL  137 (138)
                      +|+||+.|.+.+
T Consensus       105 vv~T~~~l~~~~  116 (494)
T 1wp9_A          105 IVATPQTIENDL  116 (494)
T ss_dssp             EEECHHHHHHHH
T ss_pred             EEecHHHHHHHH
Confidence            999999998754

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.41  E-value=7.2e-13  Score=111.13  Aligned_cols=80  Identities=14%  Similarity=0.199  Sum_probs=67.3

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCC-cEEEEechHHHHHHHHHHHHHh--cC--ceEEEecCCcCC----CCCCEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQ-RVIYTSSLKALSNQKYRELHKE--FK--DVGLMTGDVTLS----PNASCL  126 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~-rviyv~P~kaLv~Q~~~~l~~~--f~--~v~~~tGd~~~~----~~~~Ii  126 (138)
                      .+.++++|||+|||++++.++...+..++ +++|++|+++|++|++++|++.  +.  .+..+.|+....    .+.+|+
T Consensus       129 ~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~I~  208 (510)
T 2oca_A          129 RRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIGGGASKDDKYKNDAPVV  208 (510)
T ss_dssp             SEEEEECCSTTTHHHHHHHHHHHHHHHCSSEEEEEESSHHHHHHHHHHHHHTTSSCGGGEEECGGGCCTTGGGCTTCSEE
T ss_pred             CCcEEEeCCCCCHHHHHHHHHHHHHhCCCCeEEEEECcHHHHHHHHHHHHHhhcCCccceEEEecCCccccccccCCcEE
Confidence            57889999999999999988888776654 9999999999999999999874  22  577787776654    578999


Q ss_pred             EecHHHHHH
Q 042424          127 VMTTEILRG  135 (138)
Q Consensus       127 VtTpe~l~~  135 (138)
                      |+|++.+..
T Consensus       209 i~T~~~l~~  217 (510)
T 2oca_A          209 VGTWQTVVK  217 (510)
T ss_dssp             EEEHHHHTT
T ss_pred             EEeHHHHhh
Confidence            999998754

>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=99.40  E-value=4.2e-13  Score=120.55  Aligned_cols=80  Identities=25%  Similarity=0.334  Sum_probs=70.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC-----------
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS-----------  120 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~-----------  120 (138)
                      .+.++++|||||||++++++++.++..|.+++|++|+++|++|++++|++.+.    .++.++|+...+           
T Consensus       390 ~~~Ll~a~TGSGKTlvall~il~~l~~g~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~  469 (780)
T 1gm5_A          390 MNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRN  469 (780)
T ss_dssp             CCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHS
T ss_pred             CcEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhc
Confidence            47789999999999999999999988899999999999999999999999774    788899987532           


Q ss_pred             CCCCEEEecHHHHHH
Q 042424          121 PNASCLVMTTEILRG  135 (138)
Q Consensus       121 ~~~~IiVtTpe~l~~  135 (138)
                      .+.+|+|+||+.|..
T Consensus       470 g~~~IvVgT~~ll~~  484 (780)
T 1gm5_A          470 GQIDVVIGTHALIQE  484 (780)
T ss_dssp             SCCCEEEECTTHHHH
T ss_pred             CCCCEEEECHHHHhh
Confidence            258999999998864

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.40  E-value=5.7e-13  Score=114.26  Aligned_cols=82  Identities=15%  Similarity=0.100  Sum_probs=64.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC-------CcEEEEechHHHHHHHHHHHHHhcC--------ceEEEecCCcCC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK-------QRVIYTSSLKALSNQKYRELHKEFK--------DVGLMTGDVTLS  120 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~-------~rviyv~P~kaLv~Q~~~~l~~~f~--------~v~~~tGd~~~~  120 (138)
                      .+.++++|||+|||+++.+++++.+..+       .++||++|+++|+.|+++++++.+.        .+..+.|+....
T Consensus        61 ~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lvl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~  140 (579)
T 3sqw_A           61 HDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFR  140 (579)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHH
T ss_pred             CeEEEEcCCCcHHHHHHHHHHHHHHHhccccccCCCeEEEEcchHHHHHHHHHHHHHHHhhcccccceEEEEEECCccHH
Confidence            5677999999999999998888777543       4899999999999999999998541        345555554321


Q ss_pred             --------CCCCEEEecHHHHHHhh
Q 042424          121 --------PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 --------~~~~IiVtTpe~l~~lL  137 (138)
                              .+.+|+|+||++|..+|
T Consensus       141 ~~~~~l~~~~~~IlV~Tp~~l~~~l  165 (579)
T 3sqw_A          141 AAMNKMNKLRPNIVIATPGRLIDVL  165 (579)
T ss_dssp             HHHHHHHHHCCSEEEECHHHHHHHH
T ss_pred             HHHHHHhcCCCCEEEECHHHHHHHH
Confidence                    26899999999998654

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.37  E-value=1.6e-12  Score=120.24  Aligned_cols=81  Identities=16%  Similarity=0.129  Sum_probs=70.2

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC----------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS----------  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~----------  120 (138)
                      .++.++++|||||||++++.++.+.+..+.++||++|+++|+.|++++|++ |.    .++.++|+....          
T Consensus        93 g~dvlv~ApTGSGKTl~~l~~il~~~~~~~~~Lil~PtreLa~Q~~~~l~~-l~~~~i~v~~l~Gg~~~~er~~~~~~l~  171 (1104)
T 4ddu_A           93 GKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQK-LADEKVKIFGFYSSMKKEEKEKFEKSFE  171 (1104)
T ss_dssp             TCCEEECCSTTCCHHHHHHHHHHHHHTTTCCEEEEESSHHHHHHHHHHHHT-TSCTTSCEEEECTTCCTTHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCcHHHHHHHHHHHHHhcCCeEEEEechHHHHHHHHHHHHH-hhCCCCeEEEEeCCCCHHHHHHHHHHHh
Confidence            467889999999999988888888887899999999999999999999999 43    788899987651          


Q ss_pred             -CCCCEEEecHHHHHHh
Q 042424          121 -PNASCLVMTTEILRGM  136 (138)
Q Consensus       121 -~~~~IiVtTpe~l~~l  136 (138)
                       .+.+|+|+||++|..+
T Consensus       172 ~g~~~IlV~Tp~rL~~~  188 (1104)
T 4ddu_A          172 EDDYHILVFSTQFVSKN  188 (1104)
T ss_dssp             TSCCSEEEEEHHHHHHS
T ss_pred             CCCCCEEEECHHHHHHH
Confidence             2489999999999665

>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=99.36  E-value=9.9e-13  Score=119.47  Aligned_cols=83  Identities=19%  Similarity=0.318  Sum_probs=69.0

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc-----CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC----
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD-----KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP----  121 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~-----~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~----  121 (138)
                      ..+.++++|||+|||+++.+++.+.+.+     +.++||++|+++|+.|++++|++.+.    .+..++|+...+.    
T Consensus       263 g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~v~~~~G~~~~~~~~~~  342 (936)
T 4a2w_A          263 GKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEK  342 (936)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTCCEEEECCC-----CCHH
T ss_pred             CCCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEECCcchhhHHHH
Confidence            4678899999999999999998887765     78899999999999999999999753    7888999875442    


Q ss_pred             ---CCCEEEecHHHHHHhh
Q 042424          122 ---NASCLVMTTEILRGML  137 (138)
Q Consensus       122 ---~~~IiVtTpe~l~~lL  137 (138)
                         +.+|+|+||++|..++
T Consensus       343 ~~~~~~IvI~Tp~~L~~~l  361 (936)
T 4a2w_A          343 VIEDSDIIVVTPQILVNSF  361 (936)
T ss_dssp             HHHHCSEEEECHHHHHHHH
T ss_pred             hccCCCEEEecHHHHHHHH
Confidence               6799999999998764

>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=99.35  E-value=2.3e-12  Score=107.09  Aligned_cols=75  Identities=25%  Similarity=0.206  Sum_probs=65.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-c-eEEEecCCcCCCCCCEEEecHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-D-VGLMTGDVTLSPNASCLVMTTEIL  133 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~-v~~~tGd~~~~~~~~IiVtTpe~l  133 (138)
                      .+.++++|||+|||++++.++...   +.++++++|+++|+.|++++|++ |+ . +++++|+...  ..+|+|+|++.+
T Consensus       109 ~~~ll~~~TGsGKT~~~l~~i~~~---~~~~Lvl~P~~~L~~Q~~~~~~~-~~~~~v~~~~g~~~~--~~~Ivv~T~~~l  182 (472)
T 2fwr_A          109 KRGCIVLPTGSGKTHVAMAAINEL---STPTLIVVPTLALAEQWKERLGI-FGEEYVGEFSGRIKE--LKPLTVSTYDSA  182 (472)
T ss_dssp             TEEEEECCTTSCHHHHHHHHHHHH---CSCEEEEESSHHHHHHHHHHGGG-GCGGGEEEBSSSCBC--CCSEEEEEHHHH
T ss_pred             CCEEEEeCCCCCHHHHHHHHHHHc---CCCEEEEECCHHHHHHHHHHHHh-CCCcceEEECCCcCC--cCCEEEEEcHHH
Confidence            457899999999999998877654   88999999999999999999999 88 6 9999987654  578999999988


Q ss_pred             HHh
Q 042424          134 RGM  136 (138)
Q Consensus       134 ~~l  136 (138)
                      ...
T Consensus       183 ~~~  185 (472)
T 2fwr_A          183 YVN  185 (472)
T ss_dssp             HHT
T ss_pred             HHH
Confidence            654

>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=99.30  E-value=8.9e-12  Score=96.52  Aligned_cols=75  Identities=25%  Similarity=0.206  Sum_probs=64.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-c-eEEEecCCcCCCCCCEEEecHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-D-VGLMTGDVTLSPNASCLVMTTEIL  133 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~-v~~~tGd~~~~~~~~IiVtTpe~l  133 (138)
                      .+.++++|||+|||+++..++...   +.+++|++|+++|++|+++++.+ |+ . ++.++|+...  ..+|+|+|++.+
T Consensus       109 ~~~ll~~~tG~GKT~~a~~~~~~~---~~~~liv~P~~~L~~q~~~~~~~-~~~~~v~~~~g~~~~--~~~i~v~T~~~l  182 (237)
T 2fz4_A          109 KRGCIVLPTGSGKTHVAMAAINEL---STPTLIVVPTLALAEQWKERLGI-FGEEYVGEFSGRIKE--LKPLTVSTYDSA  182 (237)
T ss_dssp             SEEEEEESSSTTHHHHHHHHHHHS---CSCEEEEESSHHHHHHHHHHHGG-GCGGGEEEESSSCBC--CCSEEEEEHHHH
T ss_pred             CCEEEEeCCCCCHHHHHHHHHHHc---CCCEEEEeCCHHHHHHHHHHHHh-CCCCeEEEEeCCCCC--cCCEEEEeHHHH
Confidence            457899999999999988766543   78999999999999999999999 87 5 8999887643  678999999988


Q ss_pred             HHh
Q 042424          134 RGM  136 (138)
Q Consensus       134 ~~l  136 (138)
                      ...
T Consensus       183 ~~~  185 (237)
T 2fz4_A          183 YVN  185 (237)
T ss_dssp             HHT
T ss_pred             Hhh
Confidence            643

>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=99.27  E-value=6.1e-12  Score=115.72  Aligned_cols=83  Identities=18%  Similarity=0.108  Sum_probs=67.0

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC--------ceEEEecCCcCCC-----
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK--------DVGLMTGDVTLSP-----  121 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~--------~v~~~tGd~~~~~-----  121 (138)
                      .++.++++|||||||++++.++......+.+++|++|+++|+.|+++.|++.+.        .++.++|+...+.     
T Consensus        71 g~dvlv~apTGSGKTl~~lp~l~~~~~~~~~~lil~PtreLa~Q~~~~l~~l~~~~~i~~~~~v~~~~Gg~~~~~~~~~~  150 (1054)
T 1gku_B           71 KESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFM  150 (1054)
T ss_dssp             TCCEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHH
T ss_pred             CCCEEEEcCCCCCHHHHHHHHHHHHhhcCCeEEEEeccHHHHHHHHHHHHHHHhhcCCCccceEEEEeCCCChhhHHHHH
Confidence            367889999999999955555555556689999999999999999999998654        4677888764321     


Q ss_pred             ----CCCEEEecHHHHHHhh
Q 042424          122 ----NASCLVMTTEILRGML  137 (138)
Q Consensus       122 ----~~~IiVtTpe~l~~lL  137 (138)
                          +.+|+|+||++|..++
T Consensus       151 ~~l~~~~IlV~TP~~L~~~l  170 (1054)
T 1gku_B          151 QNLRNFKIVITTTQFLSKHY  170 (1054)
T ss_dssp             HSGGGCSEEEEEHHHHHHCS
T ss_pred             hhccCCCEEEEcHHHHHHHH
Confidence                3899999999998865

>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=99.24  E-value=1.2e-11  Score=114.66  Aligned_cols=79  Identities=20%  Similarity=0.254  Sum_probs=67.5

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcC-----------CC
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTL-----------SP  121 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~-----------~~  121 (138)
                      +.++++|||+|||++++.+++.++..|.+++|++||++|++|++++|++.|.    .++.++|....           +.
T Consensus       626 d~ll~~~TGsGKT~val~aa~~~~~~g~~vlvlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g  705 (1151)
T 2eyq_A          626 DRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEG  705 (1151)
T ss_dssp             EEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTT
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHHHhCCeEEEEechHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcC
Confidence            6789999999999999988888888899999999999999999999999875    57788765432           12


Q ss_pred             CCCEEEecHHHHHH
Q 042424          122 NASCLVMTTEILRG  135 (138)
Q Consensus       122 ~~~IiVtTpe~l~~  135 (138)
                      +.+|+|+||+.+..
T Consensus       706 ~~dIvV~T~~ll~~  719 (1151)
T 2eyq_A          706 KIDILIGTHKLLQS  719 (1151)
T ss_dssp             CCSEEEECTHHHHS
T ss_pred             CCCEEEECHHHHhC
Confidence            68999999988754

>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=99.22  E-value=2.6e-11  Score=107.47  Aligned_cols=77  Identities=19%  Similarity=0.110  Sum_probs=66.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcCCCCCCEEEecHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTLSPNASCLVMTTEILR  134 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~~~~~~IiVtTpe~l~  134 (138)
                      ++.++++|||||||+++.++++   .++.+++|++|+++|+.|.++++.+.++ .++...|+.....+.+|+|+||++|.
T Consensus       233 ~~vlv~ApTGSGKT~a~~l~ll---~~g~~vLVl~PTReLA~Qia~~l~~~~g~~vg~~vG~~~~~~~~~IlV~TPGrLl  309 (666)
T 3o8b_A          233 QVAHLHAPTGSGKSTKVPAAYA---AQGYKVLVLNPSVAATLGFGAYMSKAHGIDPNIRTGVRTITTGAPVTYSTYGKFL  309 (666)
T ss_dssp             EEEEEECCTTSCTTTHHHHHHH---HTTCCEEEEESCHHHHHHHHHHHHHHHSCCCEEECSSCEECCCCSEEEEEHHHHH
T ss_pred             CeEEEEeCCchhHHHHHHHHHH---HCCCeEEEEcchHHHHHHHHHHHHHHhCCCeeEEECcEeccCCCCEEEECcHHHH
Confidence            4567999999999988877664   3578999999999999999999988787 78888898777778999999999985


Q ss_pred             H
Q 042424          135 G  135 (138)
Q Consensus       135 ~  135 (138)
                      .
T Consensus       310 ~  310 (666)
T 3o8b_A          310 A  310 (666)
T ss_dssp             H
T ss_pred             h
Confidence            3

>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=99.18  E-value=6.1e-11  Score=103.20  Aligned_cols=76  Identities=12%  Similarity=0.135  Sum_probs=63.3

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcC-------------C
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTL-------------S  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~-------------~  120 (138)
                      .++.++++|||+|||+++.++++   ..+.++||++|+++|+.|+++.|++ ++ .+..++|+...             +
T Consensus        59 g~d~lv~~pTGsGKTl~~~lpal---~~~g~~lVisP~~~L~~q~~~~l~~-~gi~~~~l~~~~~~~~~~~~~~~l~~~~  134 (591)
T 2v1x_A           59 GKEVFLVMPTGGGKSLCYQLPAL---CSDGFTLVICPLISLMEDQLMVLKQ-LGISATMLNASSSKEHVKWVHAEMVNKN  134 (591)
T ss_dssp             TCCEEEECCTTSCTTHHHHHHHH---TSSSEEEEECSCHHHHHHHHHHHHH-HTCCEEECCSSCCHHHHHHHHHHHHCTT
T ss_pred             CCCEEEEECCCChHHHHHHHHHH---HcCCcEEEEeCHHHHHHHHHHHHHh-cCCcEEEEeCCCCHHHHHHHHHHhhccc
Confidence            36788999999999999877664   3577999999999999999999998 56 77888876542             3


Q ss_pred             CCCCEEEecHHHHH
Q 042424          121 PNASCLVMTTEILR  134 (138)
Q Consensus       121 ~~~~IiVtTpe~l~  134 (138)
                      .+.+|+|+|||+|.
T Consensus       135 ~~~~Ilv~Tpe~L~  148 (591)
T 2v1x_A          135 SELKLIYVTPEKIA  148 (591)
T ss_dssp             CCCCEEEECHHHHH
T ss_pred             CCCCEEEEChhHhh
Confidence            47899999999874

>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=99.16  E-value=1.7e-10  Score=88.38  Aligned_cols=82  Identities=18%  Similarity=0.130  Sum_probs=60.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHH-cCC----cEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCC-cC-CCCC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFR-DKQ----RVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDV-TL-SPNA  123 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~-~~~----rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~-~~-~~~~  123 (138)
                      ++.++++|||||||..+...+...+. .+.    +++++.|+++|+.|.++.+.+.++     .++.-.... .. ..+.
T Consensus        77 ~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~  156 (235)
T 3llm_A           77 SVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFESILPRPHA  156 (235)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHHHHHHHTTTCCTTSSEEEEETTEEECCCSSS
T ss_pred             CEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHHHHHHHHhccccCceEEEeechhhccCCCCC
Confidence            55679999999999877666655443 333    899999999999999999988765     233221111 11 2467


Q ss_pred             CEEEecHHHHHHhh
Q 042424          124 SCLVMTTEILRGML  137 (138)
Q Consensus       124 ~IiVtTpe~l~~lL  137 (138)
                      +|+|+||+++..++
T Consensus       157 ~Ivv~Tpg~l~~~l  170 (235)
T 3llm_A          157 SIMFCTVGVLLRKL  170 (235)
T ss_dssp             EEEEEEHHHHHHHH
T ss_pred             eEEEECHHHHHHHH
Confidence            89999999998765

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.14  E-value=2.8e-11  Score=103.66  Aligned_cols=79  Identities=14%  Similarity=0.157  Sum_probs=50.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHH---------cCCcEEEEechHHHHHHHH-HHHHHhcC-ceEEEecCCcCCCCCC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFR---------DKQRVIYTSSLKALSNQKY-RELHKEFK-DVGLMTGDVTLSPNAS  124 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~---------~~~rviyv~P~kaLv~Q~~-~~l~~~f~-~v~~~tGd~~~~~~~~  124 (138)
                      ++.++++|||+|||++++.++...+.         .+.++||++|+++|++|++ +.|+. |+ .+..+.+. ..+.+.+
T Consensus       199 ~~~ll~~~TGsGKT~~~~~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~~~~-~~~~~~~~~~~-~~~~~~~  276 (590)
T 3h1t_A          199 KRSLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKTFTP-FGDARHKIEGG-KVVKSRE  276 (590)
T ss_dssp             SEEEEEECTTSCHHHHHHHHHHHHHHTTCCSSCSSSCCCEEEEEC-----------CCTT-TCSSEEECCC---CCSSCS
T ss_pred             CceEEEecCCCChHHHHHHHHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHHHHh-cchhhhhhhcc-CCCCCCc
Confidence            45689999999999998877776665         3489999999999999999 77765 65 56665543 3445789


Q ss_pred             EEEecHHHHHHh
Q 042424          125 CLVMTTEILRGM  136 (138)
Q Consensus       125 IiVtTpe~l~~l  136 (138)
                      |+|+||+.|...
T Consensus       277 I~v~T~~~l~~~  288 (590)
T 3h1t_A          277 IYFAIYQSIASD  288 (590)
T ss_dssp             EEEEEGGGC---
T ss_pred             EEEEEhhhhccc
Confidence            999999988654

>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=99.13  E-value=4.4e-11  Score=102.28  Aligned_cols=77  Identities=14%  Similarity=0.070  Sum_probs=62.9

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcCC-----------CC
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTLS-----------PN  122 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~~-----------~~  122 (138)
                      .++.++++|||+|||+++.++++   ..+.++||++|+++|++|+++.|++ ++ .+..+.|+...+           ..
T Consensus        40 g~d~lv~apTGsGKTl~~~lp~l---~~~g~~lvi~P~~aL~~q~~~~l~~-~gi~~~~l~~~~~~~~~~~~~~~~~~~~  115 (523)
T 1oyw_A           40 GRDCLVVMPTGGGKSLCYQIPAL---LLNGLTVVVSPLISLMKDQVDQLQA-NGVAAACLNSTQTREQQLEVMTGCRTGQ  115 (523)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHH---HSSSEEEEECSCHHHHHHHHHHHHH-TTCCEEEECTTSCHHHHHHHHHHHHHTC
T ss_pred             CCCEEEECCCCcHHHHHHHHHHH---HhCCCEEEECChHHHHHHHHHHHHH-cCCcEEEEeCCCCHHHHHHHHHHHhcCC
Confidence            35788999999999999887664   3467899999999999999999998 55 777787765421           25


Q ss_pred             CCEEEecHHHHHH
Q 042424          123 ASCLVMTTEILRG  135 (138)
Q Consensus       123 ~~IiVtTpe~l~~  135 (138)
                      .+|+|+|||+|.+
T Consensus       116 ~~ilv~Tpe~l~~  128 (523)
T 1oyw_A          116 IRLLYIAPERLML  128 (523)
T ss_dssp             CSEEEECHHHHTS
T ss_pred             CCEEEECHHHHhC
Confidence            8999999999853

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.07  E-value=1.7e-10  Score=96.27  Aligned_cols=78  Identities=17%  Similarity=0.129  Sum_probs=56.4

Q ss_pred             CCceEECcCCCchHHHHHHHHH-HHHHcCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcC--CCCCCEEEecHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIA-MAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTL--SPNASCLVMTTEI  132 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~-~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~--~~~~~IiVtTpe~  132 (138)
                      ++.++++|||||||++++.+++ .++..|.+++|++||++|++|+++.|.. + .++..+|....  .++.-+.++|...
T Consensus         3 ~~~lv~a~TGsGKT~~~l~~~l~~~~~~g~~~lvl~Pt~~La~Q~~~~~~~-~-~v~~~~~~~~~~~~~~~~~~~~~~~~   80 (431)
T 2v6i_A            3 ELTVLDLHPGAGKTRRVLPQLVREAVKKRLRTVILAPTRVVASEMYEALRG-E-PIRYMTPAVQSERTGNEIVDFMCHST   80 (431)
T ss_dssp             CEEEEECCTTSCTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTT-S-CEEEC---------CCCSEEEEEHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEECcHHHHHHHHHHHhCC-C-eEEEEecCccccCCCCceEEEEchHH
Confidence            4678999999999999987776 5556788999999999999999987752 2 67777665322  2355677778776


Q ss_pred             HHH
Q 042424          133 LRG  135 (138)
Q Consensus       133 l~~  135 (138)
                      +..
T Consensus        81 l~~   83 (431)
T 2v6i_A           81 FTM   83 (431)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            653

>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=99.00  E-value=7.3e-10  Score=92.86  Aligned_cols=78  Identities=13%  Similarity=0.060  Sum_probs=56.9

Q ss_pred             CceEECcCCCchHHHHHHHHH-HHHHcCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCC--cCCCCCCEEEecHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIA-MAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDV--TLSPNASCLVMTTEIL  133 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~-~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~--~~~~~~~IiVtTpe~l  133 (138)
                      ..++++|||||||++++.+++ +++..+.+++|++|+++|++|+++.+.. + .++...+..  ....+..|.++|++.+
T Consensus        21 ~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~lvl~Ptr~La~Q~~~~l~g-~-~v~~~~~~~~~~~~~~~~i~~~t~~~l   98 (451)
T 2jlq_A           21 LTIMDLHPGAGKTKRILPSIVREALLRRLRTLILAPTRVVAAEMEEALRG-L-PIRYQTPAVKSDHTGREIVDLMCHATF   98 (451)
T ss_dssp             EEEECCCTTSSCCTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTT-S-CEEECCTTCSCCCCSSCCEEEEEHHHH
T ss_pred             eEEEECCCCCCHhhHHHHHHHHHHHhcCCcEEEECCCHHHHHHHHHHhcC-c-eeeeeeccccccCCCCceEEEEChHHH
Confidence            347999999999998776554 4455688999999999999999998753 2 343332222  1223667999999987


Q ss_pred             HHh
Q 042424          134 RGM  136 (138)
Q Consensus       134 ~~l  136 (138)
                      ...
T Consensus        99 ~~~  101 (451)
T 2jlq_A           99 TTR  101 (451)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            654

>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=98.99  E-value=4.9e-10  Score=101.43  Aligned_cols=75  Identities=15%  Similarity=0.051  Sum_probs=63.4

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC-----CCCEEEec
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP-----NASCLVMT  129 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~-----~~~IiVtT  129 (138)
                      +..++||+|||+++.++++.....|.++++++||+.|+.|.++.+...+.    +|+.+.|+.....     .++|+|+|
T Consensus        91 Iaem~TGsGKTlaf~LP~l~~~l~g~~vlVltPTreLA~Q~~e~~~~l~~~lgl~v~~i~GG~~~~~r~~~~~~dIvvgT  170 (853)
T 2fsf_A           91 IAEMRTGEGKTLTATLPAYLNALTGKGVHVVTVNDYLAQRDAENNRPLFEFLGLTVGINLPGMPAPAKREAYAADITYGT  170 (853)
T ss_dssp             EEECCTTSCHHHHHHHHHHHHHTTSSCCEEEESSHHHHHHHHHHHHHHHHHTTCCEEECCTTCCHHHHHHHHHSSEEEEE
T ss_pred             eeeecCCchHHHHHHHHHHHHHHcCCcEEEEcCCHHHHHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHhcCCCEEEEC
Confidence            89999999999999988875445688999999999999999998887543    7888888765321     68999999


Q ss_pred             HHHH
Q 042424          130 TEIL  133 (138)
Q Consensus       130 pe~l  133 (138)
                      |.+|
T Consensus       171 pgrl  174 (853)
T 2fsf_A          171 NNEY  174 (853)
T ss_dssp             HHHH
T ss_pred             Cchh
Confidence            9997

>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=98.96  E-value=2e-09  Score=89.88  Aligned_cols=79  Identities=14%  Similarity=0.032  Sum_probs=63.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCCcCCC--CCCEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVTLSP--NASCLVMT  129 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~~~~--~~~IiVtT  129 (138)
                      .+.+++.+||+|||++++..+......  ..++|+|+| .+|+.|+.++|++.+.  .+.++.|+.....  +.+|+|+|
T Consensus        57 ~~~ilad~~GlGKT~~ai~~i~~~~~~~~~~~~LIv~P-~~l~~qw~~e~~~~~~~~~v~~~~g~~~~~~~~~~~ivi~t  135 (500)
T 1z63_A           57 FGICLADDMGLGKTLQTIAVFSDAKKENELTPSLVICP-LSVLKNWEEELSKFAPHLRFAVFHEDRSKIKLEDYDIILTT  135 (500)
T ss_dssp             CCEEECCCTTSCHHHHHHHHHHHHHHTTCCSSEEEEEC-STTHHHHHHHHHHHCTTSCEEECSSSTTSCCGGGSSEEEEE
T ss_pred             CCEEEEeCCCCcHHHHHHHHHHHHHhcCCCCCEEEEcc-HHHHHHHHHHHHHHCCCceEEEEecCchhccccCCcEEEee
Confidence            567899999999999998777665554  478999999 6799999999999654  6777777654322  67899999


Q ss_pred             HHHHHH
Q 042424          130 TEILRG  135 (138)
Q Consensus       130 pe~l~~  135 (138)
                      ++.+..
T Consensus       136 ~~~l~~  141 (500)
T 1z63_A          136 YAVLLR  141 (500)
T ss_dssp             HHHHTT
T ss_pred             HHHHhc
Confidence            999864

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=98.94  E-value=1.5e-09  Score=96.28  Aligned_cols=75  Identities=21%  Similarity=0.210  Sum_probs=58.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCCC-----CCCEEEecH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSP-----NASCLVMTT  130 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~~-----~~~IiVtTp  130 (138)
                      ++.+++||||||||+.++.++    ....+.+|++|+++|+.|++++|++....+++++|+.....     ..+++++|+
T Consensus       156 k~vlv~apTGSGKT~~al~~l----~~~~~gl~l~PtR~LA~Qi~~~l~~~g~~v~lltG~~~~iv~TpGr~~~il~~T~  231 (677)
T 3rc3_A          156 KIIFHSGPTNSGKTYHAIQKY----FSAKSGVYCGPLKLLAHEIFEKSNAAGVPCDLVTGEERVTVQPNGKQASHVSCTV  231 (677)
T ss_dssp             EEEEEECCTTSSHHHHHHHHH----HHSSSEEEEESSHHHHHHHHHHHHHTTCCEEEECSSCEECCSTTCCCCSEEEEEG
T ss_pred             CEEEEEcCCCCCHHHHHHHHH----HhcCCeEEEeCHHHHHHHHHHHHHhcCCcEEEEECCeeEEecCCCcccceeEecH
Confidence            456799999999998544443    33466799999999999999999884338999999865432     488999999


Q ss_pred             HHHH
Q 042424          131 EILR  134 (138)
Q Consensus       131 e~l~  134 (138)
                      |.+.
T Consensus       232 e~~~  235 (677)
T 3rc3_A          232 EMCS  235 (677)
T ss_dssp             GGCC
T ss_pred             hHhh
Confidence            8653

>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=98.92  E-value=1.8e-09  Score=98.62  Aligned_cols=79  Identities=18%  Similarity=0.188  Sum_probs=64.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC--CcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCc---------CCCCC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK--QRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVT---------LSPNA  123 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~--~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~---------~~~~~  123 (138)
                      .+.+|+.+||+|||+++..++...+..|  ++++||+|+ +|+.|+.++|.+.|+ .+.++.|+..         ...+.
T Consensus       171 ~~~LLad~tGlGKTi~Ai~~i~~l~~~g~~~rvLIVvP~-sLl~Qw~~E~~~~f~l~v~v~~~~~~~~~~~~~~~~~~~~  249 (968)
T 3dmq_A          171 PRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPE-TLQHQWLVEMLRRFNLRFALFDDERYAEAQHDAYNPFDTE  249 (968)
T ss_dssp             CEEEECCCTTSCHHHHHHHHHHHHHHTSSCCCEEEECCT-TTHHHHHHHHHHHSCCCCEECCHHHHHHHHHTTCSSSTTC
T ss_pred             CCEEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEeCH-HHHHHHHHHHHHHhCCCEEEEccchhhhhhhhcccccccC
Confidence            4677999999999999998888877765  499999999 999999999988888 7777765431         11267


Q ss_pred             CEEEecHHHHHH
Q 042424          124 SCLVMTTEILRG  135 (138)
Q Consensus       124 ~IiVtTpe~l~~  135 (138)
                      +|+|+|++.+..
T Consensus       250 dIvI~T~~~L~~  261 (968)
T 3dmq_A          250 QLVICSLDFARR  261 (968)
T ss_dssp             SEEEECHHHHHT
T ss_pred             CEEEEcHHHHhh
Confidence            899999998853

>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=98.92  E-value=1.7e-09  Score=97.99  Aligned_cols=75  Identities=17%  Similarity=0.148  Sum_probs=62.4

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC-----CCCEEEec
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP-----NASCLVMT  129 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~-----~~~IiVtT  129 (138)
                      +..++||+|||+++.+++......|..+++++|++.|+.|.++.+...+.    +|+.+.|+.....     .++|+|+|
T Consensus       100 Iaea~TGeGKTlaf~LP~~l~aL~g~~vlVltptreLA~qd~e~~~~l~~~lgl~v~~i~gg~~~~~r~~~~~~dIv~gT  179 (844)
T 1tf5_A          100 IAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAYAADITYST  179 (844)
T ss_dssp             EEECCTTSCHHHHHHHHHHHHHTTSSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEECCTTSCHHHHHHHHHSSEEEEE
T ss_pred             EEEccCCcHHHHHHHHHHHHHHHcCCCEEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHhcCCCEEEEC
Confidence            89999999999999988763334588999999999999999988887543    7888888764322     68999999


Q ss_pred             HHHH
Q 042424          130 TEIL  133 (138)
Q Consensus       130 pe~l  133 (138)
                      |..|
T Consensus       180 pgrl  183 (844)
T 1tf5_A          180 NNEL  183 (844)
T ss_dssp             HHHH
T ss_pred             chhh
Confidence            9998

>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=98.89  E-value=2.4e-09  Score=89.95  Aligned_cols=78  Identities=18%  Similarity=0.091  Sum_probs=54.7

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHH-HcCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCc--CCCCCCEEEecHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAF-RDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVT--LSPNASCLVMTTE  131 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l-~~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~--~~~~~~IiVtTpe  131 (138)
                      .++.++++|||||||+++.+++++.+ ..+.++||++|+++|++|++++|+. + .++...+...  ..+..-+.++|..
T Consensus        21 ~~~vlv~a~TGsGKT~~~~l~il~~~~~~~~~~lvl~Ptr~La~Q~~~~l~g-~-~v~~~~~~~~~~~t~~~~i~~~~~~   98 (459)
T 2z83_A           21 RQMTVLDLHPGSGKTRKILPQIIKDAIQQRLRTAVLAPTRVVAAEMAEALRG-L-PVRYQTSAVQREHQGNEIVDVMCHA   98 (459)
T ss_dssp             TCEEEECCCTTSCTTTTHHHHHHHHHHHTTCCEEEEECSHHHHHHHHHHTTT-S-CEEECC--------CCCSEEEEEHH
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEECchHHHHHHHHHHhcC-c-eEeEEecccccCCCCCcEEEEEchH
Confidence            35677999999999999877666554 4688999999999999999998863 2 3333332221  1234557777877


Q ss_pred             HHH
Q 042424          132 ILR  134 (138)
Q Consensus       132 ~l~  134 (138)
                      .+.
T Consensus        99 ~l~  101 (459)
T 2z83_A           99 TLT  101 (459)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            664

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=98.86  E-value=2.9e-09  Score=97.27  Aligned_cols=75  Identities=20%  Similarity=0.156  Sum_probs=63.5

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC-----CCCEEEec
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP-----NASCLVMT  129 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~-----~~~IiVtT  129 (138)
                      +..+.||+|||+++.+++......|..+++++||+.|+.|.++.+...+.    +|++++|+.....     .++|+|+|
T Consensus        96 IaeakTGeGKTLvf~Lp~~L~aL~G~qv~VvTPTreLA~Qdae~m~~l~~~lGLsv~~i~Gg~~~~~r~~ay~~DIvyGT  175 (997)
T 2ipc_A           96 IAEMKTGEGKTLVATLAVALNALTGKGVHVVTVNDYLARRDAEWMGPVYRGLGLSVGVIQHASTPAERRKAYLADVTYVT  175 (997)
T ss_dssp             EEECCSTHHHHHHHHHHHHHHHTTCSCCEEEESSHHHHHHHHHHHHHHHHTTTCCEEECCTTCCHHHHHHHHTSSEEEEE
T ss_pred             eeeccCCCchHHHHHHHHHHHHHhCCCEEEEeCCHHHHHHHHHHHHHHHHhcCCeEEEEeCCCCHHHHHHHcCCCEEEEC
Confidence            89999999999999988854444688999999999999999999888654    7888888765322     78999999


Q ss_pred             HHHH
Q 042424          130 TEIL  133 (138)
Q Consensus       130 pe~l  133 (138)
                      |..|
T Consensus       176 pgrl  179 (997)
T 2ipc_A          176 NSEL  179 (997)
T ss_dssp             HHHH
T ss_pred             chhh
Confidence            9998

>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=98.84  E-value=3.8e-09  Score=96.19  Aligned_cols=76  Identities=14%  Similarity=0.085  Sum_probs=62.8

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC-----CCCEEEe
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP-----NASCLVM  128 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~-----~~~IiVt  128 (138)
                      .+..++||+|||+++.+++......|..+++++|++.|+.|.++.+...+.    +|+.+.|+.....     .++|+++
T Consensus       127 ~Iaem~TGeGKTLa~~LP~~l~aL~g~~v~VvTpTreLA~Qdae~m~~l~~~lGLsv~~i~gg~~~~~r~~~y~~DIvyg  206 (922)
T 1nkt_A          127 NVAEMKTGEGKTLTCVLPAYLNALAGNGVHIVTVNDYLAKRDSEWMGRVHRFLGLQVGVILATMTPDERRVAYNADITYG  206 (922)
T ss_dssp             EEEECCTTSCHHHHTHHHHHHHHTTTSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEECCTTCCHHHHHHHHHSSEEEE
T ss_pred             CEEEecCCCccHHHHHHHHHHHHHhCCCeEEEeCCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHhcCCCEEEE
Confidence            389999999999999888754334588999999999999999988877543    7888888765322     6899999


Q ss_pred             cHHHH
Q 042424          129 TTEIL  133 (138)
Q Consensus       129 Tpe~l  133 (138)
                      ||..|
T Consensus       207 Tpgrl  211 (922)
T 1nkt_A          207 TNNEF  211 (922)
T ss_dssp             EHHHH
T ss_pred             CchHh
Confidence            99997

>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=98.83  E-value=1.7e-09  Score=90.49  Aligned_cols=51  Identities=14%  Similarity=0.052  Sum_probs=44.4

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEechHHHHHHHHHHHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .++.++++|||||||++++.++++.+. .+.+++|++||++|+.|+++.|+.
T Consensus         8 g~~vlv~a~TGSGKT~~~l~~~l~~~~~~~~~~lil~Ptr~La~Q~~~~l~~   59 (440)
T 1yks_A            8 GMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHG   59 (440)
T ss_dssp             TCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTT
T ss_pred             CCCEEEEcCCCCCHHHHHHHHHHHHHHhcCCeEEEEcchHHHHHHHHHHHhc
Confidence            467789999999999999887777554 567999999999999999998875

>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=98.78  E-value=9.8e-09  Score=91.92  Aligned_cols=82  Identities=15%  Similarity=0.138  Sum_probs=57.5

Q ss_pred             CCceEECcCCCchHHHH-HHHHHHHHHc--CCcEEEEechHHHHHHHHHHHHHhcC-ceEEEec-----CCcCCCCCCEE
Q 042424           56 THGTLTNPVYNGKTAVA-EYAIAMAFRD--KQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTG-----DVTLSPNASCL  126 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva-~~ai~~~l~~--~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tG-----d~~~~~~~~Ii  126 (138)
                      .+.++++|||||||+.. .+.+...+..  |.+++++.|+++|+.|+++.+.+.++ .++...|     +.....+.+|+
T Consensus       110 ~~vii~gpTGSGKTtllp~ll~~~~~~~~~g~~ilvl~P~r~La~q~~~~l~~~~~~~v~~~vG~~i~~~~~~~~~~~I~  189 (773)
T 2xau_A          110 QIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFENKTSNKTILK  189 (773)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHHHCGGGGTCEEEEEESCHHHHHHHHHHHHHHTTCCBTTTEEEEETTEEECCTTCSEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhccccCCCceEEecCchHHHHHHHHHHHHHHhCCchhheecceeccccccCCCCCEE
Confidence            45779999999999943 2322222223  66799999999999999999988765 3322222     12233478999


Q ss_pred             EecHHHHHHhh
Q 042424          127 VMTTEILRGML  137 (138)
Q Consensus       127 VtTpe~l~~lL  137 (138)
                      |+||+++...+
T Consensus       190 v~T~G~l~r~l  200 (773)
T 2xau_A          190 YMTDGMLLREA  200 (773)
T ss_dssp             EEEHHHHHHHH
T ss_pred             EECHHHHHHHH
Confidence            99999987653

>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=98.77  E-value=1.1e-08  Score=89.50  Aligned_cols=78  Identities=9%  Similarity=0.040  Sum_probs=57.2

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHH-HcCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCC---cCCCCCCEEEecH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAF-RDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDV---TLSPNASCLVMTT  130 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l-~~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~---~~~~~~~IiVtTp  130 (138)
                      .++.++++|||||||+++++++++.+ ..+.++||++|+++|++|+++.|+. + .++ +.++.   ...+...+.++|.
T Consensus       186 g~dvlv~a~TGSGKT~~~~lpil~~l~~~~~~vLvl~PtreLa~Qi~~~l~~-~-~v~-~~~~~l~~~~tp~~~i~~~t~  262 (618)
T 2whx_A          186 KRLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALRG-L-PIR-YQTPAVKSDHTGREIVDLMCH  262 (618)
T ss_dssp             TCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTT-S-CEE-ECCTTSSCCCCSSSCEEEEEH
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHHHHhCCCeEEEEcChHHHHHHHHHHhcC-C-cee-EecccceeccCCCceEEEECh
Confidence            46778999999999999877666554 4578999999999999999988763 2 455 33322   1223556778888


Q ss_pred             HHHHH
Q 042424          131 EILRG  135 (138)
Q Consensus       131 e~l~~  135 (138)
                      ..+..
T Consensus       263 ~~l~~  267 (618)
T 2whx_A          263 ATFTT  267 (618)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87764

>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=98.69  E-value=9.5e-09  Score=94.84  Aligned_cols=79  Identities=20%  Similarity=0.252  Sum_probs=57.2

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCc------C-CCCCCE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVT------L-SPNASC  125 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~------~-~~~~~I  125 (138)
                      ++.+++++||||||++++.++ +.+..   ..++|+++|+++|+.|..++|.. |....+..+...      . +.+.+|
T Consensus       301 ~~gli~~~TGSGKT~t~~~l~-~ll~~~~~~~rvLvlvpr~eL~~Q~~~~f~~-f~~~~v~~~~s~~~l~~~L~~~~~~I  378 (1038)
T 2w00_A          301 SGGYIWHTTGSGKTLTSFKAA-RLATELDFIDKVFFVVDRKDLDYQTMKEYQR-FSPDSVNGSENTAGLKRNLDKDDNKI  378 (1038)
T ss_dssp             GSEEEEECTTSSHHHHHHHHH-HHHTTCTTCCEEEEEECGGGCCHHHHHHHHT-TSTTCSSSSCCCHHHHHHHHCSSCCE
T ss_pred             CCEEEEecCCCCHHHHHHHHH-HHHHhcCCCceEEEEeCcHHHHHHHHHHHHH-hcccccccccCHHHHHHHhcCCCCCE
Confidence            457899999999999985544 44442   36999999999999999999988 541111111110      1 236899


Q ss_pred             EEecHHHHHHh
Q 042424          126 LVMTTEILRGM  136 (138)
Q Consensus       126 iVtTpe~l~~l  136 (138)
                      +|+|+++|..+
T Consensus       379 iVtTiqkl~~~  389 (1038)
T 2w00_A          379 IVTTIQKLNNL  389 (1038)
T ss_dssp             EEEEHHHHHHH
T ss_pred             EEEEHHHHHHH
Confidence            99999999764

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=98.67  E-value=1.7e-08  Score=86.55  Aligned_cols=57  Identities=21%  Similarity=0.224  Sum_probs=46.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhc---C-ceEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEF---K-DVGLMTG  115 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f---~-~v~~~tG  115 (138)
                      ++.++.+|||+|||++++++++.   .+.+++|++||++|++|..+++....   + .+..+.|
T Consensus        23 ~~~~~~a~TGtGKT~~~l~p~l~---~~~~v~i~~pt~~l~~q~~~~~~~l~~~~~~~~~~l~g   83 (551)
T 3crv_A           23 FLVALNAPTGSGKTLFSLLVSLE---VKPKVLFVVRTHNEFYPIYRDLTKIREKRNITFSFLVG   83 (551)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH---HCSEEEEEESSGGGHHHHHHHHTTCCCSSCCCEEECCC
T ss_pred             CcEEEECCCCccHHHHHHHHHHh---CCCeEEEEcCCHHHHHHHHHHHHHHhhhcCccEEEEcc
Confidence            56779999999999999887765   58899999999999999999998732   2 4555555

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.64  E-value=5.6e-08  Score=83.33  Aligned_cols=49  Identities=16%  Similarity=0.095  Sum_probs=42.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      ++.++.+|||+|||+++++++.   ..+.+++|++||++|++|.++++.+ ++
T Consensus        27 ~~~~~~a~TGtGKT~~~l~~~~---~~~~~~~~~~~t~~l~~q~~~~~~~-l~   75 (540)
T 2vl7_A           27 KTLLLNAKPGLGKTVFVEVLGM---QLKKKVLIFTRTHSQLDSIYKNAKL-LG   75 (540)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH---HHTCEEEEEESCHHHHHHHHHHHGG-GT
T ss_pred             CCEEEEcCCCCcHHHHHHHHHH---hCCCcEEEEcCCHHHHHHHHHHHHh-cC
Confidence            5677999999999998877653   4589999999999999999999877 54

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=98.63  E-value=1.6e-08  Score=89.41  Aligned_cols=51  Identities=14%  Similarity=0.034  Sum_probs=44.5

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHH-HcCCcEEEEechHHHHHHHHHHHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAF-RDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l-~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .++.++++|||||||+++++++++.+ ..+.+++|++|+++|+.|+++.|+.
T Consensus       241 g~dvlv~apTGSGKTl~~ll~il~~l~~~~~~~lilaPTr~La~Q~~~~l~~  292 (673)
T 2wv9_A          241 RQLTVLDLHPGAGKTRRILPQIIKDAIQKRLRTAVLAPTRVVAAEMAEALRG  292 (673)
T ss_dssp             TCEEEECCCTTTTTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTT
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEccHHHHHHHHHHHHhc
Confidence            46778999999999999988777664 4578999999999999999998875

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=98.48  E-value=3.4e-07  Score=81.77  Aligned_cols=80  Identities=15%  Similarity=0.046  Sum_probs=63.1

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHH---cCCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCCc-----------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFR---DKQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVT-----------  118 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~---~~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~-----------  118 (138)
                      ..+.+|+.++|.|||+.++.++...+.   .++.+|+|+| .+|+.|+.++|.+.+.  .+.++.|+..           
T Consensus       255 ~~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P-~sll~qW~~E~~~~~p~~~v~~~~g~~~~r~~~~~~~~~  333 (800)
T 3mwy_W          255 GDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVP-LSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFY  333 (800)
T ss_dssp             TCCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECC-TTTHHHHHHHHHHHSTTCCEEECCCSSHHHHHHHHHHSC
T ss_pred             CCCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEEC-chHHHHHHHHHHHHCCCceEEEEeCCHHHHHHHHHHHhh
Confidence            367889999999999999866665543   2678999999 7899999999999664  6777777642           


Q ss_pred             --------CCCCCCEEEecHHHHHH
Q 042424          119 --------LSPNASCLVMTTEILRG  135 (138)
Q Consensus       119 --------~~~~~~IiVtTpe~l~~  135 (138)
                              ...+.+|+|+|++.+..
T Consensus       334 ~~~~~~~~~~~~~dvvitTy~~l~~  358 (800)
T 3mwy_W          334 TNPRAKGKKTMKFNVLLTTYEYILK  358 (800)
T ss_dssp             SCC-----CCCCCSEEEECTTHHHH
T ss_pred             ccccccccccccCCEEEecHHHHHh
Confidence                    11267899999999865

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=98.42  E-value=3.3e-07  Score=80.17  Aligned_cols=52  Identities=23%  Similarity=0.210  Sum_probs=45.3

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEechHHHHHHHHHHHHHh
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLKALSNQKYRELHKE  106 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~kaLv~Q~~~~l~~~  106 (138)
                      .++.++.+|||+|||++++++++..+. .+.+++|++||++|+.|..+++...
T Consensus        22 ~~~~~~~apTGtGKT~a~l~p~l~~~~~~~~kvli~t~T~~l~~Qi~~el~~l   74 (620)
T 4a15_A           22 SYGVALESPTGSGKTIMALKSALQYSSERKLKVLYLVRTNSQEEQVIKELRSL   74 (620)
T ss_dssp             SSEEEEECCTTSCHHHHHHHHHHHHHHHHTCEEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHhhhhcCCeEEEECCCHHHHHHHHHHHHHH
Confidence            356789999999999999987776654 4899999999999999999998873

>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=98.34  E-value=1.3e-06  Score=76.28  Aligned_cols=79  Identities=19%  Similarity=0.154  Sum_probs=59.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC-------CcEEEEechHHHHHHHHHHHHHhcC---ceEEEecCCcC------
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK-------QRVIYTSSLKALSNQKYRELHKEFK---DVGLMTGDVTL------  119 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~-------~rviyv~P~kaLv~Q~~~~l~~~f~---~v~~~tGd~~~------  119 (138)
                      .+.+|..+||.|||+.++..+...+..+       +++|+|+|. +|+.|+.++|.+.+.   .+..+.|....      
T Consensus        80 ~g~ILad~mGlGKT~~~i~~i~~l~~~~~~~~p~~~~~LiV~P~-sll~qW~~E~~~~~~~~~~~~~~~~g~~~~~~~~~  158 (644)
T 1z3i_X           80 YGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEVGKWLGGRVQPVAIDGGSKDEIDSKL  158 (644)
T ss_dssp             CEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHHHHHHGGGCCEEEECSSCHHHHHHHH
T ss_pred             CCeEeeeCCCchHHHHHHHHHHHHHHhCccccCCCCcEEEEecH-HHHHHHHHHHHHHcCCCeeEEEEeCCCHHHHHHHH
Confidence            4578999999999999987777766542       469999997 899999999999654   23334433211      


Q ss_pred             ---------CCCCCEEEecHHHHHH
Q 042424          120 ---------SPNASCLVMTTEILRG  135 (138)
Q Consensus       120 ---------~~~~~IiVtTpe~l~~  135 (138)
                               ....+|+|+|++.+..
T Consensus       159 ~~~~~~~~~~~~~~vvi~ty~~l~~  183 (644)
T 1z3i_X          159 VNFISQQGMRIPTPILIISYETFRL  183 (644)
T ss_dssp             HHHHCCCSSCCSCCEEEEEHHHHHH
T ss_pred             HHHHHhcCCCCCCcEEEeeHHHHHh
Confidence                     1247899999999864

>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=97.44  E-value=0.00046  Score=62.35  Aligned_cols=59  Identities=17%  Similarity=0.092  Sum_probs=48.2

Q ss_pred             CCceEECcCCCchHHHHHHHHH-HHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIA-MAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTG  115 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~-~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tG  115 (138)
                      ...+....||+|||+++.+++. .+| .|+.+.+|.|+.-|+.|-++.+...|.    +|+.+..
T Consensus        89 ~G~iaEM~TGEGKTLva~lp~~lnAL-~G~~vhVvT~ndyLA~rdae~m~~l~~~Lglsvg~i~~  152 (822)
T 3jux_A           89 EGKVAEMKTGEGKTLAATMPIYLNAL-IGKGVHLVTVNDYLARRDALWMGPVYLFLGLRVGVINS  152 (822)
T ss_dssp             TTCEEECCTTSCHHHHTHHHHHHHHT-TSSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEEEET
T ss_pred             CCChhhccCCCCccHHHHHHHHHHHh-cCCceEEEeccHHHHHhHHHHHHHHHHHhCCEEEEEcC
Confidence            4457889999999999987665 554 589999999999999999888777553    7887776

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=97.33  E-value=0.00043  Score=60.24  Aligned_cols=48  Identities=17%  Similarity=0.173  Sum_probs=44.2

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .+|.||.|+|||.+....|.+.+.++.++++++|+..-+++..+.+.+
T Consensus       208 ~lI~GPPGTGKT~ti~~~I~~l~~~~~~ILv~a~TN~AvD~i~erL~~  255 (646)
T 4b3f_X          208 AIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNLVERLAL  255 (646)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHHHH
T ss_pred             eEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEcCchHHHHHHHHHHHh
Confidence            459999999999999888888888899999999999999999999876

>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=97.01  E-value=0.0019  Score=56.78  Aligned_cols=48  Identities=23%  Similarity=0.178  Sum_probs=40.1

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      ..+.+.||||||+++...+.+.   ++.+|+|+|.+.++.|.+.+|+..|.
T Consensus        31 ~~l~g~tgs~kt~~~a~~~~~~---~~~~lvv~~~~~~A~ql~~el~~~~~   78 (664)
T 1c4o_A           31 VTLLGATGTGKTVTMAKVIEAL---GRPALVLAPNKILAAQLAAEFRELFP   78 (664)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHH---TCCEEEEESSHHHHHHHHHHHHHHCT
T ss_pred             EEEEcCCCcHHHHHHHHHHHHh---CCCEEEEecCHHHHHHHHHHHHHHCC
Confidence            4689999999998776544322   67899999999999999999999775

>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=96.92  E-value=0.0017  Score=55.58  Aligned_cols=53  Identities=11%  Similarity=0.032  Sum_probs=45.7

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC----CcEEEEechHHHHHHHHHHHHHhcC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK----QRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~----~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      ++.+|.|+.|||||.+...-+.+.+..+    .+++++++++..+.++.+++.+.++
T Consensus        23 ~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~~~   79 (647)
T 3lfu_A           23 SNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLMG   79 (647)
T ss_dssp             SCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHHHHHHHHHHHHHhc
Confidence            5667999999999999988887777653    6899999999999999999988653

>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=96.83  E-value=0.002  Score=55.97  Aligned_cols=49  Identities=16%  Similarity=0.192  Sum_probs=41.6

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEechHHHHHHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      ..+|.||.|+|||.+....+.+.+. .+.++++++|+...+++..+.+.+
T Consensus       197 ~~li~GppGTGKT~~~~~~i~~l~~~~~~~ilv~a~tn~A~~~l~~~l~~  246 (624)
T 2gk6_A          197 LSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQ  246 (624)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTSSSCCEEEEESSHHHHHHHHHHHHT
T ss_pred             CeEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEeCcHHHHHHHHHHHHh
Confidence            3469999999999988766666555 578999999999999999998876

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=96.58  E-value=0.0041  Score=55.92  Aligned_cols=48  Identities=15%  Similarity=0.211  Sum_probs=41.7

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEechHHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .+|.||.|+|||.+....+.+.+. .+.++++++|+..-+++..+.+.+
T Consensus       378 ~lI~GppGTGKT~~i~~~i~~l~~~~~~~ILv~a~tn~A~d~l~~rL~~  426 (802)
T 2xzl_A          378 SLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAVDHLAAKLRD  426 (802)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEESSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhCCCCeEEEEcCcHHHHHHHHHHHHh
Confidence            569999999999988766666555 589999999999999999999887

>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=96.52  E-value=0.0041  Score=54.04  Aligned_cols=50  Identities=14%  Similarity=0.135  Sum_probs=37.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHH----HcCCcEEEEechHHHHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAF----RDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l----~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      +..++++|+|+|||.+....+....    ..+.++++++||..++.+..+.+..
T Consensus       165 ~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~~~~~vll~APTg~AA~~L~e~~~~  218 (608)
T 1w36_D          165 RISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGK  218 (608)
T ss_dssp             SEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHTH
T ss_pred             CCEEEEeCCCCCHHHHHHHHHHHHHHhhhcCCCeEEEEeCChhHHHHHHHHHHH
Confidence            4566999999999966544333322    2356999999999999998877654

>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=96.26  E-value=0.0072  Score=54.37  Aligned_cols=48  Identities=17%  Similarity=0.209  Sum_probs=40.7

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEechHHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .+|.||.|+|||.+....+.+.+. .+.++++++|+..-+++..+.+.+
T Consensus       374 ~lI~GppGTGKT~ti~~~i~~l~~~~~~~ilv~a~tn~A~~~l~~~l~~  422 (800)
T 2wjy_A          374 SLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQ  422 (800)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTTCSSCEEEEESSHHHHHHHHHHHHT
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCCcEEEEcCcHHHHHHHHHHHHH
Confidence            469999999999988766665555 578999999999999999988876

>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=96.11  E-value=0.012  Score=49.03  Aligned_cols=47  Identities=17%  Similarity=0.252  Sum_probs=36.8

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCC-cEEEEechHHHHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQ-RVIYTSSLKALSNQKYREL  103 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~-rviyv~P~kaLv~Q~~~~l  103 (138)
                      ..+|.||.|+|||.++...+......+. ++++++||...+.+..+.+
T Consensus        47 ~~li~G~aGTGKT~ll~~~~~~l~~~~~~~il~~a~T~~Aa~~l~~~~   94 (459)
T 3upu_A           47 HVTINGPAGTGATTLTKFIIEALISTGETGIILAAPTHAAKKILSKLS   94 (459)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCCEEEEESSHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhcCCceEEEecCcHHHHHHHHhhh
Confidence            5679999999999988766655555665 8999999988887766544

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=95.94  E-value=0.0087  Score=44.37  Aligned_cols=46  Identities=15%  Similarity=0.079  Sum_probs=32.8

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELH  104 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~  104 (138)
                      .++.+|+|+|||..+...+......+.+++|+.-... ..+..+.+.
T Consensus        26 ~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~~e~~-~~~~~~~~~   71 (247)
T 2dr3_A           26 VLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVALEEH-PVQVRQNMA   71 (247)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEESSSC-HHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEccCC-HHHHHHHHH
Confidence            3599999999999988666666667889999875433 344444443

>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=95.90  E-value=0.014  Score=50.66  Aligned_cols=53  Identities=13%  Similarity=0.084  Sum_probs=44.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc-C---CcEEEEechHHHHHHHHHHHHHhcC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD-K---QRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~-~---~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      ++.+|.|+.|||||.+...-+.+.+.. +   .+++++..|+..+.++.+++.+.++
T Consensus        16 ~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~Aa~em~~Rl~~~l~   72 (673)
T 1uaa_A           16 GPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLG   72 (673)
T ss_dssp             SEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CCEEEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHcC
Confidence            566799999999999988777777654 3   6899999999999999999988653

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=95.82  E-value=0.01  Score=43.22  Aligned_cols=43  Identities=12%  Similarity=-0.037  Sum_probs=27.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQK   99 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~   99 (138)
                      .+.++++|+|+|||.++.........++.+++|+. ...+..+.
T Consensus        55 ~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~~-~~~~~~~~   97 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVY-VPELFREL   97 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEE-HHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEE-hHHHHHHH
Confidence            45669999999999987644444434566776654 33444443

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=95.73  E-value=0.012  Score=45.14  Aligned_cols=35  Identities=17%  Similarity=0.131  Sum_probs=30.0

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLK   93 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~k   93 (138)
                      ++++|+|+|||..++..+.++..+|.+++++-|..
T Consensus        16 litG~mGsGKTT~ll~~~~r~~~~g~kVli~~~~~   50 (223)
T 2b8t_A           16 FITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKI   50 (223)
T ss_dssp             EEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECC
T ss_pred             EEECCCCCcHHHHHHHHHHHHHhcCCEEEEEEecc
Confidence            48999999999999888877777899999997765

>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=95.73  E-value=0.017  Score=50.58  Aligned_cols=48  Identities=25%  Similarity=0.249  Sum_probs=39.7

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      ..+.+-||||||++....+.+   .++.+|+|+|.+.++.|.+.+|+..|.
T Consensus        35 ~~l~g~~gs~k~~~~a~~~~~---~~~~~lvv~~~~~~A~~l~~el~~~~~   82 (661)
T 2d7d_A           35 QTLLGATGTGKTFTVSNLIKE---VNKPTLVIAHNKTLAGQLYSEFKEFFP   82 (661)
T ss_dssp             EEEEECTTSCHHHHHHHHHHH---HCCCEEEECSSHHHHHHHHHHHHHHCT
T ss_pred             EEEECcCCcHHHHHHHHHHHH---hCCCEEEEECCHHHHHHHHHHHHHHcC
Confidence            468899999999876544432   267899999999999999999999765

>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=95.69  E-value=0.021  Score=49.33  Aligned_cols=47  Identities=13%  Similarity=-0.060  Sum_probs=36.7

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRE  102 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~  102 (138)
                      +..+|.+|.|+|||.+....+......|.++++++||...+.+..+.
T Consensus       205 ~~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl~~ApT~~Aa~~L~e~  251 (574)
T 3e1s_A          205 RLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPTGKAARRLGEV  251 (574)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEecCcHHHHHHhHhh
Confidence            45669999999999887654444445689999999999888877654

>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=95.65  E-value=0.015  Score=41.62  Aligned_cols=47  Identities=17%  Similarity=0.092  Sum_probs=29.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHH-HcCCcEEEEechHHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAF-RDKQRVIYTSSLKALSNQKYREL  103 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l-~~~~rviyv~P~kaLv~Q~~~~l  103 (138)
                      ...++.+|+|+|||..+........ ..|..++|+ ....+.++....+
T Consensus        39 ~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~-~~~~~~~~~~~~~   86 (180)
T 3ec2_A           39 KGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFF-DTKDLIFRLKHLM   86 (180)
T ss_dssp             CEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEE-EHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEE-EHHHHHHHHHHHh
Confidence            3456999999999998865444433 346666664 4555555554443

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=95.56  E-value=0.016  Score=42.94  Aligned_cols=46  Identities=20%  Similarity=0.101  Sum_probs=31.0

Q ss_pred             ceEECcCCCchHHHHHHHHHHH-HHcCCcEEEEechHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMA-FRDKQRVIYTSSLKALSNQKYRELH  104 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~-l~~~~rviyv~P~kaLv~Q~~~~l~  104 (138)
                      .+++|++|+|||..++..+.++ ...+..++|+.-..+ .++..+.+.
T Consensus        33 ~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s~E~~-~~~~~~~~~   79 (251)
T 2zts_A           33 VLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTLEER-ARDLRREMA   79 (251)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEESSSC-HHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeecccCC-HHHHHHHHH
Confidence            3499999999999998655554 445788888874422 344444443

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=95.56  E-value=0.014  Score=46.36  Aligned_cols=43  Identities=7%  Similarity=-0.123  Sum_probs=29.7

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHH-HcCCcEEEEechHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAF-RDKQRVIYTSSLKALSNQK   99 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l-~~~~rviyv~P~kaLv~Q~   99 (138)
                      .+.++.||+|+|||.++......+. ..|.+++|+.- -.|..+.
T Consensus       153 ~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~~-~~l~~~l  196 (308)
T 2qgz_A          153 KGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHF-PSFAIDV  196 (308)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEEH-HHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEH-HHHHHHH
Confidence            4567999999999999875555555 56777776643 2444443

>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=95.48  E-value=0.029  Score=49.39  Aligned_cols=54  Identities=11%  Similarity=0.057  Sum_probs=45.7

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc-C---CcEEEEechHHHHHHHHHHHHHhcC
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD-K---QRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~-~---~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      .++.+|.|+.|||||.+...-+.+.+.. +   .+++++..|+..+.++.+++.+.++
T Consensus        24 ~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vTFTnkAA~Em~~Rl~~~l~   81 (724)
T 1pjr_A           24 EGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLG   81 (724)
T ss_dssp             SSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHHG
T ss_pred             CCCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHhc
Confidence            3567799999999999998888877764 3   6899999999999999999988653

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=95.46  E-value=0.016  Score=42.61  Aligned_cols=35  Identities=23%  Similarity=0.263  Sum_probs=28.8

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLK   93 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~k   93 (138)
                      ++++|.|+|||..++-.+.++...|.+++++.|..
T Consensus         7 vi~G~~gsGKTT~ll~~~~~~~~~g~~v~~~~~~~   41 (184)
T 2orw_A            7 VITGPMYSGKTTELLSFVEIYKLGKKKVAVFKPKI   41 (184)
T ss_dssp             EEEESTTSSHHHHHHHHHHHHHHTTCEEEEEEEC-
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeecc
Confidence            48999999999998777766667788999988874

>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=95.46  E-value=0.023  Score=53.09  Aligned_cols=53  Identities=13%  Similarity=0.120  Sum_probs=45.0

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcC------CcEEEEechHHHHHHHHHHHHHhc
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDK------QRVIYTSSLKALSNQKYRELHKEF  107 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~------~rviyv~P~kaLv~Q~~~~l~~~f  107 (138)
                      ..+.+|.|.-|||||.+...-+.+.+.++      .+++++.+|++.++++.+++.+.+
T Consensus        23 ~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~aa~e~~~ri~~~l   81 (1232)
T 3u4q_A           23 GQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAEAL   81 (1232)
T ss_dssp             SSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHHHHHHHHHHHHHH
Confidence            35778999999999999887777777653      489999999999999999998855

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=95.34  E-value=0.02  Score=42.77  Aligned_cols=35  Identities=23%  Similarity=0.234  Sum_probs=29.7

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLK   93 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~k   93 (138)
                      ++++|.|||||..++-.+.++..+|.+++++-|.+
T Consensus        12 v~~G~mgsGKTT~ll~~a~r~~~~g~kV~v~k~~~   46 (191)
T 1xx6_A           12 VIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPEI   46 (191)
T ss_dssp             EEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEEC-
T ss_pred             EEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEecc
Confidence            38999999999988877777777899999998874

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=95.26  E-value=0.023  Score=41.53  Aligned_cols=36  Identities=28%  Similarity=0.227  Sum_probs=24.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      .+.+++||+|+|||.++..........+.+++|+..
T Consensus        53 ~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~   88 (242)
T 3bos_A           53 QAIYLWGPVKSGRTHLIHAACARANELERRSFYIPL   88 (242)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEG
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEH
Confidence            456799999999999886544444344566666543

>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=95.03  E-value=0.027  Score=46.05  Aligned_cols=43  Identities=9%  Similarity=0.089  Sum_probs=35.2

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSN   97 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~   97 (138)
                      ..+.++.||||||||......+.+.+..|..++++=|--.+..
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            4788999999999999865566677777889999988877754

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=95.02  E-value=0.03  Score=40.78  Aligned_cols=34  Identities=32%  Similarity=0.327  Sum_probs=25.3

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      .++.+|+|+|||..+...+......+.+++|+.-
T Consensus        26 ~~i~G~~GsGKTtl~~~l~~~~~~~~~~v~~~~~   59 (235)
T 2w0m_A           26 IALTGEPGTGKTIFSLHFIAKGLRDGDPCIYVTT   59 (235)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHHTCCEEEEES
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEEc
Confidence            3499999999999887555444456778888763

>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=94.78  E-value=0.089  Score=41.09  Aligned_cols=43  Identities=26%  Similarity=0.179  Sum_probs=28.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQK   99 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~   99 (138)
                      .+.+++||+|+|||.++..........+.+++|+... .+..+.
T Consensus        38 ~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~~~-~~~~~~   80 (324)
T 1l8q_A           38 NPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSAD-DFAQAM   80 (324)
T ss_dssp             SSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHH-HHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEHH-HHHHHH
Confidence            3567999999999998765444444447778777543 334433

>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=94.57  E-value=0.045  Score=44.27  Aligned_cols=49  Identities=18%  Similarity=0.292  Sum_probs=35.8

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      +.+.++.+|||||||...-..+.+....|.+++++=|..+     +..+.+.++
T Consensus        35 ~~~~~i~G~~G~GKs~~~~~~~~~~~~~~~~~~~~D~~~~-----~~~~~~~~g   83 (392)
T 4ag6_A           35 NSNWTILAKPGAGKSFTAKMLLLREYMQGSRVIIIDPERE-----YKEMCRKLG   83 (392)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEESSCC-----SHHHHHHTT
T ss_pred             cCceEEEcCCCCCHHHHHHHHHHHHHHCCCEEEEEeCCcC-----HHHHHHHcC
Confidence            4678899999999999887666666667888888877644     334444454

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=94.44  E-value=0.053  Score=37.68  Aligned_cols=23  Identities=26%  Similarity=0.133  Sum_probs=17.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAM   78 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~   78 (138)
                      .+.+++||+|+|||.++......
T Consensus        44 ~~~ll~G~~G~GKT~l~~~~~~~   66 (195)
T 1jbk_A           44 NNPVLIGEPGVGKTAIVEGLAQR   66 (195)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CceEEECCCCCCHHHHHHHHHHH
Confidence            45679999999999988644443

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=94.43  E-value=0.035  Score=39.47  Aligned_cols=34  Identities=15%  Similarity=0.092  Sum_probs=23.8

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      ...+.+|+|+|||..+..........|.+++|+.
T Consensus        38 ~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~   71 (149)
T 2kjq_A           38 FIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYID   71 (149)
T ss_dssp             EEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEc
Confidence            3459999999999887654443334566777764

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=94.37  E-value=0.046  Score=43.35  Aligned_cols=35  Identities=20%  Similarity=-0.037  Sum_probs=28.0

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      .+|+|++|+|||..++..+..+..+|.+++|++--
T Consensus        71 ~li~G~pG~GKTtl~l~ia~~~a~~g~~vl~~slE  105 (315)
T 3bh0_A           71 VLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSLE  105 (315)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHTTTCEEEEEESS
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEECC
Confidence            44999999999999986666666667889998743

>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=94.36  E-value=0.028  Score=46.09  Aligned_cols=39  Identities=13%  Similarity=0.116  Sum_probs=32.3

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKALS   96 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~kaLv   96 (138)
                      ..|.+|.|+|||.+++.++..+.+.  |.+++|+..-.++-
T Consensus        31 teI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~   71 (333)
T 3io5_A           31 LILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGIT   71 (333)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhh
Confidence            3599999999999999888877775  78999988766654

>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=94.32  E-value=0.064  Score=42.48  Aligned_cols=46  Identities=11%  Similarity=0.198  Sum_probs=28.8

Q ss_pred             ceEECcCCCchHHHHH-HHHHHHHHcCCcEEEEe--chHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTS--SLKALSNQKYREL  103 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~--P~kaLv~Q~~~~l  103 (138)
                      .++.+|+|+|||..+. ++...+..+|++++++.  +.++-+.++.+.+
T Consensus       108 i~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~~D~~r~~a~eqL~~~  156 (296)
T 2px0_A          108 IVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFITTDTYRIAAVEQLKTY  156 (296)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEECCCSSTTHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEecCcccchHHHHHHHH
Confidence            4499999999998886 44443333577887764  3344444444443

>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=94.28  E-value=0.046  Score=39.73  Aligned_cols=32  Identities=22%  Similarity=0.240  Sum_probs=24.3

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      .++.+|+|+|||..+...+.   ..+.+++|+.-.
T Consensus        23 ~~i~G~~GsGKTtl~~~l~~---~~~~~v~~i~~~   54 (220)
T 2cvh_A           23 TQVYGPYASGKTTLALQTGL---LSGKKVAYVDTE   54 (220)
T ss_dssp             EEEECSTTSSHHHHHHHHHH---HHCSEEEEEESS
T ss_pred             EEEECCCCCCHHHHHHHHHH---HcCCcEEEEECC
Confidence            34999999999998874443   457888888643

>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=94.12  E-value=0.095  Score=44.27  Aligned_cols=50  Identities=12%  Similarity=0.069  Sum_probs=35.6

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEe--chHHHHHHHHHHHHHhc
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS--SLKALSNQKYRELHKEF  107 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~--P~kaLv~Q~~~~l~~~f  107 (138)
                      .++++++|+|||..+.........+|.+++++.  |+++-+.++.+.+.+..
T Consensus       103 IlivG~~G~GKTTt~~kLA~~l~~~G~kVllv~~D~~R~aa~eqL~~~~~~~  154 (443)
T 3dm5_A          103 LLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSDTWRPGAYHQLRQLLDRY  154 (443)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECCCSSTHHHHHHHHHHGGG
T ss_pred             EEEECcCCCCHHHHHHHHHHHHHHCCCeEEEEeCCCcchhHHHHHHHHHHhc
Confidence            349999999999998743333335688888777  66776666666666644

>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=94.10  E-value=0.045  Score=44.87  Aligned_cols=37  Identities=27%  Similarity=0.197  Sum_probs=29.7

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKAL   95 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaL   95 (138)
                      .|.+|.|+|||..++..+..+...+.+++|+..-.++
T Consensus        65 ~I~GppGsGKSTLal~la~~~~~~gg~VlyId~E~s~  101 (356)
T 3hr8_A           65 EIFGQESSGKTTLALHAIAEAQKMGGVAAFIDAEHAL  101 (356)
T ss_dssp             EEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCC
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhcCCeEEEEeccccc
Confidence            4999999999999987776666678889998765544

>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=94.05  E-value=0.39  Score=40.77  Aligned_cols=52  Identities=10%  Similarity=-0.073  Sum_probs=40.4

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceE
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVG  111 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~  111 (138)
                      +..+.+-|||||+++....+.   ..++.+|+|+|....+.|.+++|+..++ +|.
T Consensus        16 ~~~l~g~~gs~ka~~~a~l~~---~~~~p~lvv~~~~~~A~~l~~~l~~~~~~~v~   68 (483)
T 3hjh_A           16 QRLLGELTGAACATLVAEIAE---RHAGPVVLIAPDMQNALRLHDEISQFTDQMVM   68 (483)
T ss_dssp             EEEEECCCTTHHHHHHHHHHH---HSSSCEEEEESSHHHHHHHHHHHHHTCSSCEE
T ss_pred             eEEEeCCCchHHHHHHHHHHH---HhCCCEEEEeCCHHHHHHHHHHHHhhCCCcEE
Confidence            456999999999976543332   2367899999999999999999998655 443

>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=94.01  E-value=0.044  Score=44.74  Aligned_cols=34  Identities=24%  Similarity=0.314  Sum_probs=28.8

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      .+|.+|.|+|||.+++..+..+...|.+++|+.-
T Consensus        66 i~I~G~pGsGKTtLal~la~~~~~~g~~vlyid~   99 (356)
T 1u94_A           66 VEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDA   99 (356)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeC
Confidence            4599999999999998777777677889999876

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=93.97  E-value=0.051  Score=37.89  Aligned_cols=23  Identities=26%  Similarity=0.106  Sum_probs=17.7

Q ss_pred             CCceEECcCCCchHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAM   78 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~   78 (138)
                      .+.++++|+|+|||.++......
T Consensus        44 ~~vll~G~~G~GKT~la~~~~~~   66 (187)
T 2p65_A           44 NNPILLGDPGVGKTAIVEGLAIK   66 (187)
T ss_dssp             CEEEEESCGGGCHHHHHHHHHHH
T ss_pred             CceEEECCCCCCHHHHHHHHHHH
Confidence            45579999999999988654443

>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=93.96  E-value=0.058  Score=43.76  Aligned_cols=35  Identities=26%  Similarity=0.172  Sum_probs=29.0

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      .+|.+|.|+|||..++..+..+...|.+++|+.--
T Consensus        64 v~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~~E   98 (349)
T 2zr9_A           64 IEIYGPESSGKTTVALHAVANAQAAGGIAAFIDAE   98 (349)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECC
Confidence            44999999999999987777777778899988744

>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=93.58  E-value=0.077  Score=43.47  Aligned_cols=35  Identities=20%  Similarity=0.216  Sum_probs=28.7

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      .+|.+|.|+|||..++..+..+...|.+++|+..-
T Consensus        77 i~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~~E  111 (366)
T 1xp8_A           77 TEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAE  111 (366)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             EEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEECC
Confidence            44999999999999987777766778889888754

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=93.48  E-value=0.15  Score=42.79  Aligned_cols=50  Identities=14%  Similarity=0.056  Sum_probs=33.4

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEe--chHHHHHHHHHHHHHhc
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS--SLKALSNQKYRELHKEF  107 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~--P~kaLv~Q~~~~l~~~f  107 (138)
                      .++++|+|+|||..+.........+|++++++.  ++++-+.++.+.+.+..
T Consensus       100 I~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv~~D~~r~~a~eqL~~~~~~~  151 (433)
T 3kl4_A          100 IMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVAADVYRPAAYDQLLQLGNQI  151 (433)
T ss_dssp             EEECCCTTSCHHHHHHHHHHHHHHTTCCEEEEEECCSCHHHHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEecCccchhHHHHHHHHHHhc
Confidence            348999999999988633333335688887766  55655555566665543

>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=93.47  E-value=0.05  Score=43.16  Aligned_cols=37  Identities=11%  Similarity=0.083  Sum_probs=27.8

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHc------CCcEEEEechHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRD------KQRVIYTSSLKA   94 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~------~~rviyv~P~ka   94 (138)
                      .++.+|+|+|||.++...+..+...      +.+++|+.--.+
T Consensus       110 ~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~  152 (324)
T 2z43_A          110 TEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGT  152 (324)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSC
T ss_pred             EEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCC
Confidence            4499999999999998666554333      678999876554

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=93.46  E-value=0.075  Score=44.44  Aligned_cols=35  Identities=20%  Similarity=-0.037  Sum_probs=28.4

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      .+|.|++|+|||..++..+.++..+|.+++|++--
T Consensus       200 iiIaG~pG~GKTtlal~ia~~~a~~g~~vl~fSlE  234 (444)
T 3bgw_A          200 VLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSLE  234 (444)
T ss_dssp             EEEEECSSSSHHHHHHHHHHHHHHTTCEEEEECSS
T ss_pred             EEEEeCCCCChHHHHHHHHHHHHHcCCEEEEEECC
Confidence            44999999999999986666666668899998754

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=93.40  E-value=0.095  Score=39.70  Aligned_cols=33  Identities=9%  Similarity=0.156  Sum_probs=29.8

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      +++|.|||||.-.+.++.+....+.+++|+-|.
T Consensus        25 iyG~MgsGKTt~Ll~~i~n~~~~~~kvl~~kp~   57 (195)
T 1w4r_A           25 ILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYA   57 (195)
T ss_dssp             EEECTTSCHHHHHHHHHHHHHHTTCCEEEEEET
T ss_pred             EECCCCCcHHHHHHHHHHHHHHcCCeEEEEccc
Confidence            999999999988888888887889999999887

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=93.20  E-value=0.073  Score=45.10  Aligned_cols=41  Identities=10%  Similarity=-0.063  Sum_probs=32.2

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHH
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      +.|+.|+|||.....    .+. ..+.++++|+++++++..+.+.+
T Consensus       166 I~G~aGsGKTt~I~~----~~~-~~~~lVlTpT~~aa~~l~~kl~~  206 (446)
T 3vkw_A          166 VDGVPGCGKTKEILS----RVN-FEEDLILVPGRQAAEMIRRRANA  206 (446)
T ss_dssp             EEECTTSCHHHHHHH----HCC-TTTCEEEESCHHHHHHHHHHHTT
T ss_pred             EEcCCCCCHHHHHHH----Hhc-cCCeEEEeCCHHHHHHHHHHhhh
Confidence            999999999975432    222 36789999999999988888754

>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=93.15  E-value=0.2  Score=39.41  Aligned_cols=34  Identities=18%  Similarity=0.164  Sum_probs=23.9

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHc--------CCcEEEEe
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRD--------KQRVIYTS   90 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~--------~~rviyv~   90 (138)
                      ..+|++|+|+|||.++..........        +..++++.
T Consensus        47 ~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~   88 (384)
T 2qby_B           47 SNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVN   88 (384)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEE
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEE
Confidence            45699999999999886544443333        66677775

>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=93.12  E-value=0.074  Score=39.20  Aligned_cols=35  Identities=11%  Similarity=0.169  Sum_probs=24.4

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH------cCCcEEEEech
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR------DKQRVIYTSSL   92 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~------~~~rviyv~P~   92 (138)
                      ..|.+|+|+|||..+...+..++.      .+..++|+.-.
T Consensus        27 ~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~   67 (243)
T 1n0w_A           27 TEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTE   67 (243)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESS
T ss_pred             EEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECC
Confidence            349999999999998755544322      25678887643

>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=93.01  E-value=0.13  Score=39.42  Aligned_cols=35  Identities=14%  Similarity=0.126  Sum_probs=29.4

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEechHH
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKA   94 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~ka   94 (138)
                      +++|-|||||..++-.+.++...|.+++++-|.+.
T Consensus        33 itG~MgsGKTT~lL~~a~r~~~~g~kVli~k~~~d   67 (214)
T 2j9r_A           33 ICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPCID   67 (214)
T ss_dssp             EECSTTSCHHHHHHHHHHHHHHTTCCEEEEECC--
T ss_pred             EECCCCCcHHHHHHHHHHHHHHCCCEEEEEEeccC
Confidence            89999999999888777777788999999988864

>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=93.00  E-value=0.073  Score=42.71  Aligned_cols=37  Identities=14%  Similarity=0.133  Sum_probs=27.7

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH------cCCcEEEEechHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR------DKQRVIYTSSLKA   94 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~------~~~rviyv~P~ka   94 (138)
                      ..|.+|.|+|||..+...+..+..      .+.+++|+.-..+
T Consensus       125 ~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~  167 (343)
T 1v5w_A          125 TEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENT  167 (343)
T ss_dssp             EEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCC
Confidence            349999999999999866655433      3678999876554

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=92.84  E-value=0.056  Score=37.65  Aligned_cols=20  Identities=20%  Similarity=0.081  Sum_probs=16.6

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      .+.++.+|+|+|||.+|...
T Consensus        25 ~~vll~G~~GtGKt~lA~~i   44 (145)
T 3n70_A           25 IAVWLYGAPGTGRMTGARYL   44 (145)
T ss_dssp             SCEEEESSTTSSHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHH
Confidence            56779999999999988643

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=92.78  E-value=0.14  Score=38.77  Aligned_cols=34  Identities=21%  Similarity=-0.065  Sum_probs=29.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      ++.++..+.|.|||.+|+-..++++.+|.|++++
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalRA~g~G~rV~~v   62 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVV   62 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            4556999999999999997777788899999998

>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=92.71  E-value=0.23  Score=41.15  Aligned_cols=45  Identities=20%  Similarity=0.129  Sum_probs=28.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKALSNQKYR  101 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~kaLv~Q~~~  101 (138)
                      .+.++.||+|+|||..+..........  +.+++|+... .+.++...
T Consensus       131 ~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~~-~~~~~~~~  177 (440)
T 2z4s_A          131 NPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSE-KFLNDLVD  177 (440)
T ss_dssp             CCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEHH-HHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHH-HHHHHHHH
Confidence            456799999999999876443333333  6777777544 34444443

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=92.69  E-value=0.12  Score=41.91  Aligned_cols=35  Identities=20%  Similarity=0.084  Sum_probs=28.1

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      .+|.|++|+|||..++..+..+...|.+++|++--
T Consensus        49 iiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~fSlE   83 (338)
T 4a1f_A           49 VIIGARPSMGKTSLMMNMVLSALNDDRGVAVFSLE   83 (338)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHTTCEEEEEESS
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeCC
Confidence            34999999999999986666655678899998754

>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=92.66  E-value=0.3  Score=38.90  Aligned_cols=46  Identities=13%  Similarity=0.189  Sum_probs=28.0

Q ss_pred             eEECcCCCchHHHHH-HHHHHHHHcCCcEEEEe--chHHHHHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTS--SLKALSNQKYRELHK  105 (138)
Q Consensus        59 ~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~--P~kaLv~Q~~~~l~~  105 (138)
                      ++++|+|+|||..+. +|.... ..|++++++.  ++++-+.++.+.|.+
T Consensus       108 ~ivG~~GsGKTTl~~~LA~~l~-~~g~kV~lv~~D~~r~~a~eqL~~~~~  156 (306)
T 1vma_A          108 MVVGVNGTGKTTSCGKLAKMFV-DEGKSVVLAAADTFRAAAIEQLKIWGE  156 (306)
T ss_dssp             EEECCTTSSHHHHHHHHHHHHH-HTTCCEEEEEECTTCHHHHHHHHHHHH
T ss_pred             EEEcCCCChHHHHHHHHHHHHH-hcCCEEEEEccccccHHHHHHHHHHHH
Confidence            499999999998875 443332 4577776654  334433344444444

>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=92.28  E-value=0.087  Score=39.89  Aligned_cols=20  Identities=15%  Similarity=0.039  Sum_probs=16.2

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      .+.++.+|+|+|||.++...
T Consensus        30 ~~vll~G~~GtGKt~la~~i   49 (265)
T 2bjv_A           30 KPVLIIGERGTGKELIASRL   49 (265)
T ss_dssp             SCEEEECCTTSCHHHHHHHH
T ss_pred             CCEEEECCCCCcHHHHHHHH
Confidence            45679999999999877543

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=92.28  E-value=0.15  Score=42.19  Aligned_cols=35  Identities=23%  Similarity=-0.046  Sum_probs=27.1

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEech
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSL   92 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~   92 (138)
                      .+|.|++|+|||..++..+..+.. .|.+++|+.--
T Consensus       203 ~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~slE  238 (444)
T 2q6t_A          203 NIIAARPAMGKTAFALTIAQNAALKEGVGVGIYSLE  238 (444)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEESS
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEECC
Confidence            349999999999999865555554 47889998754

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=92.24  E-value=0.17  Score=42.04  Aligned_cols=35  Identities=20%  Similarity=-0.030  Sum_probs=26.9

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEech
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSL   92 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~   92 (138)
                      .+|.|++|+|||..+...+..... .|.+++|+.--
T Consensus       206 iiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s~E  241 (454)
T 2r6a_A          206 IIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLE  241 (454)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEESS
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEECC
Confidence            449999999999999855555544 57789998743

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=92.21  E-value=0.11  Score=39.80  Aligned_cols=33  Identities=24%  Similarity=0.228  Sum_probs=21.1

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      +.++.+|+|+|||.++..........+..++++
T Consensus        49 ~~ll~G~~GtGKt~la~~la~~~~~~~~~~~~~   81 (311)
T 4fcw_A           49 SFLFLGPTGVGKTELAKTLAATLFDTEEAMIRI   81 (311)
T ss_dssp             EEEEESCSSSSHHHHHHHHHHHHHSCGGGEEEE
T ss_pred             EEEEECCCCcCHHHHHHHHHHHHcCCCcceEEe
Confidence            456999999999998864333322233444444

>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=92.14  E-value=0.18  Score=38.93  Aligned_cols=33  Identities=12%  Similarity=-0.093  Sum_probs=23.4

Q ss_pred             eEECcCCCchHHHHHHHHHHHHH-cCCcEEEEec
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSS   91 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P   91 (138)
                      +|.+|+|+|||..+...+..... .|.+++|+.-
T Consensus        39 ~i~G~~G~GKTTl~~~ia~~~~~~~G~~v~~~~~   72 (296)
T 1cr0_A           39 MVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAML   72 (296)
T ss_dssp             EEEESTTSSHHHHHHHHHHHHHHTSCCCEEEEES
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHHHcCCeEEEEeC
Confidence            49999999999988644333333 3668888753

>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=92.01  E-value=0.11  Score=50.60  Aligned_cols=40  Identities=25%  Similarity=0.294  Sum_probs=35.8

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHH
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQK   99 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~   99 (138)
                      +.+|.|||||.+++.++..+.+.|.+++|+.+-.+|--..
T Consensus      1436 i~g~~~sGkttl~~~~~a~~~~~g~~~~~i~~e~~~~~~~ 1475 (1706)
T 3cmw_A         1436 IYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIY 1475 (1706)
T ss_dssp             EECSTTSSHHHHHHHHHHHHHHTTCCEEEECTTSCCCHHH
T ss_pred             EEcCCCCCHHHHHHHHHHHHHhcCCeEEEEecCCCCCHHH
Confidence            9999999999999999999988999999999977665554

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=91.82  E-value=0.2  Score=38.79  Aligned_cols=33  Identities=24%  Similarity=0.075  Sum_probs=24.3

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      +.++.++.|.|||..+.........+|.+++++
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            345999999999999875555555678776543

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=91.77  E-value=0.093  Score=39.32  Aligned_cols=34  Identities=18%  Similarity=0.046  Sum_probs=22.0

Q ss_pred             eEECcCCCchHHHHHHHHHHHH-----HcCCcEEEEech
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAF-----RDKQRVIYTSSL   92 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l-----~~~~rviyv~P~   92 (138)
                      +++|+.|||||..+...+....     +.|.|.+|++..
T Consensus         9 l~tG~pGsGKT~~a~~~~~~~~~~~~~~~g~r~v~~~~~   47 (199)
T 2r2a_A            9 LITGTPGSGKTLKMVSMMANDEMFKPDENGIRRKVFTNI   47 (199)
T ss_dssp             EEECCTTSSHHHHHHHHHHHCGGGSCCTTSCCCCEEECC
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHhhcccccCceEEEEecC
Confidence            4999999999998864333322     334366665543

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=91.74  E-value=0.19  Score=38.52  Aligned_cols=36  Identities=25%  Similarity=0.219  Sum_probs=22.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc----CCcEEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD----KQRVIYTSS   91 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~----~~rviyv~P   91 (138)
                      .+.++.+|+|+|||.++.......-..    ...++++.+
T Consensus        68 ~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~  107 (309)
T 3syl_A           68 LHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTR  107 (309)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECG
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcH
Confidence            356799999999999886433332222    235666554

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=91.65  E-value=0.36  Score=37.61  Aligned_cols=35  Identities=26%  Similarity=0.231  Sum_probs=23.4

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc------CCcEEEEe
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD------KQRVIYTS   90 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~------~~rviyv~   90 (138)
                      .+.+|+||+|+|||.++..........      +..++++-
T Consensus        45 ~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~   85 (387)
T 2v1u_A           45 SNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVN   85 (387)
T ss_dssp             CCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEE
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEE
Confidence            456699999999999886544433222      45566664

>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=91.64  E-value=0.11  Score=43.60  Aligned_cols=35  Identities=6%  Similarity=-0.269  Sum_probs=28.0

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHc-CCcEEEEech
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRD-KQRVIYTSSL   92 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~-~~rviyv~P~   92 (138)
                      .+|.+++|+|||..++..+.++... |.+++|+.--
T Consensus       245 ~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s~E  280 (503)
T 1q57_A          245 IMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAMLE  280 (503)
T ss_dssp             EEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEESS
T ss_pred             EEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEecc
Confidence            3499999999999998666666555 8899998754

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=91.62  E-value=0.12  Score=51.11  Aligned_cols=38  Identities=21%  Similarity=0.241  Sum_probs=32.2

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLK   93 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~k   93 (138)
                      .+.++++|+|+|||.+|...+..+..+|.+++|+..--
T Consensus      1428 ~~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~~e~ 1465 (2050)
T 3cmu_A         1428 RIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEH 1465 (2050)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEEccc
Confidence            45669999999999999877777778899999998663

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=91.29  E-value=0.24  Score=38.39  Aligned_cols=16  Identities=25%  Similarity=0.304  Sum_probs=13.5

Q ss_pred             ceEECcCCCchHHHHH
Q 042424           58 GTLTNPVYNGKTAVAE   73 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~   73 (138)
                      .++++|||||||....
T Consensus        28 v~i~Gp~GsGKSTll~   43 (261)
T 2eyu_A           28 ILVTGPTGSGKSTTIA   43 (261)
T ss_dssp             EEEECSTTCSHHHHHH
T ss_pred             EEEECCCCccHHHHHH
Confidence            3599999999998764

>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=91.29  E-value=0.12  Score=36.62  Aligned_cols=22  Identities=32%  Similarity=0.200  Sum_probs=17.0

Q ss_pred             CceEECcCCCchHHHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAM   78 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~   78 (138)
                      +.+++||+|+|||.++......
T Consensus        40 ~~ll~G~~G~GKT~l~~~l~~~   61 (226)
T 2chg_A           40 HLLFSGPPGTGKTATAIALARD   61 (226)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4569999999999988644443

>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=91.21  E-value=0.36  Score=36.98  Aligned_cols=35  Identities=29%  Similarity=0.321  Sum_probs=24.3

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHc-----------CCcEEEEechH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRD-----------KQRVIYTSSLK   93 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~-----------~~rviyv~P~k   93 (138)
                      .+|.+|.|+|||..+...+.. +..           +.+++|+.-..
T Consensus        33 ~~i~G~~GsGKTtl~~~l~~~-~~~g~~~~g~~~~~~~~v~~~~~e~   78 (279)
T 1nlf_A           33 GALVSPGGAGKSMLALQLAAQ-IAGGPDLLEVGELPTGPVIYLPAED   78 (279)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH-HHTCCCTTCCCCCCCCCEEEEESSS
T ss_pred             EEEEcCCCCCHHHHHHHHHHH-HhcCCCcCCCccCCCccEEEEECCC
Confidence            349999999999998754443 234           35788876443

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens}

Probab=91.18  E-value=0.74  Score=33.31  Aligned_cols=65  Identities=15%  Similarity=0.023  Sum_probs=40.9

Q ss_pred             CCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCCC-----------CCCEEEecH
Q 042424           65 YNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSP-----------NASCLVMTT  130 (138)
Q Consensus        65 GsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~~-----------~~~IiVtTp  130 (138)
                      .+.|... +.-++.....+.++|+.++++.-++..++.|++.--.+..++|+.....           ..+|+|+|.
T Consensus        29 ~~~K~~~-L~~ll~~~~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vLvaT~  104 (185)
T 2jgn_A           29 ESDKRSF-LLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATA  104 (185)
T ss_dssp             GGGHHHH-HHHHHHHC-CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------CHHHHHHHHTSSSEEEEEC
T ss_pred             cHHHHHH-HHHHHHhcCCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHHHHHHHHHHcCCCeEEEEcC
Confidence            4566432 3333332234688999999999999999999873227888888765432           678999984

>3u4q_B ATP-dependent helicase/deoxyribonuclease subunit; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_B*

Probab=90.81  E-value=0.39  Score=44.39  Aligned_cols=46  Identities=22%  Similarity=0.160  Sum_probs=34.6

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      +|.|..|||||.+...-|.+.+.+   +.+++++||... .-++.+++.+
T Consensus         5 lV~agAGSGKT~~l~~ri~~ll~~~~~~~~il~lVP~q~-TFt~~~rl~~   53 (1166)
T 3u4q_B            5 FLVGRSGSGKTKLIINSIQDELRRAPFGKPIIFLVPDQM-TFLMEYELAK   53 (1166)
T ss_dssp             EEEECTTSSHHHHHHHHHHHHHHHCTTSSCEEEECCGGG-HHHHHHHHTC
T ss_pred             EEEeCCCCChHHHHHHHHHHHHHhCCCCCcEEEEecCcc-cHHHHHHHHH
Confidence            588999999999999888877765   478999999863 3334444444

>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=90.80  E-value=0.1  Score=38.91  Aligned_cols=43  Identities=21%  Similarity=0.321  Sum_probs=27.4

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      +|.+++|||||..|+....   . +.+++|++.-.+.-.++.+++..
T Consensus         3 lV~Gg~~SGKS~~A~~la~---~-~~~~~yiaT~~~~d~e~~~rI~~   45 (180)
T 1c9k_A            3 LVTGGARSGKSRHAEALIG---D-APQVLYIATSQILDDEMAARIQH   45 (180)
T ss_dssp             EEEECTTSSHHHHHHHHHC---S-CSSEEEEECCCC------CHHHH
T ss_pred             EEECCCCCcHHHHHHHHHh---c-CCCeEEEecCCCCCHHHHHHHHH
Confidence            5899999999988774332   2 67899999876655555555443

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=90.77  E-value=0.11  Score=36.09  Aligned_cols=18  Identities=22%  Similarity=0.004  Sum_probs=15.2

Q ss_pred             CCceEECcCCCchHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAE   73 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~   73 (138)
                      .+.++.+|+|+|||.+|.
T Consensus        28 ~~vll~G~~GtGKt~lA~   45 (143)
T 3co5_A           28 SPVFLTGEAGSPFETVAR   45 (143)
T ss_dssp             SCEEEEEETTCCHHHHHG
T ss_pred             CcEEEECCCCccHHHHHH
Confidence            566799999999998764

>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=90.75  E-value=0.28  Score=36.50  Aligned_cols=33  Identities=18%  Similarity=0.119  Sum_probs=21.7

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      .+.++.+|+|+|||.++...... +  +...+++..
T Consensus        40 ~~vll~G~~GtGKT~la~~la~~-~--~~~~~~~~~   72 (262)
T 2qz4_A           40 KGALLLGPPGCGKTLLAKAVATE-A--QVPFLAMAG   72 (262)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHH-H--TCCEEEEET
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH-h--CCCEEEech
Confidence            45679999999999987643322 2  455555443

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=90.56  E-value=0.33  Score=38.12  Aligned_cols=33  Identities=21%  Similarity=0.137  Sum_probs=22.3

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      .+.++.+|+|+|||.++......   .+...+++..
T Consensus        52 ~~vLl~GppGtGKT~la~aia~~---~~~~~~~v~~   84 (322)
T 3eie_A           52 SGILLYGPPGTGKSYLAKAVATE---ANSTFFSVSS   84 (322)
T ss_dssp             CEEEEECSSSSCHHHHHHHHHHH---HTCEEEEEEH
T ss_pred             CeEEEECCCCCcHHHHHHHHHHH---HCCCEEEEch
Confidence            45679999999999988643322   2555555543

>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=90.50  E-value=0.31  Score=37.95  Aligned_cols=35  Identities=11%  Similarity=0.175  Sum_probs=30.1

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEechHH
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKA   94 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~ka   94 (138)
                      +++|-|||||..++-.+.++...|.+++++-|.+.
T Consensus        24 ~~G~MgsGKTT~lL~~~~r~~~~g~kvli~kp~~D   58 (234)
T 2orv_A           24 ILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKD   58 (234)
T ss_dssp             EECCTTSCHHHHHHHHHHHHHTTTCCEEEEEETTC
T ss_pred             EECCCCCcHHHHHHHHHHHHHHCCCeEEEEeecCC
Confidence            88999999999888777777778999999988753

>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=90.40  E-value=0.34  Score=36.81  Aligned_cols=32  Identities=19%  Similarity=0.126  Sum_probs=21.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      .+.++.+|+|+|||.++..... .+  +...+++.
T Consensus        51 ~~vll~G~~GtGKT~la~~la~-~l--~~~~~~i~   82 (310)
T 1ofh_A           51 KNILMIGPTGVGKTEIARRLAK-LA--NAPFIKVE   82 (310)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHH-HH--TCCEEEEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHH-Hh--CCCEEEEc
Confidence            4567999999999998864332 22  44555543

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=90.28  E-value=0.79  Score=32.17  Aligned_cols=48  Identities=21%  Similarity=0.175  Sum_probs=39.0

Q ss_pred             cCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcC-----------CCCCCEEEecH
Q 042424           82 DKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTL-----------SPNASCLVMTT  130 (138)
Q Consensus        82 ~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~-----------~~~~~IiVtTp  130 (138)
                      .+.++|+.++++.-+++.++.|.+ .+ .+..++|+...           +...+|+|+|.
T Consensus        34 ~~~~~lVF~~~~~~~~~l~~~L~~-~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~   93 (163)
T 2hjv_A           34 NPDSCIIFCRTKEHVNQLTDELDD-LGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATD   93 (163)
T ss_dssp             CCSSEEEECSSHHHHHHHHHHHHH-TTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECG
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHH-cCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECC
Confidence            467899999999999999999988 44 88889988643           22678999984

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=90.26  E-value=0.14  Score=41.83  Aligned_cols=17  Identities=18%  Similarity=0.087  Sum_probs=14.3

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .+|++|||+|||.++..
T Consensus        43 IvI~GPTgsGKTtLa~~   59 (339)
T 3a8t_A           43 LVLMGATGTGKSRLSID   59 (339)
T ss_dssp             EEEECSTTSSHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            45999999999988753

>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=90.22  E-value=0.22  Score=36.19  Aligned_cols=35  Identities=20%  Similarity=0.149  Sum_probs=22.9

Q ss_pred             eEECcCCCchHHHHHHHHHHHHH------cCCcEEEEechH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFR------DKQRVIYTSSLK   93 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~------~~~rviyv~P~k   93 (138)
                      .|.+|+|||||..+...+.....      .+.+++|+....
T Consensus        29 ~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~~   69 (231)
T 4a74_A           29 EVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTEN   69 (231)
T ss_dssp             EEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSS
T ss_pred             EEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECCC
Confidence            49999999999887644332222      145677776543

>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=90.12  E-value=0.33  Score=39.47  Aligned_cols=31  Identities=16%  Similarity=0.194  Sum_probs=19.3

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHH-c-CCcEEE
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFR-D-KQRVIY   88 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~-~-~~rviy   88 (138)
                      ..++++|||||||.... ++...+. . +.+++.
T Consensus       125 ~i~I~GptGSGKTTlL~-~l~g~~~~~~~~~i~t  157 (356)
T 3jvv_A          125 LVLVTGPTGSGKSTTLA-AMLDYLNNTKYHHILT  157 (356)
T ss_dssp             EEEEECSTTSCHHHHHH-HHHHHHHHHCCCEEEE
T ss_pred             EEEEECCCCCCHHHHHH-HHHhcccCCCCcEEEE
Confidence            34599999999998754 3333333 2 455544

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=90.11  E-value=0.26  Score=48.71  Aligned_cols=37  Identities=22%  Similarity=0.242  Sum_probs=32.2

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      .+.++++|+|+|||..+...+..++++|.+++|+.=-
T Consensus      1082 ~~vll~G~~GtGKT~la~~~~~ea~k~Ge~~~Fit~e 1118 (2050)
T 3cmu_A         1082 RIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAE 1118 (2050)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTT
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEcc
Confidence            4567999999999999998888888889999998644

>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=90.06  E-value=0.33  Score=39.45  Aligned_cols=18  Identities=22%  Similarity=0.200  Sum_probs=14.4

Q ss_pred             CceEECcCCCchHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~   74 (138)
                      ..++++|||||||.....
T Consensus       138 ~i~ivG~~GsGKTTll~~  155 (372)
T 2ewv_A          138 LILVTGPTGSGKSTTIAS  155 (372)
T ss_dssp             EEEEECSSSSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            345999999999987643

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=90.02  E-value=0.38  Score=38.43  Aligned_cols=57  Identities=23%  Similarity=0.194  Sum_probs=32.5

Q ss_pred             eEECcCCCchHHHHH-HHHHHHHHcCCcEEEEe--chHHHHHHHHHHHHHh--cCceEEE-ecC
Q 042424           59 TLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTS--SLKALSNQKYRELHKE--FKDVGLM-TGD  116 (138)
Q Consensus        59 ~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~--P~kaLv~Q~~~~l~~~--f~~v~~~-tGd  116 (138)
                      .+++|+|+|||..+. +|...+ ..|++++++-  +.+.-+.+....|.+.  ..++.++ .+.
T Consensus       109 ~ivG~~G~GKTT~~~~LA~~l~-~~g~kVllid~D~~r~~a~~ql~~~~~~~~~~~l~vip~~~  171 (320)
T 1zu4_A          109 MLVGVNGTGKTTSLAKMANYYA-ELGYKVLIAAADTFRAGATQQLEEWIKTRLNNKVDLVKANK  171 (320)
T ss_dssp             EEESSTTSSHHHHHHHHHHHHH-HTTCCEEEEECCCSCHHHHHHHHHHHTTTSCTTEEEECCSS
T ss_pred             EEECCCCCCHHHHHHHHHHHHH-HCCCeEEEEeCCCcchhHHHHHHHHHhccccCCceEEeCCC
Confidence            488999999998875 444332 4577877763  2333333333444321  1256666 443

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=89.95  E-value=0.46  Score=33.82  Aligned_cols=32  Identities=25%  Similarity=0.124  Sum_probs=21.5

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      .+++++.|||||.++.......-..|.++.++
T Consensus        16 i~l~G~~GsGKsT~~~~L~~~l~~~~~~~~~~   47 (186)
T 2yvu_A           16 VWLTGLPGSGKTTIATRLADLLQKEGYRVEVL   47 (186)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEe
Confidence            34999999999998864333322346666555

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=89.83  E-value=0.69  Score=32.42  Aligned_cols=31  Identities=16%  Similarity=0.041  Sum_probs=20.7

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH-cCCcEEEE
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYT   89 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv   89 (138)
                      .+++++.|||||.++..... .+. .|..+.++
T Consensus         4 I~i~G~~GsGKsT~~~~L~~-~l~~~g~~~~~~   35 (194)
T 1nks_A            4 GIVTGIPGVGKSTVLAKVKE-ILDNQGINNKII   35 (194)
T ss_dssp             EEEEECTTSCHHHHHHHHHH-HHHTTTCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHH-HHHhcCceEEEE
Confidence            35999999999998864433 233 34455555

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=89.79  E-value=0.42  Score=38.50  Aligned_cols=33  Identities=27%  Similarity=0.211  Sum_probs=22.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      .+.+|.+|+|+|||.++.....   ..+..++++..
T Consensus       149 ~~vLL~GppGtGKT~la~aia~---~~~~~~~~v~~  181 (389)
T 3vfd_A          149 RGLLLFGPPGNGKTMLAKAVAA---ESNATFFNISA  181 (389)
T ss_dssp             SEEEEESSTTSCHHHHHHHHHH---HTTCEEEEECS
T ss_pred             ceEEEECCCCCCHHHHHHHHHH---hhcCcEEEeeH
Confidence            4677999999999998864422   23555555544

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=89.76  E-value=0.22  Score=38.10  Aligned_cols=20  Identities=35%  Similarity=0.242  Sum_probs=16.3

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      .+.++.||+|+|||.++...
T Consensus        55 ~~vll~Gp~GtGKT~la~~l   74 (297)
T 3b9p_A           55 KGLLLFGPPGNGKTLLARAV   74 (297)
T ss_dssp             SEEEEESSSSSCHHHHHHHH
T ss_pred             CeEEEECcCCCCHHHHHHHH
Confidence            45679999999999987643

>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=89.75  E-value=0.3  Score=38.29  Aligned_cols=34  Identities=21%  Similarity=0.202  Sum_probs=22.9

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHc-CCcEEEEe
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRD-KQRVIYTS   90 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~-~~rviyv~   90 (138)
                      ..+|+||+|+|||.++.......... +..++++-
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            45699999999999886444332223 45677765

>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=89.73  E-value=0.37  Score=37.47  Aligned_cols=35  Identities=20%  Similarity=0.306  Sum_probs=23.7

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEe
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTS   90 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~   90 (138)
                      ...+|.||.|+|||.++..........   +..++++.
T Consensus        46 ~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~   83 (386)
T 2qby_A           46 NNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYIN   83 (386)
T ss_dssp             CCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEE
Confidence            345699999999999886544433233   55667665

>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=89.72  E-value=0.32  Score=47.35  Aligned_cols=38  Identities=21%  Similarity=0.241  Sum_probs=31.4

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLK   93 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~k   93 (138)
                      ...+|++|+|+|||..++..+..++..|.+++|+.-..
T Consensus        35 ~i~lI~G~pGsGKT~LAlqla~~~~~~G~~vlYI~te~   72 (1706)
T 3cmw_A           35 RIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEH   72 (1706)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTTS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhhCCCceEEEEecC
Confidence            34569999999999999977777778899999987643

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=89.66  E-value=0.44  Score=38.16  Aligned_cols=32  Identities=22%  Similarity=0.147  Sum_probs=21.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      .+.+|.+|+|+|||.++.......   +...+++.
T Consensus        85 ~~iLL~GppGtGKT~la~ala~~~---~~~~~~v~  116 (355)
T 2qp9_X           85 SGILLYGPPGTGKSYLAKAVATEA---NSTFFSVS  116 (355)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHHHH---TCEEEEEE
T ss_pred             ceEEEECCCCCcHHHHHHHHHHHh---CCCEEEee
Confidence            456799999999999886433322   44444443

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=89.62  E-value=0.29  Score=38.12  Aligned_cols=32  Identities=16%  Similarity=-0.024  Sum_probs=21.9

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      ..++.+|+|+|||.++.......   +..++++..
T Consensus        38 ~lLl~GppGtGKT~la~aiA~~l---~~~~i~v~~   69 (293)
T 3t15_A           38 ILGIWGGKGQGKSFQCELVFRKM---GINPIMMSA   69 (293)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHH---TCCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh---CCCEEEEeH
Confidence            34588999999999876443322   566666653

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=89.59  E-value=0.22  Score=38.04  Aligned_cols=16  Identities=31%  Similarity=0.409  Sum_probs=14.0

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      +|++|+|||||.++..
T Consensus         5 ~I~G~~GSGKSTla~~   20 (253)
T 2ze6_A            5 LIYGPTCSGKTDMAIQ   20 (253)
T ss_dssp             EEECCTTSSHHHHHHH
T ss_pred             EEECCCCcCHHHHHHH
Confidence            5899999999998863

>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=89.58  E-value=0.16  Score=34.94  Aligned_cols=17  Identities=24%  Similarity=0.215  Sum_probs=14.4

Q ss_pred             eEECcCCCchHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~a   75 (138)
                      +++||.|||||.++...
T Consensus         5 ~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            5 LITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             EEECCTTSCHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHH
Confidence            49999999999988644

>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=89.51  E-value=0.26  Score=41.00  Aligned_cols=31  Identities=16%  Similarity=0.184  Sum_probs=19.9

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHc-CCcEEEE
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRD-KQRVIYT   89 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~-~~rviyv   89 (138)
                      .+|++|||||||.... ++...+.. .++++++
T Consensus       170 i~I~GpnGSGKTTlL~-allg~l~~~~g~I~~~  201 (418)
T 1p9r_A          170 ILVTGPTGSGKSTTLY-AGLQELNSSERNILTV  201 (418)
T ss_dssp             EEEECSTTSCHHHHHH-HHHHHHCCTTSCEEEE
T ss_pred             EEEECCCCCCHHHHHH-HHHhhcCCCCCEEEEe
Confidence            4599999999998643 34444443 4455543

>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=89.51  E-value=0.25  Score=38.73  Aligned_cols=37  Identities=11%  Similarity=0.134  Sum_probs=26.6

Q ss_pred             ceEECcCCCchHHHHHHHHHHH-H-----------HcC----CcEEEEechHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMA-F-----------RDK----QRVIYTSSLKA   94 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~-l-----------~~~----~rviyv~P~ka   94 (138)
                      .+|.+|+|+|||..++..+..+ +           ..|    .+++|+.--.+
T Consensus       101 ~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~  153 (322)
T 2i1q_A          101 TEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGT  153 (322)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCC
Confidence            3499999999999998655543 2           124    68899876554

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=89.41  E-value=0.45  Score=38.02  Aligned_cols=33  Identities=18%  Similarity=0.125  Sum_probs=21.7

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      .+.+|.+|+|+|||.++......   .+...+++..
T Consensus       118 ~~vLl~GppGtGKT~la~aia~~---~~~~~~~i~~  150 (357)
T 3d8b_A          118 KGILLFGPPGTGKTLIGKCIASQ---SGATFFSISA  150 (357)
T ss_dssp             SEEEEESSTTSSHHHHHHHHHHH---TTCEEEEEEG
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH---cCCeEEEEeh
Confidence            45679999999999988643322   2455555443

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}

Probab=89.40  E-value=0.72  Score=32.69  Aligned_cols=47  Identities=17%  Similarity=0.203  Sum_probs=38.2

Q ss_pred             CCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcCC-----------CCCCEEEecH
Q 042424           83 KQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTLS-----------PNASCLVMTT  130 (138)
Q Consensus        83 ~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~~-----------~~~~IiVtTp  130 (138)
                      +.++|+.++++.-++..++.|++ .+ .+..++|+....           ...+|+|+|.
T Consensus        34 ~~~~lVF~~~~~~~~~l~~~L~~-~~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~   92 (175)
T 2rb4_A           34 IGQAIIFCQTRRNAKWLTVEMIQ-DGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTN   92 (175)
T ss_dssp             CSEEEEECSCHHHHHHHHHHHHT-TTCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHH-cCCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEec
Confidence            67899999999999999999987 44 788898886432           2678999983

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=89.27  E-value=0.22  Score=35.68  Aligned_cols=18  Identities=11%  Similarity=-0.005  Sum_probs=14.5

Q ss_pred             ceEECcCCCchHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~a   75 (138)
                      .+|++|+|||||.++-..
T Consensus         8 i~i~GpsGsGKSTL~~~L   25 (180)
T 1kgd_A            8 LVLLGAHGVGRRHIKNTL   25 (180)
T ss_dssp             EEEECCTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            349999999999887543

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=89.23  E-value=0.27  Score=41.04  Aligned_cols=34  Identities=15%  Similarity=-0.030  Sum_probs=24.1

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      ..++++++|+|||..+.........+|.+++++.
T Consensus       101 vI~ivG~~GvGKTTla~~La~~l~~~G~kVllv~  134 (432)
T 2v3c_C          101 VILLVGIQGSGKTTTAAKLARYIQKRGLKPALIA  134 (432)
T ss_dssp             CEEEECCSSSSTTHHHHHHHHHHHHHHCCEEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            4559999999999988633333335578887764

>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=89.21  E-value=0.19  Score=40.84  Aligned_cols=15  Identities=27%  Similarity=0.403  Sum_probs=13.2

Q ss_pred             eEECcCCCchHHHHH
Q 042424           59 TLTNPVYNGKTAVAE   73 (138)
Q Consensus        59 ~l~aPTGsGKTlva~   73 (138)
                      +|++|||+|||.++.
T Consensus         7 ~i~GptgsGKt~la~   21 (322)
T 3exa_A            7 AIVGPTAVGKTKTSV   21 (322)
T ss_dssp             EEECCTTSCHHHHHH
T ss_pred             EEECCCcCCHHHHHH
Confidence            489999999998775

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=89.11  E-value=0.38  Score=36.45  Aligned_cols=33  Identities=21%  Similarity=0.123  Sum_probs=21.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      .+.++.+|+|+|||.++......   -+...+++..
T Consensus        52 ~~~ll~G~~GtGKT~la~~la~~---~~~~~~~v~~   84 (285)
T 3h4m_A           52 KGILLYGPPGTGKTLLAKAVATE---TNATFIRVVG   84 (285)
T ss_dssp             SEEEEESSSSSSHHHHHHHHHHH---TTCEEEEEEG
T ss_pred             CeEEEECCCCCcHHHHHHHHHHH---hCCCEEEEeh
Confidence            45679999999999887543322   2555555543

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=89.04  E-value=0.25  Score=40.09  Aligned_cols=15  Identities=47%  Similarity=0.536  Sum_probs=13.3

Q ss_pred             eEECcCCCchHHHHH
Q 042424           59 TLTNPVYNGKTAVAE   73 (138)
Q Consensus        59 ~l~aPTGsGKTlva~   73 (138)
                      +|++|||||||.++.
T Consensus        14 ~i~GptgsGKt~la~   28 (316)
T 3foz_A           14 FLMGPTASGKTALAI   28 (316)
T ss_dssp             EEECCTTSCHHHHHH
T ss_pred             EEECCCccCHHHHHH
Confidence            489999999998775

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=89.02  E-value=0.58  Score=34.26  Aligned_cols=32  Identities=28%  Similarity=0.217  Sum_probs=21.0

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      .++++.|||||.+....+...-.+|.++-++-
T Consensus         8 ~i~G~sGsGKTTl~~~L~~~l~~~g~~v~~ik   39 (169)
T 1xjc_A            8 QVVGYKHSGKTTLMEKWVAAAVREGWRVGTVK   39 (169)
T ss_dssp             EEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEECCCCCCHHHHHHHHHHhhHhcCCeeeEEE
Confidence            48999999999887644433223466655444

>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=88.95  E-value=0.24  Score=36.44  Aligned_cols=17  Identities=35%  Similarity=0.391  Sum_probs=14.1

Q ss_pred             eEECcCCCchHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~a   75 (138)
                      +|++|+|||||.++...
T Consensus        12 ~l~GpsGsGKsTl~~~L   28 (208)
T 3tau_A           12 VLSGPSGVGKGTVREAV   28 (208)
T ss_dssp             EEECCTTSCHHHHHHHH
T ss_pred             EEECcCCCCHHHHHHHH
Confidence            49999999999887543

>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=88.91  E-value=0.89  Score=37.97  Aligned_cols=47  Identities=17%  Similarity=0.132  Sum_probs=29.1

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEe--chHHHHHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS--SLKALSNQKYRELHK  105 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~--P~kaLv~Q~~~~l~~  105 (138)
                      .+++|+|+|||.++.........+|++++++.  +.++.+.++.+.+.+
T Consensus       102 ~i~G~~GsGKTT~~~~LA~~l~~~g~~Vllvd~D~~r~aa~~qL~~~~~  150 (425)
T 2ffh_A          102 FLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGE  150 (425)
T ss_dssp             EEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECCSSCHHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHcCCeEEEeeccccCchhHHHHHHhcc
Confidence            48899999999887633322224577777665  445555544444544

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=88.78  E-value=0.28  Score=34.72  Aligned_cols=18  Identities=28%  Similarity=0.176  Sum_probs=15.2

Q ss_pred             CceEECcCCCchHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~   74 (138)
                      ..++++|+|||||.++..
T Consensus         7 ~i~l~G~~GsGKst~a~~   24 (185)
T 3trf_A            7 NIYLIGLMGAGKTSVGSQ   24 (185)
T ss_dssp             EEEEECSTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            456999999999999864

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=88.76  E-value=0.21  Score=39.28  Aligned_cols=20  Identities=20%  Similarity=0.081  Sum_probs=16.3

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      .+.++.+|+|+|||.++...
T Consensus        26 ~~vLi~Ge~GtGKt~lAr~i   45 (304)
T 1ojl_A           26 ATVLIHGDSGTGKELVARAL   45 (304)
T ss_dssp             SCEEEESCTTSCHHHHHHHH
T ss_pred             CcEEEECCCCchHHHHHHHH
Confidence            46679999999999887543

>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=88.76  E-value=0.62  Score=33.73  Aligned_cols=16  Identities=25%  Similarity=0.121  Sum_probs=13.9

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      .|.+|.|||||.++..
T Consensus        29 ~l~G~sGsGKSTl~~~   44 (200)
T 3uie_A           29 WVTGLSGSGKSTLACA   44 (200)
T ss_dssp             EEECSTTSSHHHHHHH
T ss_pred             EEECCCCCCHHHHHHH
Confidence            4999999999998853

>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=88.64  E-value=0.29  Score=40.54  Aligned_cols=35  Identities=11%  Similarity=0.158  Sum_probs=23.9

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH------cCCcEEEEech
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR------DKQRVIYTSSL   92 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~------~~~rviyv~P~   92 (138)
                      ..|.+|.|+|||..+...+...+.      .+.+++|+.-.
T Consensus       181 ~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E  221 (400)
T 3lda_A          181 TELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTE  221 (400)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESS
T ss_pred             EEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCC
Confidence            349999999999998744333322      24678887644

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=88.62  E-value=0.26  Score=37.39  Aligned_cols=31  Identities=26%  Similarity=0.178  Sum_probs=21.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      .+.++++|+|+|||.++......   .+...+.+
T Consensus        65 ~~vLl~G~~GtGKT~la~~ia~~---~~~~~~~i   95 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTALAAKIAEE---SNFPFIKI   95 (272)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH---HTCSEEEE
T ss_pred             eEEEEECCCCCcHHHHHHHHHHH---hCCCEEEE
Confidence            45679999999999987643322   25555554

>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=88.55  E-value=0.33  Score=38.63  Aligned_cols=20  Identities=35%  Similarity=0.351  Sum_probs=16.6

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      .+.++.+|+|+|||.+|...
T Consensus        52 ~~vll~GppGtGKT~la~~i   71 (363)
T 3hws_A           52 SNILLIGPTGSGKTLLAETL   71 (363)
T ss_dssp             CCEEEECCTTSSHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHH
Confidence            56779999999999987543

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=88.52  E-value=0.54  Score=39.24  Aligned_cols=43  Identities=14%  Similarity=0.072  Sum_probs=27.3

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHc-CCcEEEEe--chHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRD-KQRVIYTS--SLKALSNQKY  100 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~-~~rviyv~--P~kaLv~Q~~  100 (138)
                      .++++++|+|||.++.........+ |++++++.  |.++.+.++.
T Consensus       103 I~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd~D~~r~~a~~ql  148 (433)
T 2xxa_A          103 VLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADVYRPAAIKQL  148 (433)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEECCCSSTTHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEecCCCCccHHHHH
Confidence            3488999999999987333333345 88887765  4444443333

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=88.49  E-value=0.34  Score=38.29  Aligned_cols=20  Identities=25%  Similarity=0.160  Sum_probs=16.2

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      +..++.+|+|+|||.++...
T Consensus        46 ~~iLL~GppGtGKT~la~al   65 (322)
T 1xwi_A           46 RGILLFGPPGTGKSYLAKAV   65 (322)
T ss_dssp             SEEEEESSSSSCHHHHHHHH
T ss_pred             ceEEEECCCCccHHHHHHHH
Confidence            45679999999999987633

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=88.49  E-value=0.58  Score=37.01  Aligned_cols=32  Identities=13%  Similarity=0.066  Sum_probs=20.6

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      .+.+|+|||||..........-.+++++.+..
T Consensus       104 ~lvG~nGsGKTTll~~Lag~l~~~~g~V~l~g  135 (302)
T 3b9q_A          104 MIVGVNGGGKTTSLGKLAHRLKNEGTKVLMAA  135 (302)
T ss_dssp             EEECCTTSCHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            49999999999877532222223466766653

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=88.40  E-value=0.6  Score=33.98  Aligned_cols=31  Identities=16%  Similarity=0.036  Sum_probs=19.9

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      .|++|.|||||.++.......-..+..++++
T Consensus        26 ~i~G~~GsGKstl~~~l~~~~~~~~~~v~~~   56 (201)
T 1rz3_A           26 GIDGLSRSGKTTLANQLSQTLREQGISVCVF   56 (201)
T ss_dssp             EEEECTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEECCCCCCHHHHHHHHHHHHhhcCCeEEEe
Confidence            3999999999998754332211235566554

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=88.37  E-value=0.41  Score=42.07  Aligned_cols=20  Identities=25%  Similarity=0.155  Sum_probs=16.3

Q ss_pred             CceEECcCCCchHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai   76 (138)
                      +.++.+|||+|||.+|....
T Consensus       523 ~~Ll~Gp~GtGKT~lA~ala  542 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELARALA  542 (758)
T ss_dssp             EEEEESCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            46799999999999986433

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=88.31  E-value=0.29  Score=36.83  Aligned_cols=21  Identities=29%  Similarity=0.230  Sum_probs=16.5

Q ss_pred             CCceEECcCCCchHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai   76 (138)
                      .+.++.+|+|+|||.++....
T Consensus        45 ~~vll~G~~GtGKT~la~~la   65 (268)
T 2r62_A           45 KGVLLVGPPGTGKTLLAKAVA   65 (268)
T ss_dssp             SCCCCBCSSCSSHHHHHHHHH
T ss_pred             ceEEEECCCCCcHHHHHHHHH
Confidence            345699999999999886433

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=88.30  E-value=0.35  Score=35.88  Aligned_cols=21  Identities=14%  Similarity=0.215  Sum_probs=15.9

Q ss_pred             CCceEECcCCCchHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai   76 (138)
                      +..+|+||.|+|||.+.-..+
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~   22 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLF   22 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHH
Confidence            345799999999998765433

>1byi_A Dethiobiotin synthase; biotin synthesis, cyclo-ligase, ligase; 0.97A {Escherichia coli} SCOP: c.37.1.10 PDB: 1bs1_A* 1a82_A 1dad_A* 1dae_A* 1daf_A* 1dag_A* 1dah_A* 1dai_A* 1dak_A* 1dam_A* 1dbs_A 1dts_A

Probab=88.26  E-value=0.7  Score=33.65  Aligned_cols=32  Identities=16%  Similarity=-0.044  Sum_probs=21.5

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      .+.-+|.|||.++........++|.|++++=|
T Consensus         7 ~s~kgGvGKTt~a~nLa~~la~~G~rVll~dp   38 (224)
T 1byi_A            7 TGTDTEVGKTVASCALLQAAKAAGYRTAGYKP   38 (224)
T ss_dssp             EESSTTSCHHHHHHHHHHHHHHTTCCEEEECS
T ss_pred             EECCCCCCHHHHHHHHHHHHHHCCCCEEEEcc
Confidence            44458999999997333322356889888644

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=88.24  E-value=0.18  Score=41.11  Aligned_cols=31  Identities=16%  Similarity=0.037  Sum_probs=22.9

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      .++.+|+|+|||..+...+..   .|.+++|+.-
T Consensus       126 iLI~GpPGsGKTtLAlqlA~~---~G~~VlyIs~  156 (331)
T 2vhj_A          126 VIVTGKGNSGKTPLVHALGEA---LGGKDKYATV  156 (331)
T ss_dssp             EEEECSCSSSHHHHHHHHHHH---HHTTSCCEEE
T ss_pred             EEEEcCCCCCHHHHHHHHHHh---CCCCEEEEEe
Confidence            369999999999998755443   4667666655

>3bs4_A Uncharacterized protein PH0321; structural genomics, unknown function, PSI-2, protein struct initiative; 1.60A {Pyrococcus horikoshii}

Probab=88.19  E-value=0.5  Score=37.01  Aligned_cols=35  Identities=9%  Similarity=-0.037  Sum_probs=27.6

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      .++++.+|+|||..++..+...+++|.+++|+.=.
T Consensus        24 ~li~g~p~~~~~~l~~qfl~~g~~~Ge~~~~~~~~   58 (260)
T 3bs4_A           24 LIHEEDASSRGKDILFYILSRKLKSDNLVGMFSIS   58 (260)
T ss_dssp             EEEECSGGGCHHHHHHHHHHHHHHTTCEEEEEECS
T ss_pred             EEEEeCCCccHHHHHHHHHHHHHHCCCcEEEEEEe
Confidence            34777888888877787777788889999998754

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=87.93  E-value=0.49  Score=37.69  Aligned_cols=19  Identities=32%  Similarity=0.354  Sum_probs=16.0

Q ss_pred             CCceEECcCCCchHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~   74 (138)
                      .+.++.+|+|+|||.++..
T Consensus        73 ~~ill~Gp~GtGKT~la~~   91 (376)
T 1um8_A           73 SNILLIGPTGSGKTLMAQT   91 (376)
T ss_dssp             CCEEEECCTTSSHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHH
Confidence            4567999999999998863

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=87.92  E-value=0.61  Score=35.79  Aligned_cols=20  Identities=35%  Similarity=0.282  Sum_probs=16.1

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      .+.++++|+|+|||.++...
T Consensus        39 ~~vll~G~~GtGKT~la~~i   58 (324)
T 1hqc_A           39 EHLLLFGPPGLGKTTLAHVI   58 (324)
T ss_dssp             CCCEEECCTTCCCHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHH
Confidence            45579999999999987543

>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=87.91  E-value=0.54  Score=37.11  Aligned_cols=46  Identities=17%  Similarity=0.135  Sum_probs=28.2

Q ss_pred             eEECcCCCchHHHHH-HHHHHHHHcCCcEEEEe--chHHHHHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTS--SLKALSNQKYRELHK  105 (138)
Q Consensus        59 ~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~--P~kaLv~Q~~~~l~~  105 (138)
                      ++++++|+|||..+. ++... ...|++++++.  +.++.+.++.+.+.+
T Consensus       102 ~i~G~~G~GKTT~~~~la~~~-~~~g~~v~l~~~D~~r~~a~~ql~~~~~  150 (297)
T 1j8m_F          102 MLVGVQGTGKTTTAGKLAYFY-KKKGFKVGLVGADVYRPAALEQLQQLGQ  150 (297)
T ss_dssp             EEECSSCSSTTHHHHHHHHHH-HHTTCCEEEEECCCSSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHH-HHCCCeEEEEecCCCCHHHHHHHHHHhc
Confidence            488999999998876 44333 34577776654  234444444444444

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=87.82  E-value=0.32  Score=34.87  Aligned_cols=16  Identities=25%  Similarity=0.401  Sum_probs=13.7

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      .|.||+|||||.++-.
T Consensus        11 ~l~Gp~GsGKSTl~~~   26 (205)
T 3tr0_A           11 IISAPSGAGKTSLVRA   26 (205)
T ss_dssp             EEECCTTSCHHHHHHH
T ss_pred             EEECcCCCCHHHHHHH
Confidence            4999999999988753

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=87.81  E-value=0.36  Score=36.22  Aligned_cols=19  Identities=26%  Similarity=0.246  Sum_probs=15.7

Q ss_pred             CCceEECcCCCchHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~   74 (138)
                      .+.++.+|+|+|||.++..
T Consensus        46 ~~vll~G~~GtGKT~la~~   64 (257)
T 1lv7_A           46 KGVLMVGPPGTGKTLLAKA   64 (257)
T ss_dssp             CEEEEECCTTSCHHHHHHH
T ss_pred             CeEEEECcCCCCHHHHHHH
Confidence            4567999999999988753

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=87.80  E-value=1.3  Score=31.08  Aligned_cols=49  Identities=10%  Similarity=0.114  Sum_probs=38.9

Q ss_pred             cCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCC-----------CCCCEEEecH
Q 042424           82 DKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLS-----------PNASCLVMTT  130 (138)
Q Consensus        82 ~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~-----------~~~~IiVtTp  130 (138)
                      .+.++|+.++++.-++..++.|++.--.+..++|+....           ...+|+|+|.
T Consensus        29 ~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~   88 (165)
T 1fuk_A           29 SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD   88 (165)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcC
Confidence            468899999999999999999988322788888886532           2678999984

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=87.79  E-value=0.56  Score=39.57  Aligned_cols=36  Identities=22%  Similarity=0.141  Sum_probs=26.2

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLK   93 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~k   93 (138)
                      .+|.+|+|+|||..+...+......|.+++|+++-.
T Consensus       284 ~~i~G~~GsGKSTLl~~l~g~~~~~G~~vi~~~~ee  319 (525)
T 1tf7_A          284 ILATGATGTGKTLLVSRFVENACANKERAILFAYEE  319 (525)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEESSS
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhCCCCEEEEEEeC
Confidence            349999999999988644433334577888988653

>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=87.64  E-value=0.64  Score=36.82  Aligned_cols=32  Identities=13%  Similarity=0.040  Sum_probs=20.2

Q ss_pred             ceEECcCCCchHHHHH-HHHHHHHHcCCcEEEEe
Q 042424           58 GTLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~   90 (138)
                      ..+.+|+|||||.... ++-+. -..++++++..
T Consensus       105 i~lvG~nGsGKTTll~~Lagll-~~~~g~V~l~g  137 (304)
T 1rj9_A          105 VLVVGVNGVGKTTTIAKLGRYY-QNLGKKVMFCA  137 (304)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH-HTTTCCEEEEC
T ss_pred             EEEECCCCCcHHHHHHHHHHHH-HhcCCEEEEEe
Confidence            3489999999998765 33322 12456665543

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=87.47  E-value=0.36  Score=39.07  Aligned_cols=17  Identities=35%  Similarity=0.280  Sum_probs=14.4

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .+|++|||||||.++..
T Consensus         8 i~i~GptGsGKTtla~~   24 (323)
T 3crm_A            8 IFLMGPTAAGKTDLAMA   24 (323)
T ss_dssp             EEEECCTTSCHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            45999999999988753

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=87.43  E-value=0.44  Score=33.56  Aligned_cols=16  Identities=13%  Similarity=0.250  Sum_probs=13.4

Q ss_pred             ceEECcCCCchHHHHH
Q 042424           58 GTLTNPVYNGKTAVAE   73 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~   73 (138)
                      .+|.+|+|||||.+..
T Consensus        26 ~~I~G~NGsGKStil~   41 (149)
T 1f2t_A           26 NLIIGQNGSGKSSLLD   41 (149)
T ss_dssp             EEEECCTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            3599999999998853

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=87.41  E-value=0.36  Score=39.36  Aligned_cols=17  Identities=24%  Similarity=0.292  Sum_probs=14.3

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .+|++|||||||.++..
T Consensus        10 I~I~GptgSGKTtla~~   26 (340)
T 3d3q_A           10 IVIVGPTASGKTELSIE   26 (340)
T ss_dssp             EEEECSTTSSHHHHHHH
T ss_pred             EEEECCCcCcHHHHHHH
Confidence            35999999999998853

>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=87.30  E-value=0.74  Score=36.93  Aligned_cols=47  Identities=15%  Similarity=0.039  Sum_probs=25.9

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEe-ch-HHHHHHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS-SL-KALSNQKYRELHK  105 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~-P~-kaLv~Q~~~~l~~  105 (138)
                      .+.+|+|+|||.............++++++.. ++ +.-+.++.+.+.+
T Consensus       133 ~lvG~nGaGKTTll~~Lag~l~~~~g~V~l~g~D~~r~~a~eql~~~~~  181 (328)
T 3e70_C          133 MFVGFNGSGKTTTIAKLANWLKNHGFSVVIAASDTFRAGAIEQLEEHAK  181 (328)
T ss_dssp             EEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEECCSSTTHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhcCCEEEEEeecccccchHHHHHHHHH
Confidence            49999999999876532222223466665542 32 2233344444444

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=87.27  E-value=0.26  Score=42.05  Aligned_cols=32  Identities=22%  Similarity=0.264  Sum_probs=19.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIY   88 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviy   88 (138)
                      .+.++++|||||||.... ++...+....+++.
T Consensus       261 ~~i~I~GptGSGKTTlL~-aL~~~i~~~~giit  292 (511)
T 2oap_1          261 FSAIVVGETASGKTTTLN-AIMMFIPPDAKVVS  292 (511)
T ss_dssp             CCEEEEESTTSSHHHHHH-HHGGGSCTTCCEEE
T ss_pred             CEEEEECCCCCCHHHHHH-HHHhhCCCCCCEEE
Confidence            356699999999997643 33333333444443

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=87.18  E-value=1.6  Score=31.73  Aligned_cols=48  Identities=17%  Similarity=0.028  Sum_probs=38.7

Q ss_pred             CCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCC-----------CCCCEEEecH
Q 042424           83 KQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLS-----------PNASCLVMTT  130 (138)
Q Consensus        83 ~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~-----------~~~~IiVtTp  130 (138)
                      +.++|++++++.-++..++.|++.--.+..++|+....           .+.+|+|+|.
T Consensus        54 ~~~~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~  112 (191)
T 2p6n_A           54 PPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATD  112 (191)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECH
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcC
Confidence            67899999999999999999987422788899986532           2678999994

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=87.08  E-value=0.42  Score=38.41  Aligned_cols=24  Identities=13%  Similarity=-0.074  Sum_probs=19.2

Q ss_pred             CCceEECcCCCchHHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMA   79 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~   79 (138)
                      .+..|+||+|+|||.++...+...
T Consensus        46 ~~lli~GpPGTGKT~~v~~v~~~L   69 (318)
T 3te6_A           46 KLFYITNADDSTKFQLVNDVMDEL   69 (318)
T ss_dssp             CEEEEECCCSHHHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHH
Confidence            455699999999999987766554

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=86.92  E-value=0.71  Score=38.79  Aligned_cols=33  Identities=24%  Similarity=0.221  Sum_probs=22.4

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      +..++.+|.|+|||++|.....+   -+...+++..
T Consensus       216 rGvLL~GPPGtGKTllAkAiA~e---~~~~~~~v~~  248 (437)
T 4b4t_L          216 KGVLLYGPPGTGKTLLAKAVAAT---IGANFIFSPA  248 (437)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHH---HTCEEEEEEG
T ss_pred             CeEEEECCCCCcHHHHHHHHHHH---hCCCEEEEeh
Confidence            45669999999999887643332   2566665554

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=86.90  E-value=0.82  Score=35.86  Aligned_cols=31  Identities=23%  Similarity=0.214  Sum_probs=21.8

Q ss_pred             eEECcCCCchHHHHH-HHHHHHHHcCCcEEEEe
Q 042424           59 TLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        59 ~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~   90 (138)
                      .+++++|+|||..+. ++...+ ..+++++++-
T Consensus       102 ~i~g~~G~GKTT~~~~la~~~~-~~~~~v~l~~  133 (295)
T 1ls1_A          102 FLVGLQGSGKTTTAAKLALYYK-GKGRRPLLVA  133 (295)
T ss_dssp             EEECCTTTTHHHHHHHHHHHHH-HTTCCEEEEE
T ss_pred             EEECCCCCCHHHHHHHHHHHHH-HcCCeEEEec
Confidence            388999999998875 444433 4577776654

>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=86.89  E-value=0.29  Score=34.33  Aligned_cols=17  Identities=18%  Similarity=0.196  Sum_probs=14.3

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .+++++.|||||.++-.
T Consensus         6 i~l~G~~GsGKST~a~~   22 (178)
T 1qhx_A            6 IILNGGSSAGKSGIVRC   22 (178)
T ss_dssp             EEEECCTTSSHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            35999999999998853

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=86.86  E-value=0.81  Score=38.19  Aligned_cols=34  Identities=24%  Similarity=0.147  Sum_probs=23.4

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      +..++.+|.|+|||++|.....+   -+...+.+...
T Consensus       183 rGvLL~GPPGTGKTllAkAiA~e---~~~~f~~v~~s  216 (405)
T 4b4t_J          183 KGVILYGPPGTGKTLLARAVAHH---TDCKFIRVSGA  216 (405)
T ss_dssp             CCEEEESCSSSSHHHHHHHHHHH---HTCEEEEEEGG
T ss_pred             CceEEeCCCCCCHHHHHHHHHHh---hCCCceEEEhH
Confidence            45669999999999887544332   25666666553

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=86.84  E-value=0.44  Score=37.04  Aligned_cols=20  Identities=30%  Similarity=0.356  Sum_probs=16.5

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      .+.++.+|+|+|||.++...
T Consensus        56 ~~vll~G~~GtGKT~la~~i   75 (338)
T 3pfi_A           56 DHILFSGPAGLGKTTLANII   75 (338)
T ss_dssp             CCEEEECSTTSSHHHHHHHH
T ss_pred             CeEEEECcCCCCHHHHHHHH
Confidence            45679999999999988644

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=86.83  E-value=0.72  Score=38.71  Aligned_cols=33  Identities=18%  Similarity=0.186  Sum_probs=22.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      +..++.||.|+|||++|.....+   -+...+.+..
T Consensus       216 rGvLLyGPPGTGKTllAkAiA~e---~~~~f~~v~~  248 (434)
T 4b4t_M          216 KGALMYGPPGTGKTLLARACAAQ---TNATFLKLAA  248 (434)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHH---HTCEEEEEEG
T ss_pred             CeeEEECcCCCCHHHHHHHHHHH---hCCCEEEEeh
Confidence            45669999999999887543332   2555555544

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=86.77  E-value=0.38  Score=37.74  Aligned_cols=21  Identities=24%  Similarity=0.088  Sum_probs=16.7

Q ss_pred             CCceEECcCCCchHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai   76 (138)
                      .+.+++||+|+|||.++....
T Consensus        71 ~~vLl~GppGtGKT~la~~la   91 (368)
T 3uk6_A           71 RAVLIAGQPGTGKTAIAMGMA   91 (368)
T ss_dssp             CEEEEEESTTSSHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHH
Confidence            356799999999999876443

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=86.72  E-value=0.41  Score=37.22  Aligned_cols=19  Identities=26%  Similarity=0.158  Sum_probs=15.6

Q ss_pred             CCceEECcCCCchHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~   74 (138)
                      ...++.+|+|+|||.++..
T Consensus        50 ~~vLL~Gp~GtGKT~la~a   68 (301)
T 3cf0_A           50 KGVLFYGPPGCGKTLLAKA   68 (301)
T ss_dssp             SEEEEECSSSSSHHHHHHH
T ss_pred             ceEEEECCCCcCHHHHHHH
Confidence            4466999999999998763

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19

Probab=86.70  E-value=1.9  Score=30.63  Aligned_cols=49  Identities=10%  Similarity=-0.076  Sum_probs=39.0

Q ss_pred             cCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcC-----------CCCCCEEEecH
Q 042424           82 DKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTL-----------SPNASCLVMTT  130 (138)
Q Consensus        82 ~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~-----------~~~~~IiVtTp  130 (138)
                      .+.++|+.++++.-++..++.|.+.--.+..++|+...           +...+|+|+|.
T Consensus        30 ~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~   89 (172)
T 1t5i_A           30 EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN   89 (172)
T ss_dssp             CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESS
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECC
Confidence            46799999999999999999998832278888888653           22678999984

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=86.64  E-value=0.42  Score=38.43  Aligned_cols=34  Identities=21%  Similarity=0.211  Sum_probs=23.3

Q ss_pred             eEECcCCCchHHHHHHHHHHHHH---c---CCcEEEEech
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFR---D---KQRVIYTSSL   92 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~---~---~~rviyv~P~   92 (138)
                      .|.+|.|||||..+...+.....   .   +.+++|+.-.
T Consensus       135 ~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e  174 (349)
T 1pzn_A          135 EVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTE  174 (349)
T ss_dssp             EEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESS
T ss_pred             EEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCC
Confidence            39999999999998754443311   2   3577887543

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=86.58  E-value=0.49  Score=32.66  Aligned_cols=17  Identities=29%  Similarity=0.108  Sum_probs=14.4

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .+|+||.|||||.++..
T Consensus         4 i~l~G~~GsGKsT~~~~   20 (173)
T 3kb2_A            4 IILEGPDCCFKSTVAAK   20 (173)
T ss_dssp             EEEECSSSSSHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            35999999999998864

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=86.54  E-value=0.81  Score=35.20  Aligned_cols=36  Identities=17%  Similarity=0.232  Sum_probs=27.8

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHH
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKA   94 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~ka   94 (138)
                      ++++|-|||||...+-.+.++...|.+++++-|.+.
T Consensus        32 vitG~M~sGKTT~Llr~~~r~~~~g~kvli~kp~~D   67 (219)
T 3e2i_A           32 CITGSMFSGKSEELIRRLRRGIYAKQKVVVFKPAID   67 (219)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEEC--
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHcCCceEEEEeccC
Confidence            389999999998776666666667899999988753

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A

Probab=86.51  E-value=1.6  Score=32.10  Aligned_cols=50  Identities=18%  Similarity=0.178  Sum_probs=39.8

Q ss_pred             HcCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCC-----------CCCCEEEecH
Q 042424           81 RDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLS-----------PNASCLVMTT  130 (138)
Q Consensus        81 ~~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~-----------~~~~IiVtTp  130 (138)
                      ..+.++|+.++++.-+++.++.|.+.--.+..++|+....           ...+|+|+|.
T Consensus        29 ~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~   89 (212)
T 3eaq_A           29 ASPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATD   89 (212)
T ss_dssp             HCCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECT
T ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecC
Confidence            3478999999999999999999987433788899986532           2678999994

>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=86.26  E-value=1.5  Score=37.56  Aligned_cols=53  Identities=11%  Similarity=0.069  Sum_probs=41.8

Q ss_pred             CCceEECcCCCchHHHHH-HHHHHHHHc-CCcEEEEechHHHHHHHHHHHHHhcC
Q 042424           56 THGTLTNPVYNGKTAVAE-YAIAMAFRD-KQRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~-~ai~~~l~~-~~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      +..++..|-++|||.+.. +++..++.. +.++++++|++..+.+.++.++..+.
T Consensus       179 r~~~i~~~Rq~GKS~~~a~~~l~~~~~~~~~~i~~va~t~~qA~~~~~~i~~~i~  233 (592)
T 3cpe_A          179 RMTVCNLSRQLGKTTVVAIFLAHFVCFNKDKAVGILAHKGSMSAEVLDRTKQAIE  233 (592)
T ss_dssp             SEEEEEECSSSCHHHHHHHHHHHHHHTSSSCEEEEEESSHHHHHHHHHHHHHHHT
T ss_pred             cEEEEEEcCccChHHHHHHHHHHHHHhCCCCeEEEEECCHHHHHHHHHHHHHHHH
Confidence            346699999999999875 555555554 56899999999999999988877554

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=86.22  E-value=0.9  Score=37.04  Aligned_cols=32  Identities=13%  Similarity=0.066  Sum_probs=20.6

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      .+.+|+|||||..........-.+++++++..
T Consensus       161 ~lvG~nGsGKTTll~~Lag~l~~~~G~V~l~g  192 (359)
T 2og2_A          161 MIVGVNGGGKTTSLGKLAHRLKNEGTKVLMAA  192 (359)
T ss_dssp             EEECCTTSCHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             EEEcCCCChHHHHHHHHHhhccccCCEEEEec
Confidence            49999999999877532222223466766654

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=86.21  E-value=0.43  Score=34.84  Aligned_cols=18  Identities=22%  Similarity=0.285  Sum_probs=14.7

Q ss_pred             ceEECcCCCchHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~a   75 (138)
                      .+|++|+|||||.+.-..
T Consensus         7 i~lvGpsGaGKSTLl~~L   24 (198)
T 1lvg_A            7 VVLSGPSGAGKSTLLKKL   24 (198)
T ss_dssp             EEEECCTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            459999999999887543

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=86.11  E-value=0.34  Score=33.75  Aligned_cols=17  Identities=18%  Similarity=-0.113  Sum_probs=14.3

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .++++|.|||||.++..
T Consensus         5 I~i~G~~GsGKST~a~~   21 (181)
T 1ly1_A            5 ILTIGCPGSGKSTWARE   21 (181)
T ss_dssp             EEEECCTTSSHHHHHHH
T ss_pred             EEEecCCCCCHHHHHHH
Confidence            35999999999998853

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=86.04  E-value=0.54  Score=34.04  Aligned_cols=19  Identities=26%  Similarity=0.123  Sum_probs=15.4

Q ss_pred             CceEECcCCCchHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~a   75 (138)
                      ..+|++|.|||||.++...
T Consensus        27 ~i~l~G~~GsGKsTl~~~L   45 (199)
T 3vaa_A           27 RIFLTGYMGAGKTTLGKAF   45 (199)
T ss_dssp             EEEEECCTTSCHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHH
Confidence            4559999999999988633

>1g3q_A MIND ATPase, cell division inhibitor; alpha-beta-alpha layered, protein-ADP complex, cell cycle, hydrolase; HET: ADP; 2.00A {Pyrococcus furiosus} SCOP: c.37.1.10 PDB: 1g3r_A* 1ion_A*

Probab=86.00  E-value=0.95  Score=33.12  Aligned_cols=30  Identities=20%  Similarity=0.336  Sum_probs=20.9

Q ss_pred             EECcCCCchHHHHH-HHHHHHHHcCCcEEEEe
Q 042424           60 LTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        60 l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~   90 (138)
                      .+.-.|.|||.++. +|..-+ ++|+|++++=
T Consensus         8 ~s~kgGvGKTt~a~~LA~~la-~~g~~VlliD   38 (237)
T 1g3q_A            8 VSGKGGTGKTTVTANLSVALG-DRGRKVLAVD   38 (237)
T ss_dssp             ECSSTTSSHHHHHHHHHHHHH-HTTCCEEEEE
T ss_pred             ecCCCCCCHHHHHHHHHHHHH-hcCCeEEEEe
Confidence            45668899999997 444332 4588888764

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=85.97  E-value=0.84  Score=38.19  Aligned_cols=34  Identities=21%  Similarity=0.126  Sum_probs=22.4

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      +..++.||.|+|||++|.....+   -+...+.+...
T Consensus       207 rGiLL~GPPGtGKT~lakAiA~~---~~~~~~~v~~~  240 (428)
T 4b4t_K          207 RGVLLYGPPGTGKTMLVKAVANS---TKAAFIRVNGS  240 (428)
T ss_dssp             CEEEEESCTTTTHHHHHHHHHHH---HTCEEEEEEGG
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH---hCCCeEEEecc
Confidence            44669999999999887643322   25555555543

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=85.88  E-value=0.47  Score=33.93  Aligned_cols=16  Identities=31%  Similarity=0.372  Sum_probs=13.9

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      +|+||.|||||.++..
T Consensus        10 ~l~G~~GsGKSTl~~~   25 (207)
T 2j41_A           10 VLSGPSGVGKGTVRKR   25 (207)
T ss_dssp             EEECSTTSCHHHHHHH
T ss_pred             EEECCCCCCHHHHHHH
Confidence            4999999999988754

>1ihu_A Arsenical pump-driving ATPase; aluminum fluoride, ADP, ARSA ATPase, ATP binding site, hydro; HET: ADP; 2.15A {Escherichia coli} SCOP: c.37.1.10 c.37.1.10 PDB: 1f48_A* 1ii0_A* 1ii9_A*

Probab=85.76  E-value=0.91  Score=38.64  Aligned_cols=30  Identities=30%  Similarity=0.323  Sum_probs=22.9

Q ss_pred             eEECcCCCchHHHHH-HHHHHHHHcCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv   89 (138)
                      ++++..|.|||.++. +|..-+ +.|+|+++|
T Consensus        12 ~~sgkGGvGKTT~a~~lA~~lA-~~G~rVLlv   42 (589)
T 1ihu_A           12 FFTGKGGVGKTSISCATAIRLA-EQGKRVLLV   42 (589)
T ss_dssp             EEECSTTSSHHHHHHHHHHHHH-HTTCCEEEE
T ss_pred             EEeCCCcCHHHHHHHHHHHHHH-HCCCcEEEE
Confidence            488999999999997 454433 568888884

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=85.71  E-value=0.9  Score=32.35  Aligned_cols=30  Identities=23%  Similarity=0.211  Sum_probs=20.5

Q ss_pred             EECcCCCchHHHHH-HHHHHHHHcCCcEEEEe
Q 042424           60 LTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        60 l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~   90 (138)
                      .+.-.|+|||.++. +|..-+ +.|.+++++=
T Consensus         7 ~s~kgG~GKTt~a~~la~~la-~~g~~vlliD   37 (206)
T 4dzz_A            7 LNPKGGSGKTTAVINIATALS-RSGYNIAVVD   37 (206)
T ss_dssp             CCSSTTSSHHHHHHHHHHHHH-HTTCCEEEEE
T ss_pred             EeCCCCccHHHHHHHHHHHHH-HCCCeEEEEE
Confidence            34567899999997 444333 4688887764

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=85.64  E-value=0.69  Score=38.26  Aligned_cols=19  Identities=26%  Similarity=0.167  Sum_probs=15.8

Q ss_pred             CCceEECcCCCchHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~   74 (138)
                      .+.+|.+|+|+|||.++..
T Consensus       168 ~~vLL~GppGtGKT~lA~a  186 (444)
T 2zan_A          168 RGILLFGPPGTGKSYLAKA  186 (444)
T ss_dssp             SEEEEECSTTSSHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            4567999999999988753

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=85.53  E-value=0.57  Score=34.03  Aligned_cols=19  Identities=16%  Similarity=0.177  Sum_probs=15.1

Q ss_pred             ceEECcCCCchHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai   76 (138)
                      .++++|.|||||.++....
T Consensus        15 i~l~G~sGsGKsTl~~~L~   33 (204)
T 2qor_A           15 LVVCGPSGVGKGTLIKKVL   33 (204)
T ss_dssp             EEEECCTTSCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            3499999999999876433

>3of5_A Dethiobiotin synthetase; structural genomics, center for structural genomics of infec diseases, csgid, ligase; 1.52A {Francisella tularensis subsp}

Probab=85.52  E-value=1.2  Score=33.60  Aligned_cols=31  Identities=13%  Similarity=0.115  Sum_probs=21.8

Q ss_pred             ECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           61 TNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        61 ~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      ..-||+|||.++...+....++|.++.|.=|
T Consensus        11 gt~t~vGKT~vt~~L~~~l~~~G~~V~~~KP   41 (228)
T 3of5_A           11 GTDTEVGKTYISTKLIEVCEHQNIKSLCLKP   41 (228)
T ss_dssp             ESSSSSCHHHHHHHHHHHHHHTTCCEEEECS
T ss_pred             eCCCCCCHHHHHHHHHHHHHHCCCeeEEecc
Confidence            3448999999987555444456888877644

>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=85.51  E-value=0.63  Score=33.09  Aligned_cols=19  Identities=21%  Similarity=0.139  Sum_probs=15.4

Q ss_pred             ceEECcCCCchHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai   76 (138)
                      .++.+|.|+|||.++....
T Consensus        48 ~ll~G~~G~GKT~l~~~~~   66 (250)
T 1njg_A           48 YLFSGTRGVGKTSIARLLA   66 (250)
T ss_dssp             EEEECSTTSCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            4699999999999876443

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=85.48  E-value=0.46  Score=39.81  Aligned_cols=16  Identities=13%  Similarity=0.154  Sum_probs=13.8

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      +|++|||+|||.++..
T Consensus         6 ~i~GptgsGKttla~~   21 (409)
T 3eph_A            6 VIAGTTGVGKSQLSIQ   21 (409)
T ss_dssp             EEEECSSSSHHHHHHH
T ss_pred             EEECcchhhHHHHHHH
Confidence            4999999999988753

>1hyq_A MIND, cell division inhibitor (MIND-1); MINC, FTSZ, bacterial cell division, cell cycle; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.10

Probab=85.48  E-value=1.2  Score=33.26  Aligned_cols=30  Identities=20%  Similarity=0.235  Sum_probs=21.6

Q ss_pred             EECcCCCchHHHHH-HHHHHHHHcCCcEEEEe
Q 042424           60 LTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        60 l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~   90 (138)
                      .++-.|.|||.++. +|..-+ +.|.+++++=
T Consensus         8 ~s~kgGvGKTt~a~~LA~~la-~~g~~VlliD   38 (263)
T 1hyq_A            8 ASGKGGTGKTTITANLGVALA-QLGHDVTIVD   38 (263)
T ss_dssp             EESSSCSCHHHHHHHHHHHHH-HTTCCEEEEE
T ss_pred             ECCCCCCCHHHHHHHHHHHHH-hCCCcEEEEE
Confidence            56778999999997 444333 4588888864

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=85.47  E-value=1.3  Score=31.09  Aligned_cols=30  Identities=17%  Similarity=-0.017  Sum_probs=19.3

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIY   88 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviy   88 (138)
                      .++|+.|||||.++.....+.-..|..++.
T Consensus         4 ~l~G~~GsGKsT~~~~L~~~l~~~g~~~i~   33 (195)
T 2pbr_A            4 AFEGIDGSGKTTQAKKLYEYLKQKGYFVSL   33 (195)
T ss_dssp             EEECSTTSCHHHHHHHHHHHHHHTTCCEEE
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCeEEE
Confidence            489999999999886443322123554444

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=85.24  E-value=1.3  Score=32.24  Aligned_cols=29  Identities=17%  Similarity=0.014  Sum_probs=18.6

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcE
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRV   86 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rv   86 (138)
                      ..+++|.|||||......+...-..+.++
T Consensus         9 i~i~G~sGsGKTTl~~~l~~~l~~~g~~v   37 (174)
T 1np6_A            9 LAFAAWSGTGKTTLLKKLIPALCARGIRP   37 (174)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHTTCCE
T ss_pred             EEEEeCCCCCHHHHHHHHHHhccccCCce
Confidence            34999999999987654443322345444

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=85.23  E-value=0.56  Score=41.92  Aligned_cols=33  Identities=24%  Similarity=0.228  Sum_probs=21.0

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      +.++.+|+|+|||.++..........+...+++
T Consensus       590 ~vLl~Gp~GtGKT~lA~~la~~~~~~~~~~i~i  622 (854)
T 1qvr_A          590 SFLFLGPTGVGKTELAKTLAATLFDTEEAMIRI  622 (854)
T ss_dssp             EEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcCCCCcEEEE
Confidence            457999999999998864333322234444444

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=85.05  E-value=1.2  Score=33.78  Aligned_cols=31  Identities=19%  Similarity=0.132  Sum_probs=20.1

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH-cCCcEEEE
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYT   89 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv   89 (138)
                      .+++|+.|||||.++...... +. .|..++++
T Consensus         7 Ivl~G~pGSGKSTla~~La~~-L~~~g~~~i~~   38 (260)
T 3a4m_A            7 IILTGLPGVGKSTFSKNLAKI-LSKNNIDVIVL   38 (260)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH-HHHTTCCEEEE
T ss_pred             EEEEcCCCCCHHHHHHHHHHH-HHhCCCEEEEE
Confidence            359999999999988643332 23 35555533

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=84.85  E-value=0.72  Score=32.08  Aligned_cols=17  Identities=24%  Similarity=0.387  Sum_probs=14.4

Q ss_pred             CceEECcCCCchHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAE   73 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~   73 (138)
                      ...|++|.|||||.++.
T Consensus         6 ~i~l~G~~GsGKSTl~~   22 (173)
T 1kag_A            6 NIFLVGPMGAGKSTIGR   22 (173)
T ss_dssp             CEEEECCTTSCHHHHHH
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            34599999999999875

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=84.78  E-value=0.43  Score=33.99  Aligned_cols=15  Identities=27%  Similarity=0.350  Sum_probs=13.4

Q ss_pred             eEECcCCCchHHHHH
Q 042424           59 TLTNPVYNGKTAVAE   73 (138)
Q Consensus        59 ~l~aPTGsGKTlva~   73 (138)
                      .+.+|.|||||..+.
T Consensus        13 ~l~G~nGsGKSTl~~   27 (171)
T 4gp7_A           13 VLIGSSGSGKSTFAK   27 (171)
T ss_dssp             EEECCTTSCHHHHHH
T ss_pred             EEECCCCCCHHHHHH
Confidence            499999999998876

>3fgn_A Dethiobiotin synthetase; biotin biosynthesis, BIOD, ATP-BIND ligase, magnesium, nucleotide-binding; 1.85A {Mycobacterium tuberculosis} PDB: 3fmf_A* 3fmi_A* 3fpa_A*

Probab=84.78  E-value=1.3  Score=34.29  Aligned_cols=32  Identities=19%  Similarity=0.017  Sum_probs=21.5

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      ....||+|||.++...+....++|.++.|+=|
T Consensus        32 tgt~t~vGKT~vt~gL~~~l~~~G~~V~~fKP   63 (251)
T 3fgn_A           32 TGTGTGVGKTVVCAALASAARQAGIDVAVCKP   63 (251)
T ss_dssp             EESSTTSCHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             EeCCCCCcHHHHHHHHHHHHHHCCCeEEEEee
Confidence            44458999999987544444456777777643

>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=84.75  E-value=0.76  Score=38.65  Aligned_cols=33  Identities=18%  Similarity=0.178  Sum_probs=22.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      ...+++||+|+|||.++...... +  +..++++-.
T Consensus        78 ~~lLL~GppGtGKTtla~~la~~-l--~~~~i~in~  110 (516)
T 1sxj_A           78 RAAMLYGPPGIGKTTAAHLVAQE-L--GYDILEQNA  110 (516)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHH-T--TCEEEEECT
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH-c--CCCEEEEeC
Confidence            45669999999999887644332 2  666666643

>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=84.72  E-value=0.51  Score=33.42  Aligned_cols=17  Identities=29%  Similarity=0.257  Sum_probs=14.0

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .+|.+|.|||||.++..
T Consensus        12 i~l~G~~GsGKSTl~~~   28 (191)
T 1zp6_A           12 LLLSGHPGSGKSTIAEA   28 (191)
T ss_dssp             EEEEECTTSCHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            34999999999988753

>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=84.65  E-value=0.73  Score=32.48  Aligned_cols=19  Identities=26%  Similarity=0.146  Sum_probs=15.6

Q ss_pred             CCceEECcCCCchHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~   74 (138)
                      ...+++++.|||||.++..
T Consensus        12 ~~i~i~G~~GsGKst~~~~   30 (180)
T 3iij_A           12 PNILLTGTPGVGKTTLGKE   30 (180)
T ss_dssp             CCEEEECSTTSSHHHHHHH
T ss_pred             CeEEEEeCCCCCHHHHHHH
Confidence            3456999999999998864

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=84.63  E-value=0.54  Score=35.89  Aligned_cols=17  Identities=24%  Similarity=0.030  Sum_probs=13.9

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .++++|||+|||..++.
T Consensus        37 ilI~GpsGsGKStLA~~   53 (205)
T 2qmh_A           37 VLITGDSGVGKSETALE   53 (205)
T ss_dssp             EEEECCCTTTTHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            45999999999977653

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=84.52  E-value=0.72  Score=33.55  Aligned_cols=16  Identities=25%  Similarity=0.341  Sum_probs=14.0

Q ss_pred             ceEECcCCCchHHHHH
Q 042424           58 GTLTNPVYNGKTAVAE   73 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~   73 (138)
                      ..|.+|.|||||.++-
T Consensus         8 i~i~G~~GsGKSTl~~   23 (227)
T 1cke_A            8 ITIDGPSGAGKGTLCK   23 (227)
T ss_dssp             EEEECCTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            4599999999999985

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=84.51  E-value=0.67  Score=34.74  Aligned_cols=19  Identities=11%  Similarity=0.099  Sum_probs=14.8

Q ss_pred             ceEECcCCCchHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai   76 (138)
                      .+|++|+|+|||.+....+
T Consensus        22 ivl~GPSGaGKsTL~~~L~   40 (197)
T 3ney_A           22 LVLIGASGVGRSHIKNALL   40 (197)
T ss_dssp             EEEECCTTSSHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHH
Confidence            3499999999998775433

>1w36_B RECB, exodeoxyribonuclease V beta chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 c.52.1.24 PDB: 3k70_B*

Probab=84.51  E-value=2.6  Score=39.16  Aligned_cols=53  Identities=8%  Similarity=0.040  Sum_probs=42.3

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc-C-----------CcEEEEechHHHHHHHHHHHHHhcC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD-K-----------QRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~-~-----------~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      ++.+|.|.-|||||.+-..-+++.+.. |           .+++.|.=|++=+.++.+++++.+.
T Consensus        17 g~~lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~~L~   81 (1180)
T 1w36_B           17 GERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNIH   81 (1180)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHHHHH
Confidence            455899999999998876656665542 2           4799999999999999999988654

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=84.50  E-value=0.41  Score=37.14  Aligned_cols=20  Identities=10%  Similarity=-0.067  Sum_probs=16.3

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      .+.++.||+|+|||.++...
T Consensus        46 ~~vLl~G~~GtGKT~la~~l   65 (350)
T 1g8p_A           46 GGVLVFGDRGTGKSTAVRAL   65 (350)
T ss_dssp             CCEEEECCGGGCTTHHHHHH
T ss_pred             ceEEEECCCCccHHHHHHHH
Confidence            45679999999999988643

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=84.41  E-value=0.74  Score=35.66  Aligned_cols=17  Identities=35%  Similarity=0.253  Sum_probs=14.4

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      ..|+|+.|||||.++..
T Consensus        78 I~I~G~~GSGKSTva~~   94 (281)
T 2f6r_A           78 LGLTGISGSGKSSVAQR   94 (281)
T ss_dssp             EEEEECTTSCHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            34999999999999853

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=84.28  E-value=0.68  Score=34.58  Aligned_cols=18  Identities=33%  Similarity=0.222  Sum_probs=14.8

Q ss_pred             CceEECcCCCchHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~   74 (138)
                      ..++.+|+|+|||..+..
T Consensus        51 g~ll~G~~G~GKTtl~~~   68 (254)
T 1ixz_A           51 GVLLVGPPGVGKTHLARA   68 (254)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            356999999999987753

>3zq6_A Putative arsenical pump-driving ATPase; tail-anchored, membrane protein; HET: ADP; 2.11A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=84.21  E-value=1.2  Score=35.16  Aligned_cols=30  Identities=27%  Similarity=0.303  Sum_probs=22.6

Q ss_pred             EECcCCCchHHHHH-HHHHHHHHcCCcEEEEe
Q 042424           60 LTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        60 l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~   90 (138)
                      .++..|.|||.++. +|..-+ +.|+|++++-
T Consensus        19 ~sgKGGvGKTTvA~~LA~~lA-~~G~rVLlvD   49 (324)
T 3zq6_A           19 IGGKGGVGKTTISAATALWMA-RSGKKTLVIS   49 (324)
T ss_dssp             EEESTTSSHHHHHHHHHHHHH-HTTCCEEEEE
T ss_pred             EeCCCCchHHHHHHHHHHHHH-HCCCcEEEEe
Confidence            78889999999996 455433 4588887764

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=84.18  E-value=1.6  Score=30.71  Aligned_cols=16  Identities=38%  Similarity=0.190  Sum_probs=13.8

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      .++++.|||||.++-.
T Consensus         9 ~l~G~~GsGKST~~~~   24 (179)
T 2pez_A            9 WLTGLSGAGKTTVSMA   24 (179)
T ss_dssp             EEECCTTSSHHHHHHH
T ss_pred             EEECCCCCCHHHHHHH
Confidence            4999999999998853

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=84.16  E-value=1.5  Score=31.93  Aligned_cols=15  Identities=20%  Similarity=0.392  Sum_probs=13.1

Q ss_pred             eEECcCCCchHHHHH
Q 042424           59 TLTNPVYNGKTAVAE   73 (138)
Q Consensus        59 ~l~aPTGsGKTlva~   73 (138)
                      .|.+|+|||||..+.
T Consensus        26 ~I~G~sGsGKSTl~~   40 (208)
T 3c8u_A           26 ALSGAPGSGKSTLSN   40 (208)
T ss_dssp             EEECCTTSCTHHHHH
T ss_pred             EEECCCCCCHHHHHH
Confidence            499999999998774

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=84.14  E-value=0.61  Score=32.91  Aligned_cols=16  Identities=13%  Similarity=0.314  Sum_probs=13.5

Q ss_pred             ceEECcCCCchHHHHH
Q 042424           58 GTLTNPVYNGKTAVAE   73 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~   73 (138)
                      .+|++|+|||||.+..
T Consensus        29 ~~i~G~NGsGKStll~   44 (182)
T 3kta_A           29 TAIVGANGSGKSNIGD   44 (182)
T ss_dssp             EEEEECTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            3599999999998764

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=84.06  E-value=2.7  Score=32.41  Aligned_cols=56  Identities=14%  Similarity=0.227  Sum_probs=43.2

Q ss_pred             cCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCc
Q 042424           63 PVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVT  118 (138)
Q Consensus        63 PTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~  118 (138)
                      ...+||.....-.+...+..+.++|+.+.++..++...+.|.+.++ .+..++|+..
T Consensus        92 ~~~s~K~~~L~~ll~~~~~~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~  148 (271)
T 1z5z_A           92 VRRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELS  148 (271)
T ss_dssp             STTCHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSC
T ss_pred             cccCHHHHHHHHHHHHHHhCCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCC
Confidence            3568897765545555455689999999999999999999987656 7778888765

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=83.96  E-value=0.72  Score=33.44  Aligned_cols=18  Identities=28%  Similarity=0.043  Sum_probs=14.9

Q ss_pred             ceEECcCCCchHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~a   75 (138)
                      .+|+||.|||||.++...
T Consensus         3 I~l~G~~GsGKsT~a~~L   20 (216)
T 3fb4_A            3 IVLMGLPGAGKGTQAEQI   20 (216)
T ss_dssp             EEEECSTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            358999999999988643

>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=83.88  E-value=0.83  Score=32.01  Aligned_cols=17  Identities=18%  Similarity=0.065  Sum_probs=14.5

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .++++|.|||||.++..
T Consensus         6 I~i~G~~GsGKsT~~~~   22 (192)
T 1kht_A            6 VVVTGVPGVGSTTSSQL   22 (192)
T ss_dssp             EEEECCTTSCHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            35999999999998864

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=83.80  E-value=0.67  Score=32.97  Aligned_cols=17  Identities=24%  Similarity=0.339  Sum_probs=14.2

Q ss_pred             eEECcCCCchHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~a   75 (138)
                      ++++|.|||||.++-..
T Consensus         6 ~l~G~~GaGKSTl~~~L   22 (189)
T 2bdt_A            6 IITGPAGVGKSTTCKRL   22 (189)
T ss_dssp             EEECSTTSSHHHHHHHH
T ss_pred             EEECCCCCcHHHHHHHH
Confidence            48999999999987543

>2ph1_A Nucleotide-binding protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; 2.70A {Archaeoglobus fulgidus dsm 4304} PDB: 3kb1_A*

Probab=83.76  E-value=1.3  Score=33.36  Aligned_cols=29  Identities=24%  Similarity=0.266  Sum_probs=19.9

Q ss_pred             EECcCCCchHHHHH-HHHHHHHHcCCcEEEE
Q 042424           60 LTNPVYNGKTAVAE-YAIAMAFRDKQRVIYT   89 (138)
Q Consensus        60 l~aPTGsGKTlva~-~ai~~~l~~~~rviyv   89 (138)
                      .+.-.|.|||.++. +|..-+ +.|.+++++
T Consensus        24 ~s~kGGvGKTT~a~nLA~~la-~~G~~Vlli   53 (262)
T 2ph1_A           24 MSGKGGVGKSTVTALLAVHYA-RQGKKVGIL   53 (262)
T ss_dssp             ECSSSCTTHHHHHHHHHHHHH-HTTCCEEEE
T ss_pred             EcCCCCCCHHHHHHHHHHHHH-HCCCeEEEE
Confidence            55678899999996 444333 457777764

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=83.76  E-value=1.3  Score=37.69  Aligned_cols=35  Identities=11%  Similarity=-0.052  Sum_probs=24.8

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      ..++++++|+|||..+..........|.+++++..
T Consensus       103 vI~ivG~~GvGKTTl~~kLA~~l~~~G~kVllVd~  137 (504)
T 2j37_W          103 VIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICA  137 (504)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEec
Confidence            34589999999999886433333345888877765

>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=83.73  E-value=4.6  Score=31.60  Aligned_cols=67  Identities=15%  Similarity=0.172  Sum_probs=46.2

Q ss_pred             CCCchHHHHHHHHHHHH--HcCCcEEEEechHHHHHHHHHHHHHhcCceEEEec--------CCcCC-----------CC
Q 042424           64 VYNGKTAVAEYAIAMAF--RDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTG--------DVTLS-----------PN  122 (138)
Q Consensus        64 TGsGKTlva~~ai~~~l--~~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tG--------d~~~~-----------~~  122 (138)
                      ..++|.....-.+...+  ..+.++|++++++.-++..++.|++.--.+..++|        +....           .+
T Consensus       340 ~~~~k~~~l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~  419 (494)
T 1wp9_A          340 LDHPKMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGE  419 (494)
T ss_dssp             CSCHHHHHHHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHHTS
T ss_pred             CCChHHHHHHHHHHHHhccCCCCeEEEEEccHHHHHHHHHHHHHcCCCcEEEeccccccccccCCHHHHHHHHHHHhcCC
Confidence            55667655444444444  34889999999999999999999884227888888        44332           15


Q ss_pred             CCEEEecH
Q 042424          123 ASCLVMTT  130 (138)
Q Consensus       123 ~~IiVtTp  130 (138)
                      .+|+|+|.
T Consensus       420 ~~vLv~T~  427 (494)
T 1wp9_A          420 FNVLVATS  427 (494)
T ss_dssp             CSEEEECG
T ss_pred             ceEEEECC
Confidence            78999984

>3q9l_A Septum site-determining protein MIND; ATPase, bacterial cell division inhibitor, MINC, MINE, cell hydrolase; HET: ATP; 2.34A {Escherichia coli} PDB: 3r9i_A* 3r9j_A*

Probab=83.71  E-value=1.4  Score=32.65  Aligned_cols=29  Identities=17%  Similarity=0.195  Sum_probs=20.5

Q ss_pred             EECcCCCchHHHHH-HHHHHHHHcCCcEEEE
Q 042424           60 LTNPVYNGKTAVAE-YAIAMAFRDKQRVIYT   89 (138)
Q Consensus        60 l~aPTGsGKTlva~-~ai~~~l~~~~rviyv   89 (138)
                      .+.-.|.|||.++. +|..-+ +.|++++++
T Consensus         8 ~s~kgGvGKTt~a~~LA~~la-~~g~~Vlli   37 (260)
T 3q9l_A            8 TSGKGGVGKTTSSAAIATGLA-QKGKKTVVI   37 (260)
T ss_dssp             ECSSTTSSHHHHHHHHHHHHH-HTTCCEEEE
T ss_pred             ECCCCCCcHHHHHHHHHHHHH-hCCCcEEEE
Confidence            45667899999997 444433 568888875

>2woo_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; 3.01A {Schizosaccharomyces pombe}

Probab=83.53  E-value=1.3  Score=35.10  Aligned_cols=30  Identities=23%  Similarity=0.218  Sum_probs=22.7

Q ss_pred             eEECcCCCchHHHHH-HHHHHHHHcCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv   89 (138)
                      +.++..|.|||.++. +|..-+ +.|+|++++
T Consensus        23 v~sgkGGvGKTTva~~LA~~lA-~~G~rVllv   53 (329)
T 2woo_A           23 FVGGKGGVGKTTTSCSLAIQMS-KVRSSVLLI   53 (329)
T ss_dssp             EEECSSSSSHHHHHHHHHHHHH-TSSSCEEEE
T ss_pred             EEeCCCCCcHHHHHHHHHHHHH-HCCCeEEEE
Confidence            378889999999986 555433 568888875

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=83.52  E-value=0.83  Score=35.89  Aligned_cols=15  Identities=20%  Similarity=0.270  Sum_probs=13.3

Q ss_pred             eEECcCCCchHHHHH
Q 042424           59 TLTNPVYNGKTAVAE   73 (138)
Q Consensus        59 ~l~aPTGsGKTlva~   73 (138)
                      .|++|+|||||.++.
T Consensus        35 ~I~G~sGsGKSTla~   49 (290)
T 1odf_A           35 FFSGPQGSGKSFTSI   49 (290)
T ss_dssp             EEECCTTSSHHHHHH
T ss_pred             EEECCCCCCHHHHHH
Confidence            399999999999885

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=83.46  E-value=0.72  Score=38.12  Aligned_cols=34  Identities=29%  Similarity=0.174  Sum_probs=21.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      .+.++.+|+|+|||.+|.. +...+..+...+.+.
T Consensus        64 ~~iLl~GppGtGKT~la~a-la~~l~~~~~~~~~~   97 (456)
T 2c9o_A           64 RAVLLAGPPGTGKTALALA-IAQELGSKVPFCPMV   97 (456)
T ss_dssp             CEEEEECCTTSSHHHHHHH-HHHHHCTTSCEEEEE
T ss_pred             CeEEEECCCcCCHHHHHHH-HHHHhCCCceEEEEe
Confidence            4567999999999998863 333333234444444

>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=83.45  E-value=2.4  Score=34.83  Aligned_cols=52  Identities=12%  Similarity=0.063  Sum_probs=39.6

Q ss_pred             CCceEECcCCCchHHHHH-HHHHHHHHc-CCcEEEEechHHHHHHHHHHHHHhc
Q 042424           56 THGTLTNPVYNGKTAVAE-YAIAMAFRD-KQRVIYTSSLKALSNQKYRELHKEF  107 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~-~ai~~~l~~-~~rviyv~P~kaLv~Q~~~~l~~~f  107 (138)
                      +..++..+-+.|||.++. .++..++.. +.++++++|++.-+.+.++.++..+
T Consensus       179 R~~vi~~sRq~GKT~l~a~~~l~~a~~~~g~~v~~vA~t~~qA~~vf~~i~~mi  232 (385)
T 2o0j_A          179 RMTVCNLSRQLGKTTVVAIFLAHFVCFNKDKAVGILAHKGSMSAEVLDRTKQAI  232 (385)
T ss_dssp             SEEEEEECSSSCHHHHHHHHHHHHHHSSSSCEEEEEESSHHHHHHHHHHHHHHH
T ss_pred             cEEEEEEcCcCChhHHHHHHHHHHHHhCCCCeEEEEeCCHHHHHHHHHHHHHHH
Confidence            335699999999999876 444444443 6789999999999988887776643

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=83.38  E-value=1.1  Score=38.02  Aligned_cols=33  Identities=21%  Similarity=0.080  Sum_probs=21.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      +..++.+|.|+|||++|.....+   -+...+.+..
T Consensus       244 rGILLyGPPGTGKTlLAkAiA~e---~~~~fi~vs~  276 (467)
T 4b4t_H          244 KGILLYGPPGTGKTLCARAVANR---TDATFIRVIG  276 (467)
T ss_dssp             SEEEECSCTTSSHHHHHHHHHHH---HTCEEEEEEG
T ss_pred             CceEeeCCCCCcHHHHHHHHHhc---cCCCeEEEEh
Confidence            45669999999999887543322   2555555544

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=83.33  E-value=0.62  Score=33.65  Aligned_cols=15  Identities=27%  Similarity=0.415  Sum_probs=13.3

Q ss_pred             eEECcCCCchHHHHH
Q 042424           59 TLTNPVYNGKTAVAE   73 (138)
Q Consensus        59 ~l~aPTGsGKTlva~   73 (138)
                      .|.+|+|||||.++-
T Consensus        10 ~i~G~~GsGKSTl~~   24 (211)
T 3asz_A           10 GIAGGTASGKTTLAQ   24 (211)
T ss_dssp             EEEESTTSSHHHHHH
T ss_pred             EEECCCCCCHHHHHH
Confidence            499999999998875

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=83.32  E-value=0.74  Score=33.46  Aligned_cols=18  Identities=22%  Similarity=0.008  Sum_probs=14.9

Q ss_pred             ceEECcCCCchHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~a   75 (138)
                      .+|++|.|||||.++...
T Consensus         3 I~l~G~~GsGKsT~a~~L   20 (216)
T 3dl0_A            3 LVLMGLPGAGKGTQGERI   20 (216)
T ss_dssp             EEEECSTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            358999999999988643

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=83.31  E-value=1.4  Score=37.84  Aligned_cols=31  Identities=13%  Similarity=0.005  Sum_probs=20.7

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      .|.+|+|||||.............++++++.
T Consensus       297 ~LVGpNGSGKTTLl~~LAgll~~~~G~V~l~  327 (503)
T 2yhs_A          297 LMVGVNGVGKTTTIGKLARQFEQQGKSVMLA  327 (503)
T ss_dssp             EEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEECCCcccHHHHHHHHHHHhhhcCCeEEEe
Confidence            3999999999987753222222346777775

>3qxc_A Dethiobiotin synthetase; DTBS, structural genomics, ATP BIND biology, protein structure initiative, midwest center for S genomics, MCSG; HET: ATP; 1.34A {Helicobacter pylori} PDB: 3mle_A* 3qxh_A* 3qxj_A* 3qxs_A* 3qxx_A* 3qy0_A* 2qmo_A

Probab=83.31  E-value=1.7  Score=33.39  Aligned_cols=32  Identities=16%  Similarity=0.071  Sum_probs=22.3

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      ...-||+|||.++...+....++|.++.|+=|
T Consensus        27 tgT~t~vGKT~vs~gL~~~L~~~G~~V~~fKP   58 (242)
T 3qxc_A           27 SATNTNAGKTTCARLLAQYCNACGVKTILLKP   58 (242)
T ss_dssp             EESSTTSSHHHHHHHHHHHHHHTTCCEEEECC
T ss_pred             EeCCCCCcHHHHHHHHHHHHHhCCCceEEEee
Confidence            34449999999987555444456888888754

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=83.31  E-value=0.62  Score=37.59  Aligned_cols=18  Identities=17%  Similarity=0.145  Sum_probs=14.5

Q ss_pred             CCceEECcCCCchHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAE   73 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~   73 (138)
                      ...+|++|||||||...-
T Consensus       176 ~~i~ivG~sGsGKSTll~  193 (361)
T 2gza_A          176 RVIVVAGETGSGKTTLMK  193 (361)
T ss_dssp             CCEEEEESSSSCHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            455699999999997654

>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=83.30  E-value=0.79  Score=32.76  Aligned_cols=18  Identities=33%  Similarity=0.311  Sum_probs=15.2

Q ss_pred             CceEECcCCCchHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~   74 (138)
                      +.+|+++.|||||.++..
T Consensus        12 ~I~l~G~~GsGKSTv~~~   29 (184)
T 1y63_A           12 NILITGTPGTGKTSMAEM   29 (184)
T ss_dssp             EEEEECSTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            456999999999999863

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=83.23  E-value=0.83  Score=32.88  Aligned_cols=17  Identities=24%  Similarity=0.176  Sum_probs=14.5

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .+|+|+.|||||.++..
T Consensus        21 I~l~G~~GsGKSTla~~   37 (202)
T 3t61_A           21 IVVMGVSGSGKSSVGEA   37 (202)
T ss_dssp             EEEECSTTSCHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            45999999999998853

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=83.17  E-value=1.2  Score=37.53  Aligned_cols=34  Identities=9%  Similarity=-0.007  Sum_probs=23.3

Q ss_pred             ceEECcCCCchHHHHHHH-HHHHHHcCCcEEEEec
Q 042424           58 GTLTNPVYNGKTAVAEYA-IAMAFRDKQRVIYTSS   91 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~a-i~~~l~~~~rviyv~P   91 (138)
                      .+|.+|+|||||..+... +.-.+..+...+|+.-
T Consensus        42 ~~l~G~nGsGKSTL~~~~ll~Gl~~~~~g~i~v~g   76 (525)
T 1tf7_A           42 TLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTF   76 (525)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEES
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEE
Confidence            349999999999988653 3333333666777754

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=83.07  E-value=2.1  Score=33.67  Aligned_cols=34  Identities=18%  Similarity=0.224  Sum_probs=22.5

Q ss_pred             CceE--ECcCCCchHHHHHHHHHHHHHc------CCcEEEEe
Q 042424           57 HGTL--TNPVYNGKTAVAEYAIAMAFRD------KQRVIYTS   90 (138)
Q Consensus        57 ~~~l--~aPTGsGKTlva~~ai~~~l~~------~~rviyv~   90 (138)
                      ..+|  ++|.|+|||.++.......-..      +..++|+.
T Consensus        52 ~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~   93 (412)
T 1w5s_A           52 NMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVN   93 (412)
T ss_dssp             EEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEE
T ss_pred             EEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEE
Confidence            3457  8999999999886554443221      44566665

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=82.88  E-value=1.3  Score=39.48  Aligned_cols=23  Identities=26%  Similarity=0.133  Sum_probs=17.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAM   78 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~   78 (138)
                      .+.+++||+|+|||.++......
T Consensus       192 ~~vlL~G~pG~GKT~la~~la~~  214 (854)
T 1qvr_A          192 NNPVLIGEPGVGKTAIVEGLAQR  214 (854)
T ss_dssp             CCCEEEECTTSCHHHHHHHHHHH
T ss_pred             CceEEEcCCCCCHHHHHHHHHHH
Confidence            46779999999999988644433

>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga maritima} PDB: 3qg5_A 3tho_A*

Probab=82.68  E-value=0.76  Score=37.12  Aligned_cols=16  Identities=25%  Similarity=0.368  Sum_probs=13.4

Q ss_pred             ceEECcCCCchHHHHH
Q 042424           58 GTLTNPVYNGKTAVAE   73 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~   73 (138)
                      .+|++|||||||.+..
T Consensus        26 ~~i~G~NGaGKTTll~   41 (365)
T 3qf7_A           26 TVVEGPNGAGKSSLFE   41 (365)
T ss_dssp             EEEECCTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            3499999999998764

>3ug7_A Arsenical pump-driving ATPase; tail-anchored, membrane protein, targeting factor, ATP-bindi TRC40, ARSA, nucleotide-binding; HET: ADP; 2.90A {Methanocaldococcus jannaschii} PDB: 3ug6_A*

Probab=82.65  E-value=1.6  Score=34.90  Aligned_cols=30  Identities=20%  Similarity=0.228  Sum_probs=22.7

Q ss_pred             EECcCCCchHHHHH-HHHHHHHHcCCcEEEEe
Q 042424           60 LTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        60 l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~   90 (138)
                      .++..|.|||.++. +|..-+ +.|+|++++-
T Consensus        31 ~sgKGGvGKTTvA~~LA~~lA-~~G~rVLlvD   61 (349)
T 3ug7_A           31 FGGKGGVGKTTMSAATGVYLA-EKGLKVVIVS   61 (349)
T ss_dssp             EECSSSTTHHHHHHHHHHHHH-HSSCCEEEEE
T ss_pred             EeCCCCccHHHHHHHHHHHHH-HCCCeEEEEe
Confidence            78889999999996 454433 4588887765

>3auy_A DNA double-strand break repair RAD50 ATPase; DNA repair, ABC transporter ATPase domain-like; HET: DNA ADP; 2.70A {Methanocaldococcus jannaschii} PDB: 3aux_A* 3av0_B*

Probab=82.61  E-value=0.52  Score=37.89  Aligned_cols=16  Identities=19%  Similarity=0.229  Sum_probs=13.6

Q ss_pred             ceEECcCCCchHHHHH
Q 042424           58 GTLTNPVYNGKTAVAE   73 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~   73 (138)
                      .+++||||+|||.+..
T Consensus        28 ~vi~G~NGaGKT~ile   43 (371)
T 3auy_A           28 VAIIGENGSGKSSIFE   43 (371)
T ss_dssp             EEEEECTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            3599999999998854

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=82.52  E-value=0.97  Score=35.64  Aligned_cols=19  Identities=37%  Similarity=0.387  Sum_probs=15.4

Q ss_pred             CCceEECcCCCchHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~   74 (138)
                      .+.++.+|+|+|||..+..
T Consensus        52 ~~~ll~Gp~G~GKTTLa~~   70 (334)
T 1in4_A           52 DHVLLAGPPGLGKTTLAHI   70 (334)
T ss_dssp             CCEEEESSTTSSHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHH
Confidence            3456999999999998753

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=82.39  E-value=0.88  Score=37.86  Aligned_cols=20  Identities=35%  Similarity=0.235  Sum_probs=16.7

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      .+.++.+|+|+|||.++...
T Consensus       202 ~~~LL~G~pG~GKT~la~~l  221 (468)
T 3pxg_A          202 NNPVLIGEPGVGKTAIAEGL  221 (468)
T ss_dssp             CEEEEESCTTTTTHHHHHHH
T ss_pred             CCeEEECCCCCCHHHHHHHH
Confidence            46779999999999988643

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=82.30  E-value=0.97  Score=31.68  Aligned_cols=17  Identities=12%  Similarity=-0.111  Sum_probs=14.3

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .+++++.|||||.++..
T Consensus         6 I~l~G~~GsGKsT~a~~   22 (196)
T 1tev_A            6 VFVLGGPGAGKGTQCAR   22 (196)
T ss_dssp             EEEECCTTSSHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            35999999999998853

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=82.25  E-value=1.4  Score=37.70  Aligned_cols=25  Identities=12%  Similarity=0.076  Sum_probs=19.2

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAF   80 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l   80 (138)
                      .+.+|.++||||||.+....+...+
T Consensus       168 pHlLIaG~TGSGKSt~L~~li~sLl  192 (512)
T 2ius_A          168 PHLLVAGTTGSGASVGVNAMILSML  192 (512)
T ss_dssp             CSEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHH
Confidence            6788999999999998765444433

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=82.23  E-value=1.6  Score=34.83  Aligned_cols=32  Identities=19%  Similarity=0.016  Sum_probs=21.1

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      .+++++.|+|||.++..........|.++.++
T Consensus        82 I~i~G~~G~GKSTl~~~L~~~l~~~g~kV~vi  113 (355)
T 3p32_A           82 VGITGVPGVGKSTAIEALGMHLIERGHRVAVL  113 (355)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhCCCceEEE
Confidence            45999999999998863333323446665544

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=82.18  E-value=1  Score=31.64  Aligned_cols=18  Identities=17%  Similarity=0.141  Sum_probs=15.0

Q ss_pred             CceEECcCCCchHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~   74 (138)
                      +.+|++|.|||||.++..
T Consensus         6 ~i~i~G~~GsGKsTla~~   23 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARA   23 (175)
T ss_dssp             CEEEECCTTSCHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHH
Confidence            356999999999998853

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=82.13  E-value=1.5  Score=32.60  Aligned_cols=31  Identities=19%  Similarity=0.178  Sum_probs=22.3

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      ++++..|+|||..+........ .|.+++++-
T Consensus        18 ~~~GkgGvGKTTl~~~La~~l~-~g~~v~vvd   48 (262)
T 1yrb_A           18 VFVGTAGSGKTTLTGEFGRYLE-DNYKVAYVN   48 (262)
T ss_dssp             EEECSTTSSHHHHHHHHHHHHT-TTSCEEEEE
T ss_pred             EEeCCCCCCHHHHHHHHHHHHH-CCCeEEEEe
Confidence            4899999999998863333323 677887765

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=82.08  E-value=0.82  Score=33.88  Aligned_cols=17  Identities=18%  Similarity=0.161  Sum_probs=14.0

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      ..|.+|+|||||...-.
T Consensus        26 ~~lvGpsGsGKSTLl~~   42 (218)
T 1z6g_A           26 LVICGPSGVGKGTLIKK   42 (218)
T ss_dssp             EEEECSTTSSHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            34999999999987753

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=82.05  E-value=0.51  Score=34.00  Aligned_cols=18  Identities=17%  Similarity=0.100  Sum_probs=14.8

Q ss_pred             eEECcCCCchHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai   76 (138)
                      ++.||.|||||..+....
T Consensus         4 ~i~G~~GsGKsTl~~~L~   21 (214)
T 1gtv_A            4 AIEGVDGAGKRTLVEKLS   21 (214)
T ss_dssp             EEEEEEEEEHHHHHHHHH
T ss_pred             EEEcCCCCCHHHHHHHHH
Confidence            489999999999886543

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=82.03  E-value=1.9  Score=31.31  Aligned_cols=31  Identities=16%  Similarity=0.013  Sum_probs=19.7

Q ss_pred             eEECcCCCchHHHHHHHHHHHH-HcCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAF-RDKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l-~~~~rviyv   89 (138)
                      +++++.|||||.++.......- ..|..++++
T Consensus        29 ~~~G~~GsGKsT~~~~l~~~l~~~~g~~~~~~   60 (211)
T 1m7g_A           29 WLTGLSASGKSTLAVELEHQLVRDRRVHAYRL   60 (211)
T ss_dssp             EEECSTTSSHHHHHHHHHHHHHHHHCCCEEEE
T ss_pred             EEECCCCCCHHHHHHHHHHHhccccCCcEEEE
Confidence            4999999999998864322211 235555555

>3kjh_A CO dehydrogenase/acetyl-COA synthase complex, accessory protein COOC; Zn-bound dimer, nickel binding protein, ATPase; 1.90A {Carboxydothermus hydrogenoformans} PDB: 3kjg_A* 3kje_A 3kji_A*

Probab=82.02  E-value=1  Score=32.84  Aligned_cols=30  Identities=27%  Similarity=0.237  Sum_probs=21.6

Q ss_pred             eEECcCCCchHHHHH-HHHHHHHHcCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv   89 (138)
                      ++++.-|.|||.++. +|..-+ +.|+|++++
T Consensus         4 ~vs~kGGvGKTt~a~~LA~~la-~~g~~Vlli   34 (254)
T 3kjh_A            4 AVAGKGGVGKTTVAAGLIKIMA-SDYDKIYAV   34 (254)
T ss_dssp             EEECSSSHHHHHHHHHHHHHHT-TTCSCEEEE
T ss_pred             EEecCCCCCHHHHHHHHHHHHH-HCCCeEEEE
Confidence            367888999999997 444322 458888776

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=81.99  E-value=1.8  Score=34.00  Aligned_cols=49  Identities=16%  Similarity=0.037  Sum_probs=39.6

Q ss_pred             cCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCC-----------CCCCEEEecH
Q 042424           82 DKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLS-----------PNASCLVMTT  130 (138)
Q Consensus        82 ~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~-----------~~~~IiVtTp  130 (138)
                      .+.++|++++++.-+++.++.|++.--.+..++|+....           .+.+|+|||.
T Consensus       275 ~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~  334 (417)
T 2i4i_A          275 KDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATA  334 (417)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECH
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECC
Confidence            468899999999999999999988323888899887532           2678999996

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=81.93  E-value=0.51  Score=34.93  Aligned_cols=16  Identities=44%  Similarity=0.515  Sum_probs=9.7

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      .|.+|+|||||.++..
T Consensus        31 ~l~Gp~GsGKSTl~~~   46 (231)
T 3lnc_A           31 VLSSPSGCGKTTVANK   46 (231)
T ss_dssp             EEECSCC----CHHHH
T ss_pred             EEECCCCCCHHHHHHH
Confidence            4999999999988753

>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=81.89  E-value=1.1  Score=41.61  Aligned_cols=57  Identities=18%  Similarity=0.097  Sum_probs=45.8

Q ss_pred             HHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCCcCC-----------CCCCEEEecH
Q 042424           74 YAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVTLS-----------PNASCLVMTT  130 (138)
Q Consensus        74 ~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~~~-----------~~~~IiVtTp  130 (138)
                      .++...+.+|.+++++++++.-+++.++.|++.+.  .+..++|+....           .+.+|+|||.
T Consensus       803 ~~il~~l~~g~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~  872 (1151)
T 2eyq_A          803 EAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT  872 (1151)
T ss_dssp             HHHHHHHTTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS
T ss_pred             HHHHHHHhcCCeEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECC
Confidence            45555566789999999999999999999999764  788899987532           2678999995

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=81.88  E-value=1  Score=31.45  Aligned_cols=17  Identities=35%  Similarity=0.216  Sum_probs=14.3

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      ..|++|.|||||.++..
T Consensus        11 i~l~G~~GsGKSTl~~~   27 (175)
T 1knq_A           11 YVLMGVSGSGKSAVASE   27 (175)
T ss_dssp             EEEECSTTSCHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHH
Confidence            34999999999998754

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=81.75  E-value=0.92  Score=32.13  Aligned_cols=18  Identities=17%  Similarity=-0.034  Sum_probs=14.7

Q ss_pred             ceEECcCCCchHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~a   75 (138)
                      .+++++.|||||.++...
T Consensus        15 I~l~G~~GsGKsT~a~~L   32 (199)
T 2bwj_A           15 IFIIGGPGSGKGTQCEKL   32 (199)
T ss_dssp             EEEEECTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            349999999999988543

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=81.69  E-value=1.1  Score=31.59  Aligned_cols=18  Identities=22%  Similarity=0.115  Sum_probs=14.8

Q ss_pred             ceEECcCCCchHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~a   75 (138)
                      .+++++.|||||.++...
T Consensus         7 I~l~G~~GsGKST~~~~L   24 (186)
T 3cm0_A            7 VIFLGPPGAGKGTQASRL   24 (186)
T ss_dssp             EEEECCTTSCHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            359999999999988643

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=81.67  E-value=0.94  Score=31.72  Aligned_cols=18  Identities=11%  Similarity=-0.090  Sum_probs=14.7

Q ss_pred             ceEECcCCCchHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~a   75 (138)
                      .+++++.|||||.++...
T Consensus         9 I~l~G~~GsGKsT~~~~L   26 (194)
T 1qf9_A            9 VFVLGGPGSGKGTQCANI   26 (194)
T ss_dssp             EEEEESTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            359999999999988643

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=81.55  E-value=1.7  Score=36.65  Aligned_cols=33  Identities=15%  Similarity=0.045  Sum_probs=22.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      +..++.+|.|+|||++|.....+   -+...+.+..
T Consensus       217 rGvLLyGPPGTGKTlLAkAiA~e---~~~~fi~v~~  249 (437)
T 4b4t_I          217 KGVILYGAPGTGKTLLAKAVANQ---TSATFLRIVG  249 (437)
T ss_dssp             SEEEEESSTTTTHHHHHHHHHHH---HTCEEEEEES
T ss_pred             CCCceECCCCchHHHHHHHHHHH---hCCCEEEEEH
Confidence            45669999999999877543332   2555555544

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=81.53  E-value=0.95  Score=35.25  Aligned_cols=18  Identities=22%  Similarity=0.067  Sum_probs=14.7

Q ss_pred             ceEECcCCCchHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~a   75 (138)
                      .+++||.|||||.++...
T Consensus        36 ivl~G~sGsGKSTla~~L   53 (287)
T 1gvn_B           36 FLLGGQPGSGKTSLRSAI   53 (287)
T ss_dssp             EEEECCTTSCTHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            359999999999887543

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=81.47  E-value=1.1  Score=37.91  Aligned_cols=20  Identities=30%  Similarity=0.207  Sum_probs=16.2

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      .+.+|.+|+|+|||+++...
T Consensus       239 ~~vLL~GppGtGKT~lArai  258 (489)
T 3hu3_A          239 RGILLYGPPGTGKTLIARAV  258 (489)
T ss_dssp             CEEEEECSTTSSHHHHHHHH
T ss_pred             CcEEEECcCCCCHHHHHHHH
Confidence            45679999999999987543

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=81.47  E-value=0.92  Score=32.80  Aligned_cols=17  Identities=24%  Similarity=0.143  Sum_probs=14.3

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .+|++|.|||||.++..
T Consensus        32 i~l~G~~GsGKSTl~~~   48 (200)
T 4eun_A           32 VVVMGVSGSGKTTIAHG   48 (200)
T ss_dssp             EEEECCTTSCHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            44999999999998753

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=81.45  E-value=1  Score=35.90  Aligned_cols=17  Identities=18%  Similarity=0.292  Sum_probs=14.0

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      ..|.+|+|||||.....
T Consensus       129 vaIvGpsGsGKSTLl~l  145 (305)
T 2v9p_A          129 LAFIGPPNTGKSMLCNS  145 (305)
T ss_dssp             EEEECSSSSSHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHH
Confidence            34999999999987653

>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=81.45  E-value=3.1  Score=34.15  Aligned_cols=50  Identities=16%  Similarity=0.090  Sum_probs=39.5

Q ss_pred             HcCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCC-------CCCCEEEecH
Q 042424           81 RDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLS-------PNASCLVMTT  130 (138)
Q Consensus        81 ~~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~-------~~~~IiVtTp  130 (138)
                      ..+.++++++|++.-+++.++.|++.--.+..++|+....       .+.+|+|||.
T Consensus       175 ~~~~~~lVF~~s~~~a~~l~~~L~~~~~~v~~lhg~~R~~~~~~F~~g~~~vLVaT~  231 (440)
T 1yks_A          175 ADKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYPTIKQKKPDFILATD  231 (440)
T ss_dssp             HCCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC--------CCCSEEEESS
T ss_pred             hcCCCEEEEeCCHHHHHHHHHHHHHcCCCEEEecchhHHHHHhhhcCCCceEEEECC
Confidence            3588999999999999999999988423888888854321       1678999995

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=81.25  E-value=1.1  Score=31.55  Aligned_cols=17  Identities=18%  Similarity=0.233  Sum_probs=14.6

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .+|+++.|||||.++..
T Consensus         5 I~l~G~~GsGKsT~a~~   21 (184)
T 2iyv_A            5 AVLVGLPGSGKSTIGRR   21 (184)
T ss_dssp             EEEECSTTSSHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            45999999999999853

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=81.21  E-value=0.99  Score=31.87  Aligned_cols=17  Identities=18%  Similarity=-0.021  Sum_probs=14.4

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .+++++.|||||.++..
T Consensus        12 I~l~G~~GsGKsT~~~~   28 (196)
T 2c95_A           12 IFVVGGPGSGKGTQCEK   28 (196)
T ss_dssp             EEEEECTTSSHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            45999999999998853

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=81.16  E-value=1  Score=34.21  Aligned_cols=17  Identities=35%  Similarity=0.278  Sum_probs=14.4

Q ss_pred             CceEECcCCCchHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAE   73 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~   73 (138)
                      ..+|.+|+|+|||.++.
T Consensus        75 gvll~Gp~GtGKTtl~~   91 (278)
T 1iy2_A           75 GVLLVGPPGVGKTHLAR   91 (278)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             eEEEECCCcChHHHHHH
Confidence            35699999999998775

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=81.00  E-value=1.2  Score=30.87  Aligned_cols=17  Identities=18%  Similarity=-0.019  Sum_probs=14.5

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .+++++.|||||.++..
T Consensus         5 I~l~G~~GsGKsT~a~~   21 (173)
T 1e6c_A            5 IFMVGARGCGMTTVGRE   21 (173)
T ss_dssp             EEEESCTTSSHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            45999999999998864

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=80.91  E-value=0.98  Score=32.89  Aligned_cols=15  Identities=33%  Similarity=0.532  Sum_probs=13.1

Q ss_pred             eEECcCCCchHHHHH
Q 042424           59 TLTNPVYNGKTAVAE   73 (138)
Q Consensus        59 ~l~aPTGsGKTlva~   73 (138)
                      .|.+|+|||||....
T Consensus        24 ~l~GpnGsGKSTLl~   38 (207)
T 1znw_A           24 VLSGPSAVGKSTVVR   38 (207)
T ss_dssp             EEECSTTSSHHHHHH
T ss_pred             EEECCCCCCHHHHHH
Confidence            499999999998774

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=80.79  E-value=1  Score=31.67  Aligned_cols=17  Identities=24%  Similarity=0.204  Sum_probs=14.3

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .+++++.|||||.++..
T Consensus         8 I~l~G~~GsGKST~~~~   24 (193)
T 2rhm_A            8 IIVTGHPATGKTTLSQA   24 (193)
T ss_dssp             EEEEESTTSSHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            35999999999998853

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=80.79  E-value=1.2  Score=34.33  Aligned_cols=37  Identities=19%  Similarity=0.158  Sum_probs=23.4

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHH---cCCcEEEEech
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFR---DKQRVIYTSSL   92 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~---~~~rviyv~P~   92 (138)
                      .+.++.||.|+|||.++.........   ....++.+.+.
T Consensus        59 ~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~   98 (353)
T 1sxj_D           59 PHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNAS   98 (353)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSS
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccc
Confidence            34679999999999988643332211   23556666543

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=80.68  E-value=0.78  Score=34.30  Aligned_cols=18  Identities=22%  Similarity=0.349  Sum_probs=14.6

Q ss_pred             CceEECcCCCchHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~   74 (138)
                      ..+|.+|.|||||..+-.
T Consensus        29 ~i~l~G~~GsGKSTl~k~   46 (246)
T 2bbw_A           29 RAVILGPPGSGKGTVCQR   46 (246)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            345999999999988753

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=80.59  E-value=0.95  Score=35.66  Aligned_cols=33  Identities=15%  Similarity=0.087  Sum_probs=20.3

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      .+|+++.|||||...-..+.  +..+.|+.++.|.
T Consensus         7 ~~i~G~~GaGKTTll~~l~~--~~~~~~~aVi~~d   39 (318)
T 1nij_A            7 TLLTGFLGAGKTTLLRHILN--EQHGYKIAVIENE   39 (318)
T ss_dssp             EEEEESSSSSCHHHHHHHHH--SCCCCCEEEECSS
T ss_pred             EEEEecCCCCHHHHHHHHHh--hcCCCcEEEEEec
Confidence            35999999999976533221  1235555555553

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=80.27  E-value=1.1  Score=32.32  Aligned_cols=16  Identities=38%  Similarity=0.490  Sum_probs=13.9

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      .|.+|.|||||.++..
T Consensus         6 ~l~G~~GsGKST~~~~   21 (206)
T 1jjv_A            6 GLTGGIGSGKTTIANL   21 (206)
T ss_dssp             EEECSTTSCHHHHHHH
T ss_pred             EEECCCCCCHHHHHHH
Confidence            4999999999998853

>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=80.22  E-value=8.5  Score=33.49  Aligned_cols=64  Identities=11%  Similarity=0.031  Sum_probs=44.7

Q ss_pred             CCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcC-----------CCCCCEEEec
Q 042424           65 YNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTL-----------SPNASCLVMT  129 (138)
Q Consensus        65 GsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~-----------~~~~~IiVtT  129 (138)
                      ..|+-...+-.+...+..+.++|++++++.-++..++.|.+ .+ .+..++|+...           +...+|+|+|
T Consensus       421 ~~~~~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~L~~~L~~-~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT  496 (664)
T 1c4o_A          421 TENQILDLMEGIRERAARGERTLVTVLTVRMAEELTSFLVE-HGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGI  496 (664)
T ss_dssp             STTHHHHHHHHHHHHHHTTCEEEEECSSHHHHHHHHHHHHH-TTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEES
T ss_pred             ccchHHHHHHHHHHHHhcCCEEEEEECCHHHHHHHHHHHHh-cCCCceeecCCCCHHHHHHHHHHhhcCCceEEEcc
Confidence            34544333333444445689999999999999999999988 44 77778887532           2256788887

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=80.10  E-value=1.1  Score=32.98  Aligned_cols=17  Identities=18%  Similarity=0.212  Sum_probs=14.4

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .+++||.|||||.++..
T Consensus        10 I~l~G~~GsGKsT~a~~   26 (227)
T 1zd8_A           10 AVIMGAPGSGKGTVSSR   26 (227)
T ss_dssp             EEEEECTTSSHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            45999999999998853

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=80.08  E-value=0.9  Score=35.30  Aligned_cols=19  Identities=21%  Similarity=-0.069  Sum_probs=16.1

Q ss_pred             CCceEECcCCCchHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~   74 (138)
                      .+.++.+|+|+|||.++..
T Consensus        47 ~~vll~G~pGtGKT~la~~   65 (331)
T 2r44_A           47 GHILLEGVPGLAKTLSVNT   65 (331)
T ss_dssp             CCEEEESCCCHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHH
Confidence            5677999999999988753

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=80.07  E-value=1.3  Score=33.55  Aligned_cols=21  Identities=33%  Similarity=0.257  Sum_probs=16.4

Q ss_pred             CceEECcCCCchHHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIA   77 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~   77 (138)
                      +.+++||.|+|||.++.....
T Consensus        40 ~~ll~G~~G~GKt~la~~l~~   60 (319)
T 2chq_A           40 HLLFSGPPGTGKTATAIALAR   60 (319)
T ss_dssp             CEEEESSSSSSHHHHHHHHHH
T ss_pred             eEEEECcCCcCHHHHHHHHHH
Confidence            356999999999998864443

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=80.01  E-value=2.1  Score=32.03  Aligned_cols=29  Identities=7%  Similarity=0.085  Sum_probs=20.9

Q ss_pred             EECcCCCchHHHHH-HHHHHHHHcCCcEEEE
Q 042424           60 LTNPVYNGKTAVAE-YAIAMAFRDKQRVIYT   89 (138)
Q Consensus        60 l~aPTGsGKTlva~-~ai~~~l~~~~rviyv   89 (138)
                      +++.-|.|||.++. +|..-+ +.|+|++++
T Consensus         6 vs~KGGvGKTT~a~nLA~~la-~~G~~Vlli   35 (269)
T 1cp2_A            6 IYGKGGIGKSTTTQNLTSGLH-AMGKTIMVV   35 (269)
T ss_dssp             EEECTTSSHHHHHHHHHHHHH-TTTCCEEEE
T ss_pred             EecCCCCcHHHHHHHHHHHHH-HCCCcEEEE
Confidence            56778999999986 444333 458888774

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=80.01  E-value=1.3  Score=30.83  Aligned_cols=20  Identities=25%  Similarity=0.243  Sum_probs=16.6

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      .+..|+++.|||||.++...
T Consensus         8 ~~i~l~G~~GsGKSTva~~L   27 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQEL   27 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHH
Confidence            56679999999999998643

---

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	138
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	2e-04

>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 = 37.6 bits (86), Expect = 2e-04
 Identities = 8/72 (11%), Positives = 18/72 (25%), Gaps = 1/72 (1%)

Query: 67  GKT-AVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASC 125
           GKT       +  A +   R +  +  + ++ +    L                +     
Sbjct: 21  GKTKRYLPAIVREAIKRGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIRAEHTGREIV 80

Query: 126 LVMTTEILRGML 137
            +M        L
Sbjct: 81  DLMCHATFTMRL 92

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	138
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.63
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.62
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.59
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.51
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.5
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.49
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.47
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.45
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.44
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.42
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.41
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.4
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.39
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.37
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.3
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.28
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.23
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.21
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.2
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.13
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	97.85
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	97.62
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.56
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	97.24
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	96.87
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.6
d1okkd2	207	GTPase domain of the signal recognition particle r	96.54
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.34
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	96.21
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	96.15
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.14
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	96.09
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.04
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.02
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	95.91
d2qy9a2	211	GTPase domain of the signal recognition particle r	95.84
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	95.81
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	95.59
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	95.55
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	95.39
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	95.2
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	95.12
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	94.8
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	94.77
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	94.47
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	94.47
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	94.41
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	94.32
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	94.3
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	94.23
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	94.1
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	93.88
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	93.73
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	93.65
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	93.56
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	93.55
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	93.43
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	93.43
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	93.37
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	93.22
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	93.08
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	93.04
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	92.92
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	92.86
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	92.86
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	92.67
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	92.55
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	92.49
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	92.4
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	92.26
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	92.22
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	92.13
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	92.08
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	91.95
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	91.85
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	91.79
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	91.69
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	91.39
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	91.23
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	91.05
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	90.91
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	90.77
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	90.72
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	90.52
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	90.48
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	90.31
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	89.98
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	89.77
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	89.69
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	89.67
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	89.63
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	89.57
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	89.41
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	89.32
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	89.17
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	88.76
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	88.74
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	88.56
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	88.55
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	88.52
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	88.41
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	88.24
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	88.24
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	87.92
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	87.87
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	87.84
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	87.71
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	87.66
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	87.47
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	87.4
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	87.28
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	87.24
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	87.12
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	86.7
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	86.62
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	86.61
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	86.5
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	86.43
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	86.16
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	86.1
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	85.95
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	85.88
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	85.66
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	85.6
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	85.05
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	85.03
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	84.98
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	84.95
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	84.84
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	84.8
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	84.05
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	83.48
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	82.9
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	82.78
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	82.37
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	82.25
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	81.74
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	81.45
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	81.44
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	81.42
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	81.22
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	81.16
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	81.0
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	80.98
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	80.83
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	80.42
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	80.4
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	80.2

>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=4.7e-16  Score=114.11  Aligned_cols=94  Identities=20%  Similarity=0.242  Sum_probs=73.1

Q ss_pred             cCCCCccCCC---CCCCceEECcCCCchHHHHHHHHHHHHH-cCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEec
Q 042424           44 VPSCYTLTTD---ETTHGTLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTG  115 (138)
Q Consensus        44 ~p~~y~~~~~---~~~~~~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tG  115 (138)
                      .|+.||....   ..+|.++++|||+|||+++.+++...+. .+++++|++|+++|++|.+++|++.|.    .+..+.+
T Consensus         9 ~pr~~Q~~~~~~~~~~n~lv~~pTGsGKT~i~~~~~~~~~~~~~~~il~i~P~~~L~~q~~~~~~~~~~~~~~~v~~~~~   88 (200)
T d1wp9a1           9 QPRIYQEVIYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTG   88 (200)
T ss_dssp             CCCHHHHHHHHHGGGSCEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEECS
T ss_pred             CCCHHHHHHHHHHhcCCeEEEeCCCCcHHHHHHHHHHHHHHhcCCcEEEEcCchHHHHHHHHHHHHhhcccccceeeeec
Confidence            4666662211   2368899999999999999877766665 478999999999999999999999875    5666666


Q ss_pred             CCcCCC------CCCEEEecHHHHHHhh
Q 042424          116 DVTLSP------NASCLVMTTEILRGML  137 (138)
Q Consensus       116 d~~~~~------~~~IiVtTpe~l~~lL  137 (138)
                      +...+.      +.+++++||+.+.+++
T Consensus        89 ~~~~~~~~~~~~~~~i~i~t~~~~~~~~  116 (200)
T d1wp9a1          89 EKSPEERSKAWARAKVIVATPQTIENDL  116 (200)
T ss_dssp             CSCHHHHHHHHHHCSEEEECHHHHHHHH
T ss_pred             ccchhHHHHhhhcccccccccchhHHHH
Confidence            544321      6789999999998765

>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=99.62  E-value=6.8e-16  Score=114.50  Aligned_cols=83  Identities=28%  Similarity=0.388  Sum_probs=72.0

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC---ceEEEecCCcCCC----CCCEEE
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK---DVGLMTGDVTLSP----NASCLV  127 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~---~v~~~tGd~~~~~----~~~IiV  127 (138)
                      .++.++++|||||||.++.+++.+.+.++.+++|++|+++|++|++++|++.+.   .++..+|+...+.    ..+|++
T Consensus        40 ~~~~il~apTGsGKT~~a~l~i~~~~~~~~~vl~l~P~~~L~~q~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~ii~  119 (202)
T d2p6ra3          40 GKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGEKYESFKKWEKIGLRIGISTGDYESRDEHLGDCDIIV  119 (202)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHHTTTTTTTCCEEEECSSCBCCSSCSTTCSEEE
T ss_pred             CCCEEEEcCCCCchhHHHHHHHHHHhhccCcceeecccHHHHHHHHHHHHHHhhccccceeeccCcccccccccccceee
Confidence            467889999999999999999998888899999999999999999999988555   6777888765443    688999


Q ss_pred             ecHHHHHHhh
Q 042424          128 MTTEILRGML  137 (138)
Q Consensus       128 tTpe~l~~lL  137 (138)
                      +||..+..++
T Consensus       120 ~~~~~~~~~~  129 (202)
T d2p6ra3         120 TTSEKADSLI  129 (202)
T ss_dssp             EEHHHHHHHH
T ss_pred             eccHHHHHHH
Confidence            9999998764

>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=99.59  E-value=1.4e-15  Score=115.25  Aligned_cols=82  Identities=18%  Similarity=0.124  Sum_probs=64.8

Q ss_pred             CCCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----c----eEEEecCCcC------
Q 042424           54 ETTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----D----VGLMTGDVTL------  119 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~----v~~~tGd~~~------  119 (138)
                      ..++.++++|||+|||+++++++.....+|++++|++|+++|++|++++|++.+.    .    ++...++...      
T Consensus        57 ~g~~~~i~apTGsGKT~~~~~~~~~~~~~~~rvliv~Pt~~La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  136 (237)
T d1gkub1          57 RKESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENF  136 (237)
T ss_dssp             TTCCEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHH
T ss_pred             CCCCEEEEecCCChHHHHHHHHHHHHHHhcCeEEEEeccHHHHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhh
Confidence            3468889999999999999888887777899999999999999999999998654    2    2333333321      


Q ss_pred             ---CCCCCEEEecHHHHHH
Q 042424          120 ---SPNASCLVMTTEILRG  135 (138)
Q Consensus       120 ---~~~~~IiVtTpe~l~~  135 (138)
                         ..+.+|+|+||+.+..
T Consensus       137 l~~~~~~~Ilv~Tp~~l~~  155 (237)
T d1gkub1         137 MQNLRNFKIVITTTQFLSK  155 (237)
T ss_dssp             HHSGGGCSEEEEEHHHHHH
T ss_pred             hccccccceeccChHHHHH
Confidence               1267899999998764

>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=99.51  E-value=3.6e-14  Score=107.74  Aligned_cols=83  Identities=14%  Similarity=0.055  Sum_probs=65.4

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcC--------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTL--------  119 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~--------  119 (138)
                      .++.++++|||||||+++++++.+.+..   +.++++++|+++|+.|.++.+.....    .+..+.|+...        
T Consensus        49 g~dvl~~a~TGsGKTlayllp~l~~i~~~~~~~~alil~Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (218)
T d2g9na1          49 GYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQ  128 (218)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHHTTTTCCEEEECC--CCCSTTTSSS
T ss_pred             CCCEEEEcccchhhhhhhhhhhhheecccccCccEEEEcccchhhhhHHHHHhhhccccceeEEeeecccchhHHHHHHh
Confidence            4678899999999999999999988753   67899999999999999999988544    34444332211        


Q ss_pred             CCCCCEEEecHHHHHHhh
Q 042424          120 SPNASCLVMTTEILRGML  137 (138)
Q Consensus       120 ~~~~~IiVtTpe~l~~lL  137 (138)
                      ...++|+|+||+++..++
T Consensus       129 ~~~~~IvV~TP~rl~~~l  146 (218)
T d2g9na1         129 MEAPHIIVGTPGRVFDML  146 (218)
T ss_dssp             SCCCSEEEECHHHHHHHH
T ss_pred             cCCCEEEEeCChhHHHHH
Confidence            126789999999998875

>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=99.50  E-value=2.4e-14  Score=107.41  Aligned_cols=82  Identities=17%  Similarity=0.130  Sum_probs=67.7

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCCC------CC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLSP------NA  123 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~~------~~  123 (138)
                      .+.++++|||+|||+++.+++.+....  +.++++++|+++|+.|.++.+.+.+.    .+..+.|+...+.      ++
T Consensus        43 ~d~iv~a~TGsGKT~~~~l~~~~~~~~~~~~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~~~  122 (208)
T d1hv8a1          43 YNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALKNA  122 (208)
T ss_dssp             SEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHHTC
T ss_pred             CCeeeechhcccccceeecccccccccccCcceEEEeeccccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhcCCC
Confidence            467789999999999999888776543  67899999999999999999988654    6777888764322      78


Q ss_pred             CEEEecHHHHHHhh
Q 042424          124 SCLVMTTEILRGML  137 (138)
Q Consensus       124 ~IiVtTpe~l~~lL  137 (138)
                      +|+|+||++|..++
T Consensus       123 ~IlV~TP~~l~~~l  136 (208)
T d1hv8a1         123 NIVVGTPGRILDHI  136 (208)
T ss_dssp             SEEEECHHHHHHHH
T ss_pred             CEEEEChHHHHHHH
Confidence            99999999998765

>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=99.49  E-value=3.5e-14  Score=106.70  Aligned_cols=83  Identities=18%  Similarity=0.124  Sum_probs=68.3

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCCcCC------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDVTLS------  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~~~~------  120 (138)
                      .++.++.+|||||||+++++++.+.+..   +.++++++|+++|+.|.++.++....     .+..+.|+...+      
T Consensus        38 g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l  117 (207)
T d1t6na_          38 GMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVL  117 (207)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHH
T ss_pred             CCCeEEEeccccccccccccceeeeecccCCCceEEEEeccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHH
Confidence            4678899999999999999999887654   46799999999999999999988443     456667766432      


Q ss_pred             --CCCCEEEecHHHHHHhh
Q 042424          121 --PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 --~~~~IiVtTpe~l~~lL  137 (138)
                        ..++|+|+||+++..++
T Consensus       118 ~~~~~~ilI~TP~rl~~~~  136 (207)
T d1t6na_         118 KKNCPHIVVGTPGRILALA  136 (207)
T ss_dssp             HHSCCSEEEECHHHHHHHH
T ss_pred             HhcCCCEEEeCcchhhhhc
Confidence              26899999999998875

>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=99.47  E-value=5.5e-14  Score=107.23  Aligned_cols=83  Identities=12%  Similarity=0.057  Sum_probs=68.5

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC-------
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS-------  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~-------  120 (138)
                      .++.++.+|||||||+++++++.+.+..   +-++++++|+++|+.|.++.+++...    .+..+.|+...+       
T Consensus        54 g~dvi~~a~TGSGKTlayllPil~~l~~~~~~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~  133 (222)
T d2j0sa1          54 GRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLD  133 (222)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHH
T ss_pred             CCCeEEEcCcchhhhhhhcccccccccccccCceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhc
Confidence            4778899999999999999999988753   56799999999999999999988432    566777766533       


Q ss_pred             CCCCEEEecHHHHHHhh
Q 042424          121 PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 ~~~~IiVtTpe~l~~lL  137 (138)
                      .+.+|+|+||.++.+++
T Consensus       134 ~~~~Ilv~TPgrl~~~~  150 (222)
T d2j0sa1         134 YGQHVVAGTPGRVFDMI  150 (222)
T ss_dssp             HCCSEEEECHHHHHHHH
T ss_pred             cCCeEEeCCCCcHHhcc
Confidence            27899999999998764

>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=99.45  E-value=4.5e-14  Score=108.45  Aligned_cols=83  Identities=12%  Similarity=-0.039  Sum_probs=59.3

Q ss_pred             CCCceEECcCCCchHHHHHHHHH-HHHHcCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCCCCCCEEEecHHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIA-MAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEIL  133 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~-~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~~~~~IiVtTpe~l  133 (138)
                      .++.++.+|||||||++++.++. .++.++.+++|++|+++|++|++++|++....+.....+.....+..|+++|++.|
T Consensus         9 ~~~~lv~~~TGsGKT~~~l~~~~~~~~~~~~~~lvi~Ptr~La~q~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~t~~~l   88 (305)
T d2bmfa2           9 KRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIRAEHTGREIVDLMCHATF   88 (305)
T ss_dssp             TCEEEECCCTTSSTTTTHHHHHHHHHHHHTCCEEEEESSHHHHHHHHHHTTTSCCBCCC--------CCCSEEEEEHHHH
T ss_pred             CCcEEEEECCCCCHHHHHHHHHHHHHHhcCCEEEEEccHHHHHHHHHHHHhcCCcceeeeEEeecccCccccccCCcHHH
Confidence            35677999999999988775554 44567999999999999999999998873333322223333445788999999988


Q ss_pred             HHhh
Q 042424          134 RGML  137 (138)
Q Consensus       134 ~~lL  137 (138)
                      ...+
T Consensus        89 ~~~~   92 (305)
T d2bmfa2          89 TMRL   92 (305)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7654

>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=99.44  E-value=2.2e-13  Score=104.44  Aligned_cols=83  Identities=17%  Similarity=0.053  Sum_probs=67.9

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc------------CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCc
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD------------KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVT  118 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~------------~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~  118 (138)
                      .++.++++|||+|||+++++++++.+..            +-++++++|+++|+.|.++.+.....    .+..+.|+..
T Consensus        58 g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~~~~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~  137 (238)
T d1wrba1          58 HRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGAD  137 (238)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSC
T ss_pred             CCCEEEECCCCCCcceeeHHHHHHHHHhcccccccccCCCCceEEEeccchhhhcchheeeeecccCCCcEEEEEeccch
Confidence            4688899999999999999999988632            35799999999999999999887433    5677777654


Q ss_pred             CC-------CCCCEEEecHHHHHHhh
Q 042424          119 LS-------PNASCLVMTTEILRGML  137 (138)
Q Consensus       119 ~~-------~~~~IiVtTpe~l~~lL  137 (138)
                      .+       ..++|+|+||++|..++
T Consensus       138 ~~~~~~~~~~~~~ivV~TP~~l~~~~  163 (238)
T d1wrba1         138 THSQIREVQMGCHLLVATPGRLVDFI  163 (238)
T ss_dssp             SHHHHHHHSSCCSEEEECHHHHHHHH
T ss_pred             hhHHHhhcccCCceeecCHHHHHhHH
Confidence            32       37899999999998865

>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=99.42  E-value=1.4e-13  Score=108.13  Aligned_cols=80  Identities=25%  Similarity=0.334  Sum_probs=70.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC-----------
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS-----------  120 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~-----------  120 (138)
                      -+++|+|.||||||.|++.++..++..|.++++++||..|+.|+++.|++.|.    .+.+++|.....           
T Consensus       105 m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~  184 (264)
T d1gm5a3         105 MNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRN  184 (264)
T ss_dssp             CCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHS
T ss_pred             ceeeeeccccccccHHHHHHHHHHHhcccceeEEeehHhhhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHC
Confidence            35689999999999999999999999999999999999999999999999995    688898876532           


Q ss_pred             CCCCEEEecHHHHHH
Q 042424          121 PNASCLVMTTEILRG  135 (138)
Q Consensus       121 ~~~~IiVtTpe~l~~  135 (138)
                      .+.+|||+|..-+..
T Consensus       185 g~~~iiIGThsl~~~  199 (264)
T d1gm5a3         185 GQIDVVIGTHALIQE  199 (264)
T ss_dssp             SCCCEEEECTTHHHH
T ss_pred             CCCCEEEeehHHhcC
Confidence            378999999876653

>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=99.41  E-value=2.5e-13  Score=104.96  Aligned_cols=78  Identities=21%  Similarity=0.256  Sum_probs=68.8

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC-----------C
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS-----------P  121 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~-----------~  121 (138)
                      +.+|+|.||||||.|++.++..++.+|+++++++|+.+|+.|++++|+++|.    +|.+++|.....           .
T Consensus        78 ~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g  157 (233)
T d2eyqa3          78 DRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEG  157 (233)
T ss_dssp             EEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTT
T ss_pred             CeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCC
Confidence            5679999999999999999999999999999999999999999999999876    688888876532           2


Q ss_pred             CCCEEEecHHHHH
Q 042424          122 NASCLVMTTEILR  134 (138)
Q Consensus       122 ~~~IiVtTpe~l~  134 (138)
                      +.+|||.|-..+.
T Consensus       158 ~~~iviGths~l~  170 (233)
T d2eyqa3         158 KIDILIGTHKLLQ  170 (233)
T ss_dssp             CCSEEEECTHHHH
T ss_pred             CCCEEEeehhhhc
Confidence            7899999987664

>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=99.40  E-value=4e-13  Score=100.69  Aligned_cols=84  Identities=12%  Similarity=0.040  Sum_probs=67.0

Q ss_pred             CCCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC-----ceEEEecCCcC------
Q 042424           54 ETTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK-----DVGLMTGDVTL------  119 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~-----~v~~~tGd~~~------  119 (138)
                      ..++.++++|||||||+++++++++.+..   +.++++++|+++|+.|.++.+.....     .+....|+...      
T Consensus        39 ~g~dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  118 (206)
T d1veca_          39 SGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMR  118 (206)
T ss_dssp             TTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHH
T ss_pred             cCCCEEeeccCccccccccccchhhcccccccCcceEEEeecchhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHH
Confidence            34678899999999999999999887643   56899999999999999999987543     34455555432      


Q ss_pred             -CCCCCEEEecHHHHHHhh
Q 042424          120 -SPNASCLVMTTEILRGML  137 (138)
Q Consensus       120 -~~~~~IiVtTpe~l~~lL  137 (138)
                       +...+|+|+||+++..++
T Consensus       119 l~~~~~ivv~TPgrl~~~~  137 (206)
T d1veca_         119 LDDTVHVVIATPGRILDLI  137 (206)
T ss_dssp             TTSCCSEEEECHHHHHHHH
T ss_pred             HHhccCeEEeCCccccccc
Confidence             347899999999998764

>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=99.39  E-value=7.7e-13  Score=91.90  Aligned_cols=77  Identities=17%  Similarity=0.079  Sum_probs=61.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcCCCCCCEEEecHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTLSPNASCLVMTTEILR  134 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~~~~~~IiVtTpe~l~  134 (138)
                      +..+|.+|||||||+++..++   +..|.+++|++|+++|++|.++++.+.+. ..+...++.......+++++|...+.
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~---~~~~~~vli~~P~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAY---AAQGYKVLVLNPSVAATLGFGAYMSKAHGVDPNIRTGVRTITTGSPITYSTYGKFL   85 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHH---HTTTCCEEEEESCHHHHHHHHHHHHHHHSCCCEEECSSCEECCCCSEEEEEHHHHH
T ss_pred             CEEEEEeCCCCCHHHHHHHHH---HHcCCcEEEEcChHHHHHHHHHHHHHHhhccccccccccccccccceEEEeeeeec
Confidence            356799999999998765443   35689999999999999999999999877 55666565555667789999988775


Q ss_pred             H
Q 042424          135 G  135 (138)
Q Consensus       135 ~  135 (138)
                      .
T Consensus        86 ~   86 (136)
T d1a1va1          86 A   86 (136)
T ss_dssp             H
T ss_pred             c
Confidence            4

>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=99.37  E-value=1.4e-12  Score=98.22  Aligned_cols=84  Identities=14%  Similarity=0.046  Sum_probs=64.4

Q ss_pred             CCCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcC------C
Q 042424           54 ETTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTL------S  120 (138)
Q Consensus        54 ~~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~------~  120 (138)
                      ..++.++++|||||||+++++++.+.+..   +-++++++|+++|+.|.+..+.....    .+....|+...      .
T Consensus        46 ~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (212)
T d1qdea_          46 EGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL  125 (212)
T ss_dssp             TTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------C
T ss_pred             cCCCEEeecccccchhhhhHhhhHhhhhccCCCcceEEEcccHHHhhhhhhhhcccccccccceeeEeeccchhHHHHHh
Confidence            34678899999999999999999888753   56899999999999999999977433    33333333222      1


Q ss_pred             CCCCEEEecHHHHHHhh
Q 042424          121 PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 ~~~~IiVtTpe~l~~lL  137 (138)
                      .+++|+|+||+++.+++
T Consensus       126 ~~~~IvI~TP~~l~~~~  142 (212)
T d1qdea_         126 RDAQIVVGTPGRVFDNI  142 (212)
T ss_dssp             TTCSEEEECHHHHHHHH
T ss_pred             cCCcEEEECCCcccccc
Confidence            27899999999998875

>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=99.30  E-value=4.1e-12  Score=99.59  Aligned_cols=81  Identities=12%  Similarity=0.144  Sum_probs=62.2

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc-CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcCC----CCCCEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD-KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTLS----PNASCL  126 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~-~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~~----~~~~Ii  126 (138)
                      ++.++.+|||+|||+++...+...+.. +.++|+++|+++|++|++++|.+.+.    .+..+.++...+    .+.+|+
T Consensus       129 ~~~il~~pTGsGKT~i~~~i~~~~~~~~~~k~Liivp~~~Lv~Q~~~~f~~~~~~~~~~~~~~~~g~~~~~~~~~~~~i~  208 (282)
T d1rifa_         129 RRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIGGGASKDDKYKNDAPVV  208 (282)
T ss_dssp             SEEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEECSTTCSSTTCCCTTCSEE
T ss_pred             CCceeEEEcccCccHHHHHHHHHhhhcccceEEEEEcCchhHHHHHHHHHHhhccccccceeecceecccccccccceEE
Confidence            667899999999999998777665554 67999999999999999999998543    344444333222    278899


Q ss_pred             EecHHHHHHh
Q 042424          127 VMTTEILRGM  136 (138)
Q Consensus       127 VtTpe~l~~l  136 (138)
                      |+|++.+..+
T Consensus       209 i~t~qs~~~~  218 (282)
T d1rifa_         209 VGTWQTVVKQ  218 (282)
T ss_dssp             EECHHHHTTS
T ss_pred             EEeeehhhhh
Confidence            9999987543

>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=99.28  E-value=2.6e-12  Score=94.71  Aligned_cols=78  Identities=14%  Similarity=0.067  Sum_probs=60.6

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcC-----------CCCC
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTL-----------SPNA  123 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~-----------~~~~  123 (138)
                      .+|.++++|||||||+++.+++.   ..+++++|++|+++|++|+.++|++.+.......+....           ....
T Consensus        40 g~~vlv~apTGsGKT~~~~~~~~---~~~~~~~~v~P~~~L~~q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  116 (206)
T d1oywa2          40 GRDCLVVMPTGGGKSLCYQIPAL---LLNGLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQI  116 (206)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHH---HSSSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCC
T ss_pred             CCCEEEEcCCCCCCcchhhhhhh---hccCceEEeccchhhhhhHHHHHHhhcccccccccccccccchhHHHHHhcCCc
Confidence            36888999999999999887764   568899999999999999999999865544433322211           1268


Q ss_pred             CEEEecHHHHHH
Q 042424          124 SCLVMTTEILRG  135 (138)
Q Consensus       124 ~IiVtTpe~l~~  135 (138)
                      +|+++||+.+..
T Consensus       117 ~i~~~t~~~~~~  128 (206)
T d1oywa2         117 RLLYIAPERLML  128 (206)
T ss_dssp             SEEEECHHHHTS
T ss_pred             eEEEEechhhhc
Confidence            899999998854

>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=99.23  E-value=7.2e-12  Score=85.11  Aligned_cols=81  Identities=14%  Similarity=-0.040  Sum_probs=59.3

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHH-HcCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCCCCCCEEEecHHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAF-RDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLSPNASCLVMTTEIL  133 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l-~~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~~~~~IiVtTpe~l  133 (138)
                      ..+.+|++|||||||+++..++.... ..+.++++++|+++|++|.++.+.....++....+......+..+.++|...+
T Consensus         7 ~~~~il~~~tGsGKT~~~~~~~~~~~~~~~~~vli~~p~~~l~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   86 (140)
T d1yksa1           7 GMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGLDVKFHTQAFSAHGSGREVIDAMCHATL   86 (140)
T ss_dssp             TCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHTTTSCEEEESSCCCCCCCSSCCEEEEEHHHH
T ss_pred             CCcEEEEcCCCCChhHHHHHHHHHHhhhcCceeeeeecchhHHHHHHHHhhhhhhhhcccccccccccccchhhhhHHHH
Confidence            46778999999999999876665544 56899999999999999999887552224443344444445677888887776


Q ss_pred             HH
Q 042424          134 RG  135 (138)
Q Consensus       134 ~~  135 (138)
                      ..
T Consensus        87 ~~   88 (140)
T d1yksa1          87 TY   88 (140)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>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=99.21  E-value=2.4e-11  Score=90.36  Aligned_cols=83  Identities=17%  Similarity=0.063  Sum_probs=68.4

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC----ceEEEecCCcC-------C
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK----DVGLMTGDVTL-------S  120 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~----~v~~~tGd~~~-------~  120 (138)
                      .++.++.+|||||||+++++++.+.+..   +.++++++|+..++.|....+.....    .+...+|+...       +
T Consensus        38 g~dvi~~a~tGsGKTlay~lp~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~  117 (206)
T d1s2ma1          38 GRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLN  117 (206)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTT
T ss_pred             CCCEEEecCCcchhhhhhccccccccccccccccceeeccchhhhhhhhhhhhhcccccCeeEEeecCccchhhHHHHhc
Confidence            4678899999999999999888877643   57899999999999999988887433    67777787643       3


Q ss_pred             CCCCEEEecHHHHHHhh
Q 042424          121 PNASCLVMTTEILRGML  137 (138)
Q Consensus       121 ~~~~IiVtTpe~l~~lL  137 (138)
                      ..++|+|+||+++..++
T Consensus       118 ~~~~Ili~TP~~l~~~l  134 (206)
T d1s2ma1         118 ETVHILVGTPGRVLDLA  134 (206)
T ss_dssp             SCCSEEEECHHHHHHHH
T ss_pred             ccceEEEECCccccccc
Confidence            47899999999998875

>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=99.20  E-value=3.2e-11  Score=89.76  Aligned_cols=76  Identities=24%  Similarity=0.117  Sum_probs=60.5

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcCCCCCCEEEecHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTLSPNASCLVMTTEILR  134 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~~~~~~IiVtTpe~l~  134 (138)
                      .+.++.+|||+|||++++.++.+   .+.++|+++|+++|++|+.++|.+... .++...|+..  ...+|+|+|.+.+.
T Consensus        86 ~~~ll~~~tG~GKT~~a~~~~~~---~~~~~Liv~p~~~L~~q~~~~~~~~~~~~~~~~~~~~~--~~~~i~i~t~~~~~  160 (206)
T d2fz4a1          86 KRGCIVLPTGSGKTHVAMAAINE---LSTPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIK--ELKPLTVSTYDSAY  160 (206)
T ss_dssp             SEEEEEESSSTTHHHHHHHHHHH---SCSCEEEEESSHHHHHHHHHHHGGGCGGGEEEESSSCB--CCCSEEEEEHHHHH
T ss_pred             CCcEEEeCCCCCceehHHhHHHH---hcCceeEEEcccchHHHHHHHHHhhcccchhhcccccc--cccccccceehhhh
Confidence            56789999999999988766543   378999999999999999999988333 5777777543  36789999999876


Q ss_pred             Hh
Q 042424          135 GM  136 (138)
Q Consensus       135 ~l  136 (138)
                      ..
T Consensus       161 ~~  162 (206)
T d2fz4a1         161 VN  162 (206)
T ss_dssp             HT
T ss_pred             hh
Confidence            53

>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=99.13  E-value=4.8e-11  Score=88.06  Aligned_cols=83  Identities=17%  Similarity=0.159  Sum_probs=63.9

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHc---CCcEEEEechHHHHHHHHHHHHHhcC--------ceEEEecCCc-----
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRD---KQRVIYTSSLKALSNQKYRELHKEFK--------DVGLMTGDVT-----  118 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~---~~rviyv~P~kaLv~Q~~~~l~~~f~--------~v~~~tGd~~-----  118 (138)
                      .++.++++|||||||+++++++.+.+..   +...++++|+..++.|.++.+.....        .+..+.|+..     
T Consensus        38 G~dvii~a~TGSGKTlayllp~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  117 (209)
T d1q0ua_          38 GESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKAL  117 (209)
T ss_dssp             TCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTT
T ss_pred             CCCeEeecccccccceeeeeeeccccccccccccccccccccchhHHHHHHHHhhhccccccccccccccccchhhHHHH
Confidence            4678899999999999999888887653   46789999999999999988876433        2333444332     


Q ss_pred             --CCCCCCEEEecHHHHHHhh
Q 042424          119 --LSPNASCLVMTTEILRGML  137 (138)
Q Consensus       119 --~~~~~~IiVtTpe~l~~lL  137 (138)
                        .+.+.+|+|+||+++..++
T Consensus       118 ~~~~~~~~Ilv~TP~~l~~~~  138 (209)
T d1q0ua_         118 EKLNVQPHIVIGTPGRINDFI  138 (209)
T ss_dssp             CCCSSCCSEEEECHHHHHHHH
T ss_pred             HHhccCceEEEecCchhhhhh
Confidence              2237899999999998865

>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=97.85  E-value=3.4e-05  Score=56.69  Aligned_cols=78  Identities=14%  Similarity=0.041  Sum_probs=55.4

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHc--CCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCCcC--CCCCCEEEecH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVTL--SPNASCLVMTT  130 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~~--~~~~~IiVtTp  130 (138)
                      ..+|+=+.|.|||+.++..+.+....  ..++++|+| .++..|..+++.+.+.  .+....+....  ..+.+|+|+|.
T Consensus        33 g~iLaDe~GlGKT~~~i~~~~~~~~~~~~~~~LIv~p-~~l~~~W~~e~~~~~~~~~~~~~~~~~~~~~~~~~~vvi~~~  111 (230)
T d1z63a1          33 GICLADDMGLGKTLQTIAVFSDAKKENELTPSLVICP-LSVLKNWEEELSKFAPHLRFAVFHEDRSKIKLEDYDIILTTY  111 (230)
T ss_dssp             CEEECCCTTSCHHHHHHHHHHHHHHTTCCSSEEEEEC-STTHHHHHHHHHHHCTTSCEEECSSSTTSCCGGGSSEEEEEH
T ss_pred             CEEEEeCCCCChHHHHHHhhhhhhhcccccccceecc-hhhhhHHHHHHHhhcccccceeeccccchhhccCcCEEEeeH
Confidence            45678899999999997666655554  368899998 6888999999988554  33333222211  12779999999


Q ss_pred             HHHHH
Q 042424          131 EILRG  135 (138)
Q Consensus       131 e~l~~  135 (138)
                      +.+..
T Consensus       112 ~~~~~  116 (230)
T d1z63a1         112 AVLLR  116 (230)
T ss_dssp             HHHTT
T ss_pred             HHHHh
Confidence            88753

>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=97.62  E-value=4.3e-05  Score=57.09  Aligned_cols=53  Identities=13%  Similarity=0.088  Sum_probs=43.3

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc----CCcEEEEechHHHHHHHHHHHHHhcC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD----KQRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~----~~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      ++.+|.||.|||||.+...-+.+.+.+    ..++++++++++++++....+.+.++
T Consensus        15 ~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~a~~~i~~~~~~~~~   71 (306)
T d1uaaa1          15 GPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLG   71 (306)
T ss_dssp             SEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHHHHHHHHHHHHHhcC
Confidence            456799999999999987766666654    25899999999999999888877553

>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=97.56  E-value=7.1e-05  Score=56.60  Aligned_cols=53  Identities=13%  Similarity=0.075  Sum_probs=44.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcC----CcEEEEechHHHHHHHHHHHHHhcC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDK----QRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~----~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      ++.+|.|+.|||||.+....+.+.+.++    .++++++++++.+++....+.+.+.
T Consensus        25 g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~aa~~~~~~~~~~~~   81 (318)
T d1pjra1          25 GPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLLG   81 (318)
T ss_dssp             SCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHHG
T ss_pred             CCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHHHHHHHHHHHHhhcc
Confidence            4567999999999999988887777653    5899999999999999999887543

>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=97.24  E-value=0.00055  Score=51.93  Aligned_cols=78  Identities=19%  Similarity=0.193  Sum_probs=53.9

Q ss_pred             CceEECcCCCchHHHHHHHHHHHHHcC-------CcEEEEechHHHHHHHHHHHHHhcC---ceEEEecCCc--------
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAMAFRDK-------QRVIYTSSLKALSNQKYRELHKEFK---DVGLMTGDVT--------  118 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~~l~~~-------~rviyv~P~kaLv~Q~~~~l~~~f~---~v~~~tGd~~--------  118 (138)
                      +.+|+=..|.|||+.++..+...+.++       .++|+|+|. +|+.|..++|.+.+.   .+..+.|...        
T Consensus        81 g~iLaDemGlGKT~qaia~l~~l~~~~~~~~~~~~~~LIV~P~-sl~~qW~~Ei~k~~~~~~~~v~~~~~~~~~~~~~~~  159 (298)
T d1z3ix2          81 GCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNEVGKWLGGRVQPVAIDGGSKDEIDSKLV  159 (298)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHHHHHHHGGGCCEEEECSSCHHHHHHHHH
T ss_pred             ceEEEeCCCCCHHHHHHHHHHHHHHhcccccCCCCcEEEEccc-hhhHHHHHHHHhhcCCceeEEEEeCchHHHHHHHHH
Confidence            456777889999997765555444432       468999997 589999999998665   3334444321        


Q ss_pred             -------CCCCCCEEEecHHHHHH
Q 042424          119 -------LSPNASCLVMTTEILRG  135 (138)
Q Consensus       119 -------~~~~~~IiVtTpe~l~~  135 (138)
                             .....+++|+|++.+..
T Consensus       160 ~~~~~~~~~~~~~v~i~sy~~~~~  183 (298)
T d1z3ix2         160 NFISQQGMRIPTPILIISYETFRL  183 (298)
T ss_dssp             HHHCCCSSCCSCCEEEEEHHHHHH
T ss_pred             HhhhccCccccceEEEEeeccccc
Confidence                   11256799999998764

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=96.60  E-value=0.0024  Score=46.92  Aligned_cols=49  Identities=18%  Similarity=0.196  Sum_probs=38.1

Q ss_pred             eEECcCCCchHHHHH-HHHHHHHHcCCcEEEEec--hHHHHHHHHHHHHHhcC
Q 042424           59 TLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTSS--LKALSNQKYRELHKEFK  108 (138)
Q Consensus        59 ~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~P--~kaLv~Q~~~~l~~~f~  108 (138)
                      ++++|||+|||.... +|. +...+|+++.++.-  +|+=+-++.+.+.+.++
T Consensus        14 ~lvGp~GvGKTTTiaKLA~-~~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~   65 (207)
T d1ls1a2          14 FLVGLQGSGKTTTAAKLAL-YYKGKGRRPLLVAADTQRPAAREQLRLLGEKVG   65 (207)
T ss_dssp             EEECCTTTTHHHHHHHHHH-HHHHTTCCEEEEECCSSCHHHHHHHHHHHHHHT
T ss_pred             EEECCCCCCHHHHHHHHHH-HHHHCCCcEEEEecccccchHHHHHHHHHHhcC
Confidence            379999999998886 544 34456788776664  68999999999998775

>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=96.54  E-value=0.0025  Score=46.93  Aligned_cols=49  Identities=14%  Similarity=0.167  Sum_probs=37.2

Q ss_pred             eEECcCCCchHHHHH-HHHHHHHHcCCcEEEEec--hHHHHHHHHHHHHHhcC
Q 042424           59 TLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTSS--LKALSNQKYRELHKEFK  108 (138)
Q Consensus        59 ~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~P--~kaLv~Q~~~~l~~~f~  108 (138)
                      ++++|||+|||.... +| .+..++|+++.++.-  +|+=+-++.+.|.+.++
T Consensus        10 ~lvGptGvGKTTTiaKLA-~~~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~   61 (207)
T d1okkd2          10 LVVGVNGVGKTTTIAKLG-RYYQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLS   61 (207)
T ss_dssp             EEECSTTSSHHHHHHHHH-HHHHTTTCCEEEECCCCSSTTHHHHHHHHHHHHT
T ss_pred             EEECCCCCCHHHHHHHHH-HHHHHCCCcEEEEEeccccccchhhHhhcccccC
Confidence            489999999999987 54 344456777765543  58888899999988775

>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=96.34  E-value=0.0018  Score=46.64  Aligned_cols=35  Identities=23%  Similarity=0.133  Sum_probs=30.2

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      .+|.+|+|+|||.++...+.++++.+.+++|+.-.
T Consensus        29 ~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is~e   63 (242)
T d1tf7a2          29 ILATGATGTGKTLLVSRFVENACANKERAILFAYE   63 (242)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEESS
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHhccccceeecc
Confidence            44999999999999998888888889999998743

>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=96.21  E-value=0.0017  Score=48.32  Aligned_cols=59  Identities=17%  Similarity=0.081  Sum_probs=50.1

Q ss_pred             HHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC--ceEEEecCCcCC-----------CCCCEEEecHH
Q 042424           73 EYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK--DVGLMTGDVTLS-----------PNASCLVMTTE  131 (138)
Q Consensus        73 ~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~--~v~~~tGd~~~~-----------~~~~IiVtTpe  131 (138)
                      .-+|...+.+|.++.||+|...-+++.++.+++.|.  +|++++|..+.+           .+.+|+|||+.
T Consensus        21 ~~~I~~El~rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Ttv   92 (211)
T d2eyqa5          21 REAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTI   92 (211)
T ss_dssp             HHHHHHHHTTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESST
T ss_pred             HHHHHHHHHcCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehh
Confidence            346777788899999999999999999999999887  899999987542           27899999974

>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=96.15  E-value=0.0032  Score=42.32  Aligned_cols=31  Identities=29%  Similarity=0.184  Sum_probs=22.3

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRV   86 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rv   86 (138)
                      ++.+|++|.|+|||..+...+.....++.++
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l~~~~~~v   32 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVLKSSGVPV   32 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHHHTTCCC
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHCCCEE
Confidence            4567999999999998775555544455443

>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=96.14  E-value=0.0054  Score=49.42  Aligned_cols=50  Identities=30%  Similarity=0.337  Sum_probs=40.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      ++..|.+-||||||++..-.+.   +.++.+|+|+|...+|.|.+++|+..++
T Consensus        32 ~~q~l~GltGS~ka~~iA~l~~---~~~rp~LVVt~n~~~A~qL~~dL~~~l~   81 (413)
T d1t5la1          32 KHQTLLGATGTGKTFTISNVIA---QVNKPTLVIAHNKTLAGQLYSELKEFFP   81 (413)
T ss_dssp             SEEEEEECTTSCHHHHHHHHHH---HHTCCEEEECSSHHHHHHHHHHHHHHCT
T ss_pred             CcEEEeCCCCcHHHHHHHHHHH---HhCCCEEEEeCCHHHHHHHHHHHHHHcC
Confidence            4456999999999976543332   2378899999999999999999999776

>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=96.09  E-value=0.008  Score=46.15  Aligned_cols=77  Identities=18%  Similarity=0.135  Sum_probs=55.4

Q ss_pred             CCceEECcCCCchHHHHHH-HHHHHHHcCCcEEEEechHHHHHHHHHHHHHhc---C-ceEEEecCCcCCC-----CCCE
Q 042424           56 THGTLTNPVYNGKTAVAEY-AIAMAFRDKQRVIYTSSLKALSNQKYRELHKEF---K-DVGLMTGDVTLSP-----NASC  125 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~-ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f---~-~v~~~tGd~~~~~-----~~~I  125 (138)
                      ...+....||-|||+++.+ +.+.+| .|+.+-+|...-=|+..=++.+...|   + +|+....+.....     .++|
T Consensus        94 ~G~iaem~TGEGKTL~a~l~a~l~al-~g~~vhvvTvNdyLA~RDae~m~~iy~~lGlsvg~~~~~~~~~~r~~~Y~~di  172 (273)
T d1tf5a3          94 DGNIAEMKTGEGKTLTSTLPVYLNAL-TGKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAYAADI  172 (273)
T ss_dssp             TTSEEECCTTSCHHHHHHHHHHHHHT-TSSCEEEEESSHHHHHHHHHHHHHHHHHTTCCEEECCTTSCHHHHHHHHHSSE
T ss_pred             hhhheeecCCCcchhHHHHHHHHHHh-cCCCceEEecCccccchhhhHHhHHHHHcCCCccccccccCHHHHHHHhhCCc
Confidence            4567889999999999965 454444 47777666666678887777666654   4 7887766554332     7899


Q ss_pred             EEecHHHH
Q 042424          126 LVMTTEIL  133 (138)
Q Consensus       126 iVtTpe~l  133 (138)
                      +-+|...|
T Consensus       173 ~Ygt~~e~  180 (273)
T d1tf5a3         173 TYSTNNEL  180 (273)
T ss_dssp             EEEEHHHH
T ss_pred             eecchhhh
Confidence            99998765

>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=96.04  E-value=0.0063  Score=44.79  Aligned_cols=48  Identities=15%  Similarity=0.149  Sum_probs=32.2

Q ss_pred             EECcCCCchHHHHH-HHHHHHHHcCCcEEEEec--hHHHHHHHHHHHHHhcC
Q 042424           60 LTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTSS--LKALSNQKYRELHKEFK  108 (138)
Q Consensus        60 l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~P--~kaLv~Q~~~~l~~~f~  108 (138)
                      +++|||+|||.... +| .+...+|+++.++.-  +|+=+-++.+.|.+.++
T Consensus        17 lvGptGvGKTTTiAKLA-~~~~~~g~kV~lit~Dt~R~ga~eQL~~~a~~l~   67 (211)
T d1j8yf2          17 LVGVQGTGKATTAGKLA-YFYKKKGFKVGLVGADVYRPAALEQLQQLGQQIG   67 (211)
T ss_dssp             EECSCCC----HHHHHH-HHHHHTTCCEEEEECCCSSHHHHHHHHHHHHHHT
T ss_pred             EECCCCCCHHHHHHHHH-HHHHHCCCceEEEEeeccccchhHHHHHhccccC
Confidence            79999999999886 55 344456777655554  58888888888888765

>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=96.02  E-value=0.0076  Score=44.39  Aligned_cols=49  Identities=14%  Similarity=0.186  Sum_probs=36.1

Q ss_pred             eEECcCCCchHHHHH-HHHHHHHHcCCcEEEE-ec-hHHHHHHHHHHHHHhcC
Q 042424           59 TLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYT-SS-LKALSNQKYRELHKEFK  108 (138)
Q Consensus        59 ~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv-~P-~kaLv~Q~~~~l~~~f~  108 (138)
                      ++++|||+|||.... +| .+...+|+++.++ +- +|+=+.++.+.|.+.++
T Consensus        15 ~lvGptGvGKTTTiAKLA-a~~~~~~~kV~lit~Dt~R~gA~eQL~~~a~~l~   66 (213)
T d1vmaa2          15 MVVGVNGTGKTTSCGKLA-KMFVDEGKSVVLAAADTFRAAAIEQLKIWGERVG   66 (213)
T ss_dssp             EEECCTTSSHHHHHHHHH-HHHHHTTCCEEEEEECTTCHHHHHHHHHHHHHHT
T ss_pred             EEECCCCCCHHHHHHHHH-HHHHHCCCceEEEeecccccchhHHHHHHhhhcC
Confidence            389999999999886 54 4445667665443 33 58888888988888664

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=95.84  E-value=0.01  Score=43.62  Aligned_cols=48  Identities=13%  Similarity=0.104  Sum_probs=35.4

Q ss_pred             EECcCCCchHHHHH-HHHHHHHHcCCcEEEEe-c-hHHHHHHHHHHHHHhcC
Q 042424           60 LTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTS-S-LKALSNQKYRELHKEFK  108 (138)
Q Consensus        60 l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~-P-~kaLv~Q~~~~l~~~f~  108 (138)
                      +++|||+|||.... +| .+..++|+++.++. - +|+=+-++.+.|.+.++
T Consensus        14 lvGptGvGKTTTiAKLA-~~~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~   64 (211)
T d2qy9a2          14 MVGVNGVGKTTTIGKLA-RQFEQQGKSVMLAAGDTFRAAAVEQLQVWGQRNN   64 (211)
T ss_dssp             EECCTTSCHHHHHHHHH-HHHHTTTCCEEEECCCTTCHHHHHHHHHHHHHTT
T ss_pred             EECCCCCCHHHHHHHHH-HHHHHCCCcEEEEecccccccchhhhhhhhhhcC
Confidence            79999999999886 54 33345577765554 2 48888888889888765

>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=95.81  E-value=0.0051  Score=45.21  Aligned_cols=34  Identities=12%  Similarity=-0.069  Sum_probs=26.8

Q ss_pred             ceEECcCCCchHHHHHHHHHH-HHHcCCcEEEEec
Q 042424           58 GTLTNPVYNGKTAVAEYAIAM-AFRDKQRVIYTSS   91 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~-~l~~~~rviyv~P   91 (138)
                      .++.|++|+|||.++...+.+ +..+|.+++|+..
T Consensus        38 ~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~   72 (277)
T d1cr2a_          38 IMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAML   72 (277)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEES
T ss_pred             EEEEeCCCCCHHHHHHHHHHhhhhhcccceeEeee
Confidence            349999999999888755544 4567999999974

>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=95.59  E-value=0.0067  Score=47.25  Aligned_cols=41  Identities=10%  Similarity=0.103  Sum_probs=33.7

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHH
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKAL   95 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaL   95 (138)
                      .++.++.|+||||||......+.+.+..|..++++=|.-.+
T Consensus        50 ~~H~~I~G~tGsGKT~~l~~li~~~~~~g~~~iiiD~kge~   90 (433)
T d1e9ra_          50 PRHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPNGDM   90 (433)
T ss_dssp             GGCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEETTHH
T ss_pred             cceEEEEeCCCCcHHHHHHHHHHHHHhCCCCEEEEeCChhH
Confidence            46788999999999987666777777788889888887654

>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=95.55  E-value=0.0071  Score=42.31  Aligned_cols=35  Identities=9%  Similarity=-0.023  Sum_probs=26.1

Q ss_pred             ceEECcCCCchHHHHHH-HHHHHHHcCCcEEEEech
Q 042424           58 GTLTNPVYNGKTAVAEY-AIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~-ai~~~l~~~~rviyv~P~   92 (138)
                      .+|.+++|+|||..++. +...++..+.+++|+..-
T Consensus        29 ~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s~e   64 (242)
T d1tf7a1          29 TLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFE   64 (242)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEESS
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHhcCCCccccccc
Confidence            34999999999999974 444445557788887654

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=95.39  E-value=0.024  Score=40.95  Aligned_cols=43  Identities=26%  Similarity=0.195  Sum_probs=29.1

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYR  101 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~  101 (138)
                      ..|.||+|+|||..+-....++...+.+++|+ +...+..+...
T Consensus        39 l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~-~~~~~~~~~~~   81 (213)
T d1l8qa2          39 IFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYS-SADDFAQAMVE   81 (213)
T ss_dssp             EEEECSSSSSHHHHHHHHHHHHHHTTCCEEEE-EHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHHHhccCccceEEe-chHHHHHHHHH
Confidence            45999999999987765555555567777666 44455554443

>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=95.20  E-value=0.01  Score=44.84  Aligned_cols=39  Identities=26%  Similarity=0.319  Sum_probs=31.6

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHH
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQ   98 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q   98 (138)
                      +.+|.|+|||.+++.++..+...|.+++|+----++..+
T Consensus        59 i~G~~gsGKTtl~l~~~~~~q~~g~~~vyidtE~~~~~~   97 (263)
T d1u94a1          59 IYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPI   97 (263)
T ss_dssp             EECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHH
T ss_pred             EecCCCcHHHHHHHHHHHHHHcCCCEEEEEccccccCHH
Confidence            999999999999999998888888888877655444443

>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=95.12  E-value=0.0049  Score=49.93  Aligned_cols=18  Identities=28%  Similarity=0.329  Sum_probs=16.5

Q ss_pred             CCceEECcCCCchHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAE   73 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~   73 (138)
                      .|.++.+|||+|||++|.
T Consensus        50 sNILliGPTGvGKTlLAr   67 (443)
T d1g41a_          50 KNILMIGPTGVGKTEIAR   67 (443)
T ss_dssp             CCEEEECCTTSSHHHHHH
T ss_pred             ccEEEECCCCCCHHHHHH
Confidence            688899999999999986

>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=94.80  E-value=0.0055  Score=47.57  Aligned_cols=39  Identities=15%  Similarity=0.170  Sum_probs=27.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKAL   95 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaL   95 (138)
                      .|.++++|||||||... .++...+....|++.+--+.+|
T Consensus       167 ~nili~G~tgSGKTT~l-~al~~~i~~~~rivtiEd~~El  205 (323)
T d1g6oa_         167 KNVIVCGGTGSGKTTYI-KSIMEFIPKEERIISIEDTEEI  205 (323)
T ss_dssp             CCEEEEESTTSSHHHHH-HHHGGGSCTTCCEEEEESSCCC
T ss_pred             CCEEEEeeccccchHHH-HHHhhhcccccceeeccchhhh
Confidence            56789999999999864 4555544456777777555544

>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=94.77  E-value=0.02  Score=38.07  Aligned_cols=33  Identities=15%  Similarity=0.005  Sum_probs=25.3

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      .++++.|||||..+...+...-.+|.++.++..
T Consensus         6 ~itG~~GSGKTTL~~~L~~~l~~~g~~v~v~~~   38 (170)
T d1np6a_           6 AFAAWSGTGKTTLLKKLIPALCARGIRPGLIKH   38 (170)
T ss_dssp             EEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHHCCCeEEEecc
Confidence            499999999999887666554456888777654

>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=94.47  E-value=0.012  Score=41.81  Aligned_cols=46  Identities=20%  Similarity=0.247  Sum_probs=29.3

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHc------CCcEEEEechHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRD------KQRVIYTSSLKALSNQKYREL  103 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~------~~rviyv~P~kaLv~Q~~~~l  103 (138)
                      .+|.+|+|+|||..++..+.+...+      +.+++|+.=..+...+..+.+
T Consensus        39 ~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   90 (254)
T d1pzna2          39 TEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERIREI   90 (254)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHHHHHHHH
Confidence            3499999999999998766665432      456777654433333333333

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=94.47  E-value=0.046  Score=38.87  Aligned_cols=55  Identities=13%  Similarity=0.093  Sum_probs=44.6

Q ss_pred             HHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcCC-----------CCCCEEEecH
Q 042424           75 AIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTLS-----------PNASCLVMTT  130 (138)
Q Consensus        75 ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~~-----------~~~~IiVtTp  130 (138)
                      .+.....+|.++|+.++++.-+++.++.|++ .+ .+..++|+.+..           .+.+|+|+|.
T Consensus        23 ~i~~~~~~g~r~lvfc~t~~~~~~l~~~L~~-~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~   89 (174)
T d1c4oa2          23 GIRERAARGERTLVTVLTVRMAEELTSFLVE-HGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGIN   89 (174)
T ss_dssp             HHHHHHHTTCEEEEECSSHHHHHHHHHHHHH-TTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESC
T ss_pred             HHHHHHhcCCcEEEEEcchhHHHHHHHHHHh-cCCceEEEecccchHHHHHHHHHHHCCCeEEEEeee
Confidence            3444456789999999999999999999998 55 899999987642           2788999884

>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=94.41  E-value=0.019  Score=43.43  Aligned_cols=36  Identities=25%  Similarity=0.286  Sum_probs=29.9

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHH
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKAL   95 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaL   95 (138)
                      +.+|.|+|||.+++.++..+.+.|.+++|+=---++
T Consensus        62 i~G~~~sGKT~l~l~~~~~aqk~g~~v~yiDtE~~~   97 (268)
T d1xp8a1          62 IYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHAL   97 (268)
T ss_dssp             EEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCC
T ss_pred             EecCCccchHHHHHHHHHHHHhCCCEEEEEECCccC
Confidence            999999999999998888888778888887554444

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=94.32  E-value=0.046  Score=38.78  Aligned_cols=54  Identities=15%  Similarity=0.166  Sum_probs=44.5

Q ss_pred             HHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcCCC-----------CCCEEEecH
Q 042424           76 IAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTLSP-----------NASCLVMTT  130 (138)
Q Consensus        76 i~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~~~-----------~~~IiVtTp  130 (138)
                      +.....++.++|++++++.-++..+..|++ .+ .+..++|+.+.+.           +.+|+|||.
T Consensus        24 i~~~~~~~~~~iif~~~~~~~~~~~~~l~~-~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTd   89 (181)
T d1t5la2          24 IRERVERNERTLVTTLTKKMAEDLTDYLKE-AGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN   89 (181)
T ss_dssp             HHHHHHTTCEEEEECSSHHHHHHHHHHHHT-TTCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESC
T ss_pred             HHHHHhcCCeEEEEeehhhhhHHHHHHHHh-CCcceeEecCCccHHHHHHHHHHHHCCCCCEEEehh
Confidence            444556688999999999999999999987 55 8999999986532           889999994

>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=94.30  E-value=0.02  Score=43.46  Aligned_cols=43  Identities=26%  Similarity=0.234  Sum_probs=34.5

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHH
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRE  102 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~  102 (138)
                      +.+|.|+|||.+++.++..+...|.+++|+---.++..+.++.
T Consensus        65 ~~G~~~~GKT~l~l~~~~~~q~~g~~~vyIDtE~~~~~e~a~~  107 (269)
T d1mo6a1          65 IYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKK  107 (269)
T ss_dssp             EECSSSSSHHHHHHHHHHHHHHTTCEEEEEESSCCCCHHHHHH
T ss_pred             EecCCCcHHHHHHHHHHHHHhcCCCEEEEEECCccCCHHHHHH
Confidence            9999999999999988888888888888877666665554433

>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=94.23  E-value=0.048  Score=42.55  Aligned_cols=48  Identities=15%  Similarity=0.175  Sum_probs=34.6

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH----cCCcEEEEechHHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR----DKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~----~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .+|++|.|+|||.+....+...+.    .+.+++.++||-.-+.+..+.+..
T Consensus       166 ~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~~~  217 (359)
T d1w36d1         166 SVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGK  217 (359)
T ss_dssp             EEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHHTH
T ss_pred             EEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHHHH
Confidence            459999999999886433322222    367999999998777777766544

>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=94.10  E-value=0.017  Score=41.27  Aligned_cols=21  Identities=33%  Similarity=0.325  Sum_probs=17.0

Q ss_pred             CCceEECcCCCchHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai   76 (138)
                      ++.+++||+|+|||.+|....
T Consensus        36 ~~~L~~GPpGtGKT~lA~~la   56 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLAHIIA   56 (238)
T ss_dssp             CCEEEESSTTSSHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHH
Confidence            456799999999999886443

>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=93.88  E-value=0.019  Score=43.73  Aligned_cols=24  Identities=25%  Similarity=0.243  Sum_probs=18.1

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAF   80 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l   80 (138)
                      ++.++++|||+|||++|- +++..+
T Consensus        50 ~~iLl~GPpG~GKT~lAk-alA~~~   73 (309)
T d1ofha_          50 KNILMIGPTGVGKTEIAR-RLAKLA   73 (309)
T ss_dssp             CCEEEECCTTSSHHHHHH-HHHHHH
T ss_pred             ceEEEECCCCCCHHHHHH-HHhhcc
Confidence            566799999999999985 343433

>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=93.73  E-value=0.025  Score=39.92  Aligned_cols=48  Identities=13%  Similarity=0.213  Sum_probs=32.9

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHc------CCcEEEEechHHHHHHHHHHHHHh
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRD------KQRVIYTSSLKALSNQKYRELHKE  106 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~------~~rviyv~P~kaLv~Q~~~~l~~~  106 (138)
                      +|++|+|+|||.+++..+.++...      +..++|+.....+..+..+.+...
T Consensus        41 ~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   94 (258)
T d1v5wa_          41 EAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIADR   94 (258)
T ss_dssp             EEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHHHHHHHHhh
Confidence            499999999999998777655432      245677766666555555555443

>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=93.65  E-value=0.023  Score=44.97  Aligned_cols=24  Identities=21%  Similarity=0.140  Sum_probs=17.0

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHc
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRD   82 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~   82 (138)
                      .++++|||||||.... +++..+.+
T Consensus       161 iLvtGpTGSGKSTTl~-~~l~~~~~  184 (401)
T d1p9ra_         161 ILVTGPTGSGKSTTLY-AGLQELNS  184 (401)
T ss_dssp             EEEECSTTSCHHHHHH-HHHHHHCC
T ss_pred             EEEEcCCCCCccHHHH-HHhhhhcC
Confidence            4599999999998654 44444543

>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=93.56  E-value=0.025  Score=36.74  Aligned_cols=20  Identities=20%  Similarity=0.278  Sum_probs=16.2

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      ++.+++||.|||||.+|-..
T Consensus         3 k~I~l~G~~GsGKSTvak~L   22 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQL   22 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHH
Confidence            45679999999999988533

>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=93.55  E-value=0.034  Score=38.38  Aligned_cols=31  Identities=19%  Similarity=0.005  Sum_probs=21.6

Q ss_pred             eEECc-CCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           59 TLTNP-VYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        59 ~l~aP-TGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      .|++- ||.|||.++.......-++|.|++++
T Consensus         5 ~i~gt~~GVGKTtvs~~La~aLa~~G~rVl~i   36 (224)
T d1byia_           5 FVTGTDTEVGKTVASCALLQAAKAAGYRTAGY   36 (224)
T ss_dssp             EEEESSTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEECCCCccHHHHHHHHHHHHHHCCCeEEEE
Confidence            35555 79999999974333333569999886

>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=93.43  E-value=0.038  Score=39.13  Aligned_cols=33  Identities=24%  Similarity=0.341  Sum_probs=21.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHc--CCcEEEE
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRD--KQRVIYT   89 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~--~~rviyv   89 (138)
                      .+.++.||+|+|||.++.. +.+.+..  +.+.+++
T Consensus        44 ~~lll~GppGtGKT~l~~~-l~~~l~~~~~~~~~~~   78 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTLRK-LWELYKDKTTARFVYI   78 (276)
T ss_dssp             CEEEEECCTTSSHHHHHHH-HHHHHTTSCCCEEEEE
T ss_pred             CceEEECCCCCCHHHHHHH-HHHHHhcccCCcEEEe
Confidence            4567999999999988754 4444443  3444444

>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=93.43  E-value=0.12  Score=39.57  Aligned_cols=54  Identities=7%  Similarity=0.033  Sum_probs=40.9

Q ss_pred             CCCceEECcCCCchHHHHHHHHHHHHHcC------------CcEEEEechHHHHHHHHHHHHHhcC
Q 042424           55 TTHGTLTNPVYNGKTAVAEYAIAMAFRDK------------QRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        55 ~~~~~l~aPTGsGKTlva~~ai~~~l~~~------------~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      .+..+|.|.-|||||.+...-+++.+..+            .+++.|.=|+.=+.++.+++.+.++
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            36778999999999998876666665431            3588888888888888888776553

>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=93.37  E-value=0.013  Score=41.13  Aligned_cols=36  Identities=11%  Similarity=0.144  Sum_probs=25.3

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH------cCCcEEEEechH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR------DKQRVIYTSSLK   93 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~------~~~rviyv~P~k   93 (138)
                      .+|.+|+|+|||.+++..+..++.      .+..++|+.-..
T Consensus        37 ~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~   78 (251)
T d1szpa2          37 TELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEG   78 (251)
T ss_dssp             EEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSS
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecc
Confidence            449999999999999865554432      256778875443

>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=93.22  E-value=0.021  Score=39.82  Aligned_cols=24  Identities=13%  Similarity=0.066  Sum_probs=19.3

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR   81 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~   81 (138)
                      .+|.+|+|+|||.+++..+.+++.
T Consensus        37 ~~i~G~~G~GKT~~~l~~a~~~~~   60 (258)
T d2i1qa2          37 TEFAGVFGSGKTQIMHQSCVNLQN   60 (258)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTTC
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHh
Confidence            349999999999999876666543

>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=93.08  E-value=0.033  Score=36.98  Aligned_cols=20  Identities=25%  Similarity=0.119  Sum_probs=16.3

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      .+.+|+||.|||||.+|...
T Consensus         5 ~~I~i~G~pGsGKTTia~~L   24 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKEL   24 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            45679999999999988643

>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=93.04  E-value=0.018  Score=38.76  Aligned_cols=23  Identities=13%  Similarity=0.114  Sum_probs=18.3

Q ss_pred             ceEECcCCCchHHHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAF   80 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l   80 (138)
                      .++.+|+|+|||.+++..+.++.
T Consensus        26 ~~i~G~~GsGKT~l~l~la~~~~   48 (242)
T d1n0wa_          26 TEMFGEFRTGKTQICHTLAVTCQ   48 (242)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHTT
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHH
Confidence            34999999999999986665544

>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=92.92  E-value=0.033  Score=36.68  Aligned_cols=15  Identities=27%  Similarity=0.450  Sum_probs=13.5

Q ss_pred             eEECcCCCchHHHHH
Q 042424           59 TLTNPVYNGKTAVAE   73 (138)
Q Consensus        59 ~l~aPTGsGKTlva~   73 (138)
                      +|+||.|||||.+|.
T Consensus         6 ~i~G~~GsGKTTva~   20 (176)
T d2bdta1           6 IITGPAGVGKSTTCK   20 (176)
T ss_dssp             EEECSTTSSHHHHHH
T ss_pred             EEECCCCCCHHHHHH
Confidence            599999999999885

>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=92.86  E-value=0.025  Score=44.36  Aligned_cols=18  Identities=33%  Similarity=0.409  Sum_probs=16.0

Q ss_pred             CCceEECcCCCchHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAE   73 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~   73 (138)
                      .|.++.+|||.|||.+|-
T Consensus        69 ~niLfiGPTGvGKTElAk   86 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMAQ   86 (364)
T ss_dssp             CCEEEECCTTSSHHHHHH
T ss_pred             cceeeeCCCCccHHHHHH
Confidence            567899999999999985

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=92.86  E-value=0.13  Score=34.77  Aligned_cols=49  Identities=12%  Similarity=0.035  Sum_probs=39.8

Q ss_pred             HcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcCCC----CCCEEEecH
Q 042424           81 RDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTLSP----NASCLVMTT  130 (138)
Q Consensus        81 ~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~~~----~~~IiVtTp  130 (138)
                      .+++++|+.++++.-+++.++.|++ .+ .+..++|+...+.    ..+|+|||-
T Consensus        33 ~~~~k~IVFc~t~~~ae~la~~L~~-~G~~~~~~H~~~~~~~~~~~~~~vlvaTd   86 (138)
T d1jr6a_          33 IKGGRHLIFCHSKKKCDELAAKLVA-LGINAVAYYRGLDVSVIPTNGDVVVVATD   86 (138)
T ss_dssp             HTTSCEEEECSCHHHHHHHHHHHHH-HTCEEEEECTTCCSCCCTTSSCEEEEESS
T ss_pred             cCCCCEEEEeCcHHHHHHHHHHHhc-cccchhhhhccchhhhhhhhhcceeehhH
Confidence            3578899999999999999999987 45 7778888876543    677999984

>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=92.67  E-value=0.038  Score=36.27  Aligned_cols=15  Identities=20%  Similarity=0.031  Sum_probs=13.1

Q ss_pred             eEECcCCCchHHHHH
Q 042424           59 TLTNPVYNGKTAVAE   73 (138)
Q Consensus        59 ~l~aPTGsGKTlva~   73 (138)
                      +++||+|||||.++-
T Consensus         6 ii~G~pGsGKTTla~   20 (152)
T d1ly1a_           6 LTIGCPGSGKSTWAR   20 (152)
T ss_dssp             EEECCTTSSHHHHHH
T ss_pred             EEECCCCCCHHHHHH
Confidence            489999999998775

>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=92.55  E-value=0.042  Score=39.19  Aligned_cols=21  Identities=33%  Similarity=0.256  Sum_probs=16.9

Q ss_pred             CCceEECcCCCchHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai   76 (138)
                      .+.+++||+|.|||.+|....
T Consensus        36 ~~~Ll~GPpG~GKTtla~~la   56 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLAHVIA   56 (239)
T ss_dssp             CCEEEECCTTSCHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHH
Confidence            466799999999998886433

>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=92.49  E-value=0.075  Score=35.86  Aligned_cols=16  Identities=25%  Similarity=0.295  Sum_probs=14.1

Q ss_pred             EECcCCCchHHHHHHH
Q 042424           60 LTNPVYNGKTAVAEYA   75 (138)
Q Consensus        60 l~aPTGsGKTlva~~a   75 (138)
                      |+||+|||||.+|...
T Consensus        27 I~G~~GSGKSTla~~L   42 (198)
T d1rz3a_          27 IDGLSRSGKTTLANQL   42 (198)
T ss_dssp             EEECTTSSHHHHHHHH
T ss_pred             EECCCCCCHHHHHHHH
Confidence            9999999999998644

>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=92.40  E-value=0.025  Score=40.53  Aligned_cols=16  Identities=25%  Similarity=0.138  Sum_probs=13.8

Q ss_pred             ceEECcCCCchHHHHH
Q 042424           58 GTLTNPVYNGKTAVAE   73 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~   73 (138)
                      .++.||+|+|||.++.
T Consensus        35 ilL~GpPGtGKT~la~   50 (273)
T d1gvnb_          35 FLLGGQPGSGKTSLRS   50 (273)
T ss_dssp             EEEECCTTSCTHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            4599999999998874

>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=92.26  E-value=0.16  Score=40.21  Aligned_cols=48  Identities=23%  Similarity=0.160  Sum_probs=38.5

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK  108 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~  108 (138)
                      ..|.+-+||+|+++..-.+.   ..++.+|+|+|....+.+.+++|+..++
T Consensus        31 ~~L~GlsgS~ka~~~A~l~~---~~~rp~LvVt~~~~~A~~l~~dL~~~l~   78 (408)
T d1c4oa1          31 VTLLGATGTGKTVTMAKVIE---ALGRPALVLAPNKILAAQLAAEFRELFP   78 (408)
T ss_dssp             EEEEECTTSCHHHHHHHHHH---HHTCCEEEEESSHHHHHHHHHHHHHHCT
T ss_pred             EEEecCCCCHHHHHHHHHHH---HhCCCEEEEeCCHHHHHHHHHHHHHhcC
Confidence            46899999999976442221   2377899999999999999999999765

>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=92.22  E-value=0.087  Score=34.93  Aligned_cols=30  Identities=17%  Similarity=0.163  Sum_probs=19.5

Q ss_pred             eEECcCCCchHHHHHHHHHHHHH-cCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv   89 (138)
                      ++.||.|||||.++..... .+. .+.++.++
T Consensus         5 ~i~G~~GsGKsT~~~~L~~-~l~~~~~~~~~~   35 (190)
T d1khta_           5 VVTGVPGVGSTTSSQLAMD-NLRKEGVNYKMV   35 (190)
T ss_dssp             EEECCTTSCHHHHHHHHHH-HHHTTTCCCEEE
T ss_pred             EEECCCCCCHHHHHHHHHH-HHHHcCCCeEEE
Confidence            4899999999998864333 233 34454443

>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=92.13  E-value=0.048  Score=38.42  Aligned_cols=22  Identities=23%  Similarity=0.114  Sum_probs=17.6

Q ss_pred             CceEECcCCCchHHHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAM   78 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~   78 (138)
                      +.+++||+|+|||.++...+.+
T Consensus        35 ~lll~Gp~G~GKTtl~~~i~~~   56 (237)
T d1sxjd2          35 HMLFYGPPGTGKTSTILALTKE   56 (237)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCChHHHHHHHHHH
Confidence            4579999999999988755544

>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=92.08  E-value=0.044  Score=36.50  Aligned_cols=19  Identities=32%  Similarity=0.281  Sum_probs=15.7

Q ss_pred             CceEECcCCCchHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~a   75 (138)
                      +.+|+||.|||||.++...
T Consensus         7 ~I~i~G~~GsGKTT~~~~L   25 (174)
T d1y63a_           7 NILITGTPGTGKTSMAEMI   25 (174)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHH
Confidence            4569999999999998643

>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=91.95  E-value=0.05  Score=38.58  Aligned_cols=22  Identities=27%  Similarity=0.166  Sum_probs=17.2

Q ss_pred             CCceEECcCCCchHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIA   77 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~   77 (138)
                      .+.+++||.|+|||.++...+.
T Consensus        46 ~~lll~Gp~G~GKTtla~~iak   67 (231)
T d1iqpa2          46 PHLLFAGPPGVGKTTAALALAR   67 (231)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHH
Confidence            3467999999999998864443

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=91.85  E-value=0.12  Score=38.00  Aligned_cols=35  Identities=23%  Similarity=0.154  Sum_probs=25.0

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEechH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSLK   93 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~k   93 (138)
                      +..++.+|.|+|||.++.....   .-+..++++.+..
T Consensus        43 ~giLl~GppGtGKT~la~aia~---~~~~~~~~i~~~~   77 (247)
T d1ixza_          43 KGVLLVGPPGVGKTHLARAVAG---EARVPFITASGSD   77 (247)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHH---HTTCCEEEEEHHH
T ss_pred             ceEEEecCCCCChhHHHHHHHH---HcCCCEEEEEhHH
Confidence            4467999999999998864443   2267777776654

>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=91.79  E-value=0.025  Score=37.55  Aligned_cols=18  Identities=11%  Similarity=0.163  Sum_probs=15.6

Q ss_pred             CCceEECcCCCchHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAE   73 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~   73 (138)
                      ++.+++||+|+|||..+.
T Consensus         8 K~I~i~G~~GsGKTTla~   25 (192)
T d1lw7a2           8 KTVAILGGESSGKSVLVN   25 (192)
T ss_dssp             EEEEEECCTTSHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            566799999999998875

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {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: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=91.69  E-value=0.12  Score=34.82  Aligned_cols=31  Identities=29%  Similarity=0.224  Sum_probs=23.2

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      ++++.|||||......+...-.+|.++.++.
T Consensus         6 I~G~~gSGKTTli~~l~~~L~~~g~~v~vik   36 (165)
T d1xjca_           6 VVGYKHSGKTTLMEKWVAAAVREGWRVGTVK   36 (165)
T ss_dssp             EECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEeCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            8999999999987655554445677777664

>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=91.39  E-value=0.058  Score=38.46  Aligned_cols=32  Identities=19%  Similarity=0.109  Sum_probs=20.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      ++.++.||.|+|||.++...+.+   -+..++.+-
T Consensus        53 ~~lll~GPpG~GKTt~a~~la~~---~~~~~~~~~   84 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTAAHLVAQE---LGYDILEQN   84 (253)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHH---TTCEEEEEC
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH---HHhhhhccc
Confidence            45679999999999877543322   244454443

>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=91.23  E-value=0.074  Score=37.45  Aligned_cols=22  Identities=23%  Similarity=0.108  Sum_probs=17.4

Q ss_pred             CceEECcCCCchHHHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIAM   78 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~~   78 (138)
                      +.+++||+|+|||.++...+.+
T Consensus        37 ~lLl~Gp~G~GKttl~~~la~~   58 (227)
T d1sxjc2          37 HLLFYGPPGTGKTSTIVALARE   58 (227)
T ss_dssp             CEEEECSSSSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCChhHHHHHHHHH
Confidence            4679999999999887655443

>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=91.05  E-value=0.075  Score=36.88  Aligned_cols=20  Identities=15%  Similarity=0.228  Sum_probs=15.8

Q ss_pred             CceEECcCCCchHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai   76 (138)
                      ..+|+||+|||||.++-..+
T Consensus         3 pIvl~GpsG~GK~tl~~~L~   22 (186)
T d1gkya_           3 PIVISGPSGTGKSTLLKKLF   22 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            45799999999998765443

>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=90.91  E-value=0.077  Score=37.49  Aligned_cols=23  Identities=17%  Similarity=0.043  Sum_probs=17.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAM   78 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~   78 (138)
                      .+.++.||.|+|||.++...+..
T Consensus        37 ~~~ll~Gp~G~GKTt~a~~la~~   59 (224)
T d1sxjb2          37 PHMIISGMPGIGKTTSVHCLAHE   59 (224)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCchhhHHHHHHH
Confidence            35679999999999988654443

>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=90.77  E-value=0.13  Score=34.16  Aligned_cols=31  Identities=13%  Similarity=-0.041  Sum_probs=21.2

Q ss_pred             eEECcCCCchHHHHHHHHHHHHH-cCCcEEEEe
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYTS   90 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv~   90 (138)
                      +++|+.|||||.++.... ..+. +|..+..+.
T Consensus         5 vi~G~~GsGKTT~~~~La-~~L~~~~~~~~~~~   36 (194)
T d1nksa_           5 IVTGIPGVGKSTVLAKVK-EILDNQGINNKIIN   36 (194)
T ss_dssp             EEEECTTSCHHHHHHHHH-HHHHTTTCCEEEEE
T ss_pred             EEECCCCCCHHHHHHHHH-HHHHHcCCCEEEEE
Confidence            478999999999886443 3344 466665554

>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=90.72  E-value=0.082  Score=34.86  Aligned_cols=16  Identities=19%  Similarity=0.302  Sum_probs=13.9

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      +|+||.|||||.+|..
T Consensus         7 ~l~G~~GsGKsTva~~   22 (178)
T d1qhxa_           7 ILNGGSSAGKSGIVRC   22 (178)
T ss_dssp             EEECCTTSSHHHHHHH
T ss_pred             EEECCCCCCHHHHHHH
Confidence            4899999999998864

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {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: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=90.52  E-value=0.15  Score=37.77  Aligned_cols=33  Identities=24%  Similarity=0.156  Sum_probs=23.3

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEec
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSS   91 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P   91 (138)
                      +..++.+|.|+|||.++.......   +..++++.+
T Consensus        46 ~~iLL~GppGtGKT~la~~iA~~~---~~~~~~i~~   78 (256)
T d1lv7a_          46 KGVLMVGPPGTGKTLLAKAIAGEA---KVPFFTISG   78 (256)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH---TCCEEEECS
T ss_pred             CeEEeeCCCCCCccHHHHHHHHHc---CCCEEEEEh
Confidence            446699999999999986444322   566666655

>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=90.48  E-value=0.067  Score=35.52  Aligned_cols=15  Identities=33%  Similarity=0.437  Sum_probs=13.1

Q ss_pred             eEECcCCCchHHHHH
Q 042424           59 TLTNPVYNGKTAVAE   73 (138)
Q Consensus        59 ~l~aPTGsGKTlva~   73 (138)
                      +|++|.|||||.++.
T Consensus         8 ~l~G~~GsGKSTia~   22 (176)
T d1zp6a1           8 LLSGHPGSGKSTIAE   22 (176)
T ss_dssp             EEEECTTSCHHHHHH
T ss_pred             EEECCCCCCHHHHHH
Confidence            499999999998874

>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=90.31  E-value=0.074  Score=39.06  Aligned_cols=32  Identities=25%  Similarity=0.199  Sum_probs=21.6

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEe
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~   90 (138)
                      +..++.||+|+|||.++.....   .-+..++.+.
T Consensus        41 ~~vLL~GppGtGKT~la~alA~---~~~~~~~~i~   72 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALAAKIAE---ESNFPFIKIC   72 (246)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH---HHTCSEEEEE
T ss_pred             eEEEEECcCCCCHHHHHHHHhh---cccccccccc
Confidence            3457999999999998754322   2256666553

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.98  E-value=0.13  Score=37.76  Aligned_cols=34  Identities=18%  Similarity=0.067  Sum_probs=22.9

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      +..++.+|.|+|||.++.....   .-+..++++.+.
T Consensus        39 ~giLL~GppGtGKT~l~~ala~---~~~~~~~~i~~~   72 (258)
T d1e32a2          39 RGILLYGPPGTGKTLIARAVAN---ETGAFFFLINGP   72 (258)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH---HTTCEEEEECHH
T ss_pred             ceeEEecCCCCCchHHHHHHHH---HhCCeEEEEEch
Confidence            4466999999999987653332   225666666654

>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=89.77  E-value=0.12  Score=34.22  Aligned_cols=16  Identities=38%  Similarity=0.312  Sum_probs=14.0

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      +|+||.|||||.++-.
T Consensus        10 vl~G~~GsGKsT~a~~   25 (171)
T d1knqa_          10 VLMGVSGSGKSAVASE   25 (171)
T ss_dssp             EEECSTTSCHHHHHHH
T ss_pred             EEECCCCCCHHHHHHH
Confidence            4899999999999864

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.69  E-value=0.09  Score=37.26  Aligned_cols=21  Identities=24%  Similarity=0.178  Sum_probs=16.7

Q ss_pred             CceEECcCCCchHHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAIA   77 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai~   77 (138)
                      +.+++||.|+|||.++...+.
T Consensus        35 ~lll~Gp~G~GKTt~~~~la~   55 (252)
T d1sxje2          35 HLLLYGPNGTGKKTRCMALLE   55 (252)
T ss_dssp             CEEEECSTTSSHHHHHHTHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            467999999999998864443

>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=89.67  E-value=0.12  Score=36.10  Aligned_cols=20  Identities=20%  Similarity=0.255  Sum_probs=15.6

Q ss_pred             CceEECcCCCchHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai   76 (138)
                      ..+|+||+|||||.++-..+
T Consensus         2 pIvl~GPsGsGK~tl~~~L~   21 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLF   21 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            35699999999998765443

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {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: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=89.63  E-value=0.19  Score=36.09  Aligned_cols=34  Identities=29%  Similarity=0.301  Sum_probs=23.0

Q ss_pred             ceEECcCCCchHHHHHHHHHHHHH----------cCCcEEEEec
Q 042424           58 GTLTNPVYNGKTAVAEYAIAMAFR----------DKQRVIYTSS   91 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~~l~----------~~~rviyv~P   91 (138)
                      .+|++++|+|||.+++..+.....          .+.+++|+.-
T Consensus        32 ~~i~G~~G~GKS~l~l~la~~ia~g~~~~~~~~~~~~~vl~~~~   75 (274)
T d1nlfa_          32 GALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPA   75 (274)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEES
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHcCCCcccccccCCCceEEEec
Confidence            459999999999998743333221          1357888764

>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=89.57  E-value=0.2  Score=32.77  Aligned_cols=15  Identities=40%  Similarity=0.463  Sum_probs=13.5

Q ss_pred             EECcCCCchHHHHHH
Q 042424           60 LTNPVYNGKTAVAEY   74 (138)
Q Consensus        60 l~aPTGsGKTlva~~   74 (138)
                      ++|+.|||||.+|..
T Consensus        11 l~G~~GsGKTTia~~   25 (183)
T d1m8pa3          11 LTGYMNSGKDAIARA   25 (183)
T ss_dssp             EECSTTSSHHHHHHH
T ss_pred             EECCCCCCHHHHHHH
Confidence            899999999999853

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {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: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.41  E-value=0.07  Score=37.36  Aligned_cols=14  Identities=21%  Similarity=0.408  Sum_probs=12.8

Q ss_pred             EECcCCCchHHHHH
Q 042424           60 LTNPVYNGKTAVAE   73 (138)
Q Consensus        60 l~aPTGsGKTlva~   73 (138)
                      |+||+|||||.++-
T Consensus         7 I~G~~gSGKSTla~   20 (213)
T d1uj2a_           7 VSGGTASGKSSVCA   20 (213)
T ss_dssp             EECSTTSSHHHHHH
T ss_pred             EECCCCCCHHHHHH
Confidence            89999999999884

>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=89.32  E-value=0.096  Score=35.01  Aligned_cols=16  Identities=25%  Similarity=0.171  Sum_probs=13.4

Q ss_pred             ceEECcCCCchHHHHH
Q 042424           58 GTLTNPVYNGKTAVAE   73 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~   73 (138)
                      .+|++|+|+|||....
T Consensus         3 i~I~G~~G~GKSTLl~   18 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVK   18 (178)
T ss_dssp             EEEECCTTSSHHHHHH
T ss_pred             EEEECCCCcHHHHHHH
Confidence            4699999999998753

>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=89.17  E-value=0.15  Score=34.44  Aligned_cols=18  Identities=17%  Similarity=0.141  Sum_probs=15.3

Q ss_pred             CceEECcCCCchHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~   74 (138)
                      |.+|+|+.|||||.++-.
T Consensus         2 ~I~liG~~GsGKsTi~k~   19 (161)
T d1viaa_           2 NIVFIGFMGSGKSTLARA   19 (161)
T ss_dssp             CEEEECCTTSCHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHH
Confidence            567999999999998854

>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=88.76  E-value=0.14  Score=34.47  Aligned_cols=18  Identities=28%  Similarity=0.038  Sum_probs=15.1

Q ss_pred             ceEECcCCCchHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~a   75 (138)
                      .+|.||.|||||.++.+.
T Consensus         3 I~i~G~pGSGKsT~a~~L   20 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKI   20 (182)
T ss_dssp             EEEECSTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            459999999999998643

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=88.74  E-value=0.53  Score=31.48  Aligned_cols=57  Identities=16%  Similarity=0.120  Sum_probs=42.0

Q ss_pred             HHHHHHHc-CCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCC-----------CCCCEEEecHH
Q 042424           75 AIAMAFRD-KQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLS-----------PNASCLVMTTE  131 (138)
Q Consensus        75 ai~~~l~~-~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~-----------~~~~IiVtTpe  131 (138)
                      ++.+.+.+ +.++|+.++++.-+++.++.|++..-.+..++|+....           .+.+|+|||..
T Consensus        19 ~L~~ll~~~~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~   87 (155)
T d1hv8a2          19 ALCRLLKNKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDV   87 (155)
T ss_dssp             HHHHHHCSTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTT
T ss_pred             HHHHHHccCCCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhhhhhhcccceeeeehhH
Confidence            33444443 67899999999999999999988333888888886432           26789999953

>d1z5za1 c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=88.56  E-value=0.5  Score=33.80  Aligned_cols=68  Identities=15%  Similarity=0.282  Sum_probs=48.1

Q ss_pred             CCCchHHHHHHHHHHHHHcCCcEEEEechHHHHHHHHHHHHHhcC-ceEEEecCCcCC------------CCCCEEEecH
Q 042424           64 VYNGKTAVAEYAIAMAFRDKQRVIYTSSLKALSNQKYRELHKEFK-DVGLMTGDVTLS------------PNASCLVMTT  130 (138)
Q Consensus        64 TGsGKTlva~~ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~~f~-~v~~~tGd~~~~------------~~~~IiVtTp  130 (138)
                      ..|||.....-.+...+..|.++|+.+.++.-.+-....+.+.++ .+..++|+.+.+            .+..++|+++
T Consensus        66 ~~S~K~~~l~~~l~~~~~~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vll~~~  145 (244)
T d1z5za1          66 RRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSV  145 (244)
T ss_dssp             TTCHHHHHHHHHHHHHHHTTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCCEEEEEC
T ss_pred             hhhhHHHHHHHHHHhhcccccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccchhccccc
Confidence            458897665545555556789999999999888776666666555 778888987532            2456787775


Q ss_pred             H
Q 042424          131 E  131 (138)
Q Consensus       131 e  131 (138)
                      .
T Consensus       146 ~  146 (244)
T d1z5za1         146 K  146 (244)
T ss_dssp             C
T ss_pred             c
Confidence            4

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.55  E-value=0.49  Score=32.19  Aligned_cols=49  Identities=10%  Similarity=0.092  Sum_probs=39.7

Q ss_pred             CCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCC-----------CCCCEEEecHH
Q 042424           83 KQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLS-----------PNASCLVMTTE  131 (138)
Q Consensus        83 ~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~-----------~~~~IiVtTpe  131 (138)
                      ..++|+.+.++.-+++.++.|++..-.+..++|+...+           .+.+|+|||-.
T Consensus        27 ~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Tdv   86 (162)
T d1fuka_          27 VTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDL   86 (162)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGG
T ss_pred             CCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHHHHhhcccceeecccc
Confidence            67899999999999999999988433888888887542           27789999953

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

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-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=88.52  E-value=0.093  Score=37.17  Aligned_cols=19  Identities=26%  Similarity=0.324  Sum_probs=15.3

Q ss_pred             EECcCCCchHHHHHHHHHH
Q 042424           60 LTNPVYNGKTAVAEYAIAM   78 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~   78 (138)
                      ++||+|+|||.++...+..
T Consensus        51 l~GppGtGKT~l~~~l~~~   69 (287)
T d1w5sa2          51 SIGRVGIGKTTLAKFTVKR   69 (287)
T ss_dssp             CTTCCSSSHHHHHHHHHHH
T ss_pred             eECCCCCCHHHHHHHHHHH
Confidence            6799999999988655544

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {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: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=88.41  E-value=0.17  Score=34.03  Aligned_cols=20  Identities=15%  Similarity=0.190  Sum_probs=16.3

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      ++.++.|+.|+|||.++...
T Consensus         2 p~IvliG~~G~GKSTig~~L   21 (165)
T d2iyva1           2 PKAVLVGLPGSGKSTIGRRL   21 (165)
T ss_dssp             CSEEEECSTTSSHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHH
Confidence            35678999999999998644

>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=88.24  E-value=0.15  Score=34.88  Aligned_cols=18  Identities=17%  Similarity=0.196  Sum_probs=14.9

Q ss_pred             CceEECcCCCchHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~   74 (138)
                      +.+|.||.|||||.+|.+
T Consensus         5 ~I~i~GppGsGKsT~a~~   22 (189)
T d1zaka1           5 KVMISGAPASGKGTQCEL   22 (189)
T ss_dssp             CEEEEESTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            345999999999998864

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.24  E-value=0.54  Score=32.10  Aligned_cols=49  Identities=10%  Similarity=-0.078  Sum_probs=39.1

Q ss_pred             cCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCC-----------CCCCEEEecH
Q 042424           82 DKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLS-----------PNASCLVMTT  130 (138)
Q Consensus        82 ~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~-----------~~~~IiVtTp  130 (138)
                      .+.++|+.++++.-++..++.|++.--.+..++|+.+..           .+.+|+|||-
T Consensus        26 ~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~   85 (168)
T d1t5ia_          26 EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN   85 (168)
T ss_dssp             CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESS
T ss_pred             CCCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhhhccccceeeeccc
Confidence            367899999999999999998888333888999987542           2788999984

>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=87.92  E-value=0.16  Score=34.65  Aligned_cols=19  Identities=26%  Similarity=0.214  Sum_probs=15.4

Q ss_pred             CceEECcCCCchHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~a   75 (138)
                      +.++.+|.|||||.+|.+.
T Consensus         5 riil~G~pGSGKsT~a~~L   23 (190)
T d1ak2a1           5 RAVLLGPPGAGKGTQAPKL   23 (190)
T ss_dssp             EEEEECCTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3458899999999998643

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=87.87  E-value=0.55  Score=33.19  Aligned_cols=49  Identities=10%  Similarity=0.027  Sum_probs=39.6

Q ss_pred             cCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCC-----------CCCCEEEecH
Q 042424           82 DKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLS-----------PNASCLVMTT  130 (138)
Q Consensus        82 ~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~-----------~~~~IiVtTp  130 (138)
                      .+.++|+.++++.-++..+..|+..--.+..++|+...+           ...+|+|+|-
T Consensus        29 ~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd   88 (200)
T d1oywa3          29 RGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV   88 (200)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECT
T ss_pred             CCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhcccceEEEecc
Confidence            467899999999999999999888333888899987542           2778999985

>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=87.84  E-value=0.11  Score=35.85  Aligned_cols=15  Identities=13%  Similarity=0.051  Sum_probs=12.9

Q ss_pred             eEECcCCCchHHHHH
Q 042424           59 TLTNPVYNGKTAVAE   73 (138)
Q Consensus        59 ~l~aPTGsGKTlva~   73 (138)
                      +++|+.|||||.+|.
T Consensus        18 il~G~pGsGKST~a~   32 (172)
T d1yj5a2          18 VAVGFPGAGKSTFIQ   32 (172)
T ss_dssp             EEECCTTSSHHHHHH
T ss_pred             EEECCCCCCHHHHHH
Confidence            499999999998764

>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=87.71  E-value=0.15  Score=34.47  Aligned_cols=19  Identities=21%  Similarity=0.244  Sum_probs=15.3

Q ss_pred             ceEECcCCCchHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai   76 (138)
                      .++.+|.|||||.++.+..
T Consensus         3 I~i~G~pGSGKsT~~~~La   21 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIM   21 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            4589999999999986443

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {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: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=87.66  E-value=0.35  Score=34.76  Aligned_cols=31  Identities=29%  Similarity=0.243  Sum_probs=23.5

Q ss_pred             eEECcCCCchHHHHH-HHHHHHHHcCCcEEEEe
Q 042424           59 TLTNPVYNGKTAVAE-YAIAMAFRDKQRVIYTS   90 (138)
Q Consensus        59 ~l~aPTGsGKTlva~-~ai~~~l~~~~rviyv~   90 (138)
                      ++++--|.|||.++. +|.. .-++|+|+++|-
T Consensus        12 ~~sGKGGVGKTTvaa~lA~~-lA~~G~rVLlvD   43 (296)
T d1ihua1          12 FFTGKGGVGKTSISCATAIR-LAEQGKRVLLVS   43 (296)
T ss_dssp             EEECSTTSSHHHHHHHHHHH-HHHTTCCEEEEE
T ss_pred             EEECCCcChHHHHHHHHHHH-HHHCCCCEEEEe
Confidence            389999999999997 4443 335688988765

>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=87.47  E-value=0.23  Score=33.48  Aligned_cols=20  Identities=15%  Similarity=-0.056  Sum_probs=16.0

Q ss_pred             CCceEECcCCCchHHHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~a   75 (138)
                      ++.++.||.|||||.++...
T Consensus         3 ~~Iil~G~~GsGKSTia~~L   22 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGREL   22 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHH
Confidence            34569999999999998643

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=87.40  E-value=0.77  Score=34.72  Aligned_cols=50  Identities=16%  Similarity=0.090  Sum_probs=39.8

Q ss_pred             HcCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCC-------CCCCEEEecH
Q 042424           81 RDKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLS-------PNASCLVMTT  130 (138)
Q Consensus        81 ~~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~-------~~~~IiVtTp  130 (138)
                      ..++++++++|+..-+++.++.|++.-..|..++|.....       .+.+|||+|.
T Consensus        34 ~~~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~~~~~~~~~~~~~t~   90 (299)
T d1yksa2          34 ADKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYPTIKQKKPDFILATD   90 (299)
T ss_dssp             HCCSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC--------CCCSEEEESS
T ss_pred             hcCCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHhhhhcCCcCEEEEec
Confidence            4578899999999999999999998433888888875432       2677999985

>d1ukza_ c.37.1.1 (A:) Uridylate 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: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.28  E-value=0.19  Score=34.46  Aligned_cols=19  Identities=16%  Similarity=-0.029  Sum_probs=15.0

Q ss_pred             ceEECcCCCchHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai   76 (138)
                      .++.||.|||||.+|....
T Consensus        11 I~i~GppGSGKsT~a~~La   29 (196)
T d1ukza_          11 IFVLGGPGAGKGTQCEKLV   29 (196)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            3489999999999886443

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.24  E-value=0.23  Score=36.57  Aligned_cols=34  Identities=18%  Similarity=0.034  Sum_probs=23.8

Q ss_pred             CCceEECcCCCchHHHHHHHHHHHHHcCCcEEEEech
Q 042424           56 THGTLTNPVYNGKTAVAEYAIAMAFRDKQRVIYTSSL   92 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~~ai~~~l~~~~rviyv~P~   92 (138)
                      +..++.||.|+|||.++......   -|..++++.+.
T Consensus        42 ~giLL~Gp~GtGKT~l~~ala~~---~~~~~~~~~~~   75 (265)
T d1r7ra3          42 KGVLFYGPPGCGKTLLAKAIANE---CQANFISIKGP   75 (265)
T ss_dssp             CEEEEBCCTTSSHHHHHHHHHHH---TTCEEEEECHH
T ss_pred             CeEEEECCCCCcchhHHHHHHHH---hCCcEEEEEHH
Confidence            45669999999999877644322   26777777653

>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=87.12  E-value=0.2  Score=34.06  Aligned_cols=19  Identities=21%  Similarity=0.078  Sum_probs=15.3

Q ss_pred             ceEECcCCCchHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai   76 (138)
                      .++.+|.|||||.+|....
T Consensus         3 I~i~G~pGSGKsT~a~~La   21 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADRIV   21 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            3589999999999986443

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {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: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=86.70  E-value=0.25  Score=37.51  Aligned_cols=17  Identities=29%  Similarity=0.233  Sum_probs=14.5

Q ss_pred             ceEECcCCCchHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~   74 (138)
                      .++++|||+|||.+|-.
T Consensus        56 ~lf~Gp~G~GKt~lak~   72 (315)
T d1qvra3          56 FLFLGPTGVGKTELAKT   72 (315)
T ss_dssp             EEEBSCSSSSHHHHHHH
T ss_pred             EEEECCCcchHHHHHHH
Confidence            35899999999999863

>d2cdna1 c.37.1.1 (A:1-181) Adenylate 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: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=86.62  E-value=0.22  Score=33.72  Aligned_cols=19  Identities=26%  Similarity=0.076  Sum_probs=15.6

Q ss_pred             ceEECcCCCchHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai   76 (138)
                      .++.||.|||||.+|....
T Consensus         3 I~i~G~pGsGKsT~a~~La   21 (181)
T d2cdna1           3 VLLLGPPGAGKGTQAVKLA   21 (181)
T ss_dssp             EEEECCTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            4689999999999987543

>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=86.61  E-value=0.22  Score=33.91  Aligned_cols=18  Identities=28%  Similarity=0.368  Sum_probs=14.5

Q ss_pred             eEECcCCCchHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai   76 (138)
                      +|+||.||||+.++...+
T Consensus         6 vl~GpsG~GK~tl~~~L~   23 (182)
T d1znwa1           6 VLSGPSAVGKSTVVRCLR   23 (182)
T ss_dssp             EEECSTTSSHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHH
Confidence            499999999998865443

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {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: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=86.50  E-value=0.44  Score=34.14  Aligned_cols=29  Identities=31%  Similarity=0.190  Sum_probs=21.7

Q ss_pred             EECcCCCchHHHHH-HHHHHHHHcCCcEEEE
Q 042424           60 LTNPVYNGKTAVAE-YAIAMAFRDKQRVIYT   89 (138)
Q Consensus        60 l~aPTGsGKTlva~-~ai~~~l~~~~rviyv   89 (138)
                      +++--|.|||.++. +|..-+ +.|+|+++|
T Consensus        25 ~sGKGGVGKTT~a~nLA~~lA-~~G~rVllv   54 (279)
T d1ihua2          25 LMGKGGVGKTTMAAAIAVRLA-DMGFDVHLT   54 (279)
T ss_dssp             EECSTTSSHHHHHHHHHHHHH-HTTCCEEEE
T ss_pred             EECCCCCCHHHHHHHHHHHHH-HCCCcEEEE
Confidence            88999999999996 555433 457787753

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {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: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.43  E-value=0.34  Score=36.66  Aligned_cols=16  Identities=19%  Similarity=0.247  Sum_probs=13.4

Q ss_pred             EECcCCCchHHHHHHH
Q 042424           60 LTNPVYNGKTAVAEYA   75 (138)
Q Consensus        60 l~aPTGsGKTlva~~a   75 (138)
                      |+|++|||||..+...
T Consensus        32 i~G~qGSGKSTl~~~l   47 (286)
T d1odfa_          32 FSGPQGSGKSFTSIQI   47 (286)
T ss_dssp             EECCTTSSHHHHHHHH
T ss_pred             eECCCCCCHHHHHHHH
Confidence            8999999999877543

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=86.10  E-value=0.18  Score=36.42  Aligned_cols=58  Identities=22%  Similarity=0.216  Sum_probs=38.4

Q ss_pred             HHHHHHHHHcCCcEEEEechHHH--------HHHHHHHHHHhc-C--ceEEEecCCcCCC-----------CCCEEEecH
Q 042424           73 EYAIAMAFRDKQRVIYTSSLKAL--------SNQKYRELHKEF-K--DVGLMTGDVTLSP-----------NASCLVMTT  130 (138)
Q Consensus        73 ~~ai~~~l~~~~rviyv~P~kaL--------v~Q~~~~l~~~f-~--~v~~~tGd~~~~~-----------~~~IiVtTp  130 (138)
                      .-+|...+.+|.++.||+|...=        +.+.++.+.+.+ .  .+++++|..+.+.           +.+|+|||.
T Consensus        19 ~~~I~~el~~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLVaTt   98 (206)
T d1gm5a4          19 YEFVRQEVMRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTT   98 (206)
T ss_dssp             HHHHHHHTTTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSS
T ss_pred             HHHHHHHHHcCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEEEEeh
Confidence            34566667789999999997532        333444444333 2  6889999876543           788999995

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.95  E-value=0.73  Score=31.48  Aligned_cols=49  Identities=14%  Similarity=0.129  Sum_probs=39.9

Q ss_pred             cCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCC-----------CCCCEEEecH
Q 042424           82 DKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLS-----------PNASCLVMTT  130 (138)
Q Consensus        82 ~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~-----------~~~~IiVtTp  130 (138)
                      .+.++|+.+.++.-++..++.+++..-.+..++|+...+           .+.+|+|||-
T Consensus        33 ~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~~~~~~fk~g~~~iLv~Td   92 (168)
T d2j0sa2          33 TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTD   92 (168)
T ss_dssp             TSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECG
T ss_pred             CCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHHHHHHHHhcCCccEEeccc
Confidence            468999999999999999999988433888999987643           2678999985

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=85.88  E-value=0.55  Score=31.70  Aligned_cols=30  Identities=10%  Similarity=-0.079  Sum_probs=19.2

Q ss_pred             eEECcCCCchHHHHHHHHHHHHH-cCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFR-DKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~-~~~rviyv   89 (138)
                      +++|..|||||..|.... +.+. .+.++..+
T Consensus         6 ~l~GlpgsGKSTla~~L~-~~l~~~~~~~~~~   36 (213)
T d1bifa1           6 VMVGLPARGKTYISKKLT-RYLNFIGVPTREF   36 (213)
T ss_dssp             EEECCTTSSHHHHHHHHH-HHHHHTTCCEEEE
T ss_pred             EEECCCCCCHHHHHHHHH-HHHHhcCCCCeEE
Confidence            489999999999985332 3333 34444333

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

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: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=85.66  E-value=0.25  Score=33.69  Aligned_cols=18  Identities=11%  Similarity=0.028  Sum_probs=14.7

Q ss_pred             eEECcCCCchHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai   76 (138)
                      +|.||.|||||.+|....
T Consensus        10 ~i~G~pGSGKsT~a~~La   27 (194)
T d1qf9a_          10 FVLGGPGSGKGTQCANIV   27 (194)
T ss_dssp             EEEESTTSSHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHH
Confidence            489999999999886443

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

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: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=85.60  E-value=0.46  Score=32.90  Aligned_cols=30  Identities=20%  Similarity=0.315  Sum_probs=20.5

Q ss_pred             eEECcCCCchHHHHHHHHHHHHHcCCcEEEE
Q 042424           59 TLTNPVYNGKTAVAEYAIAMAFRDKQRVIYT   89 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai~~~l~~~~rviyv   89 (138)
                      ++.+|.|||||..... +.+.+..++++.+|
T Consensus         4 ~v~G~~GsGKTTLl~~-ll~~~~~~~~~~iv   33 (244)
T d1yrba1           4 VFVGTAGSGKTTLTGE-FGRYLEDNYKVAYV   33 (244)
T ss_dssp             EEECSTTSSHHHHHHH-HHHHHTTTSCEEEE
T ss_pred             EEEcCCCCcHHHHHHH-HHHHHhhCCeEEEE
Confidence            4899999999987543 33444556666555

>d1teva_ c.37.1.1 (A:) UMP/CMP 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: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.05  E-value=0.32  Score=33.07  Aligned_cols=18  Identities=11%  Similarity=-0.001  Sum_probs=14.8

Q ss_pred             eEECcCCCchHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai   76 (138)
                      +|.+|.|||||..|.+..
T Consensus         5 ~i~GppGSGKsT~a~~La   22 (194)
T d1teva_           5 FVLGGPGAGKGTQCARIV   22 (194)
T ss_dssp             EEECCTTSSHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHH
Confidence            589999999999986433

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.03  E-value=1.2  Score=30.22  Aligned_cols=49  Identities=6%  Similarity=-0.056  Sum_probs=39.1

Q ss_pred             cCCcEEEEechHHHHHHHHHHHHHhcCceEEEecCCcCC-----------CCCCEEEecH
Q 042424           82 DKQRVIYTSSLKALSNQKYRELHKEFKDVGLMTGDVTLS-----------PNASCLVMTT  130 (138)
Q Consensus        82 ~~~rviyv~P~kaLv~Q~~~~l~~~f~~v~~~tGd~~~~-----------~~~~IiVtTp  130 (138)
                      .+.++|+.+.++.-++..++.|+..--.+..++|+....           ...+|+|||.
T Consensus        31 ~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td   90 (171)
T d1s2ma2          31 QINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSD   90 (171)
T ss_dssp             CCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESS
T ss_pred             CCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhhhhhhcccCccccccchh
Confidence            368999999999999999999988422788888887532           2778999985

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=84.98  E-value=1.4  Score=31.26  Aligned_cols=41  Identities=27%  Similarity=0.255  Sum_probs=27.3

Q ss_pred             CCceEECcCCCchHHHHH-HHHHHHHHc-----CCcEEEEechHHHH
Q 042424           56 THGTLTNPVYNGKTAVAE-YAIAMAFRD-----KQRVIYTSSLKALS   96 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~-~ai~~~l~~-----~~rviyv~P~kaLv   96 (138)
                      .|.++.+|.|.|||.+.. +|...+-.+     ..+-+|.+-.-+|+
T Consensus        44 ~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~~Li   90 (195)
T d1jbka_          44 NNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALV   90 (195)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHH
T ss_pred             CCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeHHHHh
Confidence            577899999999999886 443332211     23556666666665

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [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-3 [TaxId: 9913]

Probab=84.95  E-value=0.27  Score=34.10  Aligned_cols=20  Identities=15%  Similarity=0.177  Sum_probs=15.8

Q ss_pred             CceEECcCCCchHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai   76 (138)
                      +.+|.+|.|||||..+....
T Consensus         8 rIiliG~PGSGKtT~a~~La   27 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVSSRIT   27 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            34599999999999886433

>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=84.84  E-value=0.34  Score=32.41  Aligned_cols=15  Identities=40%  Similarity=0.279  Sum_probs=13.5

Q ss_pred             EECcCCCchHHHHHH
Q 042424           60 LTNPVYNGKTAVAEY   74 (138)
Q Consensus        60 l~aPTGsGKTlva~~   74 (138)
                      ++++.|||||.+|-.
T Consensus        24 L~G~pGSGKTTiAk~   38 (195)
T d1x6va3          24 LTGLSGAGKTTVSMA   38 (195)
T ss_dssp             EESSCHHHHHHHHHH
T ss_pred             EECCCCCCHHHHHHH
Confidence            899999999999863

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, 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: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=84.80  E-value=0.19  Score=38.11  Aligned_cols=18  Identities=28%  Similarity=0.194  Sum_probs=15.1

Q ss_pred             CceEECcCCCchHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEY   74 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~   74 (138)
                      +.++++|||+|||.+|-.
T Consensus        54 ~~lf~Gp~GvGKT~lak~   71 (315)
T d1r6bx3          54 SFLFAGPTGVGKTEVTVQ   71 (315)
T ss_dssp             EEEEECSTTSSHHHHHHH
T ss_pred             EEEEECCCcchhHHHHHH
Confidence            345999999999999864

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {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: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.05  E-value=0.38  Score=33.18  Aligned_cols=18  Identities=11%  Similarity=0.049  Sum_probs=14.5

Q ss_pred             CCceEECcCCCchHHHHH
Q 042424           56 THGTLTNPVYNGKTAVAE   73 (138)
Q Consensus        56 ~~~~l~aPTGsGKTlva~   73 (138)
                      +..+|++|+|+||+.+.-
T Consensus         4 k~ivl~Gpsg~GK~tl~~   21 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKN   21 (178)
T ss_dssp             CEEEEECCTTSSHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHH
Confidence            345699999999998764

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate 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: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.48  E-value=0.37  Score=32.64  Aligned_cols=18  Identities=28%  Similarity=0.167  Sum_probs=14.9

Q ss_pred             ceEECcCCCchHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~a   75 (138)
                      .++.||.|||||..+...
T Consensus         5 Ivl~G~pGSGKtT~a~~L   22 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNL   22 (180)
T ss_dssp             EEEECCTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            458899999999998644

>d1ckea_ c.37.1.1 (A:) CMP 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: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=82.90  E-value=0.44  Score=32.50  Aligned_cols=18  Identities=17%  Similarity=0.272  Sum_probs=14.6

Q ss_pred             EECcCCCchHHHHHHHHH
Q 042424           60 LTNPVYNGKTAVAEYAIA   77 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~   77 (138)
                      |.||.||||+..|.....
T Consensus         8 I~GppGSGKgT~ak~La~   25 (225)
T d1ckea_           8 IDGPSGAGKGTLCKAMAE   25 (225)
T ss_dssp             EECCTTSSHHHHHHHHHH
T ss_pred             EECCCCCCHHHHHHHHHH
Confidence            779999999998865443

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=82.78  E-value=0.78  Score=32.25  Aligned_cols=31  Identities=10%  Similarity=0.079  Sum_probs=24.7

Q ss_pred             HHHHHHHcCCcEEEEechHHHHHHHHHHHHH
Q 042424           75 AIAMAFRDKQRVIYTSSLKALSNQKYRELHK  105 (138)
Q Consensus        75 ai~~~l~~~~rviyv~P~kaLv~Q~~~~l~~  105 (138)
                      .+.+.+.++..+|+.+|+|.-++..+.+|.+
T Consensus        32 l~~~~i~~~~~~LVF~~sRk~~~~~A~~L~~   62 (201)
T d2p6ra4          32 LVEECVAENGGVLVFESTRRGAEKTAVKLSA   62 (201)
T ss_dssp             HHHHHHHTTCCEEEECSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCcEEEEeCCHHHHHHHHHHHHH
Confidence            3455667789999999999888888877765

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {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: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=82.37  E-value=0.71  Score=35.19  Aligned_cols=35  Identities=20%  Similarity=0.172  Sum_probs=22.1

Q ss_pred             EECcCCCchHHHHHHHHHHHHHcCCcE--EEEechHH
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFRDKQRV--IYTSSLKA   94 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~~~~rv--iyv~P~ka   94 (138)
                      |++|+|+|||......+.....+|.++  +-+=|+..
T Consensus        59 itG~pGaGKSTLi~~l~~~~~~~g~~vavlavDpss~   95 (327)
T d2p67a1          59 VTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDPSSP   95 (327)
T ss_dssp             EEECTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC--
T ss_pred             eeCCCCCCHHHHHHHHHHHHHhcCCceeeecCCCcee
Confidence            999999999987764444444456654  44445543

>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=82.25  E-value=0.44  Score=33.74  Aligned_cols=18  Identities=17%  Similarity=0.357  Sum_probs=14.1

Q ss_pred             eEECcCCCchHHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~ai   76 (138)
                      +|+||+|+||+.+.-..+
T Consensus         6 vi~GPSG~GK~tl~~~L~   23 (205)
T d1s96a_           6 IVSAPSGAGKSSLIQALL   23 (205)
T ss_dssp             EEECCTTSCHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHH
Confidence            499999999997764433

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {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: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=81.74  E-value=0.86  Score=31.33  Aligned_cols=29  Identities=21%  Similarity=0.342  Sum_probs=21.4

Q ss_pred             EECcCCCchHHHHH-HHHHHHHHcCCcEEEE
Q 042424           60 LTNPVYNGKTAVAE-YAIAMAFRDKQRVIYT   89 (138)
Q Consensus        60 l~aPTGsGKTlva~-~ai~~~l~~~~rviyv   89 (138)
                      .++-.|.|||.++. +|..-+ +.|++++++
T Consensus         8 ~~~kGGvGKTtia~nLA~~la-~~g~~Vlli   37 (237)
T d1g3qa_           8 VSGKGGTGKTTVTANLSVALG-DRGRKVLAV   37 (237)
T ss_dssp             ECSSTTSSHHHHHHHHHHHHH-HTTCCEEEE
T ss_pred             ECCCCCCcHHHHHHHHHHHHH-hCCCCEEEE
Confidence            44668999999997 554433 568888887

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {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: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=81.45  E-value=0.89  Score=32.03  Aligned_cols=16  Identities=31%  Similarity=0.264  Sum_probs=13.8

Q ss_pred             EECcCCCchHHHHHHH
Q 042424           60 LTNPVYNGKTAVAEYA   75 (138)
Q Consensus        60 l~aPTGsGKTlva~~a   75 (138)
                      ++|..|||||.+|...
T Consensus        29 ltGlsGsGKTTia~~L   44 (208)
T d1m7ga_          29 LTGLSASGKSTLAVEL   44 (208)
T ss_dssp             EECSTTSSHHHHHHHH
T ss_pred             EECCCCCCHHHHHHHH
Confidence            9999999999988533

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=81.44  E-value=0.55  Score=33.38  Aligned_cols=21  Identities=19%  Similarity=0.064  Sum_probs=16.8

Q ss_pred             ceEECcCCCchHHHHHHHHHH
Q 042424           58 GTLTNPVYNGKTAVAEYAIAM   78 (138)
Q Consensus        58 ~~l~aPTGsGKTlva~~ai~~   78 (138)
                      .++.+|.|+|||.++...+..
T Consensus        37 ~Ll~Gp~G~GKtt~a~~~~~~   57 (239)
T d1njfa_          37 YLFSGTRGVGKTSIARLLAKG   57 (239)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHHH
Confidence            469999999999988754443

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

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: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=81.42  E-value=0.54  Score=32.33  Aligned_cols=16  Identities=31%  Similarity=0.598  Sum_probs=13.5

Q ss_pred             eEECcCCCchHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEY   74 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~   74 (138)
                      +|.||.|||||.+|..
T Consensus         7 aIdGp~GsGKgT~ak~   22 (223)
T d1q3ta_           7 AIDGPASSGKSTVAKI   22 (223)
T ss_dssp             EEECSSCSSHHHHHHH
T ss_pred             EEECCCCCCHHHHHHH
Confidence            3679999999999863

>d1qhla_ c.37.1.12 (A:) Cell division protein MukB {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: ABC transporter ATPase domain-like
domain: Cell division protein MukB
species: Escherichia coli [TaxId: 562]

Probab=81.16  E-value=0.16  Score=33.49  Aligned_cols=14  Identities=29%  Similarity=0.275  Sum_probs=12.1

Q ss_pred             eEECcCCCchHHHH
Q 042424           59 TLTNPVYNGKTAVA   72 (138)
Q Consensus        59 ~l~aPTGsGKTlva   72 (138)
                      +|.||+|||||.+.
T Consensus        28 vi~G~NGsGKStil   41 (222)
T d1qhla_          28 TLSGGNGAGKSTTM   41 (222)
T ss_dssp             HHHSCCSHHHHHHH
T ss_pred             EEECCCCCCHHHHH
Confidence            48999999999764

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

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: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=81.00  E-value=0.44  Score=36.10  Aligned_cols=29  Identities=17%  Similarity=0.242  Sum_probs=16.0

Q ss_pred             EECcCCCchHHHHHHHHHHHHH-cCCcEEEE
Q 042424           60 LTNPVYNGKTAVAEYAIAMAFR-DKQRVIYT   89 (138)
Q Consensus        60 l~aPTGsGKTlva~~ai~~~l~-~~~rviyv   89 (138)
                      |+|++|||||.++... .+.+. .+.+++++
T Consensus         9 IaG~SGSGKTTva~~l-~~i~~~~~v~~~iI   38 (288)
T d1a7ja_           9 VTGSSGAGTSTVKHTF-DQIFRREGVKAVSI   38 (288)
T ss_dssp             EESCC---CCTHHHHH-HHHHHHHTCCEEEE
T ss_pred             EECCCCCcHHHHHHHH-HHHHhhcCCCeEEE
Confidence            9999999999987532 22333 35555444

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {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: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=80.98  E-value=0.36  Score=32.85  Aligned_cols=15  Identities=33%  Similarity=0.501  Sum_probs=13.4

Q ss_pred             EECcCCCchHHHHHH
Q 042424           60 LTNPVYNGKTAVAEY   74 (138)
Q Consensus        60 l~aPTGsGKTlva~~   74 (138)
                      |+|+.|||||.+|.+
T Consensus         8 itG~~gSGKstva~~   22 (191)
T d1uf9a_           8 ITGNIGSGKSTVAAL   22 (191)
T ss_dssp             EEECTTSCHHHHHHH
T ss_pred             EECCCCCCHHHHHHH
Confidence            889999999999864

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {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: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=80.83  E-value=1.2  Score=30.64  Aligned_cols=29  Identities=17%  Similarity=0.184  Sum_probs=21.2

Q ss_pred             EECcCCCchHHHHH-HHHHHHHHcCCcEEEE
Q 042424           60 LTNPVYNGKTAVAE-YAIAMAFRDKQRVIYT   89 (138)
Q Consensus        60 l~aPTGsGKTlva~-~ai~~~l~~~~rviyv   89 (138)
                      .++--|.|||.++. +|..- -+.|.+++++
T Consensus         7 ~s~KGGvGKTtia~nlA~~l-a~~g~~Vlli   36 (232)
T d1hyqa_           7 ASGKGGTGKTTITANLGVAL-AQLGHDVTIV   36 (232)
T ss_dssp             EESSSCSCHHHHHHHHHHHH-HHTTCCEEEE
T ss_pred             ECCCCCChHHHHHHHHHHHH-HhCCCCEEEE
Confidence            56778999999997 44333 2568888876

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

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: Pig (Sus scrofa) [TaxId: 9823]

Probab=80.42  E-value=0.5  Score=32.25  Aligned_cols=17  Identities=18%  Similarity=0.051  Sum_probs=14.2

Q ss_pred             eEECcCCCchHHHHHHH
Q 042424           59 TLTNPVYNGKTAVAEYA   75 (138)
Q Consensus        59 ~l~aPTGsGKTlva~~a   75 (138)
                      ++.||.||||+..|...
T Consensus        12 ~l~G~pGSGKsT~a~~L   28 (194)
T d3adka_          12 FVVGGPGSGKGTQCEKI   28 (194)
T ss_dssp             EEEECTTSSHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHH
Confidence            48999999999988643

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

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: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=80.20  E-value=0.58  Score=36.17  Aligned_cols=20  Identities=25%  Similarity=0.340  Sum_probs=15.6

Q ss_pred             CceEECcCCCchHHHHHHHH
Q 042424           57 HGTLTNPVYNGKTAVAEYAI   76 (138)
Q Consensus        57 ~~~l~aPTGsGKTlva~~ai   76 (138)
                      ..++.+|.|+|||.++...+
T Consensus       156 ~~~~~g~~~~gk~~~~~~~~  175 (362)
T d1svma_         156 YWLFKGPIDSGKTTLAAALL  175 (362)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            34599999999998875433